references.bib

@article{Eddy2011,
  title = {Accelerated {{Profile HMM Searches}}},
  volume = {7},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1002195},
  number = {10},
  urldate = {2012-01-24},
  journal = {PLoS Computational Biology},
  url = {http://dx.plos.org/10.1371/journal.pcbi.1002195},
  author = {Eddy, Sean R.},
  editor = {Pearson, William R.},
  month = oct,
  year = {2011},
  pages = {e1002195},
  file = {/home/mpetersen/bib/storage/RCSHHHK5/Eddy2011.accelerated-hmmer3-searches.pdf}
}

@article{Slater2005,
  title = {Automated Generation of Heuristics for Biological Sequence Comparison},
  volume = {6},
  doi = {10.1186/1471-2105-6-31},
  number = {1},
  journal = {Bmc Bioinformatics},
  author = {Slater, G. and Birney, E.},
  year = {2005},
  pages = {31},
  file = {/home/mpetersen/bib/storage/SG9UWSB6/1471-2105-6-31.pdf}
}

@article{Li2003,
  title = {{{OrthoMCL}}: Identification of Ortholog Groups for Eukaryotic Genomes},
  volume = {13},
  shorttitle = {{{OrthoMCL}}},
  doi = {10.1101/gr.1224503},
  number = {9},
  journal = {Genome research},
  author = {Li, L. and Stoeckert, C.J. and Roos, D.S.},
  year = {2003},
  pages = {2178--2189},
  file = {/home/mpetersen/bib/storage/8VMXD4DD/Li2003.orthomcl.pdf}
}

@article{Trachana2011,
  title = {Orthology Prediction Methods: {{A}} Quality Assessment Using Curated Protein Families},
  volume = {33},
  issn = {02659247},
  shorttitle = {Orthology Prediction Methods},
  doi = {10.1002/bies.201100062},
  number = {10},
  urldate = {2012-01-24},
  journal = {BioEssays},
  url = {http://doi.wiley.com/10.1002/bies.201100062},
  author = {Trachana, Kalliopi and Larsson, Tomas A. and Powell, Sean and Chen, Wei-Hua and Doerks, Tobias and Muller, Jean and Bork, Peer},
  month = oct,
  year = {2011},
  pages = {769-780},
  file = {/home/mpetersen/bib/storage/VKNCAGA6/Trachana2011.orthology-prediction-methods-quality-assessment.pdf}
}

@article{Kriventseva2008,
  title = {{{OrthoDB}}: The Hierarchical Catalog of Eukaryotic Orthologs},
  volume = {36},
  shorttitle = {{{OrthoDB}}},
  doi = {10.1093/nar/gkq930},
  number = {suppl 1},
  journal = {Nucleic acids research},
  author = {Kriventseva, E.V. and Rahman, N. and Espinosa, O. and Zdobnov, E.M.},
  year = {2008},
  keywords = {Animals,Phylogeny,Genomics,Fungi,Genes,Proteins,Saccharomyces cerevisiae,Databases; Genetic,Evolution; Molecular,Mice,Protein Structure; Tertiary,Molecular Sequence Annotation,Sequence Homology; Amino Acid,Arthropods,Drosophila melanogaster,Vertebrates},
  pages = {D271--D275},
  file = {/home/mpetersen/bib/storage/8JP8VRVC/Kriventseva2007.orthodb.pdf;/home/mpetersen/bib/storage/F9I3NDR4/Waterhouse2001.orthodb-2011.pdf;/home/mpetersen/bib/storage/FDBZ6YK5/Waterhouse et al. - 2011 - OrthoDB the hierarchical catalog of eukaryotic or.pdf}
}

@article{Koonin2005,
  title = {Orthologs, Paralogs, and Evolutionary Genomics.},
  volume = {39},
  doi = {10.1146/annurev.genet.39.073003.114725},
  abstract = {Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A clear distinction between orthologs and paralogs is critical for the construction of a robust evolutionary classification of genes and reliable functional annotation of newly sequenced genomes. Genome comparisons show that orthologous relationships with genes from taxonomically distant species can be established for the majority of the genes from each sequenced genome. This review examines in depth the definitions and subtypes of orthologs and paralogs, outlines the principal methodological approaches employed for identification of orthology and paralogy, and considers evolutionary and functional implications of these concepts.},
  journal = {Annu Rev Genet},
  url = {http://dx.doi.org/10.1146/annurev.genet.39.073003.114725},
  author = {Koonin, Eugene V},
  year = {2005},
  keywords = {Animals; Computational Biology; Conserved Sequence; Evolution,Molecular; Genomics},
  pages = {309--338},
  file = {/home/mpetersen/bib/storage/NJ8C2ER5/Koonin2005.orthologs-paralogs-evolutionary-genomics.pdf}
}

@article{Tatusov2003,
  title = {The {{COG}} Database: An Updated Version Includes Eukaryotes.},
  volume = {4},
  doi = {10.1186/1471-2105-4-41},
  abstract = {The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75\% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54\% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20\% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1\% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.},
  journal = {BMC Bioinformatics},
  url = {http://dx.doi.org/10.1186/1471-2105-4-41},
  author = {Tatusov, Roman L and Fedorova, Natalie D and Jackson, John D and Jacobs, Aviva R and Kiryutin, Boris and Koonin, Eugene V and Krylov, Dmitri M and Mazumder, Raja and Mekhedov, Sergei L and Nikolskaya, Anastasia N and Rao, B. Sridhar and Smirnov, Sergei and Sverdlov, Alexander V and Vasudevan, Sona and Wolf, Yuri I and Yin, Jodie J and Natale, Darren A},
  month = sep,
  year = {2003},
  keywords = {Nucleic Acid,Animals; Databases,trends; Databases,Protein,trends; Eukaryotic Cells,chemistry/physiology; Evolution,Molecular; Humans; National Institutes of Health (U.S.); Proteins,classification/genetics/physiology; Terminology as Topic; United States},
  pages = {41},
  file = {/home/mpetersen/bib/storage/P7EJDEPN/Tatusov2003.cog-database.pdf}
}

@article{Ebersberger2009,
  title = {{{HaMStR}}: {{Profile}} Hidden Markov Model Based Search for Orthologs in {{ESTs}}},
  volume = {9},
  shorttitle = {{{HaMStR}}},
  doi = {10.1186/1471-2148-9-157},
  number = {1},
  journal = {BMC Evolutionary Biology},
  author = {Ebersberger, I. and Strauss, S. and Von Haeseler, A.},
  year = {2009},
  pages = {157},
  file = {/home/mpetersen/bib/storage/2SU5AEA4/Ebersberger2009.hamstr.pdf}
}

@article{Kristensen2011,
  title = {Computational Methods for Gene Orthology Inference},
  volume = {12},
  issn = {1467-5463, 1477-4054},
  doi = {10.1093/bib/bbr030},
  number = {5},
  urldate = {2012-10-11},
  journal = {Briefings in Bioinformatics},
  url = {http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbr030},
  author = {Kristensen, D. M. and Wolf, Y. I. and Mushegian, A. R. and Koonin, E. V.},
  month = jun,
  year = {2011},
  pages = {379-391},
  file = {/home/mpetersen/bib/storage/2V92T7H9/2011 - Computational methods for Gene Orthology inference.pdf;/home/mpetersen/bib/storage/37P82GHD/Brief Bioinform-2011-Kristensen-bib-bbr030.pdf}
}

@article{Chen2007a,
  title = {Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes},
  volume = {2},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0000383},
  abstract = {Orthology detection is critically important for accurate functional annotation, and has been widely used to facilitate studies on comparative and evolutionary genomics. Although various methods are now available, there has been no comprehensive analysis of performance, due to the lack of a genomic-scale 'gold standard' orthology dataset. Even in the absence of such datasets, the comparison of results from alternative methodologies contains useful information, as agreement enhances confidence and disagreement indicates possible errors. Latent Class Analysis (LCA) is a statistical technique that can exploit this information to reasonably infer sensitivities and specificities, and is applied here to evaluate the performance of various orthology detection methods on a eukaryotic dataset. Overall, we observe a trade-off between sensitivity and specificity in orthology detection, with BLAST-based methods characterized by high sensitivity, and tree-based methods by high specificity. Two algorithms exhibit the best overall balance, with both sensitivity and specificity{$>$}80\%: INPARANOID identifies orthologs across two species while OrthoMCL clusters orthologs from multiple species. Among methods that permit clustering of ortholog groups spanning multiple genomes, the (automated) OrthoMCL algorithm exhibits better within-group consistency with respect to protein function and domain architecture than the (manually curated) KOG database, and the homolog clustering algorithm TribeMCL as well. By way of using LCA, we are also able to comprehensively assess similarities and statistical dependence between various strategies, and evaluate the effects of parameter settings on performance. In summary, we present a comprehensive evaluation of orthology detection on a divergent set of eukaryotic genomes, thus providing insights and guides for method selection, tuning and development for different applications. Many biological questions have been addressed by multiple tests yielding binary (yes/no) outcomes but no clear definition of truth, making LCA an attractive approach for computational biology.},
  number = {4},
  urldate = {2011-08-24},
  journal = {PloS One},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/17440619},
  author = {Chen, Feng and Mackey, Aaron J and Vermunt, Jeroen K and Roos, David S},
  year = {2007},
  keywords = {Algorithms,Eukaryotic Cells,Genome},
  pages = {e383},
  file = {/home/mpetersen/bib/storage/HX7FHAXC/Chen2007.orthology-detection-assesment.pdf},
  pmid = {17440619}
}

@book{MySQL2013,
  edition = {5.5},
  title = {{{MySQL}} 5.5 {{Reference Manual}}},
  volume = {1},
  abstract = {This is the MySQLTM Reference Manual. It documents MySQL 5.5 through 5.5.31, as well as MySQL Cluster
releases based on version 7.2 of NDBCLUSTER through 5.5.29-ndb-7.2.10.},
  language = {English},
  urldate = {2013-01-22},
  publisher = {{Oracle}},
  url = {http://dev.mysql.com/doc/},
  author = {{MySQL}},
  year = {2013}
}

@article{Berglund2008,
  title = {{{InParanoid}} 6: Eukaryotic Ortholog Clusters with Inparalogs},
  volume = {36},
  issn = {1362-4962},
  shorttitle = {{{InParanoid}} 6},
  doi = {10.1093/nar/gkm1020},
  abstract = {The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters.},
  number = {Database issue},
  urldate = {2011-08-24},
  journal = {Nucleic Acids Research},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/18055500},
  author = {Berglund, Ann-Charlotte and Sj\"olund, Erik and Ostlund, Gabriel and Sonnhammer, Erik L L},
  month = jan,
  year = {2008},
  keywords = {Animals,Cluster Analysis,Humans,Phylogeny,Animals; Cluster Analysis; Databases,Protein; Gene Duplication; Humans; Internet; Phylogeny; Proteins,genetics; Proteomics,Proteins,Gene Duplication,Databases; Protein,Internet,Proteomics},
  pages = {D263-266},
  file = {/home/mpetersen/bib/storage/VT7TCNPC/Berglund2008.inparanoid6.pdf},
  pmid = {18055500}
}

@article{Shedlock2000,
  title = {{{SINE}} Insertions: Powerful Tools for Molecular Systematics},
  volume = {22},
  issn = {0265-9247},
  shorttitle = {{{SINE}} Insertions},
  doi = {10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z},
  abstract = {Short interspersed repetitive elements, or SINEs, are tRNA-derived retroposons that are dispersed throughout eukaryotic genomes and can be present in well over 10(4) total copies. The enormous volume of SINE amplifications per organism makes them important evolutionary agents for shaping the diversity of genomes, and the irreversible, independent nature of their insertion allows them to be used for diagnosing common ancestry among host taxa with extreme confidence. As such, they represent a powerful new tool for systematic biology that can be strategically integrated with other conventional phylogenetic characters, most notably morphology and DNA sequences. This review covers the basic aspects of SINE evolution that are especially relevant to their use as systematic characters and describes the practical methods of characterizing SINEs for cladogram construction. It also discusses the limits of their systematic utility, clarifies some recently published misunderstandings, and illustrates the effective application of SINEs for vertebrate phylogenetics with results from selected case studies. BioEssays 22:148-160, 2000.},
  language = {eng},
  number = {2},
  journal = {BioEssays: news and reviews in molecular, cellular and developmental biology},
  author = {Shedlock, A M and Okada, N},
  month = feb,
  year = {2000},
  keywords = {Animals,Artiodactyla,Molecular,Phylogeny,Perches,Salmonidae,Short Interspersed Nucleotide Elements,Models,Whales,Genetic,Evolution,Evolution; Molecular,Models; Genetic},
  pages = {148-160},
  pmid = {10655034}
}

@article{Dutilh2007,
  title = {Assessment of Phylogenomic and Orthology Approaches for Phylogenetic Inference},
  volume = {23},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btm015},
  abstract = {MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology. RESULTS Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content. CONCLUSIONS Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.},
  number = {7},
  urldate = {2011-08-24},
  journal = {Bioinformatics (Oxford, England)},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/17237036},
  author = {Dutilh, B E and {van Noort}, V and {van der Heijden}, R T J M and Boekhout, T and Snel, B and Huynen, M A},
  month = apr,
  year = {2007},
  keywords = {Algorithms,Molecular,Phylogeny,Sequence Alignment,Sequence Analysis,DNA,Genome,Base Sequence,Chromosome Mapping,Genetic Variation,Fungal,Molecular Sequence Data,Evolution,Evolution; Molecular,Genome; Fungal,Sequence Analysis; DNA},
  pages = {815-824},
  file = {/home/mpetersen/bib/storage/NNMSHRJ2/815.full.pdf},
  pmid = {17237036}
}

@article{Altenhoff2012a,
  title = {Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs},
  volume = {8},
  shorttitle = {Resolving the {{Ortholog Conjecture}}},
  doi = {10.1371/journal.pcbi.1002514},
  number = {5},
  urldate = {2013-01-16},
  journal = {PLoS Computational Biology},
  url = {http://dx.plos.org/10.1371/journal.pcbi.1002514},
  author = {Altenhoff, A. M. and Studer, R. A. and {Robinson-Rechavi}, M. and Dessimoz, C.},
  year = {2012},
  pages = {e1002514},
  file = {/home/mpetersen/bib/storage/AZPA9Q3M/pcbi.1002514.pdf}
}

@article{Altenhoff2012,
  title = {Inferring Orthology and Paralogy},
  volume = {855},
  issn = {1940-6029},
  doi = {10.1007/978-1-61779-582-4_9},
  abstract = {The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases, and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.},
  journal = {Methods in molecular biology (Clifton, N.J.)},
  author = {Altenhoff, Adrian M and Dessimoz, Christophe},
  year = {2012},
  keywords = {Animals,Humans,Phylogeny,Computational Biology,Evolution; Molecular},
  pages = {259-279},
  file = {/home/mpetersen/bib/storage/KZEUTGZV/orthology-bookchapter.pdf},
  pmid = {22407712}
}

@article{Jothi2006,
  title = {{{COCO}}-{{CL}}: Hierarchical Clustering of Homology Relations Based on Evolutionary Correlations},
  volume = {22},
  issn = {1367-4803, 1460-2059},
  shorttitle = {{{COCO}}-{{CL}}},
  doi = {10.1093/bioinformatics/btl009},
  number = {7},
  urldate = {2013-01-18},
  journal = {Bioinformatics},
  url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btl009},
  author = {Jothi, R. and Zotenko, E. and Tasneem, A. and Przytycka, T. M.},
  month = jan,
  year = {2006},
  pages = {779-788}
}

@article{Edgar2004,
  title = {{{MUSCLE}}: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity},
  volume = {5},
  issn = {1471-2105},
  shorttitle = {{{MUSCLE}}},
  doi = {10.1186/1471-2105-5-113},
  abstract = {BACKGROUND

In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles.

RESULTS

We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer.

CONCLUSIONS

MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at http://www.drive5.com/muscle.},
  journal = {BMC bioinformatics},
  author = {Edgar, Robert C},
  month = aug,
  year = {2004},
  keywords = {Cluster Analysis,Phylogeny,Sequence Alignment,Computational Biology,Software,Time Factors,Software Design},
  pages = {113},
  pmid = {15318951}
}

@article{Waterhouse2013,
  title = {{{OrthoDB}}: A Hierarchical Catalog of Animal, Fungal and Bacterial Orthologs},
  volume = {41},
  issn = {1362-4962},
  shorttitle = {{{OrthoDB}}},
  doi = {10.1093/nar/gks1116},
  abstract = {The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB-the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon-intron architectures, syntenic orthologs and parent-child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.},
  language = {eng},
  number = {Database issue},
  journal = {Nucleic Acids Research},
  author = {Waterhouse, Robert M. and Tegenfeldt, Fredrik and Li, Jia and Zdobnov, Evgeny M. and Kriventseva, Evgenia V.},
  month = jan,
  year = {2013},
  keywords = {Animals,Cluster Analysis,Humans,Phylogeny,Genes,Synteny,Databases; Genetic,Evolution; Molecular,Genes; Fungal,Internet,Genes; Bacterial,Mice,Molecular Sequence Annotation,Phenotype},
  pages = {D358-365},
  file = {/home/mpetersen/bib/storage/78RXXRDF/Nucl. Acids Res.-2013-Waterhouse-D358-65.pdf},
  pmid = {23180791},
  pmcid = {PMC3531149}
}

@article{Terrapon2014,
  title = {Molecular Traces of Alternative Social Organization in a Termite Genome},
  volume = {5},
  issn = {2041-1723},
  doi = {10.1038/ncomms4636},
  urldate = {2014-09-30},
  journal = {Nature Communications},
  url = {http://www.nature.com/doifinder/10.1038/ncomms4636},
  author = {Terrapon, Nicolas and Li, Cai and Robertson, Hugh M. and Ji, Lu and Meng, Xuehong and Booth, Warren and Chen, Zhensheng and Childers, Christopher P. and Glastad, Karl M. and Gokhale, Kaustubh and Gowin, Johannes and Gronenberg, Wulfila and Hermansen, Russell A. and Hu, Haofu and Hunt, Brendan G. and Huylmans, Ann Kathrin and Khalil, Sayed M. S. and Mitchell, Robert D. and {Munoz-Torres}, Monica C. and Mustard, Julie A. and Pan, Hailin and Reese, Justin T. and Scharf, Michael E. and Sun, Fengming and Vogel, Heiko and Xiao, Jin and Yang, Wei and Yang, Zhikai and Yang, Zuoquan and Zhou, Jiajian and Zhu, Jiwei and Brent, Colin S. and Elsik, Christine G. and Goodisman, Michael A. D. and Liberles, David A. and Roe, R. Michael and Vargo, Edward L. and Vilcinskas, Andreas and Wang, Jun and {Bornberg-Bauer}, Erich and Korb, Judith and Zhang, Guojie and Liebig, J\"urgen},
  month = may,
  year = {2014},
  keywords = {Genome,zootermopsis}
}

@article{TheInternationalAphidGenomicsConsortium2010,
  title = {Genome {{Sequence}} of the {{Pea Aphid Acyrthosiphon}} Pisum},
  volume = {8},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.1000313},
  language = {en},
  number = {2},
  urldate = {2014-09-30},
  journal = {PLoS Biology},
  url = {http://dx.plos.org/10.1371/journal.pbio.1000313},
  author = {{The International Aphid Genomics Consortium}},
  editor = {Eisen, Jonathan A.},
  month = feb,
  year = {2010},
  keywords = {Genome},
  pages = {e1000313}
}

@article{Colbourne2011,
  title = {The {{Ecoresponsive Genome}} of {{Daphnia}} Pulex},
  volume = {331},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1197761},
  language = {en},
  number = {6017},
  urldate = {2014-10-06},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1197761},
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  month = feb,
  year = {2011},
  keywords = {Genome,sequencing,water flea},
  pages = {555-561}
}

@article{Scott2014,
  title = {Genome of the House Fly, {{Musca}} Domestica {{L}}., a Global Vector of Diseases with Adaptations to a Septic Environment},
  volume = {15},
  issn = {1465-6906},
  doi = {10.1186/s13059-014-0466-3},
  language = {en},
  number = {10},
  urldate = {2014-10-22},
  journal = {Genome Biology},
  url = {http://genomebiology.com/2014/15/10/466},
  author = {Scott, Jeffrey G and Warren, Wesley C and Beukeboom, Leo W and Bopp, Daniel and Clark, Andrew G and Giers, Sarah D and Hediger, Monika and Jones, Andrew K and Kasai, Shinji and Leichter, Cheryl A and Li, Ming and Meisel, Richard P and Minx, Patrick and Murphy, Terence D and Nelson, David R and Reid, William R and Rinkevich, Frank D and Robertson, Hugh M and Sackton, Timothy B and Sattelle, David B and {Thibaud-Nissen}, Francoise and Tomlinson, Chad and {van de Zande}, Louis and Walden, Kimberly and Wilson, Richard K and Liu, Nannan},
  year = {2014},
  keywords = {Genome,assembly,transposable element,repeat,fly,sequencing},
  pages = {466},
  file = {/home/mpetersen/bib/storage/I4WEUTIY/s13059-014-0466-3.pdf;/home/mpetersen/bib/storage/NUD5MUTU/s13059-014-0466-3.pdf}
}

@article{Werren2010,
  title = {Functional and Evolutionary Insights from the Genomes of Three Parasitoid {{Nasonia}} Species},
  volume = {327},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1178028},
  language = {en},
  number = {5963},
  urldate = {2014-10-23},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1178028},
  author = {Werren, J. H. and Richards, S. and Desjardins, C. A. and Niehuis, O. and Gadau, J. and Colbourne, J. K. and {The Nasonia Genome Working Group} and Beukeboom, L. W. and Desplan, C. and Elsik, C. G. and Grimmelikhuijzen, C. J. P. and Kitts, P. and Lynch, J. A. and Murphy, T. and Oliveira, D. C. S. G. and Smith, C. D. and v. d. Zande, L. and Worley, K. C. and Zdobnov, E. M. and Aerts, M. and Albert, S. and Anaya, V. H. and Anzola, J. M. and Barchuk, A. R. and Behura, S. K. and Bera, A. N. and Berenbaum, M. R. and Bertossa, R. C. and Bitondi, M. M. G. and Bordenstein, S. R. and Bork, P. and {Bornberg-Bauer}, E. and Brunain, M. and Cazzamali, G. and Chaboub, L. and Chacko, J. and Chavez, D. and Childers, C. P. and Choi, J.-H. and Clark, M. E. and Claudianos, C. and Clinton, R. A. and Cree, A. G. and Cristino, A. S. and Dang, P. M. and Darby, A. C. and {de Graaf}, D. C. and Devreese, B. and Dinh, H. H. and Edwards, R. and Elango, N. and Elhaik, E. and Ermolaeva, O. and Evans, J. D. and Foret, S. and Fowler, G. R. and Gerlach, D. and Gibson, J. D. and Gilbert, D. G. and Graur, D. and Grunder, S. and Hagen, D. E. and Han, Y. and Hauser, F. and Hultmark, D. and Hunter, H. C. and Hurst, G. D. D. and Jhangian, S. N. and Jiang, H. and Johnson, R. M. and Jones, A. K. and Junier, T. and Kadowaki, T. and Kamping, A. and Kapustin, Y. and Kechavarzi, B. and Kim, J. and Kim, J. and Kiryutin, B. and Koevoets, T. and Kovar, C. L. and Kriventseva, E. V. and Kucharski, R. and Lee, H. and Lee, S. L. and Lees, K. and Lewis, L. R. and Loehlin, D. W. and Logsdon, J. M. and Lopez, J. A. and Lozado, R. J. and Maglott, D. and Maleszka, R. and Mayampurath, A. and Mazur, D. J. and McClure, M. A. and Moore, A. D. and Morgan, M. B. and Muller, J. and {Munoz-Torres}, M. C. and Muzny, D. M. and Nazareth, L. V. and Neupert, S. and Nguyen, N. B. and Nunes, F. M. F. and Oakeshott, J. G. and Okwuonu, G. O. and Pannebakker, B. A. and Pejaver, V. R. and Peng, Z. and Pratt, S. C. and Predel, R. and Pu, L.-L. and Ranson, H. and Raychoudhury, R. and Rechtsteiner, A. and Reid, J. G. and Riddle, M. and {Romero-Severson}, J. and Rosenberg, M. and Sackton, T. B. and Sattelle, D. B. and Schluns, H. and Schmitt, T. and Schneider, M. and Schuler, A. and Schurko, A. M. and Shuker, D. M. and Simoes, Z. L. P. and Sinha, S. and Smith, Z. and Souvorov, A. and Springauf, A. and Stafflinger, E. and Stage, D. E. and Stanke, M. and Tanaka, Y. and Telschow, A. and Trent, C. and Vattathil, S. and Viljakainen, L. and Wanner, K. W. and Waterhouse, R. M. and Whitfield, J. B. and Wilkes, T. E. and Williamson, M. and Willis, J. H. and Wolschin, F. and Wyder, S. and Yamada, T. and Yi, S. V. and Zecher, C. N. and Zhang, L. and Gibbs, R. A.},
  month = jan,
  year = {2010},
  keywords = {Animals,Sequence Analysis,DNA,Genetic Speciation,Genome,Genetic,Genetic Variation,Molecular Sequence Data,Genes,Insect Proteins,Biological Evolution,Sequence Analysis; DNA,Arthropods,Quantitative Trait Loci,nasonia,wasp,Male,DNA Transposable Elements,Female,Genes; Insect,Genome; Insect,DNA Methylation,Gene Transfer; Horizontal,Host-Parasite Interactions,Insect Viruses,Insects,Recombination; Genetic,Wasp Venoms,Wasps,Wolbachia,Insect,Gene Transfer,Horizontal,Recombination},
  pages = {343-348},
  file = {/home/mpetersen/bib/storage/6GT5JCVZ/NasoniaScience2010.pdf;/home/mpetersen/bib/storage/WKIWEW6X/NasoniaScience2010.pdf}
}

@article{Zhan2011,
  title = {The {{Monarch Butterfly Genome Yields Insights}} into {{Long}}-{{Distance Migration}}},
  volume = {147},
  issn = {00928674},
  doi = {10.1016/j.cell.2011.09.052},
  language = {en},
  number = {5},
  urldate = {2014-10-31},
  journal = {Cell},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867411012682},
  author = {Zhan, Shuai and Merlin, Christine and Boore, Jeffrey L. and Reppert, Steven M.},
  month = nov,
  year = {2011},
  pages = {1171-1185},
  file = {/home/mpetersen/bib/storage/BIWLVEZK/1-s2.0-S0092867411012682-main.pdf;/home/mpetersen/bib/storage/WG45RMJA/1-s2.0-S0092867411012682-main.pdf},
  note = {Danaus Plexippus}
}

@article{Schreiber2009,
  title = {{{OrthoSelect}}: A Protocol for Selecting Orthologous Groups in Phylogenomics},
  volume = {10},
  issn = {1471-2105},
  shorttitle = {{{OrthoSelect}}},
  doi = {10.1186/1471-2105-10-219},
  language = {en},
  number = {1},
  urldate = {2014-11-15},
  journal = {BMC Bioinformatics},
  url = {http://www.biomedcentral.com/1471-2105/10/219},
  author = {Schreiber, Fabian and Pick, Kerstin and Erpenbeck, Dirk and W\"orheide, Gert and Morgenstern, Burkhard},
  year = {2009},
  pages = {219}
}

@article{Arensburger2010,
  title = {Sequencing of {{Culex}} Quinquefasciatus {{Establishes}} a {{Platform}} for {{Mosquito Comparative Genomics}}},
  volume = {330},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1191864},
  language = {en},
  number = {6000},
  urldate = {2014-11-17},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1191864},
  author = {Arensburger, P. and Megy, K. and Waterhouse, R. M. and Abrudan, J. and Amedeo, P. and Antelo, B. and Bartholomay, L. and Bidwell, S. and Caler, E. and Camara, F. and Campbell, C. L. and Campbell, K. S. and Casola, C. and Castro, M. T. and Chandramouliswaran, I. and Chapman, S. B. and Christley, S. and Costas, J. and Eisenstadt, E. and Feschotte, C. and {Fraser-Liggett}, C. and Guigo, R. and Haas, B. and Hammond, M. and Hansson, B. S. and Hemingway, J. and Hill, S. R. and Howarth, C. and Ignell, R. and Kennedy, R. C. and Kodira, C. D. and Lobo, N. F. and Mao, C. and Mayhew, G. and Michel, K. and Mori, A. and Liu, N. and Naveira, H. and Nene, V. and Nguyen, N. and Pearson, M. D. and Pritham, E. J. and Puiu, D. and Qi, Y. and Ranson, H. and Ribeiro, J. M. C. and Roberston, H. M. and Severson, D. W. and Shumway, M. and Stanke, M. and Strausberg, R. L. and Sun, C. and Sutton, G. and Tu, Z. and Tubio, J. M. C. and Unger, M. F. and Vanlandingham, D. L. and Vilella, A. J. and White, O. and White, J. R. and Wondji, C. S. and Wortman, J. and Zdobnov, E. M. and Birren, B. and Christensen, B. M. and Collins, F. H. and Cornel, A. and Dimopoulos, G. and Hannick, L. I. and Higgs, S. and Lanzaro, G. C. and Lawson, D. and Lee, N. H. and Muskavitch, M. A. T. and Raikhel, A. S. and Atkinson, P. W.},
  month = oct,
  year = {2010},
  pages = {86-88},
  file = {/home/mpetersen/bib/storage/IEXJYIPX/Arensburger_Science_2010.pdf;/home/mpetersen/bib/storage/PCJSXTDZ/Arensburger_Science_2010.pdf}
}

@article{Bohne2008,
  title = {Transposable Elements as Drivers of Genomic and Biological Diversity in Vertebrates},
  volume = {16},
  issn = {0967-3849, 1573-6849},
  doi = {10.1007/s10577-007-1202-6},
  language = {en},
  number = {1},
  urldate = {2015-01-07},
  journal = {Chromosome Research},
  url = {http://link.springer.com/10.1007/s10577-007-1202-6},
  author = {B\"ohne, Astrid and Brunet, Fr\'ed\'eric and {Galiana-Arnoux}, Delphine and Schultheis, Christina and Volff, Jean-Nicolas},
  month = mar,
  year = {2008},
  pages = {203-215},
  file = {/home/mpetersen/bib/storage/KQIA9G5W/review vert evolution.pdf}
}

@article{Kriventseva2015,
  title = {{{OrthoDB}} v8: Update of the Hierarchical Catalog of Orthologs and the Underlying Free Software},
  volume = {43},
  issn = {0305-1048, 1362-4962},
  shorttitle = {{{OrthoDB}} V8},
  doi = {10.1093/nar/gku1220},
  language = {en},
  number = {D1},
  urldate = {2015-02-26},
  journal = {Nucleic Acids Research},
  url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1220},
  author = {Kriventseva, E. V. and Tegenfeldt, F. and Petty, T. J. and Waterhouse, R. M. and Simao, F. A. and Pozdnyakov, I. A. and Ioannidis, P. and Zdobnov, E. M.},
  month = jan,
  year = {2015},
  pages = {D250-D256},
  file = {/home/mpetersen/bib/storage/A42ELKZM/gku1220.pdf}
}

@article{Struck2014,
  title = {Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of {{Spiralia}}},
  volume = {31},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msu143},
  language = {en},
  number = {7},
  urldate = {2015-03-06},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msu143},
  author = {Struck, T. H. and {Wey-Fabrizius}, A. R. and Golombek, A. and Hering, L. and Weigert, A. and Bleidorn, C. and Klebow, S. and Iakovenko, N. and Hausdorf, B. and Petersen, M. and Kuck, P. and Herlyn, H. and Hankeln, T.},
  month = jul,
  year = {2014},
  pages = {1833-1849},
  file = {/home/mpetersen/bib/storage/UQBKJ798/0000000e.Struck_MolBiolEvol2014AdvancedPublication.pdf}
}

@article{Cong2015a,
  title = {Tiger {{Swallowtail Genome Reveals Mechanisms}} for {{Speciation}} and {{Caterpillar Chemical Defense}}},
  volume = {10},
  issn = {22111247},
  doi = {10.1016/j.celrep.2015.01.026},
  language = {en},
  number = {6},
  urldate = {2015-03-06},
  journal = {Cell Reports},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S2211124715000510},
  author = {Cong, Qian and Borek, Dominika and Otwinowski, Zbyszek and Grishin, Nick V.},
  month = feb,
  year = {2015},
  pages = {910-919},
  file = {/home/mpetersen/bib/storage/GJQXQKVZ/Papilio.pdf;/home/mpetersen/bib/storage/TV5AYKAE/Papilio.pdf}
}

@article{Barron2014,
  title = {Population {{Genomics}} of {{Transposable Elements}} in {{Drosophila}}},
  volume = {48},
  issn = {0066-4197, 1545-2948},
  doi = {10.1146/annurev-genet-120213-092359},
  language = {en},
  number = {1},
  urldate = {2015-11-25},
  journal = {Annual Review of Genetics},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-genet-120213-092359},
  author = {Barr\'on, Maite G. and {Fiston-Lavier}, Anna-Sophie and Petrov, Dmitri A. and Gonz\'alez, Josefa},
  month = nov,
  year = {2014},
  pages = {561-581},
  file = {/home/mpetersen/bib/storage/389HWMIX/annurev-genet-120213-092359.pdf}
}

@article{Peters2014,
  title = {The Evolutionary History of Holometabolous Insects Inferred from Transcriptome-Based Phylogeny and Comprehensive Morphological Data},
  volume = {14},
  issn = {1471-2148},
  doi = {10.1186/1471-2148-14-52},
  language = {en},
  number = {1},
  urldate = {2015-05-05},
  journal = {BMC Evolutionary Biology},
  url = {http://www.biomedcentral.com/1471-2148/14/52},
  author = {Peters, Ralph S and Meusemann, Karen and Petersen, Malte and Mayer, Christoph and Wilbrandt, Jeanne and Ziesmann, Tanja and Donath, Alexander and Kjer, Karl M and Asp\"ock, Ulrike and Asp\"ock, Horst and Aberer, Andre and Stamatakis, Alexandros and Friedrich, Frank and H\"unefeld, Frank and Niehuis, Oliver and Beutel, Rolf G and Misof, Bernhard},
  year = {2014},
  pages = {52},
  file = {/home/mpetersen/bib/storage/N8X4AUGR/Peters et al. - 2014 - The evolutionary history of holometabolous insects}
}

@article{DellAmpio2014,
  title = {Decisive {{Data Sets}} in {{Phylogenomics}}: {{Lessons}} from {{Studies}} on the {{Phylogenetic Relationships}} of {{Primarily Wingless Insects}}},
  volume = {31},
  issn = {0737-4038, 1537-1719},
  shorttitle = {Decisive {{Data Sets}} in {{Phylogenomics}}},
  doi = {10.1093/molbev/mst196},
  language = {en},
  number = {1},
  urldate = {2015-05-05},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/mst196},
  author = {Dell'Ampio, E. and Meusemann, K. and Szucsich, N. U. and Peters, R. S. and Meyer, B. and Borner, J. and Petersen, M. and Aberer, A. J. and Stamatakis, A. and Walzl, M. G. and Minh, B. Q. and {von Haeseler}, A. and Ebersberger, I. and Pass, G. and Misof, B.},
  month = jan,
  year = {2014},
  pages = {239-249},
  file = {/home/mpetersen/bib/storage/QAUZZE57/Dell'Ampio et al. - 2014 - Decisive Data Sets in Phylogenomics Lessons from .pdf}
}

@article{Wright2014,
  title = {Metabolic 'engines' of Flight Drive Genome Size Reduction in Birds},
  volume = {281},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2013.2780},
  language = {en},
  number = {1779},
  urldate = {2015-05-08},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2013.2780},
  author = {Wright, N. A. and Gregory, T. R. and Witt, C. C.},
  month = jan,
  year = {2014},
  pages = {20132780-20132780}
}

@article{Hubley2015,
  title = {The {{Dfam}} Database of Repetitive {{DNA}} Families},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkv1272},
  abstract = {Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.},
  language = {en},
  urldate = {2015-12-03},
  journal = {Nucleic Acids Research},
  url = {http://nar.oxfordjournals.org/content/early/2015/11/25/nar.gkv1272},
  author = {Hubley, Robert and Finn, Robert D. and Clements, Jody and Eddy, Sean R. and Jones, Thomas A. and Bao, Weidong and Smit, Arian F. A. and Wheeler, Travis J.},
  month = nov,
  year = {2015},
  pages = {gkv1272},
  file = {/home/mpetersen/bib/storage/J8KXHHH8/gkv1272.pdf;/home/mpetersen/bib/storage/DTJUWPVQ/nar.gkv1272.html},
  pmid = {26612867}
}

@article{Lander2001,
  title = {Initial Sequencing and Analysis of the Human Genome},
  volume = {409},
  issn = {0028-0836},
  doi = {10.1038/35057062},
  abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.},
  language = {eng},
  number = {6822},
  journal = {Nature},
  author = {Lander, E. S. and Linton, L. M. and Birren, B. and Nusbaum, C. and Zody, M. C. and Baldwin, J. and Devon, K. and Dewar, K. and Doyle, M. and FitzHugh, W. and Funke, R. and Gage, D. and Harris, K. and Heaford, A. and Howland, J. and Kann, L. and Lehoczky, J. and LeVine, R. and McEwan, P. and McKernan, K. and Meldrim, J. and Mesirov, J. P. and Miranda, C. and Morris, W. and Naylor, J. and Raymond, C. and Rosetti, M. and Santos, R. and Sheridan, A. and Sougnez, C. and {Stange-Thomann}, N. and Stojanovic, N. and Subramanian, A. and Wyman, D. and Rogers, J. and Sulston, J. and Ainscough, R. and Beck, S. and Bentley, D. and Burton, J. and Clee, C. and Carter, N. and Coulson, A. and Deadman, R. and Deloukas, P. and Dunham, A. and Dunham, I. and Durbin, R. and French, L. and Grafham, D. and Gregory, S. and Hubbard, T. and Humphray, S. and Hunt, A. and Jones, M. and Lloyd, C. and McMurray, A. and Matthews, L. and Mercer, S. and Milne, S. and Mullikin, J. C. and Mungall, A. and Plumb, R. and Ross, M. and Shownkeen, R. and Sims, S. and Waterston, R. H. and Wilson, R. K. and Hillier, L. W. and McPherson, J. D. and Marra, M. A. and Mardis, E. R. and Fulton, L. A. and Chinwalla, A. T. and Pepin, K. H. and Gish, W. R. and Chissoe, S. L. and Wendl, M. C. and Delehaunty, K. D. and Miner, T. L. and Delehaunty, A. and Kramer, J. B. and Cook, L. L. and Fulton, R. S. and Johnson, D. L. and Minx, P. J. and Clifton, S. W. and Hawkins, T. and Branscomb, E. and Predki, P. and Richardson, P. and Wenning, S. and Slezak, T. and Doggett, N. and Cheng, J. F. and Olsen, A. and Lucas, S. and Elkin, C. and Uberbacher, E. and Frazier, M. and Gibbs, R. A. and Muzny, D. M. and Scherer, S. E. and Bouck, J. B. and Sodergren, E. J. and Worley, K. C. and Rives, C. M. and Gorrell, J. H. and Metzker, M. L. and Naylor, S. L. and Kucherlapati, R. S. and Nelson, D. L. and Weinstock, G. M. and Sakaki, Y. and Fujiyama, A. and Hattori, M. and Yada, T. and Toyoda, A. and Itoh, T. and Kawagoe, C. and Watanabe, H. and Totoki, Y. and Taylor, T. and Weissenbach, J. and Heilig, R. and Saurin, W. and Artiguenave, F. and Brottier, P. and Bruls, T. and Pelletier, E. and Robert, C. and Wincker, P. and Smith, D. R. and {Doucette-Stamm}, L. and Rubenfield, M. and Weinstock, K. and Lee, H. M. and Dubois, J. and Rosenthal, A. and Platzer, M. and Nyakatura, G. and Taudien, S. and Rump, A. and Yang, H. and Yu, J. and Wang, J. and Huang, G. and Gu, J. and Hood, L. and Rowen, L. and Madan, A. and Qin, S. and Davis, R. W. and Federspiel, N. A. and Abola, A. P. and Proctor, M. J. and Myers, R. M. and Schmutz, J. and Dickson, M. and Grimwood, J. and Cox, D. R. and Olson, M. V. and Kaul, R. and Raymond, C. and Shimizu, N. and Kawasaki, K. and Minoshima, S. and Evans, G. A. and Athanasiou, M. and Schultz, R. and Roe, B. A. and Chen, F. and Pan, H. and Ramser, J. and Lehrach, H. and Reinhardt, R. and McCombie, W. R. and {de la Bastide}, M. and Dedhia, N. and Bl\"ocker, H. and Hornischer, K. and Nordsiek, G. and Agarwala, R. and Aravind, L. and Bailey, J. A. and Bateman, A. and Batzoglou, S. and Birney, E. and Bork, P. and Brown, D. G. and Burge, C. B. and Cerutti, L. and Chen, H. C. and Church, D. and Clamp, M. and Copley, R. R. and Doerks, T. and Eddy, S. R. and Eichler, E. E. and Furey, T. S. and Galagan, J. and Gilbert, J. G. and Harmon, C. and Hayashizaki, Y. and Haussler, D. and Hermjakob, H. and Hokamp, K. and Jang, W. and Johnson, L. S. and Jones, T. A. and Kasif, S. and Kaspryzk, A. and Kennedy, S. and Kent, W. J. and Kitts, P. and Koonin, E. V. and Korf, I. and Kulp, D. and Lancet, D. and Lowe, T. M. and McLysaght, A. and Mikkelsen, T. and Moran, J. V. and Mulder, N. and Pollara, V. J. and Ponting, C. P. and Schuler, G. and Schultz, J. and Slater, G. and Smit, A. F. and Stupka, E. and Szustakowski, J. and {Thierry-Mieg}, D. and {Thierry-Mieg}, J. and Wagner, L. and Wallis, J. and Wheeler, R. and Williams, A. and Wolf, Y. I. and Wolfe, K. H. and Yang, S. P. and Yeh, R. F. and Collins, F. and Guyer, M. S. and Peterson, J. and Felsenfeld, A. and Wetterstrand, K. A. and Patrinos, A. and Morgan, M. J. and {de Jong}, P. and Catanese, J. J. and Osoegawa, K. and Shizuya, H. and Choi, S. and Chen, Y. J. and Szustakowki, J. and {International Human Genome Sequencing Consortium}},
  month = feb,
  year = {2001},
  keywords = {Animals,Conserved Sequence,Humans,Proteome,Chromosome Mapping,Databases; Factual,Genes,Proteins,RNA,Gene Duplication,Evolution; Molecular,Mutation,Sequence Analysis; DNA,Genome; Human,Species Specificity,DNA Transposable Elements,Drug Industry,CpG Islands,Forecasting,GC Rich Sequence,Genetic Diseases; Inborn,Genetics; Medical,Human Genome Project,Private Sector,Public Sector,Repetitive Sequences; Nucleic Acid},
  pages = {860-921},
  file = {/home/mpetersen/bib/storage/FEC923SA/409860a0.pdf},
  pmid = {11237011}
}

@article{You2013,
  title = {A Heterozygous Moth Genome Provides Insights into Herbivory and Detoxification},
  volume = {45},
  issn = {1061-4036, 1546-1718},
  doi = {10.1038/ng.2524},
  number = {2},
  urldate = {2015-06-25},
  journal = {Nature Genetics},
  url = {http://www.nature.com/doifinder/10.1038/ng.2524},
  author = {You, Minsheng and Yue, Zhen and He, Weiyi and Yang, Xinhua and Yang, Guang and Xie, Miao and Zhan, Dongliang and Baxter, Simon W and Vasseur, Liette and Gurr, Geoff M and Douglas, Carl J and Bai, Jianlin and Wang, Ping and Cui, Kai and Huang, Shiguo and Li, Xianchun and Zhou, Qing and Wu, Zhangyan and Chen, Qilin and Liu, Chunhui and Wang, Bo and Li, Xiaojing and Xu, Xiufeng and Lu, Changxin and Hu, Min and Davey, John W and Smith, Sandy M and Chen, Mingshun and Xia, Xiaofeng and Tang, Weiqi and Ke, Fushi and Zheng, Dandan and Hu, Yulan and Song, Fengqin and You, Yanchun and Ma, Xiaoli and Peng, Lu and Zheng, Yunkai and Liang, Yong and Chen, Yaqiong and Yu, Liying and Zhang, Younan and Liu, Yuanyuan and Li, Guoqing and Fang, Lin and Li, Jingxiang and Zhou, Xin and Luo, Yadan and Gou, Caiyun and Wang, Junyi and Wang, Jian and Yang, Huanming and Wang, Jun},
  month = jan,
  year = {2013},
  pages = {220-225}
}

@article{Staton2015a,
  title = {Transposome: A Toolkit for Annotation of Transposable Element Families from Unassembled Sequence Reads},
  volume = {31},
  issn = {1367-4803, 1460-2059},
  shorttitle = {Transposome},
  doi = {10.1093/bioinformatics/btv059},
  language = {en},
  number = {11},
  urldate = {2015-06-25},
  journal = {Bioinformatics},
  url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btv059},
  author = {Staton, S. E. and Burke, J. M.},
  month = jun,
  year = {2015},
  pages = {1827-1829},
  file = {/home/mpetersen/bib/storage/IMK879P3/Bioinformatics-2015-Staton-bioinformatics_btv059.pdf}
}

@article{Gonzalez2008,
  title = {High {{Rate}} of {{Recent Transposable Element}}\textendash{{Induced Adaptation}} in {{Drosophila}} Melanogaster},
  volume = {6},
  issn = {1544-9173, 1545-7885},
  doi = {10.1371/journal.pbio.0060251},
  language = {en},
  number = {10},
  urldate = {2015-07-15},
  journal = {PLoS Biology},
  url = {http://biology.plosjournals.org/perlserv/?request=get-document\&doi=10.1371\%2Fjournal.pbio.0060251},
  author = {Gonz\'alez, Josefa and Lenkov, Kapa and Lipatov, Mikhail and Macpherson, J. Michael and Petrov, Dmitri A.},
  editor = {Noor, Mohamed A. F.},
  year = {2008},
  pages = {e251}
}

@article{Camacho2009,
  title = {{{BLAST}}+: Architecture and Applications},
  volume = {10},
  issn = {1471-2105},
  shorttitle = {{{BLAST}}+},
  doi = {10.1186/1471-2105-10-421},
  language = {en},
  number = {1},
  urldate = {2015-08-04},
  journal = {BMC Bioinformatics},
  url = {http://www.biomedcentral.com/1471-2105/10/421},
  author = {Camacho, Christiam and Coulouris, George and Avagyan, Vahram and Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden, Thomas L},
  year = {2009},
  keywords = {Sequence Alignment,Computational Biology,Software,Databases; Genetic},
  pages = {421}
}

@article{Buchon2006,
  title = {{{RNAi}}: A Defensive {{RNA}}-Silencing against Viruses and Transposable Elements},
  volume = {96},
  issn = {0018-067X, 1365-2540},
  shorttitle = {{{RNAi}}},
  doi = {10.1038/sj.hdy.6800789},
  number = {2},
  urldate = {2015-08-07},
  journal = {Heredity},
  url = {http://www.nature.com/doifinder/10.1038/sj.hdy.6800789},
  author = {Buchon, N and Vaury, C},
  month = feb,
  year = {2006},
  pages = {195-202}
}

@book{Fedoroff2013,
  address = {Oxford, UK},
  title = {Plant {{Transposons}} and {{Genome Dynamics}} in {{Evolution}}: {{Fedoroff}}/{{Plant Transposons}} and {{Genome Dynamics}} in {{Evolution}}},
  isbn = {978-1-118-50015-6 978-0-470-95994-7},
  shorttitle = {Plant {{Transposons}} and {{Genome Dynamics}} in {{Evolution}}},
  language = {en},
  urldate = {2015-08-07},
  publisher = {{Wiley-Blackwell}},
  url = {http://doi.wiley.com/10.1002/9781118500156},
  editor = {Fedoroff, Nina V.},
  month = apr,
  year = {2013}
}

@article{Nygaard2011,
  title = {The Genome of the Leaf-Cutting Ant {{Acromyrmex}} Echinatior Suggests Key Adaptations to Advanced Social Life and Fungus Farming},
  volume = {21},
  issn = {1549-5469},
  doi = {10.1101/gr.121392.111},
  abstract = {We present a high-quality ({$>$}100\texttimes{} depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. We compare this genome with three previously sequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet of A. echinatior, where we find gene loss in the ant's arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of "garden manuring" fungal enzymes that are unaffected by ant digestion. The second is multiple mating of queens and ejaculate competition, which may be associated with a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of the feminizer gene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae in A. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the transition from single to multiple queen mating 10 million years ago.},
  language = {eng},
  number = {8},
  journal = {Genome Research},
  author = {Nygaard, Sanne and Zhang, Guojie and Schi\o{}tt, Morten and Li, Cai and Wurm, Yannick and Hu, Haofu and Zhou, Jiajian and Ji, Lu and Qiu, Feng and Rasmussen, Morten and Pan, Hailin and Hauser, Frank and Krogh, Anders and Grimmelikhuijzen, Cornelis J. P. and Wang, Jun and Boomsma, Jacobus J.},
  month = aug,
  year = {2011},
  keywords = {Animals,Phylogeny,Genome,Fungal,Molecular Sequence Data,Fungi,Genes,Insect Proteins,Genes; Fungal,Symbiosis,Male,Adaptation; Physiological,Ants,Sexual Behavior; Animal,Adaptation,Animal,Physiological,Sexual Behavior},
  pages = {1339-1348},
  pmid = {21719571},
  pmcid = {PMC3149500}
}

@article{Honeybee2006,
  title = {Insights into Social Insects from the Genome of the Honeybee {{Apis}} Mellifera},
  volume = {443},
  issn = {1476-4687},
  doi = {10.1038/nature05260},
  abstract = {Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A+T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A. mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A. mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.},
  language = {eng},
  number = {7114},
  journal = {Nature},
  author = {{Honeybee Genome Sequencing Consortium}},
  month = oct,
  year = {2006},
  keywords = {Animals,Molecular,Phylogeny,Proteome,Genome,Genomics,Molecular Sequence Data,Genes,Evolution,Evolution; Molecular,Male,DNA Transposable Elements,Female,Base Composition,Bees,Behavior; Animal,Gene Expression Regulation,Genes; Insect,Genome; Insect,Immunity,Physical Chromosome Mapping,Reproduction,Signal Transduction,Social Behavior,Telomere,Insect,Animal,Behavior},
  pages = {931-949},
  pmid = {17073008},
  pmcid = {PMC2048586}
}

@article{Bonasio2010,
  title = {Genomic Comparison of the Ants {{Camponotus}} Floridanus and {{Harpegnathos}} Saltator},
  volume = {329},
  issn = {1095-9203},
  doi = {10.1126/science.1192428},
  abstract = {The organized societies of ants include short-lived worker castes displaying specialized behavior and morphology and long-lived queens dedicated to reproduction. We sequenced and compared the genomes of two socially divergent ant species: Camponotus floridanus and Harpegnathos saltator. Both genomes contained high amounts of CpG, despite the presence of DNA methylation, which in non-Hymenoptera correlates with CpG depletion. Comparison of gene expression in different castes identified up-regulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of microRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Our findings provide clues on the molecular differences between castes in these two ants and establish a new experimental model to study epigenetics in aging and behavior.},
  language = {eng},
  number = {5995},
  journal = {Science (New York, N.Y.)},
  author = {Bonasio, Roberto and Zhang, Guojie and Ye, Chaoyang and Mutti, Navdeep S. and Fang, Xiaodong and Qin, Nan and Donahue, Greg and Yang, Pengcheng and Li, Qiye and Li, Cai and Zhang, Pei and Huang, Zhiyong and Berger, Shelley L. and Reinberg, Danny and Wang, Jun and Liebig, J\"urgen},
  month = aug,
  year = {2010},
  keywords = {Animals,Proteome,Sequence Analysis,DNA,Amino Acid Sequence,Genome,Genetic,Molecular Sequence Data,Genes,Nucleic Acid,Insect Proteins,Sequence Analysis; DNA,Species Specificity,Repetitive Sequences; Nucleic Acid,Ants,Behavior; Animal,Gene Expression Regulation,Genes; Insect,Social Behavior,Aging,Dinucleoside Phosphates,Epigenesis; Genetic,Gene Expression Profiling,Group III Histone Deacetylases,Hydrocarbons,MicroRNAs,Protein Methyltransferases,Telomerase,Insect,Animal,Behavior,Epigenesis,Repetitive Sequences},
  pages = {1068-1071},
  pmid = {20798317},
  pmcid = {PMC3772619}
}

@article{Suen2011,
  title = {The Genome Gequence of the Leaf-Cutter Ant {{Atta}} Cephalotes Reveals Insights into {{Its}} Obligate Symbiotic Lifestyle},
  volume = {7},
  doi = {10.1371/journal.pgen.1002007},
  abstract = {Author Summary
Leaf-cutter ant workers forage for and cut leaves that they use to support the growth of a specialized fungus, which serves as the colony's primary food source. The ability of these ants to grow their own food likely facilitated their emergence as one of the most dominant herbivores in New World tropical ecosystems, where leaf-cutter ants harvest more plant biomass than any other herbivore species. These ants have also evolved one of the most complex forms of division of labor, with colonies composed of different-sized workers specialized for different tasks. To gain insight into the biology of these ants, we sequenced the first genome of a leaf-cutter ant, Atta cephalotes. Our analysis of this genome reveals characteristics reflecting the obligate nutritional dependency of these ants on their fungus. These findings represent the first genetic evidence of a reduced capacity for nutrient acquisition in leaf-cutter ants, which is likely compensated for by their fungal symbiont. These findings parallel other nutritional host\textendash{}microbe symbioses, suggesting convergent genomic modifications in these types of associations.},
  number = {2},
  urldate = {2015-08-10},
  journal = {PLoS Genet},
  url = {http://dx.doi.org/10.1371/journal.pgen.1002007},
  author = {Suen, Garret and Teiling, Clotilde and Li, Lewyn and Holt, Carson and Abouheif, Ehab and {Bornberg-Bauer}, Erich and Bouffard, Pascal and Caldera, Eric J. and Cash, Elizabeth and Cavanaugh, Amy and Denas, Olgert and Elhaik, Eran and Fav\'e, Marie-Julie and Gadau, J\"urgen and Gibson, Joshua D. and Graur, Dan and Grubbs, Kirk J. and Hagen, Darren E. and Harkins, Timothy T. and Helmkampf, Martin and Hu, Hao and Johnson, Brian R. and Kim, Jay and Marsh, Sarah E. and Moeller, Joseph A. and {Mu\~noz-Torres}, M\'onica C. and Murphy, Marguerite C. and Naughton, Meredith C. and Nigam, Surabhi and Overson, Rick and Rajakumar, Rajendhran and Reese, Justin T. and Scott, Jarrod J. and Smith, Chris R. and Tao, Shu and Tsutsui, Neil D. and Viljakainen, Lumi and Wissler, Lothar and Yandell, Mark D. and Zimmer, Fabian and Taylor, James and Slater, Steven C. and Clifton, Sandra W. and Warren, Wesley C. and Elsik, Christine G. and Smith, Christopher D. and Weinstock, George M. and Gerardo, Nicole M. and Currie, Cameron R.},
  month = feb,
  year = {2011},
  pages = {e1002007},
  file = {/home/mpetersen/bib/storage/PRMMGPI8/Suen et al. - 2011 - The Genome Sequence of the Leaf-Cutter Ant Atta ce.pdf;/home/mpetersen/bib/storage/QGBDBVWS/Suen et al. - 2011 - The Genome Sequence of the Leaf-Cutter Ant Atta ce.pdf}
}

@article{Chenais2012,
  title = {The Impact of Transposable Elements on Eukaryotic Genomes: {{From}} Genome Size Increase to Genetic Adaptation to Stressful Environments},
  volume = {509},
  issn = {03781119},
  shorttitle = {The Impact of Transposable Elements on Eukaryotic Genomes},
  doi = {10.1016/j.gene.2012.07.042},
  language = {en},
  number = {1},
  urldate = {2015-08-12},
  journal = {Gene},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0378111912008931},
  author = {Ch\'enais, Beno\^it and Caruso, Aurore and Hiard, Sophie and Casse, Nathalie},
  month = nov,
  year = {2012},
  keywords = {Genome evolution,Gene expression,Insecticide resistance,Mutagenesis,genome evolution,gene expression,Genetic adaptation,Insecticide Resistance,mutagenesis,Stress response},
  pages = {7-15},
  file = {/home/mpetersen/bib/storage/7TWXBFZG/Chénais et al. - 2012 - The impact of transposable elements on eukaryotic .pdf;/home/mpetersen/bib/storage/MCC338P2/S0378111912008931.html}
}

@article{Kvist2013,
  title = {Phylogenomics of {{Annelida}} Revisited: A Cladistic Approach Using Genome-Wide Expressed Sequence Tag Data Mining and Examining the Effects of Missing Data},
  volume = {29},
  copyright = {\textcopyright{} The Willi Hennig Society 2013},
  issn = {1096-0031},
  shorttitle = {Phylogenomics of {{Annelida}} Revisited},
  doi = {10.1111/cla.12015},
  abstract = {We present phylogenomic analyses of the most comprehensive molecular character set compiled for Annelida and its constituent taxa, including over 347~000 aligned nucleotide sites for 39 taxa. The nucleotide data set was recovered using a pre-existing amino acid data set of almost 48~000 aligned sites as a backbone for tBLASTn searches against NCBI. In addition, orthology determinations of the loci in the original amino acid data set were scrutinized using an All vs All Reciprocal Best Hit approach, employing BLASTp, and examining for statistical interdependency among the loci. This approach revealed considerable sequence redundancy among the loci in the original data set and a new data set was compiled, with the redundancy removed. The newly compiled nucleotide data set, the original amino acid data set, and the new reduced amino acid data set were subjected to parsimony analyses and two forms of bootstrap resampling. The last-named data set also was analysed using a maximum-likelihood approach. There were two main objectives to these analyses: (i) to examine the general topology, including support, resulting from the analyses of the new data sets and (ii) to assess the consistency of the branching patterns across optimality criteria by comparison with previous probabilistic approaches. The phylogenetic hypotheses resulting from analyses of the three data sets are largely unsupported, reflecting the continued difficulty of finding numerous, reliable, and suitable loci for a group as ancient as Annelida. Resulting parsimonious hypotheses disagree, in some respects, with the previous probabilistic approaches; Sedentaria and, in most cases, Errantia are not supported as monophyletic groups but Pleistoannelida is recovered as a (unsupported) monophyletic group in one of the three parsimony analyses as well as the likelihood analysis. In addition, we performed missing data titration studies to estimate the impact of missing data on overall support and support for specific clades.},
  language = {en},
  number = {4},
  urldate = {2015-09-09},
  journal = {Cladistics},
  url = {http://onlinelibrary.wiley.com/doi/10.1111/cla.12015/abstract},
  author = {Kvist, Sebastian and Siddall, Mark E.},
  month = aug,
  year = {2013},
  pages = {435-448},
  file = {/home/mpetersen/bib/storage/DFPZ34ZC/Kvist & Siddall, 2013 Annelida.pdf;/home/mpetersen/bib/storage/WNA3WWZC/abstract.html}
}

@article{Ellison2013,
  title = {Dosage {{Compensation}} via {{Transposable Element Mediated Rewiring}} of a {{Regulatory Network}}},
  volume = {342},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1239552},
  language = {en},
  number = {6160},
  urldate = {2015-08-24},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1239552},
  author = {Ellison, C. E. and Bachtrog, D.},
  month = nov,
  year = {2013},
  pages = {846-850}
}

@article{Altenhoff2015,
  title = {The {{OMA}} Orthology Database in 2015: Function Predictions, Better Plant Support, Synteny View and Other Improvements},
  volume = {43},
  issn = {0305-1048, 1362-4962},
  shorttitle = {The {{OMA}} Orthology Database in 2015},
  doi = {10.1093/nar/gku1158},
  language = {en},
  number = {D1},
  urldate = {2015-09-03},
  journal = {Nucleic Acids Research},
  url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1158},
  author = {Altenhoff, A. M. and {\v S}kunca, N. and Glover, N. and Train, C.-M. and Sueki, A. and Pili{\v z}ota, I. and Gori, K. and Tomiczek, B. and M\"uller, S. and Redestig, H. and Gonnet, G. H. and Dessimoz, C.},
  month = jan,
  year = {2015},
  pages = {D240-D249}
}

@article{Sonnhammer2015,
  title = {{{InParanoid}} 8: Orthology Analysis between 273 Proteomes, Mostly Eukaryotic},
  volume = {43},
  issn = {1362-4962},
  shorttitle = {{{InParanoid}} 8},
  doi = {10.1093/nar/gku1203},
  abstract = {The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173\% and the number of pairwise species comparisons by 650\%. In turn, the number of ortholog groups has increased by 423\%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.},
  language = {eng},
  number = {Database issue},
  journal = {Nucleic Acids Research},
  author = {Sonnhammer, Erik L. L. and \"Ostlund, Gabriel},
  month = jan,
  year = {2015},
  keywords = {Algorithms,Proteome,Databases; Protein,Sequence Homology; Amino Acid},
  pages = {D234-239},
  pmid = {25429972},
  pmcid = {PMC4383983}
}

@article{Elliott2015a,
  title = {What's in a Genome? {{The C}}-Value Enigma and the Evolution of Eukaryotic Genome Content},
  volume = {370},
  copyright = {\textcopyright{} 2015 The Author(s). Published by the Royal Society. All rights reserved.},
  issn = {0962-8436, 1471-2970},
  shorttitle = {What's in a Genome?},
  doi = {10.1098/rstb.2014.0331},
  abstract = {Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of `complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.},
  language = {en},
  number = {1678},
  urldate = {2015-09-03},
  journal = {Phil. Trans. R. Soc. B},
  url = {http://rstb.royalsocietypublishing.org/content/370/1678/20140331},
  author = {Elliott, Tyler A. and Gregory, T. Ryan},
  month = sep,
  year = {2015},
  pages = {20140331},
  file = {/home/mpetersen/bib/storage/C785CRK3/20140331.html;/home/mpetersen/bib/storage/CHVDMK26/20140331.html},
  pmid = {26323762}
}

@article{Cong2015,
  title = {Skipper Genome Sheds Light on Unique Phenotypic Traits and Phylogeny},
  volume = {16},
  issn = {1471-2164},
  doi = {10.1186/s12864-015-1846-0},
  language = {en},
  number = {1},
  urldate = {2015-09-03},
  journal = {BMC Genomics},
  url = {http://www.biomedcentral.com/1471-2164/16/639},
  author = {Cong, Qian and Borek, Dominika and Otwinowski, Zbyszek and Grishin, Nick V.},
  month = dec,
  year = {2015},
  keywords = {Phylogeny,Lerema accius,Skipper butterflies,Whole genome,Comparative genomics,Lepidoptera,Genotype and phenotype},
  file = {/home/mpetersen/bib/storage/VEBN7VS5/Cong et al. - 2015 - Skipper genome sheds light on unique phenotypic tr.pdf;/home/mpetersen/bib/storage/3X3QQXPW/639.html}
}

@article{Zhang2006,
  title = {Comparison of Multiple Vertebrate Genomes Reveals the Birth and Evolution of Human Exons},
  volume = {103},
  number = {36},
  urldate = {2015-09-10},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/103/36/13427.short},
  author = {Zhang, Xiang H.-F. and Chasin, Lawrence A.},
  year = {2006},
  keywords = {repeats,splicing},
  pages = {13427--13432},
  file = {/home/mpetersen/bib/storage/E93FU5N9/0a85e5315e097bef1c000000.pdf}
}

@article{Kim2014,
  title = {Divergence of {{Drosophila}} Melanogaster Repeatomes in Response to a Sharp Microclimate Contrast in {{Evolution Canyon}}, {{Israel}}},
  volume = {111},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1410372111},
  language = {en},
  number = {29},
  urldate = {2015-10-08},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1410372111},
  author = {Kim, Y. B. and Oh, J. H. and McIver, L. J. and Rashkovetsky, E. and Michalak, K. and Garner, H. R. and Kang, L. and Nevo, E. and Korol, A. B. and Michalak, P.},
  month = jul,
  year = {2014},
  keywords = {genome sequencing,adaptive evolution,incipient speciation,microsatellite},
  pages = {10630-10635}
}

@article{Perrat2013,
  title = {Transposition-{{Driven Genomic Heterogeneity}} in the {{Drosophila Brain}}},
  volume = {340},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1231965},
  language = {en},
  number = {6128},
  urldate = {2015-10-08},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1231965},
  author = {Perrat, P. N. and DasGupta, S. and Wang, J. and Theurkauf, W. and Weng, Z. and Rosbash, M. and Waddell, S.},
  month = apr,
  year = {2013},
  pages = {91-95}
}

@article{Li2013,
  title = {Activation of Transposable Elements during Aging and Neuronal Decline in {{Drosophila}}},
  volume = {16},
  issn = {1097-6256, 1546-1726},
  doi = {10.1038/nn.3368},
  number = {5},
  urldate = {2015-10-08},
  journal = {Nature Neuroscience},
  url = {http://www.nature.com/doifinder/10.1038/nn.3368},
  author = {Li, Wanhe and Prazak, Lisa and Chatterjee, Nabanita and Gr\"uninger, Servan and Krug, Lisa and Theodorou, Delphine and Dubnau, Josh},
  month = apr,
  year = {2013},
  pages = {529-531}
}

@article{Denton2014,
  title = {Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies},
  volume = {10},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1003998},
  abstract = {Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40\% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.},
  language = {eng},
  number = {12},
  journal = {PLoS computational biology},
  author = {Denton, James F. and {Lugo-Martinez}, Jose and Tucker, Abraham E. and Schrider, Daniel R. and Warren, Wesley C. and Hahn, Matthew W.},
  month = dec,
  year = {2014},
  keywords = {Animals,Genome,Genomics,Chromosome Mapping,Sequence Analysis; DNA,Drosophila melanogaster,Chickens,Pan troglodytes,Sequence Analysis; RNA},
  pages = {e1003998},
  pmid = {25474019},
  pmcid = {PMC4256071}
}

@article{Jarvis2014,
  title = {Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds},
  volume = {346},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1253451},
  language = {en},
  number = {6215},
  urldate = {2015-10-08},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1253451},
  author = {Jarvis, E. D. and Mirarab, S. and Aberer, A. J. and Li, B. and Houde, P. and Li, C. and Ho, S. Y. W. and Faircloth, B. C. and Nabholz, B. and Howard, J. T. and Suh, A. and Weber, C. C. and {da Fonseca}, R. R. and Li, J. and Zhang, F. and Li, H. and Zhou, L. and Narula, N. and Liu, L. and Ganapathy, G. and Boussau, B. and Bayzid, M. S. and Zavidovych, V. and Subramanian, S. and Gabaldon, T. and {Capella-Gutierrez}, S. and {Huerta-Cepas}, J. and Rekepalli, B. and Munch, K. and Schierup, M. and Lindow, B. and Warren, W. C. and Ray, D. and Green, R. E. and Bruford, M. W. and Zhan, X. and Dixon, A. and Li, S. and Li, N. and Huang, Y. and Derryberry, E. P. and Bertelsen, M. F. and Sheldon, F. H. and Brumfield, R. T. and Mello, C. V. and Lovell, P. V. and Wirthlin, M. and Schneider, M. P. C. and Prosdocimi, F. and Samaniego, J. A. and Velazquez, A. M. V. and {Alfaro-Nunez}, A. and Campos, P. F. and Petersen, B. and {Sicheritz-Ponten}, T. and Pas, A. and Bailey, T. and Scofield, P. and Bunce, M. and Lambert, D. M. and Zhou, Q. and Perelman, P. and Driskell, A. C. and Shapiro, B. and Xiong, Z. and Zeng, Y. and Liu, S. and Li, Z. and Liu, B. and Wu, K. and Xiao, J. and Yinqi, X. and Zheng, Q. and Zhang, Y. and Yang, H. and Wang, J. and Smeds, L. and Rheindt, F. E. and Braun, M. and Fjeldsa, J. and Orlando, L. and Barker, F. K. and Jonsson, K. A. and Johnson, W. and Koepfli, K.-P. and O'Brien, S. and Haussler, D. and Ryder, O. A. and Rahbek, C. and Willerslev, E. and Graves, G. R. and Glenn, T. C. and McCormack, J. and Burt, D. and Ellegren, H. and Alstrom, P. and Edwards, S. V. and Stamatakis, A. and Mindell, D. P. and Cracraft, J. and Braun, E. L. and Warnow, T. and Jun, W. and Gilbert, M. T. P. and Zhang, G.},
  month = dec,
  year = {2014},
  pages = {1320-1331}
}

@article{Smith2011a,
  title = {Draft Genome of the Globally Widespread and Invasive {{Argentine}} Ant ({{Linepithema}} Humile)},
  volume = {108},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1008617108},
  abstract = {Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of {$>$}1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes ({$>$}110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.},
  language = {en},
  number = {14},
  urldate = {2015-10-15},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/108/14/5673},
  author = {Smith, Christopher D. and Zimin, Aleksey and Holt, Carson and Abouheif, Ehab and Benton, Richard and Cash, Elizabeth and Croset, Vincent and Currie, Cameron R. and Elhaik, Eran and Elsik, Christine G. and Fave, Marie-Julie and Fernandes, Vilaiwan and Gadau, J\"urgen and Gibson, Joshua D. and Graur, Dan and Grubbs, Kirk J. and Hagen, Darren E. and Helmkampf, Martin and Holley, Jo-Anne and Hu, Hao and Viniegra, Ana Sofia Ibarraran and Johnson, Brian R. and Johnson, Reed M. and Khila, Abderrahman and Kim, Jay W. and Laird, Joseph and Mathis, Kaitlyn A. and Moeller, Joseph A. and {Mu\~noz-Torres}, Monica C. and Murphy, Marguerite C. and Nakamura, Rin and Nigam, Surabhi and Overson, Rick P. and Placek, Jennifer E. and Rajakumar, Rajendhran and Reese, Justin T. and Robertson, Hugh M. and Smith, Chris R. and Suarez, Andrew V. and Suen, Garret and Suhr, Elissa L. and Tao, Shu and Torres, Candice W. and van Wilgenburg, Ellen and Viljakainen, Lumi and Walden, Kimberly K. O. and Wild, Alexander L. and Yandell, Mark and Yorke, James A. and Tsutsui, Neil D.},
  month = may,
  year = {2011},
  keywords = {invasive species,transcriptome,chemoreception,Hymenoptera,sociality},
  pages = {5673-5678},
  file = {/home/mpetersen/bib/storage/2XAHRNI7/Smith et al. - 2011 - Draft genome of the globally widespread and invasi.pdf;/home/mpetersen/bib/storage/TIZS575U/5673.html},
  pmid = {21282631}
}

@article{Chalopin2015,
  title = {Comparative {{Analysis}} of {{Transposable Elements Highlights Mobilome Diversity}} and {{Evolution}} in {{Vertebrates}}},
  volume = {7},
  issn = {1759-6653},
  doi = {10.1093/gbe/evv005},
  language = {en},
  number = {2},
  urldate = {2015-10-13},
  journal = {Genome Biology and Evolution},
  url = {http://gbe.oxfordjournals.org/cgi/doi/10.1093/gbe/evv005},
  author = {Chalopin, D. and Naville, M. and Plard, F. and Galiana, D. and Volff, J.-N.},
  month = feb,
  year = {2015},
  pages = {567-580},
  file = {/home/mpetersen/bib/storage/C8BECIZX/Chalopin_submitted_GBE-Supp.docx;/home/mpetersen/bib/storage/QASD2FFS/Genome Biol Evol-2015-Chalopin-567-80.pdf}
}

@article{Gray2000,
  title = {It Takes Two Transposons to Tango: Transposable-Element-Mediated Chromosomal Rearrangements},
  volume = {16},
  issn = {0168-9525},
  shorttitle = {It Takes Two Transposons to Tango},
  abstract = {Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes(1-3). One explanation of such events is homologous recombination between multiple copies of a TE present in a genome. Although this does occur, strong evidence from a number of TE systems in bacteria, plants and animals suggests that another mechanism - alternative transposition - induces a large proportion of TE-associated chromosomal rearrangements. This paper reviews evidence for alternative transposition from a number of unrelated but structurally similar TEs. The similarities between alternative transposition and V(D)J recombination are also discussed, as is the use of alternative transposition as a genetic tool.},
  language = {eng},
  number = {10},
  journal = {Trends in genetics: TIG},
  author = {Gray, Y. H.},
  month = oct,
  year = {2000},
  keywords = {Animals,Humans,Evolution,Models; Genetic,Drosophila melanogaster,Male,DNA Transposable Elements,Mutagenesis; Insertional,Plants,Recombination; Genetic,Chromosomes,DNA Nucleotidyltransferases,VDJ Recombinases,Deletions,Duplications,Genome plasticity,Inversions,Transposon},
  pages = {461-468},
  file = {/home/mpetersen/bib/storage/GGAKM4P7/1-s2.0-S0168952500021041-main.pdf},
  pmid = {11050333}
}

@article{Emms2015,
  title = {{{OrthoFinder}}: Solving Fundamental Biases in Whole Genome Comparisons Dramatically Improves Orthogroup Inference Accuracy},
  volume = {16},
  copyright = {2015 Emms and Kelly.},
  issn = {1465-6906},
  shorttitle = {{{OrthoFinder}}},
  doi = {10.1186/s13059-015-0721-2},
  abstract = {Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 \% and 33 \%. Furthermore, we demonstrate the utility of OrthoFinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships.},
  language = {en},
  number = {1},
  urldate = {2016-01-08},
  journal = {Genome Biology},
  url = {http://genomebiology.com/2015/16/1/157/abstract},
  author = {Emms, David M. and Kelly, Steven},
  month = aug,
  year = {2015},
  pages = {157},
  file = {/home/mpetersen/bib/storage/AH2M9IUH/Emms and Kelly - 2015 - OrthoFinder solving fundamental biases in whole g.pdf;/home/mpetersen/bib/storage/PPM8DBRN/157.html},
  pmid = {26243257}
}

@article{Consortium2013,
  title = {The {{i5K Initiative}}: {{Advancing Arthropod Genomics}} for {{Knowledge}}, {{Human Health}}, {{Agriculture}}, and the {{Environment}}},
  volume = {104},
  issn = {0022-1503, 1465-7333},
  shorttitle = {The {{i5K Initiative}}},
  doi = {10.1093/jhered/est050},
  abstract = {Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.},
  language = {en},
  number = {5},
  urldate = {2014-03-15},
  journal = {Journal of Heredity},
  url = {http://jhered.oxfordjournals.org/content/104/5/595},
  author = {Consortium, i5K},
  month = sep,
  year = {2013},
  keywords = {comparative genomics,agriculture,disease vector,genome sequencing,insect evolution},
  pages = {595-600},
  pmid = {23940263}
}

@article{Adams2000,
  title = {The {{Genome Sequence}} of {{Drosophila}} Melanogaster},
  volume = {287},
  issn = {00368075, 10959203},
  doi = {10.1126/science.287.5461.2185},
  number = {5461},
  urldate = {2015-05-27},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.287.5461.2185},
  author = {Adams, M. D.},
  month = mar,
  year = {2000},
  pages = {2185-2195}
}

@book{Gregory2011,
  title = {The {{Evolution}} of the {{Genome}}},
  isbn = {978-0-08-047052-8},
  abstract = {The Evolution of the Genome provides a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. This includes the evolution of genome size, genomic parasites, gene and ancient genome duplications, polypoidy, comparative genomics, and the implications of these genome-level phenomena for evolutionary theory. In addition to reviewing the current state of knowledge of these fields in an accessible way, the various chapters also provide historical and conceptual background information, highlight the ways in which the critical questions are actually being studied, indicate some important areas for future research, and build bridges across traditional professional and taxonomic boundaries.The Evolution of the Genome will serve as a critical resource for graduate students, postdoctoral fellows, and established scientists alike who are interested in the issue of genome evolution in the broadest sense.{$\cdot$} Provides detailed, clearly written chapters authored by leading researchers in their respective fields{$\cdot$} Presents a much-needed overview of the historical and theoretical context of the various areas of genomic study{$\cdot$} Creates important links between topics in order to promote integration across subdisciplines, including descriptions of how each subject is actually studied{$\cdot$} Provides information specifically designed to be accessible to established researchers, postdoctoral fellows, and graduate students alike},
  language = {en},
  publisher = {{Academic Press}},
  author = {Gregory, T. Ryan},
  month = may,
  year = {2011},
  keywords = {Science / Life Sciences / Molecular Biology,Science / Life Sciences / Evolution,Science / Life Sciences / Developmental Biology,Science / Life Sciences / Ecology,Science / Life Sciences / Genetics \& Genomics,Science / Earth Sciences / General}
}

@article{Cridland2013,
  title = {Abundance and {{Distribution}} of {{Transposable Elements}} in {{Two Drosophila QTL Mapping Resources}}},
  volume = {30},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/mst129},
  language = {en},
  number = {10},
  urldate = {2016-01-27},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/mst129},
  author = {Cridland, J. M. and Macdonald, S. J. and Long, A. D. and Thornton, K. R.},
  month = oct,
  year = {2013},
  pages = {2311-2327}
}

@article{Kofler2015,
  title = {Tempo and {{Mode}} of {{Transposable Element Activity}} in {{Drosophila}}},
  volume = {11},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1005406},
  language = {en},
  number = {7},
  urldate = {2016-02-01},
  journal = {PLOS Genetics},
  url = {http://dx.plos.org/10.1371/journal.pgen.1005406},
  author = {Kofler, Robert and Nolte, Viola and Schl\"otterer, Christian},
  editor = {Petrov, Dmitri A.},
  month = jul,
  year = {2015},
  pages = {e1005406},
  file = {/home/mpetersen/bib/storage/3QPKRXWC/journal.pgen.1005406.pdf}
}

@article{Rognes2011,
  title = {Faster {{Smith}}-{{Waterman}} Database Searches with Inter-Sequence {{SIMD}} Parallelisation},
  volume = {12},
  issn = {1471-2105},
  doi = {10.1186/1471-2105-12-221},
  abstract = {The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation.},
  urldate = {2016-03-01},
  journal = {BMC Bioinformatics},
  url = {http://dx.doi.org/10.1186/1471-2105-12-221},
  author = {Rognes, Torbj\o{}rn},
  year = {2011},
  pages = {221},
  file = {/home/mpetersen/bib/storage/BUHDWIWI/Rognes - 2011 - Faster Smith-Waterman database searches with inter.pdf;/home/mpetersen/bib/storage/SZD9E82U/1471-2105-12-221.html}
}

@article{Casola2007,
  title = {{{PIF}}-like {{Transposons}} Are {{Common}} in {{Drosophila}} and {{Have Been Repeatedly Domesticated}} to {{Generate New Host Genes}}},
  volume = {24},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msm116},
  abstract = {The P instability factor or PIF superfamily of DNA transposons constitutes an important group of transposable elements (TEs) in plants, but it is still poorly characterized in metazoans. Taking advantage of the availability of draft genome sequences for twelve Drosophila species, we discovered 4 different lineages of Drosophila PIF-like transposons, named DPLT1-4. These lineages have experienced a complex evolutionary history during the Drosophila radiation, involving differential amplification and retention among species and probable events of horizontal transmission. Like previously described plant and animal PIF transposons, full-length DPLTs encode a putative transposase as well as a second predicted protein containing a Myb/SANT domain. In DPLTs, this domain is most closely related to the MADF DNA-binding domain found in several Drosophila transcription factors. In addition, we identified 7 distinct genes distributed across the Drosophila genus that encode proteins related to PIF transposases, but lack the hallmarks of transposons. Instead, these sequences show features of functional genes, such as an intact coding region evolving under purifying selection, the presence of orthologs in at least 2 Drosophila species, and the conservation of intron/exon structure across orthologs. We also provide evidence that most of these genes are transcribed and that some are developmentally regulated. Together the data indicate that these genes derived from PIF-transposons that have been ``domesticated'' to serve cellular functions. In one instance the recruitment of the transposase gene was accompanied by the co-recruitment of the adjacent second PIF gene, which raises the hypothesis that both proteins now function in the same pathway. The second PIF gene has retained the capacity to encode a protein with an intact MADF domain, suggesting that it may function as a transcription factor. We conclude that PIF transposons are common in the Drosophila lineage and have been a recurrent source of new genes during Drosophila evolution.},
  language = {en},
  number = {8},
  urldate = {2015-10-14},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/content/24/8/1872},
  author = {Casola, Claudio and Lawing, A. Michelle and Betr\'an, Esther and Feschotte, C\'edric},
  month = aug,
  year = {2007},
  keywords = {Drosophila,transposase,PIF superfamily,transposon domestication,MADF domain,horizontal transfer},
  pages = {1872-1888},
  file = {/home/mpetersen/bib/storage/DZUXAKUB/Casola et al. - 2007 - PIF-like Transposons are Common in Drosophila and .pdf;/home/mpetersen/bib/storage/QTQSSGM8/1872.html},
  pmid = {17556756}
}

@article{Petrov2011,
  title = {Population {{Genomics}} of {{Transposable Elements}} in {{Drosophila}} Melanogaster},
  volume = {28},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msq337},
  language = {en},
  number = {5},
  urldate = {2015-10-14},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msq337},
  author = {Petrov, D. A. and {Fiston-Lavier}, A.-S. and Lipatov, M. and Lenkov, K. and Gonzalez, J.},
  month = may,
  year = {2011},
  pages = {1633-1644},
  file = {/home/mpetersen/bib/storage/JAVAKQ35/76.pdf}
}

@article{Holt2002,
  title = {The Genome Sequence of the Malaria Mosquito {{Anopheles}} Gambiae},
  volume = {298},
  issn = {1095-9203},
  doi = {10.1126/science.1076181},
  abstract = {Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91\% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.},
  language = {eng},
  number = {5591},
  journal = {Science (New York, N.Y.)},
  author = {Holt, Robert A. and Subramanian, G. Mani and Halpern, Aaron and Sutton, Granger G. and Charlab, Rosane and Nusskern, Deborah R. and Wincker, Patrick and Clark, Andrew G. and Ribeiro, Jos\'e M. C. and Wides, Ron and Salzberg, Steven L. and Loftus, Brendan and Yandell, Mark and Majoros, William H. and Rusch, Douglas B. and Lai, Zhongwu and Kraft, Cheryl L. and Abril, Josep F. and Anthouard, Veronique and Arensburger, Peter and Atkinson, Peter W. and Baden, Holly and {de Berardinis}, Veronique and Baldwin, Danita and Benes, Vladimir and Biedler, Jim and Blass, Claudia and Bolanos, Randall and Boscus, Didier and Barnstead, Mary and Cai, Shuang and Center, Angela and Chaturverdi, Kabir and Christophides, George K. and Chrystal, Mathew A. and Clamp, Michele and Cravchik, Anibal and Curwen, Val and Dana, Ali and Delcher, Art and Dew, Ian and Evans, Cheryl A. and Flanigan, Michael and {Grundschober-Freimoser}, Anne and Friedli, Lisa and Gu, Zhiping and Guan, Ping and Guigo, Roderic and Hillenmeyer, Maureen E. and Hladun, Susanne L. and Hogan, James R. and Hong, Young S. and Hoover, Jeffrey and Jaillon, Olivier and Ke, Zhaoxi and Kodira, Chinnappa and Kokoza, Elena and Koutsos, Anastasios and Letunic, Ivica and Levitsky, Alex and Liang, Yong and Lin, Jhy-Jhu and Lobo, Neil F. and Lopez, John R. and Malek, Joel A. and McIntosh, Tina C. and Meister, Stephan and Miller, Jason and Mobarry, Clark and Mongin, Emmanuel and Murphy, Sean D. and O'Brochta, David A. and Pfannkoch, Cynthia and Qi, Rong and Regier, Megan A. and Remington, Karin and Shao, Hongguang and Sharakhova, Maria V. and Sitter, Cynthia D. and Shetty, Jyoti and Smith, Thomas J. and Strong, Renee and Sun, Jingtao and Thomasova, Dana and Ton, Lucas Q. and Topalis, Pantelis and Tu, Zhijian and Unger, Maria F. and Walenz, Brian and Wang, Aihui and Wang, Jian and Wang, Mei and Wang, Xuelan and Woodford, Kerry J. and Wortman, Jennifer R. and Wu, Martin and Yao, Alison and Zdobnov, Evgeny M. and Zhang, Hongyu and Zhao, Qi and Zhao, Shaying and Zhu, Shiaoping C. and Zhimulev, Igor and Coluzzi, Mario and {della Torre}, Alessandra and Roth, Charles W. and Louis, Christos and Kalush, Francis and Mural, Richard J. and Myers, Eugene W. and Adams, Mark D. and Smith, Hamilton O. and Broder, Samuel and Gardner, Malcolm J. and Fraser, Claire M. and Birney, Ewan and Bork, Peer and Brey, Paul T. and Venter, J. Craig and Weissenbach, Jean and Kafatos, Fotis C. and Collins, Frank H. and Hoffman, Stephen L.},
  month = oct,
  year = {2002},
  keywords = {Animals,Humans,Proteome,Sequence Analysis,DNA,Computational Biology,Genome,Expressed Sequence Tags,Genetic Variation,Molecular Sequence Data,Genes,Insect Proteins,Biological Evolution,Sequence Analysis; DNA,Drosophila melanogaster,Species Specificity,DNA Transposable Elements,Gene Expression Regulation,Genes; Insect,Physical Chromosome Mapping,Anopheles,Chromosome Inversion,Chromosomes,Transcription Factors,Blood,Chromosomes; Artificial; Bacterial,Digestion,Enzymes,Feeding Behavior,Haplotypes,Insect Vectors,Malaria; Falciparum,Mosquito Control,Plasmodium falciparum,Polymorphism; Single Nucleotide,Insect,Artificial,Bacterial,Falciparum,Malaria,Polymorphism,Single Nucleotide},
  pages = {129-149},
  pmid = {12364791}
}

@article{Munoz-Torres2011,
  title = {Hymenoptera {{Genome Database}}: Integrated Community Resources for Insect Species of the Order {{Hymenoptera}}},
  volume = {39},
  issn = {0305-1048, 1362-4962},
  shorttitle = {Hymenoptera {{Genome Database}}},
  doi = {10.1093/nar/gkq1145},
  language = {en},
  number = {Database},
  urldate = {2015-10-26},
  journal = {Nucleic Acids Research},
  url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkq1145},
  author = {{Munoz-Torres}, M. C. and Reese, J. T. and Childers, C. P. and Bennett, A. K. and Sundaram, J. P. and Childs, K. L. and Anzola, J. M. and Milshina, N. and Elsik, C. G.},
  month = jan,
  year = {2011},
  pages = {D658-D662}
}

@article{Katoh2013,
  title = {{{MAFFT}} Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability},
  volume = {30},
  issn = {1537-1719},
  shorttitle = {{{MAFFT}} Multiple Sequence Alignment Software Version 7},
  doi = {10.1093/molbev/mst010},
  abstract = {We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.},
  language = {eng},
  number = {4},
  journal = {Molecular Biology and Evolution},
  author = {Katoh, Kazutaka and Standley, Daron M.},
  month = apr,
  year = {2013},
  keywords = {Algorithms,Humans,Phylogeny,Sequence Alignment,Amino Acid Sequence,Software,Base Sequence,Molecular Sequence Data,Fungi,Models; Genetic,Protein Structure; Tertiary,DNA; Fungal,Ribonucleases,DNA; Ribosomal,multiple sequence alignment,metagemone,protein structure,progressive alignment,parallel processing,DNA; Ribosomal Spacer,Quality Improvement,RNA; Bacterial,Ribosome Subunits; Small; Bacterial},
  pages = {772-780},
  file = {/home/mpetersen/bib/storage/H5EUGGVC/Katoh and Standley - 2013 - MAFFT Multiple Sequence Alignment Software Version.pdf;/home/mpetersen/bib/storage/87NBKUJ6/772.html},
  pmid = {23329690},
  pmcid = {PMC3603318}
}

@article{Blumenstiel2014,
  title = {An {{Age}}-of-{{Allele Test}} of {{Neutrality}} for {{Transposable Element Insertions}}},
  volume = {196},
  copyright = {Copyright \textcopyright{} 2014 by the Genetics Society of America. Available freely online through the author-supported open access option.},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.113.158147},
  abstract = {How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, previous studies have used models of transposition\textendash{}selection equilibrium that assume a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence. By conditioning on the age of an individual TE insertion allele (inferred by the number of unique substitutions that have occurred within the particular TE sequence since insertion), we determine the probability distribution of the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this nonequilibrium neutral model, we are able to explain {$\sim$}80\% of the variance in TE insertion allele frequencies based on age alone. Controlling for both nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications, or other copy number variants.},
  language = {en},
  number = {2},
  urldate = {2016-03-17},
  journal = {Genetics},
  url = {http://www.genetics.org/content/196/2/523},
  author = {Blumenstiel, Justin P. and Chen, Xi and He, Miaomiao and Bergman, Casey M.},
  month = feb,
  year = {2014},
  keywords = {Drosophila melanogaster,Genome evolution,population genomics,transposable elements (TEs),test of neutrality},
  pages = {523-538},
  file = {/home/mpetersen/bib/storage/3PUB72HV/Blumenstiel et al. - 2014 - An Age-of-Allele Test of Neutrality for Transposab.pdf;/home/mpetersen/bib/storage/UZFV2A2H/523.html},
  pmid = {24336751}
}

@article{Rehan2016,
  title = {The Genome and Methylome of a Subsocial Small Carpenter Bee, {{{\emph{Ceratina}}}}{\emph{ Calcarata}}},
  issn = {1759-6653},
  doi = {10.1093/gbe/evw079},
  language = {en},
  urldate = {2016-04-12},
  journal = {Genome Biology and Evolution},
  url = {http://gbe.oxfordjournals.org/lookup/doi/10.1093/gbe/evw079},
  author = {Rehan, Sandra M. and Glastad, Karl M. and Lawson, Sarah P. and Hunt, Brendan G.},
  month = apr,
  year = {2016},
  pages = {evw079},
  file = {/home/mpetersen/bib/storage/EXWTW54F/Genome_Biol_Evol-2016-Rehan-gbe_evw079.pdf;/home/mpetersen/bib/storage/TXZH3KPD/Genome_Biol_Evol-2016-Rehan-gbe_evw079.pdf}
}

@misc{Hipp2016,
  title = {{{SQLite}}},
  copyright = {Public domain},
  shorttitle = {{{SQLite}}},
  url = {https://www.sqlite.org},
  author = {Hipp, Richard D. and Kennedy, Dan and Mistachkin, Joe},
  year = {2016}
}

@article{Hof2016,
  title = {The Industrial Melanism Mutation in {{British}} Peppered Moths Is a Transposable Element},
  volume = {534},
  copyright = {\textcopyright{} 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  issn = {0028-0836},
  doi = {10.1038/nature17951},
  abstract = {Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria\textendash{}typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of `jumping genes' as a source of major phenotypic novelty.},
  language = {en},
  number = {7605},
  urldate = {2016-06-03},
  journal = {Nature},
  url = {http://www.nature.com/nature/journal/v534/n7605/full/nature17951.html},
  author = {van't Hof, Arjen E. and Campagne, Pascal and Rigden, Daniel J. and Yung, Carl J. and Lingley, Jessica and Quail, Michael A. and Hall, Neil and Darby, Alistair C. and Saccheri, Ilik J.},
  month = jun,
  year = {2016},
  keywords = {Evolutionary genetics,Gene expression},
  pages = {102-105},
  file = {/home/mpetersen/bib/storage/N47MHRBN/nature17951.pdf;/home/mpetersen/bib/storage/4ACAKNTF/nature17951.html}
}

@article{Struck2011,
  title = {Phylogenomic Analyses Unravel Annelid Evolution},
  volume = {471},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/nature09864},
  number = {7336},
  urldate = {2016-07-21},
  journal = {Nature},
  url = {http://www.nature.com/doifinder/10.1038/nature09864},
  author = {Struck, Torsten H. and Paul, Christiane and Hill, Natascha and Hartmann, Stefanie and H\"osel, Christoph and Kube, Michael and Lieb, Bernhard and Meyer, Achim and Tiedemann, Ralph and Purschke, G\"unter and Bleidorn, Christoph},
  month = mar,
  year = {2011},
  pages = {95-98},
  file = {/home/mpetersen/bib/storage/CTZJUDI4/10.1038@nature09864.pdf}
}

@article{Xie2014,
  title = {{{SOAPdenovo}}-{{Trans}}: De Novo Transcriptome Assembly with Short {{RNA}}-{{Seq}} Reads},
  volume = {30},
  issn = {1367-4803, 1460-2059},
  shorttitle = {{{SOAPdenovo}}-{{Trans}}},
  doi = {10.1093/bioinformatics/btu077},
  language = {en},
  number = {12},
  urldate = {2016-08-18},
  journal = {Bioinformatics},
  url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu077},
  author = {Xie, Y. and Wu, G. and Tang, J. and Luo, R. and Patterson, J. and Liu, S. and Huang, W. and He, G. and Gu, S. and Li, S. and Zhou, X. and Lam, T.-W. and Li, Y. and Xu, X. and Wong, G. K.-S. and Wang, J.},
  month = jun,
  year = {2014},
  pages = {1660-1666}
}

@article{deKoning2011,
  title = {Repetitive Elements May Comprise over Two-Thirds of the Human Genome},
  volume = {7},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1002384},
  abstract = {Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds"). We show here that P-clouds predicts {$>$}840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66\%-69\% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes ({$\sim$}25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified {$\sim$}100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.},
  language = {eng},
  number = {12},
  journal = {PLoS genetics},
  author = {{de Koning}, A. P. Jason and Gu, Wanjun and Castoe, Todd A. and Batzer, Mark A. and Pollock, David D.},
  month = dec,
  year = {2011},
  keywords = {Algorithms,Humans,Computational Biology,Software,Consensus Sequence,Molecular Sequence Annotation,Genome; Human,DNA Transposable Elements,Repetitive Sequences; Nucleic Acid,Alu Elements,Long Interspersed Nucleotide Elements},
  pages = {e1002384},
  pmid = {22144907},
  pmcid = {PMC3228813}
}

@article{Szitenberg2016,
  title = {Genetic Drift, Not Life History or {{RNAi}}, Determine Long Term Evolution of Transposable Elements},
  issn = {, 1759-6653},
  doi = {10.1093/gbe/evw208},
  abstract = {Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host's genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways, have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.},
  language = {en},
  urldate = {2016-08-29},
  journal = {Genome Biology and Evolution},
  url = {http://gbe.oxfordjournals.org/content/early/2016/08/26/gbe.evw208},
  author = {Szitenberg, Amir and Cha, Soyeon and Opperman, Charles H. and Bird, David M. and Blaxter, Mark L. and Lunt, David H.},
  month = aug,
  year = {2016},
  keywords = {Nematoda,transposable elements evolution,RNA interference,mating system,parasitism},
  pages = {evw208},
  file = {/home/mpetersen/bib/storage/54XRTU2I/evw208.pdf;/home/mpetersen/bib/storage/7C6SIZS3/Szitenberg et al. - 2016 - Genetic drift, not life history or RNAi, determine.pdf;/home/mpetersen/bib/storage/UVFHZDFX/gbe.evw208.html},
  pmid = {27566762}
}

@article{Chenais2015,
  title = {Transposable Elements in Cancer and Other Human Diseases},
  volume = {15},
  issn = {1873-5576},
  abstract = {Transposable elements (TEs) are mobile DNA sequences representing a substantial fraction of most genomes. Through the creation of new genes and functions, TEs are important elements of genome plasticity and evolution. However TE insertion in human genomes may be the cause of genetic dysfunction and alteration of gene expression contributing to cancer and other human diseases. Besides the chromosome rearrangements induced by TE repeats, this mini-review shows how gene expression may be altered following TE insertion, for example by the creation of new polyadenylation sites, by the creation of new exons (exonization), by exon skipping and by other modification of alternative splicing, and also by the alteration of regulatory sequences. Through the correlation between TE mobility and the methylation status of DNA, the importance of chromatin regulation is evident in several diseases. Finally this overview ends with a brief presentation of the use of TEs as biotechnology tools for insertional mutagenesis screening and gene therapy with DNA transposons.},
  language = {eng},
  number = {3},
  journal = {Current Cancer Drug Targets},
  author = {Chenais, Benoit},
  year = {2015},
  keywords = {Humans,DNA Transposable Elements,Mutagenesis; Insertional,Female,Placenta,Pregnancy,Recombination; Genetic,Gene Expression Regulation; Developmental,Alu Elements,Alternative Splicing,Galectins,Gene Expression Regulation; Neoplastic,Genetic Predisposition to Disease,Genetic Therapy,Neoplasms,Promoter Regions; Genetic},
  pages = {227-242},
  pmid = {25808076}
}

@article{Vorechovsky2009,
  title = {Transposable Elements in Disease-Associated Cryptic Exons},
  volume = {127},
  doi = {10.1007/s00439-009-0752-4},
  number = {2},
  journal = {Hum Genet},
  url = {http://dx.doi.org/10.1007/s00439-009-0752-4},
  author = {Vorechovsky, Igor},
  month = oct,
  year = {2009},
  pages = {135-154}
}

@article{Hancks2016,
  title = {Roles for Retrotransposon Insertions in Human Disease},
  volume = {7},
  doi = {10.1186/s13100-016-0065-9},
  number = {1},
  journal = {Mobile DNA},
  url = {http://dx.doi.org/10.1186/s13100-016-0065-9},
  author = {Hancks, Dustin C. and Kazazian, Haig H.},
  month = may,
  year = {2016}
}

@article{Eickbush2008,
  title = {The Diversity of Retrotransposons and the Properties of Their Reverse Transcriptases},
  volume = {134},
  doi = {10.1016/j.virusres.2007.12.010},
  number = {1-2},
  journal = {Virus Research},
  url = {http://dx.doi.org/10.1016/j.virusres.2007.12.010},
  author = {Eickbush, Thomas H. and Jamburuthugoda, Varuni K.},
  month = jun,
  year = {2008},
  pages = {221-234}
}

@article{Robinson2011,
  title = {Creating a Buzz about Insect Genomes},
  volume = {331},
  number = {6023},
  urldate = {2016-09-09},
  journal = {Science},
  url = {https://www.researchgate.net/profile/Jay_Evans/publication/50420113_Creating_a_buzz_about_insect_genomes/links/0deec53568f92d6bf1000000.pdf},
  author = {Robinson, Gene E. and Hackett, Kevin J. and {Purcell-Miramontes}, Mary and Brown, Susan J. and Evans, Jay D. and Goldsmith, Marian R. and Lawson, Daniel and Okamuro, Jack and Robertson, Hugh M. and Schneider, David J. and others},
  year = {2011},
  pages = {1386--1386},
  file = {/home/mpetersen/bib/storage/3WTFP33D/1386.full.pdf}
}

@article{Struchiner2009,
  title = {The Tempo and Mode of Evolution of Transposable Elements as Revealed by Molecular Phylogenies Reconstructed from Mosquito Genomes},
  volume = {63},
  doi = {10.1111/j.1558-5646.2009.00788.x},
  number = {12},
  journal = {Evolution},
  url = {http://dx.doi.org/10.1111/j.1558-5646.2009.00788.x},
  author = {Struchiner, Claudio J. and Massad, Eduardo and Tu, Zhijian and Ribeiro, Jos\'e M. C.},
  month = dec,
  year = {2009},
  pages = {3136-3146},
  file = {/home/mpetersen/bib/storage/MC4WV25S/j.1558-5646.2009.00788.x.pdf}
}

@misc{Smit2015a,
  title = {{{RepeatModeler Open}}-4.0},
  url = {http://www.repeatmasker.org},
  author = {Smit, AFA and Hubley, R and Green, P},
  year = {2015}
}

@article{Jurka2005,
  title = {Repbase {{Update}}, a Database of Eukaryotic Repetitive Elements},
  volume = {110},
  issn = {1424-859X, 1424-8581},
  doi = {10.1159/000084979},
  language = {en},
  number = {1-4},
  journal = {Cytogenetic and Genome Research},
  author = {Jurka, J. and Kapitonov, V.V. and Pavlicek, A. and Klonowski, P. and Kohany, O. and Walichiewicz, J.},
  year = {2005},
  pages = {462-467}
}

@article{Burns2012,
  title = {Human {{Transposon Tectonics}}},
  volume = {149},
  doi = {10.1016/j.cell.2012.04.019},
  number = {4},
  journal = {Cell},
  url = {http://dx.doi.org/10.1016/j.cell.2012.04.019},
  author = {Burns, Kathleen H. and Boeke, Jef D.},
  month = may,
  year = {2012},
  pages = {740-752}
}

@article{Feschotte2008,
  title = {Transposable Elements and the Evolution of Regulatory Networks},
  volume = {9},
  doi = {10.1038/nrg2337},
  number = {5},
  journal = {Nat Rev Genet},
  url = {http://dx.doi.org/10.1038/nrg2337},
  author = {Feschotte, C\'edric},
  month = may,
  year = {2008},
  pages = {397-405}
}

@article{Chen2007,
  title = {Transposable Elements Are Enriched within or in Close Proximity to Xenobiotic-Metabolizing Cytochrome {{P450}} Genes},
  volume = {7},
  doi = {10.1186/1471-2148-7-46},
  number = {1},
  journal = {BMC Evol Biol},
  url = {http://dx.doi.org/10.1186/1471-2148-7-46},
  author = {Chen, Song and Li, Xianchun},
  year = {2007},
  pages = {46}
}

@article{Itokawa2010,
  title = {Genomic Structures of {{Cyp9m10}} in Pyrethroid Resistant and Susceptible Strains of {{Culex}} Quinquefasciatus},
  volume = {40},
  doi = {10.1016/j.ibmb.2010.06.001},
  number = {9},
  journal = {Insect Biochemistry and Molecular Biology},
  url = {http://dx.doi.org/10.1016/j.ibmb.2010.06.001},
  author = {Itokawa, Kentaro and Komagata, Osamu and Kasai, Shinji and Okamura, Yoshika and Masada, Masahiro and Tomita, Takashi},
  month = sep,
  year = {2010},
  pages = {631-640}
}

@article{Gahan2001,
  title = {Identification of a {{Gene Associated}} with {{Bt Resistance}} in {{Heliothis}} Virescens},
  volume = {293},
  doi = {10.1126/science.1060949},
  number = {5531},
  journal = {Science},
  url = {http://dx.doi.org/10.1126/science.1060949},
  author = {Gahan, L. J.},
  month = aug,
  year = {2001},
  pages = {857-860}
}

@article{Gonzalez2010,
  title = {Genome-{{Wide Patterns}} of {{Adaptation}} to {{Temperate Environments Associated}} with {{Transposable Elements}} in {{Drosophila}}},
  volume = {6},
  doi = {10.1371/journal.pgen.1000905},
  number = {4},
  journal = {PLoS Genetics},
  url = {http://dx.doi.org/10.1371/journal.pgen.1000905},
  author = {Gonz\'alez, Josefa and Karasov, Talia L. and Messer, Philipp W. and Petrov, Dmitri A.},
  editor = {Malik, Harmit S.},
  month = apr,
  year = {2010},
  pages = {e1000905}
}

@article{Staton2015,
  title = {Evolutionary {{Transitions}} in the {{Asteraceae Coincide}} with {{Marked Shifts}} in {{Transposable Element Abundance}}},
  volume = {16},
  issn = {1471-2164},
  doi = {10.1186/s12864-015-1830-8},
  abstract = {Background The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of Utricularia gibba to more than 80~\% in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants. Results Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of Gypsy retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in Gypsy abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner. Conclusions We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1830-8) contains supplementary material, which is available to authorized users.},
  number = {1},
  urldate = {2015-08-24},
  journal = {BMC Genomics},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546089/},
  author = {Staton, S. Evan and Burke, John M.},
  month = aug,
  year = {2015},
  file = {/home/mpetersen/bib/storage/7T9JEYE6/Staton and Burke - 2015 - Evolutionary transitions in the Asteraceae coincid.pdf;/home/mpetersen/bib/storage/7V6UWN8R/Staton and Burke - 2015 - Evolutionary transitions in the Asteraceae coincid.pdf},
  pmcid = {PMC4546089},
  pmid = {26290182}
}

@article{Malik1999,
  title = {The Age and Evolution of Non-{{LTR}} Retrotransposable Elements},
  volume = {16},
  doi = {10.1093/oxfordjournals.molbev.a026164},
  number = {6},
  journal = {Molecular Biology and Evolution},
  url = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026164},
  author = {Malik, H. S. and Burke, W. D. and Eickbush, T. H.},
  month = jun,
  year = {1999},
  pages = {793-805}
}

@article{delaChaux2011,
  title = {{{BEL}}/{{Pao}} Retrotransposons in Metazoan Genomes},
  volume = {11},
  doi = {10.1186/1471-2148-11-154},
  number = {1},
  journal = {BMC Evol Biol},
  url = {http://dx.doi.org/10.1186/1471-2148-11-154},
  author = {{de la Chaux}, Nicole and Wagner, Andreas},
  year = {2011},
  pages = {154}
}

@article{Marin2000,
  title = {Ty3/{{Gypsy Retrotransposons}}: {{Description}} of {{New Arabidopsis}} Thaliana {{Elements}} and {{Evolutionary Perspectives Derived}} from {{Comparative Genomic Data}}},
  volume = {17},
  doi = {10.1093/oxfordjournals.molbev.a026385},
  number = {7},
  journal = {Molecular Biology and Evolution},
  url = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026385},
  author = {Marin, I. and Llorens, C.},
  month = jul,
  year = {2000},
  pages = {1040-1049}
}

@article{Wicker2007,
  title = {A Unified Classification System for Eukaryotic Transposable Elements},
  volume = {8},
  doi = {10.1038/nrg2165},
  number = {12},
  journal = {Nat Rev Genet},
  url = {http://dx.doi.org/10.1038/nrg2165},
  author = {Wicker, Thomas and Sabot, Fran\c{}cois and {Hua-Van}, Aur\'elie and Bennetzen, Jeffrey L. and Capy, Pierre and Chalhoub, Boulos and Flavell, Andrew and Leroy, Philippe and Morgante, Michele and Panaud, Olivier and Paux, Etienne and SanMiguel, Phillip and Schulman, Alan H.},
  month = dec,
  year = {2007},
  pages = {973-982}
}

@article{Kapitonov2001,
  title = {Rolling-Circle Transposons in Eukaryotes},
  volume = {98},
  doi = {10.1073/pnas.151269298},
  number = {15},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://dx.doi.org/10.1073/pnas.151269298},
  author = {Kapitonov, V. V. and Jurka, J.},
  month = jul,
  year = {2001},
  pages = {8714-8719}
}

@article{Kapitonov2006,
  title = {Self-Synthesizing {{DNA}} Transposons in Eukaryotes},
  volume = {103},
  doi = {10.1073/pnas.0600833103},
  number = {12},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://dx.doi.org/10.1073/pnas.0600833103},
  author = {Kapitonov, V. V. and Jurka, J.},
  month = mar,
  year = {2006},
  pages = {4540-4545}
}

@article{Shirasawa2012,
  title = {Characterization of Active Miniature Inverted-Repeat Transposable Elements in the Peanut Genome},
  volume = {124},
  doi = {10.1007/s00122-012-1798-6},
  number = {8},
  journal = {Theor Appl Genet},
  url = {http://dx.doi.org/10.1007/s00122-012-1798-6},
  author = {Shirasawa, Kenta and Hirakawa, Hideki and Tabata, Satoshi and Hasegawa, Makoto and Kiyoshima, Hiroyuki and Suzuki, Sigeru and Sasamoto, Sigemi and Watanabe, Akiko and Fujishiro, Tsunakazu and Isobe, Sachiko},
  month = feb,
  year = {2012},
  pages = {1429-1438}
}

@article{Astrin2016,
  title = {Towards a {{DNA Barcode Reference Database}} for {{Spiders}} and {{Harvestmen}} of {{Germany}}},
  volume = {11},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0162624},
  abstract = {As part of the German Barcode of Life campaign, over 3500 arachnid specimens have been collected and analyzed: ca. 3300 Araneae and 200 Opiliones, belonging to almost 600 species (median: 4 individuals/species). This covers about 60\% of the spider fauna and more than 70\% of the harvestmen fauna recorded for Germany. The overwhelming majority of species could be readily identified through DNA barcoding: median distances between closest species lay around 9\% in spiders and 13\% in harvestmen, while in 95\% of the cases, intraspecific distances were below 2.5\% and 8\% respectively, with intraspecific medians at 0.3\% and 0.2\%. However, almost 20 spider species, most notably in the family Lycosidae, could not be separated through DNA barcoding (although many of them present discrete morphological differences). Conspicuously high interspecific distances were found in even more cases, hinting at cryptic species in some instances. A new program is presented: DiStats calculates the statistics needed to meet DNA barcode release criteria. Furthermore, new generic COI primers useful for a wide range of taxa (also other than arachnids) are introduced.},
  number = {9},
  urldate = {2016-09-29},
  journal = {PLOS ONE},
  url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162624},
  author = {Astrin, Jonas J. and H\"ofer, Hubert and Spelda, J\"org and Holstein, Joachim and Bayer, Steffen and Hendrich, Lars and Huber, Bernhard A. and Kielhorn, Karl-Hinrich and Krammer, Hans-Joachim and Lemke, Martin and Monje, Juan Carlos and Morini\`ere, J\'er\^ome and Rulik, Bj\"orn and Petersen, Malte and Janssen, Hannah and Muster, Christoph},
  month = sep,
  year = {2016},
  keywords = {Sequence Alignment,Polymerase Chain Reaction,Haplotypes,phylogenetic analysis,spiders,DNA barcoding,Mitochondria,Taxonomy},
  pages = {e0162624},
  file = {/home/mpetersen/bib/storage/KKAA7UU8/Astrin et al. - 2016 - Towards a DNA Barcode Reference Database for Spide.pdf;/home/mpetersen/bib/storage/W8ZDCW5I/article.html}
}

@article{Nakabachi2015,
  series = {Insect Genomics * {{Development}} and Regulation},
  title = {Horizontal Gene Transfers in Insects},
  volume = {7},
  issn = {2214-5745},
  doi = {10.1016/j.cois.2015.03.006},
  abstract = {Horizontal gene transfer is the transfer of genetic material across species boundaries. Although horizontal gene transfers are relatively rare in animals, the recent rapid accumulation of genomic data has identified increasing amounts of exogenous DNA inserts in insect genomes. Most of the horizontally acquired sequences appear to be non-functional; however, there is growing evidence that some genes are truly expressed and confer novel functions on the recipient insects. These include previously unavailable metabolic properties including digesting food, degrading toxins, providing resistance to pathogens, and facilitating an obligate mutualistic relationship with intracellular bacteria. A recent analysis revealed that an aphid gene of bacterial origin encodes a protein that is transported into the obligate symbiont, paralleling the evolution of endosymbiotic organelles.},
  urldate = {2016-10-16},
  journal = {Current Opinion in Insect Science},
  url = {http://www.sciencedirect.com/science/article/pii/S2214574515000371},
  author = {Nakabachi, Atsushi},
  month = feb,
  year = {2015},
  pages = {24-29},
  file = {/home/mpetersen/bib/storage/2JNSNZA8/nakabachi2015.pdf;/home/mpetersen/bib/storage/85GBMKNG/S2214574515000371.html}
}

@article{Capella-Gutierrez2014,
  title = {A Phylogenomics Approach for Selecting Robust Sets of Phylogenetic Markers},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gku071},
  abstract = {Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.},
  language = {en},
  urldate = {2016-10-18},
  journal = {Nucleic Acids Research},
  url = {http://nar.oxfordjournals.org/content/early/2014/01/28/nar.gku071},
  author = {{Capella-Gutierrez}, Salvador and Kauff, Frank and Gabald\'on, Toni},
  month = jan,
  year = {2014},
  pages = {gku071},
  file = {/home/mpetersen/bib/storage/ZEK443NX/Capella-Gutierrez et al. - 2014 - A phylogenomics approach for selecting robust sets.pdf;/home/mpetersen/bib/storage/V7D22ZZK/nar.gku071.html},
  pmid = {24476915}
}

@article{Pauli2016,
  title = {Transcriptomic Data from Panarthropods Shed New Light on the Evolution of Insulator Binding Proteins in Insects},
  volume = {17},
  issn = {1471-2164},
  doi = {10.1186/s12864-016-3205-1},
  abstract = {Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods.},
  urldate = {2016-11-03},
  journal = {BMC Genomics},
  url = {http://dx.doi.org/10.1186/s12864-016-3205-1},
  author = {Pauli, Thomas and Vedder, Lucia and Dowling, Daniel and Petersen, Malte and Meusemann, Karen and Donath, Alexander and Peters, Ralph S. and Podsiadlowski, Lars and Mayer, Christoph and Liu, Shanlin and Zhou, Xin and Heger, Peter and Wiehe, Thomas and Hering, Lars and Mayer, Georg and Misof, Bernhard and Niehuis, Oliver},
  year = {2016},
  keywords = {Insulator binding proteins,Comparative transcriptomic analyses,Gene evolution,Arthropod evolution},
  pages = {861},
  file = {/home/mpetersen/bib/storage/X8JSMR5V/Pauli et al. - 2016 - Transcriptomic data from panarthropods shed new li.pdf;/home/mpetersen/bib/storage/W8P79QPC/s12864-016-3205-1.html}
}

@article{Thompson1994,
  title = {{{CLUSTAL W}}: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice.},
  volume = {22},
  issn = {0305-1048},
  shorttitle = {{{CLUSTAL W}}},
  abstract = {The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.},
  number = {22},
  urldate = {2016-11-10},
  journal = {Nucleic Acids Research},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308517/},
  author = {Thompson, J D and Higgins, D G and Gibson, T J},
  month = nov,
  year = {1994},
  pages = {4673-4680},
  file = {/home/mpetersen/bib/storage/5HBMSAKP/Thompson et al. - 1994 - CLUSTAL W improving the sensitivity of progressiv.pdf},
  pmid = {7984417},
  pmcid = {PMC308517}
}

@article{Dowling2017,
  title = {Phylogenetic {{Origin}} and {{Diversification}} of {{RNAi Pathway Genes}} in {{Insects}}},
  issn = {1759-6653},
  doi = {10.1093/gbe/evw281},
  language = {en},
  urldate = {2017-01-11},
  journal = {Genome Biology and Evolution},
  url = {http://gbe.oxfordjournals.org/lookup/doi/10.1093/gbe/evw281},
  author = {Dowling, Daniel and Pauli, Thomas and Donath, Alexander and Meusemann, Karen and Podsiadlowski, Lars and Petersen, Malte and Peters, Ralph S. and Mayer, Christoph and Liu, Shanlin and Zhou, Xin and Misof, Bernhard and Niehuis, Oliver},
  month = jan,
  year = {2017},
  pages = {evw281},
  file = {/home/mpetersen/bib/storage/LFWM7WRK/Dowling et al. - 2017 - Phylogenetic Origin and Diversification of RNAi Pa.pdf}
}

@article{Kraaijeveld2016,
  title = {Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp},
  issn = {, 1759-6653},
  doi = {10.1093/gbe/evw273},
  abstract = {Trait loss is a widespread phenomenon with pervasive consequences for a species' evolutionary potential. The genetic changes underlying trait loss have only been clarified in a small number of cases. None of these studies can identify whether the loss of the trait under study was a result of neutral mutation accumulation or negative selection. This distinction is relatively clear-cut in the loss of sexual traits in asexual organisms. Male-specific sexual traits are not expressed and can only decay through neutral mutations, whereas female-specific traits are expressed and subject to negative selection. We present the genome of an asexual parasitoid wasp and compare it to that of a sexual lineage of the same species. We identify a short-list of 16 genes for which the asexual lineage carries deleterious SNP or indel variants, whereas the sexual lineage does not. Using tissue-specific expression data from other insects, we show that fifteen of these are expressed in male-specific reproductive tissues. Only one deleterious variant was found that is expressed in the female-specific spermathecae, a trait that is heavily degraded and thought to be under negative selection in L. clavipes. Although the phenotypic decay of male-specific sexual traits in asexuals is generally slow compared to the decay of female-specific sexual traits, we show that male-specific traits do indeed accumulate deleterious mutations as expected by theory. Our results provide an excellent starting point for detailed study of the genomics of neutral and selected trait decay.},
  language = {en},
  urldate = {2017-01-11},
  journal = {Genome Biology and Evolution},
  url = {http://gbe.oxfordjournals.org/content/early/2016/11/10/gbe.evw273},
  author = {Kraaijeveld, Ken and Anvar, Yahya and Frank, Jeroen and Schmitz, Arnoud and Bast, Jens and Wilbrandt, Jeanne and Petersen, Malte and Ziesmann, Tanja and Niehuis, Oliver and de Knijff, Peter and den Dunnen, Johan T. and Ellers, Jacintha},
  month = nov,
  year = {2016},
  keywords = {Wolbachia,Leptopilina clavipes,parthenogenesis,deleterious variants,sexual trait decay},
  pages = {evw273},
  file = {/home/mpetersen/bib/storage/27Z7AETK/evw273.pdf;/home/mpetersen/bib/storage/KH2DN27F/gbe.evw273.full.pdf;/home/mpetersen/bib/storage/UVMU4UE4/gbe.html}
}

@article{Mayer2016,
  title = {{{BaitFisher}}: {{A Software Package}} for {{Multispecies Target DNA Enrichment Probe Design}}},
  volume = {33},
  issn = {0737-4038, 1537-1719},
  shorttitle = {{{BaitFisher}}},
  doi = {10.1093/molbev/msw056},
  language = {en},
  number = {7},
  urldate = {2017-01-11},
  journal = {Molecular Biology and Evolution},
  url = {http://mbe.oxfordjournals.org/lookup/doi/10.1093/molbev/msw056},
  author = {Mayer, Christoph and Sann, Manuela and Donath, Alexander and Meixner, Martin and Podsiadlowski, Lars and Peters, Ralph S. and Petersen, Malte and Meusemann, Karen and Liere, Karsten and W\"agele, Johann-Wolfgang and Misof, Bernhard and Bleidorn, Christoph and Ohl, Michael and Niehuis, Oliver},
  month = jul,
  year = {2016},
  pages = {1875-1886},
  file = {/home/mpetersen/bib/storage/YQKNHSXU/Mayer et al. - 2016 - BaitFisher A Software Package for Multispecies Ta.pdf}
}

@article{Kapusta2017a,
  title = {Dynamics of Genome Size Evolution in Birds and Mammals},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1616702114},
  language = {en},
  urldate = {2017-02-09},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1616702114},
  author = {Kapusta, Aur\'elie and Suh, Alexander and Feschotte, C\'edric},
  month = feb,
  year = {2017},
  pages = {201616702},
  file = {/home/mpetersen/bib/storage/637ESNUC/pnas.201616702SI.pdf;/home/mpetersen/bib/storage/XEVUIT5E/Dynamics_of_genome_size_evolution_PNAS-2017-Kapusta-1616702114.pdf}
}

@article{Petersen2017,
  title = {Orthograph: A Versatile Tool for Mapping Coding Nucleotide Sequences to Clusters of Orthologous Genes},
  volume = {18},
  issn = {1471-2105},
  shorttitle = {Orthograph},
  doi = {10.1186/s12859-017-1529-8},
  abstract = {Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses.},
  urldate = {2017-02-16},
  journal = {BMC Bioinformatics},
  url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1529-8},
  author = {Petersen, Malte and Meusemann, Karen and Donath, Alexander and Dowling, Daniel and Liu, Shanlin and Peters, Ralph S. and Podsiadlowski, Lars and Vasilikopoulos, Alexandros and Zhou, Xin and Misof, Bernhard and Niehuis, Oliver},
  year = {2017},
  keywords = {Crabronidae,Orthology,Paralogy,Sphecidae,Splice variants,transcriptome},
  pages = {111},
  file = {/home/mpetersen/bib/storage/M7Q5IZHK/art%3A10.1186%2Fs12859-017-1529-8.pdf;/home/mpetersen/bib/storage/N2RUEGEN/s12859-017-1529-8.html}
}

@article{Vega2015,
  title = {Draft Genome of the Most Devastating Insect Pest of Coffee Worldwide: The Coffee Berry Borer, {{Hypothenemus}} Hampei},
  volume = {5},
  copyright = {\textcopyright{} 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
  issn = {2045-2322},
  shorttitle = {Draft Genome of the Most Devastating Insect Pest of Coffee Worldwide},
  doi = {10.1038/srep12525},
  abstract = {The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species.},
  language = {en},
  urldate = {2017-02-20},
  journal = {Scientific Reports},
  url = {http://www.nature.com/srep/2015/150731/srep12525/full/srep12525.html},
  author = {Vega, Fernando E. and Brown, Stuart M. and Chen, Hao and Shen, Eric and Nair, Mridul B. and {Ceja-Navarro}, Javier A. and Brodie, Eoin L. and Infante, Francisco and Dowd, Patrick F. and Pain, Arnab},
  month = jul,
  year = {2015},
  pages = {12525},
  file = {/home/mpetersen/bib/storage/VGG9ZMV2/srep12525.pdf;/home/mpetersen/bib/storage/M7R726W4/srep12525.html}
}

@article{Keeling2013,
  title = {Draft Genome of the Mountain Pine Beetle, {{Dendroctonus}} Ponderosae {{Hopkins}}, a Major Forest Pest},
  volume = {14},
  issn = {1465-6906},
  doi = {10.1186/gb-2013-14-3-r27},
  language = {en},
  number = {3},
  urldate = {2017-02-20},
  journal = {Genome Biology},
  url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-3-r27},
  author = {Keeling, Christopher I and Yuen, Macaire MS and Liao, Nancy Y and Roderick Docking, T and Chan, Simon K and Taylor, Greg A and Palmquist, Diana L and Jackman, Shaun D and Nguyen, Anh and Li, Maria and Henderson, Hannah and Janes, Jasmine K and Zhao, Yongjun and Pandoh, Pawan and Moore, Richard and Sperling, Felix AH and W Huber, Dezene P and Birol, Inanc and Jones, Steven JM and Bohlmann, Joerg},
  year = {2013},
  pages = {R27},
  file = {/home/mpetersen/bib/storage/GN7EMVH7/Draft-genome-of-the-mountain-pine-beetle-Dendroctonus-ponderosae-Hopkins-a-major-forest-pest.pdf;/home/mpetersen/bib/storage/VCDZ679T/Draft-genome-of-the-mountain-pine-beetle-Dendroctonus-ponderosae-Hopkins-a-major-forest-pest.pdf}
}

@article{Schwager2017,
  title = {The House Spider Genome Reveals an Ancient Whole-Genome Duplication during Arachnid Evolution},
  doi = {10.1101/106385},
  urldate = {2017-02-22},
  journal = {bioRxiv},
  url = {http://biorxiv.org/content/early/2017/02/08/106385.abstract},
  author = {Schwager, Evelyn E. and Sharma, Prashant P. and Clarke, Thomas and Leite, Daniel J. and Wierschin, Torsten and Pechmann, Matthias and {Akiyama-Oda}, Yasuko and Esposito, Lauren and Bechsgaard, Jesper and Bilde, Trine and others},
  year = {2017},
  pages = {106385},
  file = {/home/mpetersen/bib/storage/MSG4RWD3/106385.full.pdf;/home/mpetersen/bib/storage/V84REE5E/106385.full.pdf}
}

@article{Bailly-Bechet2014,
  title = {``{{One}} Code to Find Them All'': A Perl Tool to Conveniently Parse {{RepeatMasker}} Output Files},
  volume = {5},
  issn = {1759-8753},
  shorttitle = {``{{One}} Code to Find Them All''},
  doi = {10.1186/1759-8753-5-13},
  abstract = {Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker program. RepeatMasker generates several output files, including the .out file, which provides annotations for all detected repeats in a query sequence. However, a remaining challenge consists of identifying the different copies of TEs that correspond to the identified hits. This step is essential for any evolutionary/comparative analysis of the different copies within a family. Different possibilities can lead to multiple hits corresponding to a unique copy of an element, such as the presence of large deletions/insertions or undetermined bases, and distinct consensus corresponding to a single full-length sequence (like for long terminal repeat (LTR)-retrotransposons). These possibilities must be taken into account to determine the exact number of TE copies.},
  urldate = {2017-02-23},
  journal = {Mobile DNA},
  url = {http://dx.doi.org/10.1186/1759-8753-5-13},
  author = {{Bailly-Bechet}, Marc and Haudry, Annabelle and Lerat, Emmanuelle},
  year = {2014},
  keywords = {Transposable elements,RepeatMasker,Annotation},
  pages = {13},
  file = {/home/mpetersen/bib/storage/SNABT84W/Bailly-Bechet et al. - 2014 - “One code to find them all” a perl tool to conven.pdf;/home/mpetersen/bib/storage/BJ65CKEN/1759-8753-5-13.html}
}

@article{Peters2017,
  title = {Evolutionary {{History}} of the {{Hymenoptera}}},
  issn = {09609822},
  doi = {10.1016/j.cub.2017.01.027},
  language = {en},
  urldate = {2017-03-24},
  journal = {Current Biology},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982217300593},
  author = {Peters, Ralph S. and Krogmann, Lars and Mayer, Christoph and Donath, Alexander and Gunkel, Simon and Meusemann, Karen and Kozlov, Alexey and Podsiadlowski, Lars and Petersen, Malte and Lanfear, Robert and Diez, Patricia A. and Heraty, John and Kjer, Karl M. and Klopfstein, Seraina and Meier, Rudolf and Polidori, Carlo and Schmitt, Thomas and Liu, Shanlin and Zhou, Xin and Wappler, Torsten and Rust, Jes and Misof, Bernhard and Niehuis, Oliver},
  month = mar,
  year = {2017},
  file = {/home/mpetersen/bib/storage/IDHT75W3/Peters_et_al._-_2017_-_Evolutionary_history_of_the_Hymenoptera.pdf;/home/mpetersen/bib/storage/S6X3KXJM/Peters_et_al._-_2017_-_Evolutionary_history_of_the_Hymenoptera.pdf}
}

@book{RCoreTeam2017,
  address = {Vienna, Austria},
  title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
  publisher = {{R Foundation for Statistical Computing}},
  url = {https://www.R-project.org/},
  author = {{R Core Team}},
  year = {2017}
}

@article{Lindblad-Toh2005,
  title = {Genome Sequence, Comparative Analysis and Haplotype Structure of the Domestic Dog},
  volume = {438},
  copyright = {\textcopyright{} 2005 Nature Publishing Group},
  issn = {0028-0836},
  doi = {10.1038/nature04338},
  abstract = {Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.},
  language = {en},
  number = {7069},
  urldate = {2017-04-25},
  journal = {Nature},
  url = {http://www.nature.com/nature/journal/v438/n7069/full/nature04338.html},
  author = {{Lindblad-Toh}, Kerstin and Wade, Claire M. and Mikkelsen, Tarjei S. and Karlsson, Elinor K. and Jaffe, David B. and Kamal, Michael and Clamp, Michele and Chang, Jean L. and Kulbokas, Edward J. and Zody, Michael C. and Mauceli, Evan and Xie, Xiaohui and Breen, Matthew and Wayne, Robert K. and Ostrander, Elaine A. and Ponting, Chris P. and Galibert, Francis and Smith, Douglas R. and {deJong}, Pieter J. and Kirkness, Ewen and Alvarez, Pablo and Biagi, Tara and Brockman, William and Butler, Jonathan and Chin, Chee-Wye and Cook, April and Cuff, James and Daly, Mark J. and DeCaprio, David and Gnerre, Sante and Grabherr, Manfred and Kellis, Manolis and Kleber, Michael and Bardeleben, Carolyne and Goodstadt, Leo and Heger, Andreas and Hitte, Christophe and Kim, Lisa and Koepfli, Klaus-Peter and Parker, Heidi G. and Pollinger, John P. and Searle, Stephen M. J. and Sutter, Nathan B. and Thomas, Rachael and Webber, Caleb and Baldwin, Jennifer and Abebe, Adal and Abouelleil, Amr and Aftuck, Lynne and {Ait-zahra}, Mostafa and Aldredge, Tyler and Allen, Nicole and An, Peter and Anderson, Scott and Antoine, Claudel and Arachchi, Harindra and Aslam, Ali and Ayotte, Laura and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Benamara, Mostafa and Berlin, Aaron and Bessette, Daniel and Blitshteyn, Berta and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Brown, Adam and Cahill, Patrick and Calixte, Nadia and Camarata, Jody and Cheshatsang, Yama and Chu, Jeffrey and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Dawoe, Tenzin and Daza, Riza and Decktor, Karin and DeGray, Stuart and Dhargay, Norbu and Dooley, Kimberly and Dooley, Kathleen and Dorje, Passang and Dorjee, Kunsang and Dorris, Lester and Duffey, Noah and Dupes, Alan and Egbiremolen, Osebhajajeme and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Ferreira, Patricia and Fisher, Sheila and FitzGerald, Mike and Foley, Karen and Foley, Chelsea and Franke, Alicia and Friedrich, Dennis and Gage, Diane and Garber, Manuel and Gearin, Gary and Giannoukos, Georgia and Goode, Tina and Goyette, Audra and Graham, Joseph and Grandbois, Edward and Gyaltsen, Kunsang and Hafez, Nabil and Hagopian, Daniel and Hagos, Birhane and Hall, Jennifer and Healy, Claire and Hegarty, Ryan and Honan, Tracey and Horn, Andrea and Houde, Nathan and Hughes, Leanne and Hunnicutt, Leigh and Husby, M. and Jester, Benjamin and Jones, Charlien and Kamat, Asha and Kanga, Ben and Kells, Cristyn and Khazanovich, Dmitry and Kieu, Alix Chinh and Kisner, Peter and Kumar, Mayank and Lance, Krista and Landers, Thomas and Lara, Marcia and Lee, William and Leger, Jean-Pierre and Lennon, Niall and Leuper, Lisa and LeVine, Sarah and Liu, Jinlei and Liu, Xiaohong and Lokyitsang, Yeshi and Lokyitsang, Tashi and Lui, Annie and Macdonald, Jan and Major, John and Marabella, Richard and Maru, Kebede and Matthews, Charles and McDonough, Susan and Mehta, Teena and Meldrim, James and Melnikov, Alexandre and Meneus, Louis and Mihalev, Atanas and Mihova, Tanya and Miller, Karen and Mittelman, Rachel and Mlenga, Valentine and Mulrain, Leonidas and Munson, Glen and Navidi, Adam and Naylor, Jerome and Nguyen, Tuyen and Nguyen, Nga and Nguyen, Cindy and Nguyen, Thu and Nicol, Robert and Norbu, Nyima and Norbu, Choe and Novod, Nathaniel and Nyima, Tenchoe and Olandt, Peter and O'Neill, Barry and O'Neill, Keith and Osman, Sahal and Oyono, Lucien and Patti, Christopher and Perrin, Danielle and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Rachupka, Anthony and Raghuraman, Sujaa and Rameau, Rayale and Ray, Verneda and Raymond, Christina and Rege, Filip and Rise, Cecil and Rogers, Julie and Rogov, Peter and Sahalie, Julie and Settipalli, Sampath and Sharpe, Theodore and Shea, Terrance and Sheehan, Mechele and Sherpa, Ngawang and Shi, Jianying and Shih, Diana and Sloan, Jessie and Smith, Cherylyn and Sparrow, Todd and Stalker, John and {Stange-Thomann}, Nicole and Stavropoulos, Sharon and Stone, Catherine and Stone, Sabrina and Sykes, Sean and Tchuinga, Pierre and Tenzing, Pema and Tesfaye, Senait and Thoulutsang, Dawa and Thoulutsang, Yama and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Venkataraman, Vijay and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Yang, Shuli and Yang, Xiaoping and Young, Geneva and Yu, Qing and Zainoun, Joanne and Zembek, Lisa and Zimmer, Andrew and Lander, Eric S.},
  month = dec,
  year = {2005},
  pages = {803-819},
  file = {/home/mpetersen/bib/storage/PJNWMUBD/Lindblad-Toh et al. - 2005 - Genome sequence, comparative analysis and haplotyp.pdf;/home/mpetersen/bib/storage/W4IJMQ39/nature04338.html}
}

@article{Paradis2004,
  title = {{{APE}}: Analyses of Phylogenetics and Evolution in {{R}} Language},
  volume = {20},
  journal = {Bioinformatics},
  author = {Paradis, E. and Claude, J. and Strimmer, K.},
  year = {2004},
  pages = {289-290}
}

@article{Li2009,
  title = {The {{Sequence Alignment}}/{{Map}} Format and {{SAMtools}}},
  volume = {25},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btp352},
  abstract = {SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
AVAILABILITY: http://samtools.sourceforge.net.},
  language = {eng},
  number = {16},
  journal = {Bioinformatics (Oxford, England)},
  author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and {1000 Genome Project Data Processing Subgroup}},
  month = aug,
  year = {2009},
  keywords = {Algorithms,Sequence Alignment,Sequence Analysis,DNA,Computational Biology,Software,Genome,Genomics,Base Sequence,Molecular Sequence Data,Sequence Analysis; DNA},
  pages = {2078-2079},
  pmid = {19505943},
  pmcid = {PMC2723002}
}

@article{Neafsey2015,
  title = {Highly Evolvable Malaria Vectors: {{The}} Genomes of 16 {{Anopheles}} Mosquitoes},
  volume = {347},
  issn = {0036-8075, 1095-9203},
  shorttitle = {Highly Evolvable Malaria Vectors},
  doi = {10.1126/science.1258522},
  language = {en},
  number = {6217},
  urldate = {2017-06-01},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1258522},
  author = {Neafsey, D. E. and Waterhouse, R. M. and Abai, M. R. and Aganezov, S. S. and Alekseyev, M. A. and Allen, J. E. and Amon, J. and Arca, B. and Arensburger, P. and Artemov, G. and Assour, L. A. and Basseri, H. and Berlin, A. and Birren, B. W. and Blandin, S. A. and Brockman, A. I. and Burkot, T. R. and Burt, A. and Chan, C. S. and Chauve, C. and Chiu, J. C. and Christensen, M. and Costantini, C. and Davidson, V. L. M. and Deligianni, E. and Dottorini, T. and Dritsou, V. and Gabriel, S. B. and Guelbeogo, W. M. and Hall, A. B. and Han, M. V. and Hlaing, T. and Hughes, D. S. T. and Jenkins, A. M. and Jiang, X. and Jungreis, I. and Kakani, E. G. and Kamali, M. and Kemppainen, P. and Kennedy, R. C. and Kirmitzoglou, I. K. and Koekemoer, L. L. and Laban, N. and Langridge, N. and Lawniczak, M. K. N. and Lirakis, M. and Lobo, N. F. and Lowy, E. and MacCallum, R. M. and Mao, C. and Maslen, G. and Mbogo, C. and McCarthy, J. and Michel, K. and Mitchell, S. N. and Moore, W. and Murphy, K. A. and Naumenko, A. N. and Nolan, T. and Novoa, E. M. and O'Loughlin, S. and Oringanje, C. and Oshaghi, M. A. and Pakpour, N. and Papathanos, P. A. and Peery, A. N. and Povelones, M. and Prakash, A. and Price, D. P. and Rajaraman, A. and Reimer, L. J. and Rinker, D. C. and Rokas, A. and Russell, T. L. and Sagnon, N. and Sharakhova, M. V. and Shea, T. and Simao, F. A. and Simard, F. and Slotman, M. A. and Somboon, P. and Stegniy, V. and Struchiner, C. J. and Thomas, G. W. C. and Tojo, M. and Topalis, P. and Tubio, J. M. C. and Unger, M. F. and Vontas, J. and Walton, C. and Wilding, C. S. and Willis, J. H. and Wu, Y.-C. and Yan, G. and Zdobnov, E. M. and Zhou, X. and Catteruccia, F. and Christophides, G. K. and Collins, F. H. and Cornman, R. S. and Crisanti, A. and Donnelly, M. J. and Emrich, S. J. and Fontaine, M. C. and Gelbart, W. and Hahn, M. W. and Hansen, I. A. and Howell, P. I. and Kafatos, F. C. and Kellis, M. and Lawson, D. and Louis, C. and Luckhart, S. and Muskavitch, M. A. T. and Ribeiro, J. M. and Riehle, M. A. and Sharakhov, I. V. and Tu, Z. and Zwiebel, L. J. and Besansky, N. J.},
  month = jan,
  year = {2015},
  pages = {1258522-1258522},
  file = {/home/mpetersen/bib/storage/SRFKD9CG/1258522.full.pdf}
}

@article{Feschotte2007,
  title = {{{DNA Transposons}} and the {{Evolution}} of {{Eukaryotic Genomes}}},
  volume = {41},
  issn = {0066-4197},
  doi = {10.1146/annurev.genet.40.110405.090448},
  abstract = {Transposable elements are mobile genetic units that exhibit broad diversity in their structure and transposition mechanisms. Transposable elements occupy a large fraction of many eukaryotic genomes and their movement and accumulation represent a major force shaping the genes and genomes of almost all organisms. This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect. We provide an up-to-date outlook on the diversity and taxonomic distribution of all major types of DNA transposons in eukaryotes, including Helitrons and Mavericks. We discuss some of the evolutionary forces that influence their maintenance and diversification in various genomic environments. Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages.},
  urldate = {2017-06-18},
  journal = {Annual review of genetics},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2167627/},
  author = {Feschotte, C\'edric and Pritham, Ellen J.},
  year = {2007},
  pages = {331-368},
  file = {/home/mpetersen/bib/storage/8XPSPUGK/Feschotte and Pritham - 2007 - DNA Transposons and the Evolution of Eukaryotic Ge.pdf},
  pmid = {18076328},
  pmcid = {PMC2167627}
}

@article{Peccoud2017,
  title = {Massive Horizontal Transfer of Transposable Elements in Insects},
  volume = {114},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1621178114},
  abstract = {Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24\% (2.08\% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.},
  language = {en},
  number = {18},
  urldate = {2017-06-19},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/114/18/4721},
  author = {Peccoud, Jean and Loiseau, Vincent and Cordaux, Richard and Gilbert, Cl\'ement},
  month = feb,
  year = {2017},
  keywords = {Genome evolution,Insects,horizontal transfer,Transposable elements,biogeography},
  pages = {4721-4726},
  file = {/home/mpetersen/bib/storage/5UBMPBMJ/1621178114.full.pdf;/home/mpetersen/bib/storage/39PWMQBI/4721.html},
  pmid = {28416702}
}

@article{Aravin2001,
  title = {Double-Stranded {{RNA}}-Mediated Silencing of Genomic Tandem Repeats and Transposable Elements in the {{D}}. Melanogaster Germline},
  volume = {11},
  issn = {09609822},
  doi = {10.1016/S0960-9822(01)00299-8},
  language = {en},
  number = {13},
  urldate = {2017-06-20},
  journal = {Current Biology},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982201002998},
  author = {Aravin, Alexei A. and Naumova, Natalia M. and Tulin, Alexei V. and Vagin, Vasilii V. and Rozovsky, Yakov M. and Gvozdev, Vladimir A.},
  month = jul,
  year = {2001},
  pages = {1017-1027},
  file = {/home/mpetersen/bib/storage/5HCWVTLJ/Aravin et al. - 2001 - Double-stranded RNA-mediated silencing of genomic .pdf}
}

@article{LeThomas2013,
  title = {Piwi Induces {{piRNA}}-Guided Transcriptional Silencing and Establishment of a Repressive Chromatin State},
  volume = {27},
  issn = {0890-9369},
  doi = {10.1101/gad.209841.112},
  language = {en},
  number = {4},
  urldate = {2017-06-22},
  journal = {Genes \& Development},
  url = {http://genesdev.cshlp.org/cgi/doi/10.1101/gad.209841.112},
  author = {Le Thomas, A. and Rogers, A. K. and Webster, A. and Marinov, G. K. and Liao, S. E. and Perkins, E. M. and Hur, J. K. and Aravin, A. A. and Toth, K. F.},
  month = feb,
  year = {2013},
  pages = {390-399},
  file = {/home/mpetersen/bib/storage/IK8QKTIU/Genes Dev.-2013-Le Thomas-gad.209841.112.pdf}
}

@article{McClintock1950,
  title = {The Origin and Behavior of Mutable Loci in Maize},
  volume = {36},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.36.6.344},
  language = {en},
  number = {6},
  urldate = {2017-06-29},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/cgi/doi/10.1073/pnas.36.6.344},
  author = {McClintock, B.},
  month = jun,
  year = {1950},
  pages = {344-355}
}

@article{Alfsnes2017,
  title = {Genome Size in Arthropods; Different Roles of Phylogeny, Habitat and Life History in Insects and Crustaceans},
  issn = {2045-7758},
  doi = {10.1002/ece3.3163},
  abstract = {Despite the major role of genome size for physiology, ecology, and evolution, there is still mixed evidence with regard to proximate and ultimate drivers. The main causes of large genome size are proliferation of noncoding elements and/or duplication events. The relative role and interplay between these proximate causes and the evolutionary patterns shaped by phylogeny, life history traits or environment are largely unknown for the arthropods. Genome size shows a tremendous variability in this group, and it has a major impact on a range of fitness-related parameters such as growth, metabolism, life history traits, and for many species also body size. In this study, we compared genome size in two major arthropod groups, insects and crustaceans, and related this to phylogenetic patterns and parameters affecting ambient temperature (latitude, depth, or altitude), insect developmental mode, as well as crustacean body size and habitat, for species where data were available. For the insects, the genome size is clearly phylogeny-dependent, reflecting primarily their life history and mode of development, while for crustaceans there was a weaker association between genome size and phylogeny, suggesting life cycle strategies and habitat as more important determinants. Maximum observed latitude and depth, and their combined effect, showed positive, and possibly phylogenetic independent, correlations with genome size for crustaceans. This study illustrate the striking difference in genome sizes both between and within these two major groups of arthropods, and that while living in the cold with low developmental rates may promote large genomes in marine crustaceans, there is a multitude of proximate and ultimate drivers of genome size.},
  language = {en},
  urldate = {2017-07-11},
  journal = {Ecology and Evolution},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.3163/abstract},
  author = {Alfsnes, Kristian and Leinaas, Hans Petter and Hessen, Dag Olav},
  month = jun,
  year = {2017},
  keywords = {Evolution,Insects,C-value,Ecology,crustaceans,life history,temperature-size-rules},
  pages = {n/a-n/a},
  file = {/home/mpetersen/bib/storage/QUGFKX49/Alfsnes et al. - Genome size in arthropods\; different roles of phyl.pdf;/home/mpetersen/bib/storage/GCS6S73D/abstract.html}
}

@article{Faddeeva-Vakhrusheva2016,
  title = {Gene {{Family Evolution Reflects Adaptation}} to {{Soil Environmental Stressors}} in the {{Genome}} of the {{Collembolan Orchesella}} Cincta},
  volume = {8},
  doi = {10.1093/gbe/evw134},
  number = {7},
  urldate = {2017-07-13},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/8/7/2106/2466009/Gene-Family-Evolution-Reflects-Adaptation-to-Soil},
  author = {{Faddeeva-Vakhrusheva}, Anna and Derks, Martijn F. L. and Anvar, Seyed Yahya and Agamennone, Valeria and Suring, Wouter and Smit, Sandra and Straalen, Van and M, Nico and Roelofs, Dick},
  month = jul,
  year = {2016},
  pages = {2106-2117},
  file = {/home/mpetersen/bib/storage/VBCAX9IC/Faddeeva-Vakhrusheva et al. - 2016 - Gene Family Evolution Reflects Adaptation to Soil .pdf;/home/mpetersen/bib/storage/SDG2HNW5/evw134.html}
}

@article{Westerman1987,
  title = {Differences in {{DNA}} Content between Two Chromosomal Races of the Grasshopper {{Podisma}} Pedestris},
  volume = {58},
  issn = {0018-067X, 1365-2540},
  doi = {10.1038/hdy.1987.36},
  number = {2},
  urldate = {2017-08-01},
  journal = {Heredity},
  url = {http://www.nature.com/doifinder/10.1038/hdy.1987.36},
  author = {Westerman, M and Barton, N H and Hewitt, G M},
  month = apr,
  year = {1987},
  pages = {221-228},
  file = {/home/mpetersen/bib/storage/AXRZ7N64/Differences-in-DNA-content-between-two-chromosomal-races-of-the-grasshopper-Podisma-pedestris.pdf}
}

@article{Glastad2014,
  title = {Evolutionary Insights into {{DNA}} Methylation in Insects},
  volume = {1},
  issn = {22145745},
  doi = {10.1016/j.cois.2014.04.001},
  language = {en},
  urldate = {2017-08-03},
  journal = {Current Opinion in Insect Science},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S2214574514000029},
  author = {Glastad, Karl M and Hunt, Brendan G and Goodisman, Michael AD},
  month = jul,
  year = {2014},
  pages = {25-30}
}

@article{Suzuki2008,
  title = {{{DNA}} Methylation Landscapes: Provocative Insights from Epigenomics},
  volume = {9},
  issn = {1471-0056, 1471-0064},
  shorttitle = {{{DNA}} Methylation Landscapes},
  doi = {10.1038/nrg2341},
  number = {6},
  urldate = {2017-08-03},
  journal = {Nature Reviews Genetics},
  url = {http://www.nature.com/doifinder/10.1038/nrg2341},
  author = {Suzuki, Miho M. and Bird, Adrian},
  month = jun,
  year = {2008},
  pages = {465-476}
}

@article{Yoder1997,
  title = {Cytosine Methylation and the Ecology of Intragenomic Parasites},
  volume = {13},
  issn = {01689525},
  doi = {10.1016/S0168-9525(97)01181-5},
  language = {en},
  number = {8},
  urldate = {2017-08-03},
  journal = {Trends in Genetics},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952597011815},
  author = {Yoder, Jeffrey A. and Walsh, Colum P. and Bestor, Timothy H.},
  month = aug,
  year = {1997},
  pages = {335-340},
  file = {/home/mpetersen/bib/storage/PKDUY6LW/Yoder et al. - 1997 - Cytosine methylation and the ecology of intragenom.pdf}
}

@article{Gregory2002,
  title = {Genome Size and Developmental Complexity},
  volume = {115},
  number = {1},
  urldate = {2017-08-04},
  journal = {Genetica},
  url = {https://link.springer.com/article/10.1023/A:1016032400147},
  author = {Gregory, T. Ryan},
  year = {2002},
  pages = {131--146},
  file = {/home/mpetersen/bib/storage/PRSQ6B2K/10.1023A1016032400147.pdf}
}

@article{Barnosky2011,
  title = {Has the {{Earth}}'s Sixth Mass Extinction Already Arrived?},
  volume = {471},
  copyright = {\textcopyright{} 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  issn = {0028-0836},
  doi = {10.1038/nature09678},
  abstract = {Palaeontologists characterize mass extinctions as times when the Earth loses more than three-quarters of its species in a geologically short interval, as has happened only five times in the past 540 million years or so. Biologists now suggest that a sixth mass extinction may be under way, given the known species losses over the past few centuries and millennia. Here we review how differences between fossil and modern data and the addition of recently available palaeontological information influence our understanding of the current extinction crisis. Our results confirm that current extinction rates are higher than would be expected from the fossil record, highlighting the need for effective conservation measures.},
  language = {en},
  number = {7336},
  urldate = {2017-08-22},
  journal = {Nature},
  url = {http://www.nature.com/nature/journal/v471/n7336/full/nature09678.html},
  author = {Barnosky, Anthony D. and Matzke, Nicholas and Tomiya, Susumu and Wogan, Guinevere O. U. and Swartz, Brian and Quental, Tiago B. and Marshall, Charles and McGuire, Jenny L. and Lindsey, Emily L. and Maguire, Kaitlin C. and Mersey, Ben and Ferrer, Elizabeth A.},
  month = mar,
  year = {2011},
  keywords = {Ecology,Palaeontology,Environmental science,Earth science},
  pages = {51-57},
  file = {/home/mpetersen/bib/storage/A577ECZQ/nature09678.html}
}

@article{Dirzo2014,
  title = {Defaunation in the {{Anthropocene}}},
  volume = {345},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1251817},
  abstract = {We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically, declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining species show 25\% average decline in abundance. Invertebrate patterns are equally dire: 67\% of monitored populations show 45\% mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown about this ``Anthropocene defaunation''; these knowledge gaps hinder our capacity to predict and limit defaunation impacts. Clearly, however, defaunation is both a pervasive component of the planet's sixth mass extinction and also a major driver of global ecological change.},
  language = {en},
  number = {6195},
  urldate = {2017-08-22},
  journal = {Science},
  url = {http://science.sciencemag.org/content/345/6195/401},
  author = {Dirzo, Rodolfo and Young, Hillary S. and Galetti, Mauro and Ceballos, Gerardo and Isaac, Nick J. B. and Collen, Ben},
  month = jul,
  year = {2014},
  pages = {401-406},
  file = {/home/mpetersen/bib/storage/Q56XNJS8/401.html},
  pmid = {25061202}
}

@article{Pimm1995,
  title = {The {{Future}} of {{Biodiversity}}},
  volume = {269},
  copyright = {1995 by the American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.269.5222.347},
  abstract = {Recent extinction rates are 100 to 1000 times their pre-human levels in well-known, but taxonomically diverse groups from widely different environments. If all species currently deemed "threatened" become extinct in the next century, then future extinction rates will be 10 times recent rates. Some threatened species will survive the century, but many species not now threatened will succumb. Regions rich in species found only within them (endemics) dominate the global patterns of extinction. Although new technology provides details of habitat losses, estimates of future extinctions are hampered by our limited knowledge of which areas are rich in endemics.},
  language = {en},
  number = {5222},
  urldate = {2017-08-22},
  journal = {Science},
  url = {http://science.sciencemag.org/content/269/5222/347},
  author = {Pimm, Stuart L. and Russell, Gareth J. and Gittleman, John L. and Brooks, Thomas M.},
  month = jul,
  year = {1995},
  pages = {347-350},
  file = {/home/mpetersen/bib/storage/CBJ5MCBK/347.html},
  pmid = {17841251}
}

@article{Papanicolaou2016,
  title = {The Whole Genome Sequence of the {{Mediterranean}} Fruit Fly, {{Ceratitis}} Capitata ({{Wiedemann}}), Reveals Insights into the Biology and Adaptive Evolution of a Highly Invasive Pest Species},
  volume = {17},
  issn = {1474-760X},
  doi = {10.1186/s13059-016-1049-2},
  abstract = {The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.},
  urldate = {2017-10-16},
  journal = {Genome Biology},
  url = {https://doi.org/10.1186/s13059-016-1049-2},
  author = {Papanicolaou, Alexie and Schetelig, Marc F. and Arensburger, Peter and Atkinson, Peter W. and Benoit, Joshua B. and Bourtzis, Kostas and Casta\~nera, Pedro and Cavanaugh, John P. and Chao, Hsu and Childers, Christopher and Curril, Ingrid and Dinh, Huyen and Doddapaneni, HarshaVardhan and Dolan, Amanda and Dugan, Shannon and Friedrich, Markus and Gasperi, Giuliano and Geib, Scott and Georgakilas, Georgios and Gibbs, Richard A. and Giers, Sarah D. and Gomulski, Ludvik M. and {Gonz\'alez-Guzm\'an}, Miguel and {Guillem-Amat}, Ana and Han, Yi and Hatzigeorgiou, Artemis G. and {Hern\'andez-Crespo}, Pedro and Hughes, Daniel S. T. and Jones, Jeffery W. and Karagkouni, Dimitra and Koskinioti, Panagiota and Lee, Sandra L. and Malacrida, Anna R. and Manni, Mos\`e and Mathiopoulos, Kostas and Meccariello, Angela and Murali, Shwetha C. and Murphy, Terence D. and Muzny, Donna M. and Oberhofer, Georg and Ortego, F\'elix and Paraskevopoulou, Maria D. and Poelchau, Monica and Qu, Jiaxin and Reczko, Martin and Robertson, Hugh M. and Rosendale, Andrew J. and Rosselot, Andrew E. and Saccone, Giuseppe and Salvemini, Marco and Savini, Grazia and Schreiner, Patrick and Scolari, Francesca and Siciliano, Paolo and Sim, Sheina B. and Tsiamis, George and Ure\~na, Enric and Vlachos, Ioannis S. and Werren, John H. and Wimmer, Ernst A. and Worley, Kim C. and Zacharopoulou, Antigone and Richards, Stephen and Handler, Alfred M.},
  month = sep,
  year = {2016},
  keywords = {Medfly genome,Tephritid genomics,Insect orthology,Gene family evolution,Chromosomal synteny,Insect invasiveness,Insect adaptation,Medfly integrated pest management (IPM)},
  pages = {192},
  file = {/home/mpetersen/bib/storage/GBIHKCDZ/Papanicolaou et al. - 2016 - The whole genome sequence of the Mediterranean fru.pdf;/home/mpetersen/bib/storage/WEHUIQ9U/s13059-016-1049-2.html}
}

@article{McGaugh2012,
  title = {Genomic Impacts of Chromosomal Inversions in Parapatric {{Drosophila}} Species},
  volume = {367},
  issn = {0962-8436, 1471-2970},
  doi = {10.1098/rstb.2011.0250},
  language = {en},
  number = {1587},
  urldate = {2017-10-16},
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2011.0250},
  author = {McGaugh, S. E. and Noor, M. A. F.},
  month = feb,
  year = {2012},
  pages = {422-429}
}

@article{Gulia-Nuss2016,
  title = {Genomic Insights into the {{Ixodes}} Scapularis Tick Vector of {{Lyme}} Disease},
  volume = {7},
  issn = {2041-1723},
  doi = {10.1038/ncomms10507},
  urldate = {2017-10-16},
  journal = {Nature Communications},
  url = {http://www.nature.com/doifinder/10.1038/ncomms10507},
  author = {{Gulia-Nuss}, Monika and Nuss, Andrew B. and Meyer, Jason M. and Sonenshine, Daniel E. and Roe, R. Michael and Waterhouse, Robert M. and Sattelle, David B. and {de la Fuente}, Jos\'e and Ribeiro, Jose M. and Megy, Karine and Thimmapuram, Jyothi and Miller, Jason R. and Walenz, Brian P. and Koren, Sergey and Hostetler, Jessica B. and Thiagarajan, Mathangi and Joardar, Vinita S. and Hannick, Linda I. and Bidwell, Shelby and Hammond, Martin P. and Young, Sarah and Zeng, Qiandong and Abrudan, Jenica L. and Almeida, Francisca C. and Ayll\'on, Nieves and Bhide, Ketaki and Bissinger, Brooke W. and {Bonzon-Kulichenko}, Elena and Buckingham, Steven D. and Caffrey, Daniel R. and Caimano, Melissa J. and Croset, Vincent and Driscoll, Timothy and Gilbert, Don and Gillespie, Joseph J. and {Giraldo-Calder\'on}, Gloria I. and Grabowski, Jeffrey M. and Jiang, David and Khalil, Sayed M. S. and Kim, Donghun and Kocan, Katherine M. and Ko{\v c}i, Juraj and Kuhn, Richard J. and Kurtti, Timothy J. and Lees, Kristin and Lang, Emma G. and Kennedy, Ryan C. and Kwon, Hyeogsun and Perera, Rushika and Qi, Yumin and Radolf, Justin D. and Sakamoto, Joyce M. and {S\'anchez-Gracia}, Alejandro and Severo, Maiara S. and Silverman, Neal and {\v S}imo, Ladislav and Tojo, Marta and Tornador, Cristian and Van Zee, Janice P. and V\'azquez, Jes\'us and Vieira, Filipe G. and Villar, Margarita and Wespiser, Adam R. and Yang, Yunlong and Zhu, Jiwei and Arensburger, Peter and Pietrantonio, Patricia V. and Barker, Stephen C. and Shao, Renfu and Zdobnov, Evgeny M. and Hauser, Frank and Grimmelikhuijzen, Cornelis J. P. and Park, Yoonseong and Rozas, Julio and Benton, Richard and Pedra, Joao H. F. and Nelson, David R. and Unger, Maria F. and Tubio, Jose M. C. and Tu, Zhijian and Robertson, Hugh M. and Shumway, Martin and Sutton, Granger and Wortman, Jennifer R. and Lawson, Daniel and Wikel, Stephen K. and Nene, Vishvanath M. and Fraser, Claire M. and Collins, Frank H. and Birren, Bruce and Nelson, Karen E. and Caler, Elisabet and Hill, Catherine A.},
  month = feb,
  year = {2016},
  pages = {10507}
}

@article{Zhao2015,
  title = {A {{Massive Expansion}} of {{Effector Genes Underlies Gall}}-{{Formation}} in the {{Wheat Pest Mayetiola}} Destructor},
  volume = {25},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2014.12.057},
  abstract = {Summary
Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5\% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M.~destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in~vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.},
  number = {5},
  urldate = {2017-10-16},
  journal = {Current Biology},
  url = {http://www.sciencedirect.com/science/article/pii/S0960982214016959},
  author = {Zhao, Chaoyang and Escalante, Lucio Navarro and Chen, Hang and Benatti, Thiago R. and Qu, Jiaxin and Chellapilla, Sanjay and Waterhouse, Robert M. and Wheeler, David and Andersson, Martin N. and Bao, Riyue and Batterton, Matthew and Behura, Susanta K. and Blankenburg, Kerstin P. and Caragea, Doina and Carolan, James C. and Coyle, Marcus and {El-Bouhssini}, Mustapha and Francisco, Liezl and Friedrich, Markus and Gill, Navdeep and Grace, Tony and Grimmelikhuijzen, Cornelis J. P. and Han, Yi and Hauser, Frank and Herndon, Nicolae and Holder, Michael and Ioannidis, Panagiotis and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Johnson, Alisha J. and Kalra, Divya and Korchina, Viktoriya and Kovar, Christie L. and Lara, Fremiet and Lee, Sandra L. and Liu, Xuming and L\"ofstedt, Christer and Mata, Robert and Mathew, Tittu and Muzny, Donna M. and Nagar, Swapnil and Nazareth, Lynne V. and Okwuonu, Geoffrey and Ongeri, Fiona and Perales, Lora and Peterson, Brittany F. and Pu, Ling-Ling and Robertson, Hugh M. and Schemerhorn, Brandon J. and Scherer, Steven E. and Shreve, Jacob T. and Simmons, DeNard and Subramanyam, Subhashree and Thornton, Rebecca L. and Xue, Kun and Weissenberger, George M. and Williams, Christie E. and Worley, Kim C. and Zhu, Dianhui and Zhu, Yiming and Harris, Marion O. and Shukle, Richard H. and Werren, John H. and Zdobnov, Evgeny M. and Chen, Ming-Shun and Brown, Susan J. and Stuart, Jeffery J. and Richards, Stephen},
  month = mar,
  year = {2015},
  pages = {613-620},
  file = {/home/mpetersen/bib/storage/VSHWX9AT/Zhao et al. - 2015 - A Massive Expansion of Effector Genes Underlies Ga.pdf;/home/mpetersen/bib/storage/XRPPETM7/S0960982214016959.html}
}

@article{Kirkness2010,
  title = {Genome Sequences of the Human Body Louse and Its Primary Endosymbiont Provide Insights into the Permanent Parasitic Lifestyle},
  volume = {107},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1003379107},
  abstract = {As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.},
  language = {en},
  number = {27},
  urldate = {2017-10-16},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/107/27/12168},
  author = {Kirkness, Ewen F. and Haas, Brian J. and Sun, Weilin and Braig, Henk R. and Perotti, M. Alejandra and Clark, John M. and Lee, Si Hyeock and Robertson, Hugh M. and Kennedy, Ryan C. and Elhaik, Eran and Gerlach, Daniel and Kriventseva, Evgenia V. and Elsik, Christine G. and Graur, Dan and Hill, Catherine A. and Veenstra, Jan A. and Walenz, Brian and Tub\'io, Jos\'e Manuel C. and Ribeiro, Jos\'e M. C. and Rozas, Julio and Johnston, J. Spencer and Reese, Justin T. and Popadic, Aleksandar and Tojo, Marta and Raoult, Didier and Reed, David L. and Tomoyasu, Yoshinori and Kraus, Emily and Mittapalli, Omprakash and Margam, Venu M. and Li, Hong-Mei and Meyer, Jason M. and Johnson, Reed M. and {Romero-Severson}, Jeanne and VanZee, Janice Pagel and {Alvarez-Ponce}, David and Vieira, Filipe G. and Aguad\'e, Montserrat and {Guirao-Rico}, Sara and Anzola, Juan M. and Yoon, Kyong S. and Strycharz, Joseph P. and Unger, Maria F. and Christley, Scott and Lobo, Neil F. and Seufferheld, Manfredo J. and Wang, NaiKuan and Dasch, Gregory A. and Struchiner, Claudio J. and Madey, Greg and Hannick, Linda I. and Bidwell, Shelby and Joardar, Vinita and Caler, Elisabet and Shao, Renfu and Barker, Stephen C. and Cameron, Stephen and Bruggner, Robert V. and Regier, Allison and Johnson, Justin and Viswanathan, Lakshmi and Utterback, Terry R. and Sutton, Granger G. and Lawson, Daniel and Waterhouse, Robert M. and Venter, J. Craig and Strausberg, Robert L. and Berenbaum, May R. and Collins, Frank H. and Zdobnov, Evgeny M. and Pittendrigh, Barry R.},
  month = jun,
  year = {2010},
  keywords = {Comparative genomics,ectoparasite,coevolution},
  pages = {12168-12173},
  file = {/home/mpetersen/bib/storage/VUZK59WI/Kirkness et al. - 2010 - Genome sequences of the human body louse and its p.pdf;/home/mpetersen/bib/storage/GPK6JKGG/12168.html},
  pmid = {20566863}
}

@article{Smith2011,
  title = {Draft Genome of the Red Harvester Ant {{Pogonomyrmex}} Barbatus},
  volume = {108},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1007901108},
  abstract = {We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.},
  language = {en},
  number = {14},
  urldate = {2017-10-16},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/108/14/5667},
  author = {Smith, Chris R. and Smith, Christopher D. and Robertson, Hugh M. and Helmkampf, Martin and Zimin, Aleksey and Yandell, Mark and Holt, Carson and Hu, Hao and Abouheif, Ehab and Benton, Richard and Cash, Elizabeth and Croset, Vincent and Currie, Cameron R. and Elhaik, Eran and Elsik, Christine G. and Fav\'e, Marie-Julie and Fernandes, Vilaiwan and Gibson, Joshua D. and Graur, Dan and Gronenberg, Wulfila and Grubbs, Kirk J. and Hagen, Darren E. and Viniegra, Ana Sofia Ibarraran and Johnson, Brian R. and Johnson, Reed M. and Khila, Abderrahman and Kim, Jay W. and Mathis, Kaitlyn A. and {Munoz-Torres}, Monica C. and Murphy, Marguerite C. and Mustard, Julie A. and Nakamura, Rin and Niehuis, Oliver and Nigam, Surabhi and Overson, Rick P. and Placek, Jennifer E. and Rajakumar, Rajendhran and Reese, Justin T. and Suen, Garret and Tao, Shu and Torres, Candice W. and Tsutsui, Neil D. and Viljakainen, Lumi and Wolschin, Florian and Gadau, J\"urgen},
  month = may,
  year = {2011},
  keywords = {social insect,chemoreceptor,de novo genome,eusociality,genomic evolution},
  pages = {5667-5672},
  file = {/home/mpetersen/bib/storage/MN2SQWJH/Smith et al. - 2011 - Draft genome of the red harvester ant Pogonomyrmex.pdf;/home/mpetersen/bib/storage/JDENPG9D/5667.html},
  pmid = {21282651}
}

@article{Wurm2011,
  title = {The Genome of the Fire Ant {{Solenopsis}} Invicta},
  volume = {108},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1009690108},
  abstract = {Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects. S. invicta also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the transformer/feminizer sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this S. invicta telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.},
  language = {en},
  number = {14},
  urldate = {2017-10-16},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/108/14/5679},
  author = {Wurm, Yannick and Wang, John and {Riba-Grognuz}, Oksana and Corona, Miguel and Nygaard, Sanne and Hunt, Brendan G. and Ingram, Krista K. and Falquet, Laurent and Nipitwattanaphon, Mingkwan and Gotzek, Dietrich and Dijkstra, Michiel B. and Oettler, Jan and Comtesse, Fabien and Shih, Cheng-Jen and Wu, Wen-Jer and Yang, Chin-Cheng and Thomas, Jerome and Beaudoing, Emmanuel and Pradervand, Sylvain and Flegel, Volker and Cook, Erin D. and Fabbretti, Roberto and Stockinger, Heinz and Long, Li and Farmerie, William G. and Oakey, Jane and Boomsma, Jacobus J. and Pamilo, Pekka and Yi, Soojin V. and Heinze, J\"urgen and Goodisman, Michael A. D. and Farinelli, Laurent and Harshman, Keith and Hulo, Nicolas and Cerutti, Lorenzo and Xenarios, Ioannis and Shoemaker, DeWayne and Keller, Laurent},
  month = may,
  year = {2011},
  keywords = {caste differences,de novo genome assembly,nonmodel organism,social insect},
  pages = {5679-5684},
  file = {/home/mpetersen/bib/storage/8NRW7EGK/Wurm et al. - 2011 - The genome of the fire ant Solenopsis invicta.pdf;/home/mpetersen/bib/storage/2VEK5929/5679.html},
  pmid = {21282665}
}

@article{Eyun2017,
  title = {Evolutionary {{History}} of {{Chemosensory}}-{{Related Gene Families}} across the {{Arthropoda}}},
  volume = {34},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msx147},
  language = {en},
  number = {8},
  urldate = {2017-10-16},
  journal = {Molecular Biology and Evolution},
  url = {http://academic.oup.com/mbe/article/34/8/1838/3782715/Evolutionary-History-of-ChemosensoryRelated-Gene},
  author = {Eyun, Seong-il and Soh, Ho Young and Posavi, Marijan and Munro, James B. and Hughes, Daniel S.T. and Murali, Shwetha C. and Qu, Jiaxin and Dugan, Shannon and Lee, Sandra L. and Chao, Hsu and Dinh, Huyen and Han, Yi and Doddapaneni, HarshaVardhan and Worley, Kim C. and Muzny, Donna M. and Park, Eun-Ok and Silva, Joana C. and Gibbs, Richard A. and Richards, Stephen and Lee, Carol Eunmi},
  month = aug,
  year = {2017},
  pages = {1838-1862}
}

@article{Wallace2011,
  title = {Evolutionary History of the Third Chromosome Gene Arrangements of {{Drosophila}} Pseudoobscura Inferred from Inversion Breakpoints.},
  volume = {28},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msr039},
  language = {en},
  number = {8},
  urldate = {2017-11-20},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msr039},
  author = {Wallace, A. G. and Detweiler, D. and Schaeffer, S. W.},
  month = aug,
  year = {2011},
  pages = {2219-2229},
  file = {/home/mpetersen/bib/storage/ZXMRDX7W/Evolutionary_History_of_the_Third_Chromosome_Gene_.pdf}
}

@article{Traut1997,
  title = {Sex {{Chromosome Differentiation}} in {{Some Species}} of {{Lepidoptera}} ({{Insecta}})},
  volume = {5},
  issn = {0967-3849, 1573-6849},
  doi = {10.1023/B:CHRO.0000038758.08263.c3},
  abstract = {Sex chromosome morphology of eight Lepidoptera species was studied, exploiting predominantly the pachytene stage when chromosomes display a remarkable chromomere pattern. Six species had a WZ/ZZ sex chromosome system, one species a W1W2Z/ZZ system and one species was of the Z/ZZ type. Much like XY chromosomes in groups with male heterogamety, the lepidopteran sex chromosomes showed various degrees of structural differentiation. Differences between Z and W chromomere patterns ranged from undetectable to obviously non-homologous. A common property of the W chromosomes (the W1 in the W1W2Z/ZZ system) was the possession of a block of heterochromatin. The heterochromatin block comprised a small or a large segment of the W or even the entire W, depending on the species. Segments with apparent structural homology are evolutionarily young parts of the sex chromosomes \textemdash{} recently fused autosomes that have not had sufficient time for differentiation. The `primitive' lepidopteran species Micropterix calthella had a Z/ZZ sex chromosome system. This supports the hypothesis that the lepidopteran W chromosome came into being at the base of the `advanced' Lepidoptera; it was presumably an autosome whose homologue fused to the original Z chromosome.},
  language = {en},
  number = {5},
  urldate = {2017-12-01},
  journal = {Chromosome Research},
  url = {https://link.springer.com/article/10.1023/B:CHRO.0000038758.08263.c3},
  author = {Traut, Walther and Marec, Frantis{\v e}k},
  month = aug,
  year = {1997},
  pages = {283-291},
  file = {/home/mpetersen/bib/storage/UQR38I9I/10.1023BCHRO.0000038758.08263.html}
}

@article{Levis1993,
  title = {Transposons in Place of Telomeric Repeats at a {{Drosophila}} Telomere},
  volume = {75},
  issn = {0092-8674},
  doi = {10.1016/0092-8674(93)90318-K},
  abstract = {We present the first isolation of the terminal DNA of an intact Drosophila telomere. It differs from those isolated from other eukaryotes by the lack of short tandem repeats at the terminus. The terminal 14.5 kb is composed of four tandem elements derived from two families of non-long terminal repeat retrotransposons and is subject to slow terminal loss. One of these transposon families, TART (telomere-associated retrotransposon), is described for the first time here. The other element, HeT-A, has previously been shown to transpose to broken chromosome ends. Our results provide key evidence that these elements also transpose to natural chromosome ends. We propose that the telomere-associated repetitive DNA is maintained by saltatory expansions, including terminal transpositions of specialized retrotransposons, which serve to balance terminal loss.},
  number = {6},
  urldate = {2017-12-01},
  journal = {Cell},
  url = {http://www.sciencedirect.com/science/article/pii/009286749390318K},
  author = {Levis, Robert W. and Ganesan, Robin and Houtchens, Kathleen and Tolar, Leigh Anna and Sheen, Fang-miin},
  month = dec,
  year = {1993},
  pages = {1083-1093},
  file = {/home/mpetersen/bib/storage/VBI2SDU3/Levis et al. - 1993 - Transposons in place of telomeric repeats at a Dro.pdf;/home/mpetersen/bib/storage/TIFY368X/009286749390318K.html}
}

@article{Mackay1989,
  title = {Transposable Elements and Fitness in {{Drosophila}} Melanogaster},
  volume = {31},
  issn = {0831-2796, 1480-3321},
  doi = {10.1139/g89-046},
  language = {en},
  number = {1},
  urldate = {2017-12-04},
  journal = {Genome},
  url = {http://www.nrcresearchpress.com/doi/10.1139/g89-046},
  author = {Mackay, Trudy F. C.},
  month = jan,
  year = {1989},
  pages = {284-295},
  file = {/home/mpetersen/bib/storage/FL5HLFC2/Transposable_elements_and_fitness_in_Drosophila_me.pdf}
}

@article{Deininger2011,
  title = {Alu Elements: Know the {{SINEs}}},
  volume = {12},
  issn = {1465-6906},
  shorttitle = {Alu Elements},
  doi = {10.1186/gb-2011-12-12-236},
  language = {en},
  number = {12},
  urldate = {2017-12-04},
  journal = {Genome Biology},
  url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-12-236},
  author = {Deininger, Prescott},
  year = {2011},
  pages = {236}
}

@book{Grimaldi2005,
  address = {Cambridge [U.K.] ; New York},
  title = {Evolution of the Insects},
  isbn = {978-0-521-82149-0},
  lccn = {QL468.7 .G75 2005},
  publisher = {{Cambridge University Press}},
  author = {Grimaldi, David A. and Engel, Michael S.},
  year = {2005},
  keywords = {Evolution,Insects}
}

@book{Beutel2013,
  address = {Berlin ; New York},
  series = {De {{Gruyter}} Graduate},
  title = {Insect Morphology and Phylogeny},
  isbn = {978-3-11-026263-6 978-3-11-026404-3},
  lccn = {QL494 .B483 2013},
  shorttitle = {Insect Morphology and Phylogeny},
  publisher = {{De Gruyter}},
  author = {Beutel, Rolf},
  year = {2013},
  keywords = {Phylogeny,Insects,Morphology}
}

@article{Dunn2018,
  title = {Pairwise Comparisons across Species Are Problematic When Analyzing Functional Genomic Data},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1707515115},
  language = {en},
  urldate = {2018-01-08},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1707515115},
  author = {Dunn, Casey W. and Zapata, Felipe and Munro, Catriona and Siebert, Stefan and Hejnol, Andreas},
  month = jan,
  year = {2018},
  keywords = {functional genomics,gene expression,phylogenetics,hourglass,ortholog conjecture},
  pages = {201707515},
  file = {/home/mpetersen/bib/storage/3NKNLZNJ/PNAS-2018-Dunn-1707515115.pdf;/home/mpetersen/bib/storage/KQ9YR6DQ/Dunn et al. - 2018 - Pairwise comparisons across species are problemati.pdf;/home/mpetersen/bib/storage/9YS8M2Z8/E409.html}
}

@article{Nichio2017,
  title = {New {{Tools}} in {{Orthology Analysis}}: {{A Brief Review}} of {{Promising Perspectives}}},
  volume = {8},
  issn = {1664-8021},
  shorttitle = {New {{Tools}} in {{Orthology Analysis}}},
  doi = {10.3389/fgene.2017.00165},
  urldate = {2018-01-17},
  journal = {Frontiers in Genetics},
  url = {http://journal.frontiersin.org/article/10.3389/fgene.2017.00165/full},
  author = {Nichio, Bruno T. L. and Marchaukoski, Jeroniza Nunes and Raittz, Roberto Tadeu},
  month = oct,
  year = {2017},
  file = {/home/mpetersen/bib/storage/YDSINT2M/New_Tools_in_Orthology_Analysis_A_Brief_Review_of_.pdf}
}

@article{Charlesworth1983,
  title = {The Population Dynamics of Transposable Elements},
  volume = {42},
  issn = {0016-6723, 1469-5073},
  doi = {10.1017/S0016672300021455},
  language = {en},
  number = {01},
  urldate = {2018-01-24},
  journal = {Genetical Research},
  url = {http://www.journals.cambridge.org/abstract_S0016672300021455},
  author = {Charlesworth, Brian and Charlesworth, Deborah},
  month = aug,
  year = {1983},
  pages = {1}
}

@article{Sotero-Caio2017,
  title = {Evolution and {{Diversity}} of {{Transposable Elements}} in {{Vertebrate Genomes}}},
  volume = {9},
  doi = {10.1093/gbe/evw264},
  abstract = {Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4\textendash{}60\% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.},
  language = {en},
  number = {1},
  urldate = {2018-01-30},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/9/1/161/2965566},
  author = {{Sotero-Caio}, Cibele G. and Platt, Roy N. and Suh, Alexander and Ray, David A.},
  month = jan,
  year = {2017},
  pages = {161-177},
  file = {/home/mpetersen/bib/storage/HGP3YU5D/Sotero-Caio et al. - 2017 - Evolution and Diversity of Transposable Elements i.pdf;/home/mpetersen/bib/storage/VT9L7ZBU/Sotero-Caio et al. - 2017 - Evolution and Diversity of Transposable Elements i.pdf}
}

@article{Mondal2018,
  title = {Rewired {{RNAi}}-Mediated Genome Surveillance in House Dust Mites},
  volume = {14},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1007183},
  abstract = {Author summary Investigation of small RNA populations in dust mites revealed absence of the piwi-associated RNA (piRNA) pathway. Apart from several nematode and platyhelminths lineages, piRNAs are an essential component of animal genome surveillance, actively targeting and silencing transposable elements. In dust mites, expansion of Dicer produced small-interfering RNA (siRNA) biology compensates for loss of piRNAs. The dramatic difference we find in dust mites is likely a consequence of their evolutionary history, which is marked by descent from a parasite to the current free-living form. Our study highlights a correlation between perturbation of transposon surveillance and shifts in ecology.},
  language = {en},
  number = {1},
  urldate = {2018-02-14},
  journal = {PLOS Genetics},
  url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007183},
  author = {Mondal, Mosharrof and Klimov, Pavel and Flynt, Alex Sutton},
  month = jan,
  year = {2018},
  keywords = {Drosophila melanogaster,RNA interference,Invertebrate genomics,Sequence motif analysis,Double stranded RNA,Mites,RNA sequencing,Small interfering RNAs},
  pages = {e1007183},
  file = {/home/mpetersen/bib/storage/PD2LVV8W/Mondal et al. - 2018 - Rewired RNAi-mediated genome surveillance in house.pdf;/home/mpetersen/bib/storage/ETKJKQZU/article.html}
}

@article{Horvath2017,
  title = {Revisiting the {{Relationship}} between {{Transposable Elements}} and the {{Eukaryotic Stress Response}}},
  volume = {33},
  issn = {0168-9525},
  doi = {10.1016/j.tig.2017.08.007},
  abstract = {A relationship between transposable elements (TEs) and the eukaryotic stress response was suggested in the first publications describing TEs. Since then, it has often been assumed that TEs are activated by stress, and that this activation is often beneficial for the organism. In recent years, the availability of new high-throughput experimental techniques has allowed further interrogation of the relationship between TEs and stress. By reviewing the recent literature, we conclude that although there is evidence for a beneficial effect of TE activation under stress conditions, the relationship between TEs and the eukaryotic stress response is quite complex., TEs can be activated and/or repressed under stress conditions. In some cases, the repression of TEs happens after an initial activation., TEs are associated with upregulation and downregulation of nearby genes following stress. TEs can be the cause or the consequence of the changes in the nearby gene expression., TEs can be beneficial for the organism in stress conditions, however, there are studies showing that the effects of TEs are harmful under stress., To further our understanding of the relationship between TEs and stress, we need to gain more knowledge about the molecular mechanisms behind the changes in the activity of TEs and the consequences of these changes at the phenotypic level.},
  language = {English},
  number = {11},
  urldate = {2018-02-15},
  journal = {Trends in Genetics},
  url = {http://www.cell.com/trends/genetics/abstract/S0168-9525(17)30145-2},
  author = {Horv\'ath, Vivien and Merenciano, Miriam and Gonz\'alez, Josefa},
  month = nov,
  year = {2017},
  keywords = {activation,fitness effects,gene regulation,repression,silencing mechanisms},
  pages = {832-841},
  file = {/home/mpetersen/bib/storage/TLDVEHXU/S0168-9525(17)30145-2.html},
  pmid = {28947157}
}

@article{Petrov2001,
  title = {Evolution of Genome Size: New Approaches to an Old Problem},
  volume = {17},
  issn = {0168-9525},
  shorttitle = {Evolution of Genome Size},
  doi = {10.1016/S0168-9525(00)02157-0},
  abstract = {Eukaryotic genomes come in a wide variety of sizes. Haploid DNA contents (C values) range {$>$}80\hphantom{,}000-fold without an apparent correlation with either the complexity of the organism or the number of genes. This puzzling observation, the C-value paradox, has remained a mystery for almost half a century, despite much progress in the elucidation of the structure and function of genomes. Here I argue that new approaches focussing on the genetic mechanisms that generate genome-size differences could shed much light on the evolution of genome size.},
  number = {1},
  urldate = {2018-02-26},
  journal = {Trends in Genetics},
  url = {http://www.sciencedirect.com/science/article/pii/S0168952500021570},
  author = {Petrov, Dmitri A.},
  month = jan,
  year = {2001},
  keywords = {genome size,genome evolution,C-value paradox,DNA loss,junk DNA,transposable},
  pages = {23-28},
  file = {/home/mpetersen/bib/storage/JTJDEAQ7/19.pdf;/home/mpetersen/bib/storage/T34KP2PS/S0168952500021570.html}
}

@article{Petrov1996,
  title = {High Intrinsic Rate of {{DNA}} Loss in {{Drosophila}}},
  volume = {384},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/384346a0},
  language = {en},
  number = {6607},
  urldate = {2018-02-26},
  journal = {Nature},
  url = {http://www.nature.com/doifinder/10.1038/384346a0},
  author = {Petrov, Dmitri A. and Lozovskaya, Elena R. and Hartl, Daniel L.},
  month = nov,
  year = {1996},
  pages = {346-349},
  file = {/home/mpetersen/bib/storage/5H4AHWAU/08.pdf;/home/mpetersen/bib/storage/QSHXSJDQ/08.pdf}
}

@article{Zonneveld2005,
  title = {First {{Nuclear DNA Amounts}} in More than 300 {{Angiosperms}}},
  volume = {96},
  issn = {1095-8290, 0305-7364},
  doi = {10.1093/aob/mci170},
  language = {en},
  number = {2},
  urldate = {2018-02-26},
  journal = {Annals of Botany},
  url = {http://academic.oup.com/aob/article/96/2/229/299162/First-Nuclear-DNA-Amounts-in-more-than-300},
  author = {Zonneveld, B. J. M. and Leitch, I. J. and Bennett, M. D.},
  month = aug,
  year = {2005},
  pages = {229-244}
}

@article{Petrov2000,
  title = {Evidence for {{DNA Loss}} as a {{Determinant}} of {{Genome Size}}},
  volume = {287},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.287.5455.1060},
  abstract = {Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum inLaupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than inDrosophila.},
  language = {en},
  number = {5455},
  urldate = {2018-02-26},
  journal = {Science},
  url = {http://science.sciencemag.org/content/287/5455/1060},
  author = {Petrov, Dmitri A. and Sangster, Todd A. and Johnston, J. Spencer and Hartl, Daniel L. and Shaw, Kerry L.},
  month = feb,
  year = {2000},
  pages = {1060-1062},
  file = {/home/mpetersen/bib/storage/LW2GZ8RJ/Laupala.pdf;/home/mpetersen/bib/storage/JR8RAMC3/1060.html},
  pmid = {10669421}
}

@book{Gregory2005,
  address = {Burlington, MA},
  title = {The Evolution of the Genome},
  isbn = {978-0-12-301463-4},
  lccn = {QH447 .E9626 2005},
  publisher = {{Elsevier Academic}},
  editor = {Gregory, T. Ryan},
  year = {2005},
  keywords = {Evolution,Evolution; Molecular,Genome,Genomes,Molecular},
  note = {OCLC: ocm57727263}
}

@article{Canapa2015,
  title = {Transposons, {{Genome Size}}, and {{Evolutionary Insights}} in {{Animals}}},
  volume = {147},
  issn = {1424-8581, 1424-859X},
  doi = {10.1159/000444429},
  language = {en},
  number = {4},
  urldate = {2018-02-27},
  journal = {Cytogenetic and Genome Research},
  url = {https://www.karger.com/Article/FullText/444429},
  author = {Canapa, Adriana and Barucca, Marco and Biscotti, Maria A. and Forconi, Mariko and Olmo, Ettore},
  year = {2015},
  pages = {217-239}
}

@misc{Gregory2018,
  title = {Animal {{Genome Size Database}}},
  url = {http://www.genomesize.com},
  author = {Gregory, T. Ryan},
  year = {2018}
}

@article{Dufresne2011,
  title = {A Guided Tour of Large Genome Size in Animals: What We Know and Where We Are Heading},
  volume = {19},
  issn = {0967-3849, 1573-6849},
  shorttitle = {A Guided Tour of Large Genome Size in Animals},
  doi = {10.1007/s10577-011-9248-x},
  language = {en},
  number = {7},
  urldate = {2018-02-27},
  journal = {Chromosome Research},
  url = {http://link.springer.com/10.1007/s10577-011-9248-x},
  author = {Dufresne, France and Jeffery, Nicholas},
  month = oct,
  year = {2011},
  pages = {925-938}
}

@article{Bennett1977,
  title = {The {{Time}} and {{Duration}} of {{Meiosis}} [and {{Discussion}}]},
  volume = {277},
  issn = {0962-8436, 1471-2970},
  doi = {10.1098/rstb.1977.0012},
  language = {en},
  number = {955},
  urldate = {2018-02-27},
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.1977.0012},
  author = {Bennett, M. D. and Lewis, K. R. and Harberd, D. J.},
  month = mar,
  year = {1977},
  pages = {201-226}
}

@article{White2000,
  title = {Copepod Development Rates in Relation to Genome Size and {{18S rDNA}} Copy Number},
  volume = {43},
  issn = {1480-3321, 0831-2796},
  doi = {10.1139/gen-43-5-750},
  number = {5},
  urldate = {2018-02-27},
  journal = {Genome},
  url = {http://www.nrc.ca/cgi-bin/cisti/journals/rp/rp2_abst_e?gen_g00-048_43_ns_nf_gen43-00},
  author = {White, M.M. and McLaren, I.A.},
  year = {2000},
  pages = {750-755}
}

@article{Bennetzen2005,
  title = {Mechanisms of {{Recent Genome Size Variation}} in {{Flowering Plants}}},
  volume = {95},
  issn = {0305-7364},
  doi = {10.1093/aob/mci008},
  abstract = {\textbullet{} Background and Aims Plant nuclear genomes vary tremendously in DNA content, mostly due to differences in ancestral ploidy and variation in the degree of transposon amplification. These processes can increase genome size, but little is known about mechanisms of genome shrinkage and the degree to which these can attenuate or reverse genome expansion. This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species.\textbullet{} Methods Retrotransposons were analyzed for sequence variation within several element families in rice and Arabidopsis. Nucleotide sequence changes in the two termini of individual retrotransposons were used to date their time of insertion.\textbullet{} Key Results An accumulation of small deletions was found in both species, caused by unequal homologous recombination and illegitimate recombination. The relative contribution of unequal homologous recombination compared to illegitimate recombination was higher in rice than in Arabidopsis. However, retrotransposons are rapidly removed in both species, as evidenced by the similar apparent ages of intact elements (most less than 3 million years old) in these two plants and all other investigated plant species.\textbullet{} Conclusions Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor. The simplest model suggests that significant genome size variation is generated by lineage-specific differences in the molecular mechanisms of DNA amplification and removal, creating major variation in nuclear DNA content that can then serve as the substrate for fitness-based selection.},
  language = {en},
  number = {1},
  urldate = {2018-02-27},
  journal = {Annals of Botany},
  url = {https://academic.oup.com/aob/article/95/1/127/198516},
  author = {Bennetzen, Jeffrey L. and Ma, Jianxin and Devos, Katrien M.},
  month = jan,
  year = {2005},
  pages = {127-132},
  file = {/home/mpetersen/bib/storage/FQ5UMFQ2/Bennetzen et al. - 2005 - Mechanisms of Recent Genome Size Variation in Flow.pdf;/home/mpetersen/bib/storage/TE2FUYFX/198516.html}
}

@article{Piegu2006,
  title = {Doubling Genome Size without Polyploidization: {{Dynamics}} of Retrotransposition-Driven Genomic Expansions in {{Oryza}} Australiensis, a Wild Relative of Rice},
  volume = {16},
  issn = {1088-9051, 1549-5469},
  shorttitle = {Doubling Genome Size without Polyploidization},
  doi = {10.1101/gr.5290206},
  abstract = {Retrotransposons are the main components of eukaryotic genomes, representing up to 80\% of some large plant genomes. These mobile elements transpose via a ``copy and paste'' mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.},
  language = {en},
  number = {10},
  urldate = {2018-02-27},
  journal = {Genome Research},
  url = {http://genome.cshlp.org/content/16/10/1262},
  author = {Piegu, Benoit and Guyot, Romain and Picault, Nathalie and Roulin, Anne and Saniyal, Abhijit and Kim, Hyeran and Collura, Kristi and Brar, Darshan S. and Jackson, Scott and Wing, Rod A. and Panaud, Olivier},
  month = jan,
  year = {2006},
  pages = {1262-1269},
  file = {/home/mpetersen/bib/storage/XQUJVF9I/Piegu et al. - 2006 - Doubling genome size without polyploidization Dyn.pdf;/home/mpetersen/bib/storage/RKC57PAI/1262.html},
  pmid = {16963705}
}

@article{Vitte2007,
  title = {{{LTR}} Retrotransposons in Rice ({{Oryza}} Sativa, {{L}}.): Recent Burst Amplifications Followed by Rapid {{DNA}} Loss},
  volume = {8},
  issn = {1471-2164},
  shorttitle = {{{LTR}} Retrotransposons in Rice ({{Oryza}} Sativa, {{L}}.)},
  doi = {10.1186/1471-2164-8-218},
  abstract = {BACKGROUND: LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice.
RESULTS: Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal.
CONCLUSION: Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.},
  language = {eng},
  journal = {BMC genomics},
  author = {Vitte, Cl\'ementine and Panaud, Olivier and Quesneville, Hadi},
  month = jul,
  year = {2007},
  keywords = {Molecular,DNA,Genome,Evolution,Evolution; Molecular,Genome; Plant,Retroelements,Gene Amplification,Gene Deletion,DNA; Plant,Oryza,Terminal Repeat Sequences,Plant},
  pages = {218},
  pmid = {17617907},
  pmcid = {PMC1940013}
}

@article{Kelly2015,
  title = {Analysis of the Giant Genomes of {{Fritillaria}} ({{Liliaceae}}) Indicates That a Lack of {{DNA}} Removal Characterizes Extreme Expansions in Genome Size},
  volume = {208},
  issn = {0028646X},
  doi = {10.1111/nph.13471},
  language = {en},
  number = {2},
  urldate = {2018-02-27},
  journal = {New Phytologist},
  url = {http://doi.wiley.com/10.1111/nph.13471},
  author = {Kelly, Laura J. and {Renny-Byfield}, Simon and Pellicer, Jaume and Macas, Ji{\v r}\'i and Nov\'ak, Petr and Neumann, Pavel and Lysak, Martin A. and Day, Peter D. and Berger, Madeleine and Fay, Michael F. and Nichols, Richard A. and Leitch, Andrew R. and Leitch, Ilia J.},
  month = oct,
  year = {2015},
  pages = {596-607},
  file = {/home/mpetersen/bib/storage/Q8B33IAP/nph13471.pdf}
}

@article{Nystedt2013,
  title = {The {{Norway}} Spruce Genome Sequence and Conifer Genome Evolution},
  volume = {497},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/nature12211},
  language = {en},
  number = {7451},
  urldate = {2018-02-27},
  journal = {Nature},
  url = {http://www.nature.com/articles/nature12211},
  author = {Nystedt, Bj\"orn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and H\"allman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and K\"aller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittyl\"a, Totte and Olson, \AA{}ke and Rilakovic, Nemanja and Ritland, Carol and Rossell\'o, Josep A. and Sena, Juliana and Svensson, Thomas and {Talavera-L\'opez}, Carlos and Thei\ss{}en, G\"unter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and {de Jong}, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Bj\"orn and Lee Thompson, Stacey and {Van de Peer}, Yves and Andersson, Bj\"orn and Nilsson, Ove and Ingvarsson, P\"ar K. and Lundeberg, Joakim and Jansson, Stefan},
  month = may,
  year = {2013},
  pages = {579-584}
}

@article{Blass2012,
  title = {Accumulation and {{Rapid Decay}} of {{Non}}-{{LTR Retrotransposons}} in the {{Genome}} of the {{Three}}-{{Spine Stickleback}}},
  volume = {4},
  doi = {10.1093/gbe/evs044},
  abstract = {The diversity and abundance of non\textendash{}long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions.},
  language = {en},
  number = {5},
  urldate = {2018-02-27},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/4/5/687/536060},
  author = {Blass, Eryn and Bell, Michael and Boissinot, St\'ephane},
  month = jan,
  year = {2012},
  pages = {687-702},
  file = {/home/mpetersen/bib/storage/PUDXYKWQ/Blass et al. - 2012 - Accumulation and Rapid Decay of Non-LTR Retrotrans.pdf;/home/mpetersen/bib/storage/YV876RWL/536060.html}
}

@article{Neafsey2003,
  title = {Genome {{Size Evolution}} in {{Pufferfish}}: {{A Comparative Analysis}} of {{Diodontid}} and {{Tetraodontid Pufferfish Genomes}}},
  volume = {13},
  issn = {1088-9051, 1549-5469},
  shorttitle = {Genome {{Size Evolution}} in {{Pufferfish}}},
  doi = {10.1101/gr.841703},
  abstract = {Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of {$\sim$}400 million bp (Mb), which is almost eight times smaller than the human genome. Given that spiny pufferfish from the sister family Diodontidae and a fish from the outgroup Molidae have genomes twice as large as smooth puffers, it appears that the genome size of smooth puffers has contracted in the last 50\textendash{}70 million years since their divergence from the spiny puffers. Here we use renaturation kinetics to compare the repetitive nature of the smooth and spiny puffer genomes. We also estimate the rates of small ({$<$}400 bp) insertions and deletions in smooth and spiny puffers using defunct non-LTR retrotransposons. We find a significantly greater abundance of a transposon-like repetitive DNA class in spiny puffers relative to smooth puffers, in addition to nearly identical indel rates. We comment on the role that large insertions may play in the evolution of genome size in these two groups.
[The sequence data from this study have been submitted to GenBank under accession nos. AY212336\textendash{}AY212504.]},
  language = {en},
  number = {5},
  urldate = {2018-02-27},
  journal = {Genome Research},
  url = {http://genome.cshlp.org/content/13/5/821},
  author = {Neafsey, Daniel E. and Palumbi, Stephen R.},
  month = jan,
  year = {2003},
  pages = {821-830},
  file = {/home/mpetersen/bib/storage/RUXHAJR4/Neafsey and Palumbi - 2003 - Genome Size Evolution in Pufferfish A Comparative.pdf;/home/mpetersen/bib/storage/2V2UB9JM/821.html},
  pmid = {12727902}
}

@article{Sun2012,
  title = {Slow {{DNA Loss}} in the {{Gigantic Genomes}} of {{Salamanders}}},
  volume = {4},
  doi = {10.1093/gbe/evs103},
  abstract = {Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., {$\sim$}1\textendash{}30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes\textemdash{}the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis, Danio rerio, Gallus gallus, Homo sapiens, and Xenopus tropicalis. Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.},
  language = {en},
  number = {12},
  urldate = {2018-02-27},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/4/12/1340/608259},
  author = {Sun, Cheng and Arriaza, L\'opez and R, Jos\'e and Mueller, Rachel Lockridge},
  month = dec,
  year = {2012},
  pages = {1340-1348},
  file = {/home/mpetersen/bib/storage/XE5592ES/Sun et al. - 2012 - Slow DNA Loss in the Gigantic Genomes of Salamande.pdf;/home/mpetersen/bib/storage/XTJVCXPA/608259.html}
}

@article{Wang2017,
  title = {When Did the Ancestor of True Bugs Become Stinky? {{Disentangling}} the Phylogenomics of {{Hemiptera}}-{{Heteroptera}}},
  issn = {07483007},
  shorttitle = {When Did the Ancestor of True Bugs Become Stinky?},
  doi = {10.1111/cla.12232},
  language = {en},
  urldate = {2018-03-05},
  journal = {Cladistics},
  url = {http://doi.wiley.com/10.1111/cla.12232},
  author = {Wang, Yan-Hui and Wu, Hao-Yang and R\'edei, D\'avid and Xie, Qiang and Chen, Yan and Chen, Ping-Ping and Dong, Zhuo-Er and Dang, Kai and Damgaard, Jakob and {\v S}tys, Pavel and Wu, Yan-Zhuo and Luo, Jiu-Yang and Sun, Xiao-Ya and Hartung, Viktor and Kuechler, Stefan M. and Liu, Yang and Liu, Hua-Xi and Bu, Wen-Jun},
  month = dec,
  year = {2017},
  file = {/home/mpetersen/bib/storage/NG7J9P57/When_did_the_ancestor_of_true_bugs_become_stinky_D.pdf;/home/mpetersen/bib/storage/R6NE4EHW/When_did_the_ancestor_of_true_bugs_become_stinky_D.pdf}
}

@article{Zdobnov2017,
  title = {{{OrthoDB}} v9.1: Cataloging Evolutionary and Functional Annotations for Animal, Fungal, Plant, Archaeal, Bacterial and Viral Orthologs},
  volume = {45},
  issn = {1362-4962},
  shorttitle = {{{OrthoDB}} v9.1},
  doi = {10.1093/nar/gkw1119},
  abstract = {OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87\% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.},
  language = {eng},
  number = {D1},
  journal = {Nucleic Acids Research},
  author = {Zdobnov, Evgeny M. and Tegenfeldt, Fredrik and Kuznetsov, Dmitry and Waterhouse, Robert M. and Sim\~ao, Felipe A. and Ioannidis, Panagiotis and Seppey, Mathieu and Loetscher, Alexis and Kriventseva, Evgenia V.},
  month = jan,
  year = {2017},
  keywords = {Algorithms,Animals,Computational Biology,Software,Genomics,Fungi,User-Computer Interface,Databases; Genetic,Evolution; Molecular,Molecular Sequence Annotation,Archaea,Bacteria,Plants,Viruses,Web Browser},
  pages = {D744-D749},
  pmid = {27899580},
  pmcid = {PMC5210582}
}

@article{Wallau2012,
  title = {Horizontal {{Transposon Transfer}} in {{Eukarya}}: {{Detection}}, {{Bias}}, and {{Perspectives}}},
  volume = {4},
  shorttitle = {Horizontal {{Transposon Transfer}} in {{Eukarya}}},
  doi = {10.1093/gbe/evs055},
  abstract = {The genetic similarity observed among species is normally attributed to the existence of a common ancestor. However, a growing body of evidence suggests that the exchange of genetic material is not limited to the transfer from parent to offspring but can also occur through horizontal transfer (HT). Transposable elements (TEs) are DNA fragments with an innate propensity for HT; they are mobile and possess parasitic characteristics that allow them to exist and proliferate within host genomes. However, horizontal transposon transfer (HTT) is not easily detected, primarily because the complex TE life cycle can generate phylogenetic patterns similar to those expected for HTT events. The increasingly large number of new genome projects, in all branches of life, has provided an unprecedented opportunity to evaluate the TE content and HTT events in these species, although a standardized method of HTT detection is required before trends in the HTT rates can be evaluated in a wide range of eukaryotic taxa and predictions about these events can be made. Thus, we propose a straightforward hypothesis test that can be used by TE specialists and nonspecialists alike to discriminate between HTT events and natural TE life cycle patterns. We also discuss several plausible explanations and predictions for the distribution and frequency of HTT and for the inherent biases of HTT detection. Finally, we discuss some of the methodological concerns for HTT detection that may result in the underestimation and overestimation of HTT rates during eukaryotic genome evolution.},
  language = {en},
  number = {8},
  urldate = {2018-03-27},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/4/8/801/580764},
  author = {Wallau, Gabriel Luz and Ortiz, Mauro Freitas and Loreto, Elgion Lucio Silva},
  month = jan,
  year = {2012},
  pages = {801-811},
  file = {/home/mpetersen/bib/storage/4QHJDWTX/Wallau et al. - 2012 - Horizontal Transposon Transfer in Eukarya Detecti.pdf;/home/mpetersen/bib/storage/KPCLL89W/580764.html}
}

@article{Kent2017,
  title = {Coevolution between Transposable Elements and Recombination},
  volume = {372},
  copyright = {\textcopyright{} 2017 The Author(s). http://royalsocietypublishing.org/licencePublished by the Royal Society. All rights reserved.},
  issn = {0962-8436, 1471-2970},
  doi = {10.1098/rstb.2016.0458},
  abstract = {One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure.
This article is part of the themed issue `Evolutionary causes and consequences of recombination rate variation in sexual organisms'.},
  language = {en},
  number = {1736},
  urldate = {2018-03-27},
  journal = {Phil. Trans. R. Soc. B},
  url = {http://rstb.royalsocietypublishing.org/content/372/1736/20160458},
  author = {Kent, Tyler V. and Uzunovi\'c, Jasmina and Wright, Stephen I.},
  month = dec,
  year = {2017},
  pages = {20160458},
  file = {/home/mpetersen/bib/storage/6FVGRY9S/Kent et al. - 2017 - Coevolution between transposable elements and reco.pdf;/home/mpetersen/bib/storage/LV3X4D7N/20160458.html},
  pmid = {29109221}
}

@article{Marburger2018,
  title = {Whole Genome Duplication and Transposable Element Proliferation Drive Genome Expansion in {{Corydoradinae}} Catfishes},
  volume = {285},
  issn = {0962-8452},
  doi = {10.1098/rspb.2017.2732},
  abstract = {Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size\textemdash{}0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree\textemdash{}the first between 43 and 49 Ma (95\% highest posterior density (HPD) 36.2\textendash{}68.1 Ma) and the second at approximately 19 Ma (95\% HPD 15.3\textendash{}30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95\% HPD 42.56\textendash{}99.5 Ma) and the second at 20\textendash{}30 Ma (95\% HPD 15.3\textendash{}45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95\% HPD 30.29\textendash{}64.51 Ma) and 20\textendash{}30 Ma (95\% HPD 15.3\textendash{}45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20\textendash{}30 Ma (95\% HPD 15.3\textendash{}45 Ma) and an older event at 35\textendash{}44 Ma (95\% HPD 30.29\textendash{}64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.},
  number = {1872},
  urldate = {2018-04-10},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829208/},
  author = {Marburger, Sarah and Alexandrou, Markos A. and Taggart, John B. and Creer, Simon and Carvalho, Gary and Oliveira, Claudio and Taylor, Martin I.},
  month = feb,
  year = {2018},
  file = {/home/mpetersen/bib/storage/2JXSXQB3/Marburger et al. - 2018 - Whole genome duplication and transposable element .pdf;/home/mpetersen/bib/storage/S3R7NA7U/Marburger et al. - 2018 - Whole genome duplication and transposable element .pdf},
  pmid = {29445022},
  pmcid = {PMC5829208}
}

@article{Sato2010,
  title = {Teleost Fish with Specific Genome Duplication as Unique Models of Vertebrate Evolution},
  volume = {88},
  issn = {0378-1909, 1573-5133},
  doi = {10.1007/s10641-010-9628-7},
  abstract = {Whole-genome duplication (WGD) is believed to be one of the major evolutionary events that shaped the genome organization of vertebrates. Here, we review recent research on vertebrate genome evolution, specifically on WGD and its consequences for gene and genome evolution in teleost fishes. Recent genome analyses confirmed that all vertebrates experienced two rounds of WGD early in their evolution, and that teleosts experienced a subsequent additional third-round (3R)-WGD. The 3R-WGD was estimated to have occurred 320\textendash{}400 million years ago in a teleost ancestor, but after its divergence from a common ancestor with living non-teleost actinopterygians (Bichir, Sturgeon, Bowfin, and Gar) based on the analyses of teleost-specific duplicate genes. This 3R-WGD was confirmed by synteny analysis and ancestral karyotype inference using the genome sequences of Tetraodon and medaka. Most of the tetrapods, on the other hand, have not experienced an additional WGD; however, they have experienced repeated chromosomal rearrangements throughout the whole genome. Therefore, different types of chromosomal events have characterized the genomes of teleosts and tetrapods, respectively. The 3R-WGD is useful to investigate the consequences of WGD because it is an evolutionarily recent WGD and thus teleost genomes retain many more WGD-derived duplicates and ``traces'' of their evolution. In addition, the remarkable morphological, physiological, and ecological diversity of teleosts may facilitate understanding of macrophenotypic evolution on the basis of genetic/genomic information. We highlight the teleosts with 3R-WGD as unique models for future studies on ecology and evolution taking advantage of emerging genomics technologies and systems biology environments.},
  language = {en},
  number = {2},
  urldate = {2018-04-10},
  journal = {Environmental Biology of Fishes},
  url = {https://link.springer.com/article/10.1007/s10641-010-9628-7},
  author = {Sato, Yukuto and Nishida, Mutsumi},
  month = jun,
  year = {2010},
  pages = {169-188},
  file = {/home/mpetersen/bib/storage/X4D5RE9H/s10641-010-9628-7.html;/home/mpetersen/bib/storage/Y5BURP4P/s10641-010-9628-7.html}
}

@article{McKenna2015,
  title = {The Beetle Tree of Life Reveals That {{Coleoptera}} Survived End-{{Permian}} Mass Extinction to Diversify during the {{Cretaceous}} Terrestrial Revolution},
  volume = {40},
  issn = {0307-6970},
  doi = {10.1111/syen.12132},
  abstract = {Abstract Here we present a phylogeny of beetles (Insecta: Coleoptera) based on DNA sequence data from eight nuclear genes, including six single?copy nuclear protein?coding genes, for 367 species representing 172 of 183 extant families. Our results refine existing knowledge of relationships among major groups of beetles. Strepsiptera was confirmed as sister to Coleoptera and each of the suborders of Coleoptera was recovered as monophyletic. Interrelationships among the suborders, namely Polyphaga (Adephaga (Archostemata, Myxophaga)), in our study differ from previous studies. Adephaga comprised two clades corresponding to Hydradephaga and Geadephaga. The series and superfamilies of Polyphaga were mostly monophyletic. The traditional Cucujoidea were recovered in three distantly related clades. Lymexyloidea was recovered within Tenebrionoidea. Several of the series and superfamilies of Polyphaga received moderate to maximal clade support in most analyses, for example Buprestoidea, Chrysomeloidea, Coccinelloidea, Cucujiformia, Curculionoidea, Dascilloidea, Elateroidea, Histeroidea and Hydrophiloidea. However, many of the relationships within Polyphaga lacked compatible resolution under maximum?likelihood and Bayesian inference, and/or lacked consistently strong nodal support. Overall, we recovered slightly younger estimated divergence times than previous studies for most groups of beetles. The ordinal split between Coleoptera and Strepsiptera was estimated to have occurred in the Early Permian. Crown Coleoptera appeared in the Late Permian, and only one or two lineages survived the end?Permian mass extinction, with stem group representatives of all four suborders appearing by the end of the Triassic. The basal split in Polyphaga was estimated to have occurred in the Triassic, with the stem groups of most series and superfamilies originating during the Triassic or Jurassic. Most extant families of beetles were estimated to have Cretaceous origins. Overall, Coleoptera experienced an increase in diversification rate compared to the rest of Neuropteroidea. Furthermore, 10 family?level clades, all in suborder Polyphaga, were identified as having experienced significant increases in diversification rate. These include most beetle species with phytophagous habits, but also several groups not typically or primarily associated with plants. Most of these groups originated in the Cretaceous, which is also when a majority of the most species?rich beetle families first appeared. An additional 12 clades showed evidence for significant decreases in diversification rate. These clades are species?poor in the Modern fauna, but collectively exhibit diverse trophic habits. The apparent success of beetles, as measured by species numbers, may result from their associations with widespread and diverse substrates ? especially plants, but also including fungi, wood and leaf litter ? but what facilitated these associations in the first place or has allowed these associations to flourish likely varies within and between lineages. Our results provide a uniquely well?resolved temporal and phylogenetic framework for studying patterns of innovation and diversification in Coleoptera, and a foundation for further sampling and resolution of the beetle tree of life.},
  number = {4},
  urldate = {2018-04-17},
  journal = {Systematic Entomology},
  url = {https://onlinelibrary.wiley.com/doi/full/10.1111/syen.12132},
  author = {McKenna, Duane D and Wild, Alexander L and Kanda, Kojun and Bellamy, Charles L and G., Beutel Rolf and {Caterino Michael S.} and {Farnum Charles W.} and {Hawks David C.} and {Ivie Michael A.} and {Jameson Mary Liz} and {Leschen Richard a. B.} and {Marvaldi Adriana E.} and {Mchugh Joseph V.} and {Newton Alfred F.} and {Robertson James A.} and {Thayer Margaret K.} and {Whiting Michael F.} and {Lawrence John F.} and {\'Slipi\'nski Adam} and {Maddison David R.} and {Farrell Brian D.}},
  month = jul,
  year = {2015},
  pages = {835-880},
  file = {/home/mpetersen/bib/storage/NQPWM3X8/Mckenna Duane D. et al. - 2015 - The beetle tree of life reveals that Coleoptera su.pdf;/home/mpetersen/bib/storage/V53HQM79/syen.html}
}

@article{Blanco-Bercial2011,
  title = {Molecular Phylogeny of the {{Calanoida}} ({{Crustacea}}: {{Copepoda}})},
  volume = {59},
  issn = {1055-7903},
  shorttitle = {Molecular Phylogeny of the {{Calanoida}} ({{Crustacea}}},
  doi = {10.1016/j.ympev.2011.01.008},
  abstract = {The order Calanoida includes some of the most successful planktonic groups in both marine and freshwater environments. Due to the morphological complexity of the taxonomic characters in this group, subdivision and phylogenies have been complex and problematic. This study establishes a multi-gene molecular phylogeny of the calanoid copepods based upon small (18S) and large (28S) subunits of nuclear ribosomal RNA genes and mitochondrial encoded cytochrome b and cytochrome c oxidase subunit-I genes, including 29 families from 7 superfamilies of the order. This analysis is more comprehensive than earlier studies in terms of number of families, range of molecular markers, and breadth of taxonomic levels resolved. Patterns of divergence of ribosomal RNA genes are shown to be significantly heterogeneous among superfamilies, providing a likely explanation for disparate results of previous studies. The multi-gene phylogeny recovers a monophyletic Calanoida, as well as the superfamilies Augaptiloidea, Centropagoidea, Bathypontioidea, Eucalanoidea, Spinocalanoidea and Clausocalanoidea. The phylogeny largely agrees with previously-published morphological phylogenies, including e.g., enlargement of the Bathypontioidea to include the Fosshageniidae.},
  number = {1},
  urldate = {2018-04-17},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://www.sciencedirect.com/science/article/pii/S105579031100025X},
  author = {{Blanco-Bercial}, Leocadio and {Bradford-Grieve}, Janet and Bucklin, Ann},
  month = apr,
  year = {2011},
  keywords = {18S,28S,Calanoid copepods,COI,Cyt,Molecular phylogeny},
  pages = {103-113},
  file = {/home/mpetersen/bib/storage/2U8VHMF5/Blanco-Bercial et al. - 2011 - Molecular phylogeny of the Calanoida (Crustacea C.pdf;/home/mpetersen/bib/storage/6493KHZ6/Blanco-Bercial et al. - 2011 - Molecular phylogeny of the Calanoida (Crustacea C.pdf;/home/mpetersen/bib/storage/3GNWGNRX/S105579031100025X.html}
}

@article{Thum2004,
  title = {Using {{18S rDNA}} to Resolve Diaptomid Copepod ({{Copepoda}}: {{Calanoida}}: {{Diaptomidae}}) Phylogeny: An Example with the {{North American}} Genera},
  volume = {519},
  issn = {0018-8158, 1573-5117},
  shorttitle = {Using {{18S rDNA}} to Resolve Diaptomid Copepod ({{Copepoda}}},
  doi = {10.1023/B:HYDR.0000026500.27949.e9},
  abstract = {The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light's (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light's hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family's diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.},
  language = {en},
  number = {1-3},
  urldate = {2018-04-17},
  journal = {Hydrobiologia},
  url = {https://link.springer.com/article/10.1023/B:HYDR.0000026500.27949.e9},
  author = {Thum, Ryan A.},
  month = may,
  year = {2004},
  pages = {135-141},
  file = {/home/mpetersen/bib/storage/M2RXXEJT/Thum - 2004 - Using 18S rDNA to resolve diaptomid copepod (Copep.pdf;/home/mpetersen/bib/storage/9FHKUAHJ/BHYDR.0000026500.27949.html}
}

@article{Figueroa2011,
  title = {Phylogenetic {{Analysis}} of {{Ridgewayia}} ({{Copepoda}}: {{Calanoida}}) from the {{Galapagos}} and of a {{New Species}} from the {{Florida Keys With}} a {{Reevaluation}} of the {{Phylogeny}} of {{Calanoida}}},
  volume = {31},
  issn = {0278-0372, 1937-240X},
  shorttitle = {Phylogenetic {{Analysis}} of {{Ridgewayia}} ({{Copepoda}}},
  doi = {10.1651/10-3341.1},
  language = {en},
  number = {1},
  urldate = {2018-04-18},
  journal = {Journal of Crustacean Biology},
  url = {https://academic.oup.com/jcb/article-lookup/doi/10.1651/10-3341.1},
  author = {Figueroa, Diego F.},
  month = feb,
  year = {2011},
  pages = {153-165},
  file = {/home/mpetersen/bib/storage/9V26IYVD/Figueroa - 2011 - Phylogenetic Analysis of Ridgewayia (Copepoda Cal.pdf;/home/mpetersen/bib/storage/NLZLSCDR/Figueroa - 2011 - Phylogenetic Analysis of Ridgewayia (Copepoda Cal.pdf}
}

@article{Jenner2009,
  title = {Eumalacostracan Phylogeny and Total Evidence: Limitations of the Usual Suspects},
  volume = {9},
  issn = {1471-2148},
  shorttitle = {Eumalacostracan Phylogeny and Total Evidence},
  doi = {10.1186/1471-2148-9-21},
  language = {en},
  number = {1},
  urldate = {2018-04-18},
  journal = {BMC Evolutionary Biology},
  url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-21},
  author = {Jenner, Ronald A and Dhubhghaill, Ciara and Ferla, Matteo P and Wills, Matthew A},
  year = {2009},
  pages = {21},
  file = {/home/mpetersen/bib/storage/JJHEZX9H/Jenner et al. - 2009 - Eumalacostracan phylogeny and total evidence limi;/home/mpetersen/bib/storage/JMKWG9J4/Jenner et al. - 2009 - Eumalacostracan phylogeny and total evidence limi}
}

@article{Tsang2008,
  title = {Phylogeny of {{Decapoda}} Using Two Nuclear Protein-Coding Genes: {{Origin}} and Evolution of the {{Reptantia}}},
  volume = {48},
  issn = {10557903},
  shorttitle = {Phylogeny of {{Decapoda}} Using Two Nuclear Protein-Coding Genes},
  doi = {10.1016/j.ympev.2008.04.009},
  language = {en},
  number = {1},
  urldate = {2018-04-18},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790308001565},
  author = {Tsang, L.M. and Ma, K.Y. and Ahyong, S.T. and Chan, T.-Y. and Chu, K.H.},
  month = jul,
  year = {2008},
  pages = {359-368},
  file = {/home/mpetersen/bib/storage/CNIC6MJ9/Tsang et al. - 2008 - Phylogeny of Decapoda using two nuclear protein-co.pdf;/home/mpetersen/bib/storage/TRYP4UC8/Tsang et al. - 2008 - Phylogeny of Decapoda using two nuclear protein-co.pdf}
}

@article{Ahyong2004,
  title = {Phylogeny of the {{Decapoda Reptantia}}: {{Resolution}} Using Three Molecular Loci and Morphology},
  volume = {52},
  abstract = {The controversial interrelationships of the major clades of the reptant decapods are resolved by simultaneous analysis of 16S, 18S, and 28S rRNA sequences in combination with morphology. All major replant clades are represented including the first molecular data for the controversial Polychelidae, Glypheidae, and Enoplometopidae. Interrelationships of major clades in the shortest morphological cladograms were identical to those based on the molecular partition, and were congruent with those of the optimal combined analyses. The optimal tree, namely, that exhibiting minimal overall incongruence between morphological and molecular partitions was achieved under equal transition: transversion weights. Palinura, as traditionally recognised, is polyphyletic corroborating several recent studies. Infraordinal relationships are robust and insensitive to transition weight variation. For clades previously comprising the Palinura, we recognise Achelata, Polychelida and Glypheidea. Polychelida is sister to the remaining Repantia. Achelata is near basal and sister to Fractosternalia. Contrary to many previous studies, glypheideans are neither basal reptants, nor are they related to Thalassinidea, Brachyura or Anomura. Glypheidea is sister to Astacidea. A monophyletic Astacidea, comprising the freshwater crayfish (Astacida) and marine clawed lobsters (Homarida), corroborates most previous studies. The enigmatic lobster Enoplometopus (Enoplometopoidea) is confirmed as an astacidean rather than a possible thalassinidean. Unusual characters of the extinct uncinid lobsters, shared with enoplometopids, suggest close affinity, extending the fossil record of the Enoplometopoidea to the Lower Jurassic. The Sterropoda concept, comprising (Thalassinidea (Achelata + Meiura)) is not recognised. The clade formed by Brachyura, Anomura, and Thalassinidea is united by carapace lineae, for which we propose the new name Lineata. Internal relationships of Anomura recovered in our analyses suggest possible paraphyly of Galatheoidea and Paguroidea. Relationships within Brachyura indicate podotreme paraphyly, but greater taxonomic sampling is required to adequately test the status of Podotremata. The anomuran dromiid hypothesis is unsupported. Seven reptantian infraorders are recognised: Polychelida, Achelata, Glypheidea, Astacidea, Thalassinidea, Anomura and Brachyura.},
  journal = {Raffles Bulletin of Zoology},
  url = {https://www.researchgate.net/publication/279573912_Phylogeny_of_the_Decapoda_Reptantia_Resolution_using_three_molecular_loci_and_morphology},
  author = {Ahyong, Shane and O'Meally, Denis},
  month = dec,
  year = {2004},
  pages = {673-693},
  file = {/home/mpetersen/bib/storage/JBD5WT43/Ahyong and O'Meally - 2004 - Phylogeny of the Decapoda Reptantia Resolution us.pdf;/home/mpetersen/bib/storage/QWQE3GP8/Ahyong and O'Meally - 2004 - Phylogeny of the Decapoda Reptantia Resolution us.pdf}
}

@article{Lowry2017,
  title = {A {{Phylogeny}} and {{Classification}} of the {{Amphipoda}} with the Establishment of the New Order {{Ingolfiellida}} ({{Crustacea}}: {{Peracarida}})},
  volume = {4265},
  issn = {1175-5334, 1175-5326},
  shorttitle = {A {{Phylogeny}} and {{Classification}} of the {{Amphipoda}} with the Establishment of the New Order {{Ingolfiellida}} ({{Crustacea}}},
  doi = {10.11646/zootaxa.4265.1.1},
  number = {1},
  urldate = {2018-04-18},
  journal = {Zootaxa},
  url = {http://biotaxa.org/Zootaxa/article/view/zootaxa.4265.1.1},
  author = {Lowry, J.K. and Myers, A.A.},
  month = may,
  year = {2017},
  pages = {1},
  file = {/home/mpetersen/bib/storage/4ALH6HSY/Lowry and Myers - 2017 - A Phylogeny and Classification of the Amphipoda wi.pdf;/home/mpetersen/bib/storage/GW4LU7Q4/Lowry and Myers - 2017 - A Phylogeny and Classification of the Amphipoda wi.pdf}
}

@article{Richter2007,
  title = {Phylogeny of {{Branchiopoda}} ({{Crustacea}}) Based on a Combined Analysis of Morphological Data and Six Molecular Loci},
  volume = {23},
  issn = {0748-3007, 1096-0031},
  doi = {10.1111/j.1096-0031.2007.00148.x},
  language = {en},
  number = {4},
  urldate = {2018-04-18},
  journal = {Cladistics},
  url = {http://doi.wiley.com/10.1111/j.1096-0031.2007.00148.x},
  author = {Richter, Stefan and Olesen, J\o{}rgen and Wheeler, Ward C.},
  month = aug,
  year = {2007},
  pages = {301-336},
  file = {/home/mpetersen/bib/storage/3XGKQYK7/Richter et al. - 2007 - Phylogeny of Branchiopoda (Crustacea) based on a c.pdf;/home/mpetersen/bib/storage/UPJM3ISF/Richter et al. - 2007 - Phylogeny of Branchiopoda (Crustacea) based on a c.pdf}
}

@article{Magro2010,
  title = {Phylogeny of Ladybirds ({{Coleoptera}}: {{Coccinellidae}}): {{Are}} the Subfamilies Monophyletic?},
  volume = {54},
  issn = {10557903},
  shorttitle = {Phylogeny of Ladybirds ({{Coleoptera}}},
  doi = {10.1016/j.ympev.2009.10.022},
  language = {en},
  number = {3},
  urldate = {2018-04-19},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790309004163},
  author = {Magro, A. and Lecompte, E. and Magn\'e, F. and Hemptinne, J.-L. and {Crouau-Roy}, B.},
  month = mar,
  year = {2010},
  pages = {833-848},
  file = {/home/mpetersen/bib/storage/4Y3RW8UY/Magro et al. - 2010 - Phylogeny of ladybirds (Coleoptera Coccinellidae).pdf;/home/mpetersen/bib/storage/6L9B3ZW8/Magro et al. - 2010 - Phylogeny of ladybirds (Coleoptera Coccinellidae).pdf}
}

@article{Giorgi2009,
  title = {The Evolution of Food Preferences in {{Coccinellidae}}},
  volume = {51},
  issn = {10499644},
  doi = {10.1016/j.biocontrol.2009.05.019},
  language = {en},
  number = {2},
  urldate = {2018-04-19},
  journal = {Biological Control},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1049964409001455},
  author = {Giorgi, Jos\'e Adriano and Vandenberg, Natalia J. and McHugh, Joseph V. and Forrester, Juanita A. and \'Slipi\'nski, S. Adam and Miller, Kelly B. and Shapiro, Lori R. and Whiting, Michael F.},
  month = nov,
  year = {2009},
  pages = {215-231},
  file = {/home/mpetersen/bib/storage/4EGDRMRZ/Giorgi et al. - 2009 - The evolution of food preferences in Coccinellidae.pdf;/home/mpetersen/bib/storage/QANVMP5B/Giorgi et al. - 2009 - The evolution of food preferences in Coccinellidae.pdf}
}

@article{Kergoat2014,
  title = {Higher Level Molecular Phylogeny of Darkling Beetles ({{Coleoptera}}: {{Tenebrionidae}}): {{Darkling}} Beetle Phylogeny},
  volume = {39},
  issn = {03076970},
  shorttitle = {Higher Level Molecular Phylogeny of Darkling Beetles ({{Coleoptera}}},
  doi = {10.1111/syen.12065},
  language = {en},
  number = {3},
  urldate = {2018-04-20},
  journal = {Systematic Entomology},
  url = {http://doi.wiley.com/10.1111/syen.12065},
  author = {Kergoat, Gael J. and Soldati, Laurent and Clamens, Anne-Laure and Jourdan, Herve and {Jabbour-Zahab}, Roula and Genson, Gwenaelle and Bouchard, Patrice and Condamine, Fabien L.},
  month = jul,
  year = {2014},
  pages = {486-499},
  file = {/home/mpetersen/bib/storage/97LB7ZP5/Kergoat et al. - 2014 - Higher level molecular phylogeny of darkling beetl.pdf;/home/mpetersen/bib/storage/RIHPPL6L/Kergoat et al. - 2014 - Higher level molecular phylogeny of darkling beetl.pdf}
}

@article{Ahrens2014,
  title = {The Evolution of Scarab Beetles Tracks the Sequential Rise of Angiosperms and Mammals},
  volume = {281},
  issn = {0962-8452, 1471-2954},
  doi = {10.1098/rspb.2014.1470},
  language = {en},
  number = {1791},
  urldate = {2018-04-20},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2014.1470},
  author = {Ahrens, D. and Schwarzer, J. and Vogler, A. P.},
  month = aug,
  year = {2014},
  pages = {20141470-20141470},
  file = {/home/mpetersen/bib/storage/WGNAZ7SU/Ahrens et al. - 2014 - The evolution of scarab beetles tracks the sequent.pdf;/home/mpetersen/bib/storage/ZNNDCGUH/syen12037-sup-0007-syen12037-figures1.pdf}
}

@article{Novakova2013,
  title = {Reconstructing the Phylogeny of Aphids ({{Hemiptera}}: {{Aphididae}}) Using {{DNA}} of the Obligate Symbiont {{Buchnera}} Aphidicola},
  volume = {68},
  issn = {10557903},
  shorttitle = {Reconstructing the Phylogeny of Aphids ({{Hemiptera}}},
  doi = {10.1016/j.ympev.2013.03.016},
  language = {en},
  number = {1},
  urldate = {2018-04-24},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790313001176},
  author = {Nov\'akov\'a, Eva and Hyp{\v s}a, V\'aclav and Klein, Joanne and Foottit, Robert G. and {von Dohlen}, Carol D. and Moran, Nancy A.},
  month = jul,
  year = {2013},
  pages = {42-54},
  file = {/home/mpetersen/bib/storage/DX8Q4FJ2/Nováková et al. - 2013 - Reconstructing the phylogeny of aphids (Hemiptera.pdf;/home/mpetersen/bib/storage/VG2BZ9X7/Nováková et al. - 2013 - Reconstructing the phylogeny of aphids (Hemiptera.pdf}
}

@article{Ortiz-Rivas2010,
  title = {Combination of Molecular Data Support the Existence of Three Main Lineages in the Phylogeny of Aphids ({{Hemiptera}}: {{Aphididae}}) and the Basal Position of the Subfamily {{Lachninae}}},
  volume = {55},
  issn = {10557903},
  shorttitle = {Combination of Molecular Data Support the Existence of Three Main Lineages in the Phylogeny of Aphids ({{Hemiptera}}},
  doi = {10.1016/j.ympev.2009.12.005},
  language = {en},
  number = {1},
  urldate = {2018-04-24},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790309005119},
  author = {{Ortiz-Rivas}, Benjam\'in and {Mart\'inez-Torres}, David},
  month = apr,
  year = {2010},
  pages = {305-317},
  file = {/home/mpetersen/bib/storage/VTVDRSN2/Ortiz-Rivas and Martínez-Torres - 2010 - Combination of molecular data support the existenc.pdf;/home/mpetersen/bib/storage/ZFPFZ9R8/Ortiz-Rivas and Martínez-Torres - 2010 - Combination of molecular data support the existenc.pdf}
}

@article{Song2012,
  title = {A {{Molecular Phylogeny}} of {{Hemiptera Inferred}} from {{Mitochondrial Genome Sequences}}},
  volume = {7},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0048778},
  language = {en},
  number = {11},
  urldate = {2018-04-24},
  journal = {PLoS ONE},
  url = {http://dx.plos.org/10.1371/journal.pone.0048778},
  author = {Song, Nan and Liang, Ai-Ping and Bu, Cui-Ping},
  editor = {Ho, Simon},
  month = nov,
  year = {2012},
  keywords = {Insects,Mitochondria,Ribosomal RNA,Animal phylogenetics,Hemiptera,Phylogenetic analysis,Sequence alignment,Transfer RNA},
  pages = {e48778},
  file = {/home/mpetersen/bib/storage/HPXZZ49N/Song et al. - 2012 - A Molecular Phylogeny of Hemiptera Inferred from M.PDF;/home/mpetersen/bib/storage/IP86844P/Song et al. - 2012 - A Molecular Phylogeny of Hemiptera Inferred from M.PDF;/home/mpetersen/bib/storage/RUCMWS9D/Song et al. - 2012 - A Molecular Phylogeny of Hemiptera Inferred from M.pdf;/home/mpetersen/bib/storage/A3YN4V67/article.html}
}

@article{Kofler2018,
  title = {Molecular Dissection of a Natural Transposable Element Invasion},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.228627.117},
  language = {en},
  urldate = {2018-05-07},
  journal = {Genome Research},
  url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.228627.117},
  author = {Kofler, Robert and Senti, Kirsten-Andr\'e and Nolte, Viola and Tobler, Ray and Schl\"otterer, Christian},
  month = apr,
  year = {2018},
  file = {/home/mpetersen/bib/storage/5QHLFUYY/Kofler et al. - 2018 - Molecular dissection of a natural transposable ele.pdf;/home/mpetersen/bib/storage/776IH8TQ/Kofler et al. - 2018 - Molecular dissection of a natural transposable ele.pdf;/home/mpetersen/bib/storage/BE34GRDI/Kofler et al. - 2018 - Molecular dissection of a natural transposable ele.pdf}
}

@article{Morris2010,
  title = {Anthropogenic Impacts on Tropical Forest Biodiversity: A Network Structure and Ecosystem Functioning Perspective},
  volume = {365},
  copyright = {\textcopyright{} 2010 The Royal Society},
  issn = {0962-8436, 1471-2970},
  shorttitle = {Anthropogenic Impacts on Tropical Forest Biodiversity},
  doi = {10.1098/rstb.2010.0273},
  abstract = {Huge areas of diverse tropical forest are lost or degraded every year with dramatic consequences for biodiversity. Deforestation and fragmentation, over-exploitation, invasive species and climate change are the main drivers of tropical forest biodiversity loss. Most studies investigating these threats have focused on changes in species richness or species diversity. However, if we are to understand the absolute and long-term effects of anthropogenic impacts on tropical forests, we should also consider the interactions between species, how those species are organized in networks, and the function that those species perform. I discuss our current knowledge of network structure and ecosystem functioning, highlighting empirical examples of their response to anthropogenic impacts. I consider the future prospects for tropical forest biodiversity, focusing on biodiversity and ecosystem functioning in secondary forest. Finally, I propose directions for future research to help us better understand the effects of anthropogenic impacts on tropical forest biodiversity.},
  language = {en},
  number = {1558},
  urldate = {2018-05-08},
  journal = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
  url = {http://rstb.royalsocietypublishing.org/content/365/1558/3709},
  author = {Morris, Rebecca J.},
  month = nov,
  year = {2010},
  pages = {3709-3718},
  file = {/home/mpetersen/bib/storage/IINADUFW/Morris - 2010 - Anthropogenic impacts on tropical forest biodivers.pdf;/home/mpetersen/bib/storage/4REFZUEN/3709.html},
  pmid = {20980318}
}

@article{Wright2005,
  title = {Tropical Forests in a Changing Environment},
  volume = {20},
  issn = {0169-5347},
  doi = {10.1016/j.tree.2005.07.009},
  abstract = {Understanding and mitigating the impact of an ever-increasing population and global economic activity on tropical forests is one of the great challenges currently facing biologists, conservationists and policy makers. Tropical forests currently face obvious regional changes, both negative and positive, and uncertain global changes. Although deforestation rates have increased to unprecedented levels, natural secondary succession has reclaimed approximately 15\% of the area deforested during the 1990s. Governments have also protected 18\% of the remaining tropical moist forest; however, unsustainable hunting continues to threaten many keystone mammal and bird species. The structure and dynamics of old-growth forests appear to be rapidly changing, suggesting that there is a pantropical response to global anthropogenic forcing, although the evidence comes almost exclusively from censuses of tree plots and is controversial. Here, I address ongoing anthropogenic change in tropical forests and suggest how these forests might respond to increasing anthropogenic pressure.},
  number = {10},
  urldate = {2018-05-08},
  journal = {Trends in Ecology \& Evolution},
  url = {http://www.sciencedirect.com/science/article/pii/S016953470500251X},
  author = {Wright, S. Joseph},
  month = oct,
  year = {2005},
  pages = {553-560},
  file = {/home/mpetersen/bib/storage/956W22GJ/S016953470500251X.html}
}

@techreport{Wuebbles2017,
  title = {Executive Summary.  {{Climate Science Special Report}}: {{Fourth National Climate Assessment}}, {{Volume I}}},
  shorttitle = {Executive Summary.  {{Climate Science Special Report}}},
  institution = {{U.S. Global Change Research Program}},
  author = {Wuebbles, D.J. and Fahey, D.W. and Hibbard, K.A. and DeAngelo, B. and Doherty, S. and Hayhoe, K. and Horton, R. and Kossin, J.P. and Taylor, P.C. and Waple, A.M. and Weaver, C.P. and Wuebbles, D.J. and Fahey, D.W. and Hibbard, K.A. and Dokken, D.J. and Stewart, B.C. and Maycock, T.K.},
  year = {2017},
  doi = {10.7930/J0DJ5CTG}
}

@article{Cook2016,
  title = {Consensus on Consensus: A Synthesis of Consensus Estimates on Human-Caused Global Warming},
  volume = {11},
  issn = {1748-9326},
  shorttitle = {Consensus on Consensus},
  doi = {10.1088/1748-9326/11/4/048002},
  number = {4},
  urldate = {2018-05-08},
  journal = {Environmental Research Letters},
  url = {http://stacks.iop.org/1748-9326/11/i=4/a=048002?key=crossref.80d294a6c5d3b7882bc7dc12487e9f39},
  author = {Cook, John and Oreskes, Naomi and Doran, Peter T and Anderegg, William R L and Verheggen, Bart and Maibach, Ed W and Carlton, J Stuart and Lewandowsky, Stephan and Skuce, Andrew G and Green, Sarah A and Nuccitelli, Dana and Jacobs, Peter and Richardson, Mark and Winkler, B\"arbel and Painting, Rob and Rice, Ken},
  month = apr,
  year = {2016},
  pages = {048002}
}

@book{Leakey1996,
  address = {New York},
  title = {The Sixth Extinction: Patterns of Life and the Future of Humankind},
  isbn = {978-0-385-46809-1},
  shorttitle = {The Sixth Extinction},
  abstract = {"Thirty thousand species are wiped out every year-a rate matching the patterns of five previous massive extinctions. In each, 65 percent of all living species disappeared in a geological instant. In The Sixth Extinction, bestselling author Richard Leakey, the world's foremost paleoanthropologist and former head of Kenya's wildlife preservation program, and award-winning science writer Roger Lewin describe the consequences of those great extinctions and present the evidence that we have entered another such age-one brought about by human agency. A sobering but necessary call to arms, the book paints a terrifying scenario for the future of life on Earth-unless mankind mends its destructive ways. Book jacket."--Jacket.},
  language = {English},
  publisher = {{Anchor Books}},
  author = {Leakey, Richard E and Lewin, Roger},
  year = {1996},
  note = {OCLC: 36002376}
}

@article{Ceballos2015,
  title = {Accelerated Modern Human\textendash{}Induced Species Losses: {{Entering}} the Sixth Mass Extinction},
  volume = {1},
  copyright = {Copyright \textcopyright{} 2015, The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.},
  issn = {2375-2548},
  shorttitle = {Accelerated Modern Human\textendash{}Induced Species Losses},
  doi = {10.1126/sciadv.1400253},
  abstract = {The oft-repeated claim that Earth's biota is entering a sixth ``mass extinction'' depends on clearly demonstrating that current extinction rates are far above the ``background'' rates prevailing between the five previous mass extinctions. Earlier estimates of extinction rates have been criticized for using assumptions that might overestimate the severity of the extinction crisis. We assess, using extremely conservative assumptions, whether human activities are causing a mass extinction. First, we use a recent estimate of a background rate of 2 mammal extinctions per 10,000 species per 100 years (that is, 2 E/MSY), which is twice as high as widely used previous estimates. We then compare this rate with the current rate of mammal and vertebrate extinctions. The latter is conservatively low because listing a species as extinct requires meeting stringent criteria. Even under our assumptions, which would tend to minimize evidence of an incipient mass extinction, the average rate of vertebrate species loss over the last century is up to 100 times higher than the background rate. Under the 2 E/MSY background rate, the number of species that have gone extinct in the last century would have taken, depending on the vertebrate taxon, between 800 and 10,000 years to disappear. These estimates reveal an exceptionally rapid loss of biodiversity over the last few centuries, indicating that a sixth mass extinction is already under way. Averting a dramatic decay of biodiversity and the subsequent loss of ecosystem services is still possible through intensified conservation efforts, but that window of opportunity is rapidly closing.
Humans are causing a massive animal extinction without precedent in 65 million years.
Humans are causing a massive animal extinction without precedent in 65 million years.},
  language = {en},
  number = {5},
  urldate = {2018-05-08},
  journal = {Science Advances},
  url = {http://advances.sciencemag.org/content/1/5/e1400253},
  author = {Ceballos, Gerardo and Ehrlich, Paul R. and Barnosky, Anthony D. and Garc\'ia, Andr\'es and Pringle, Robert M. and Palmer, Todd M.},
  month = jun,
  year = {2015},
  pages = {e1400253},
  file = {/home/mpetersen/bib/storage/99U9HF87/Ceballos et al. - 2015 - Accelerated modern human–induced species losses E.pdf;/home/mpetersen/bib/storage/NIWQTFHD/e1400253.html}
}

@article{Dirzo2003,
  title = {Global {{State}} of {{Biodiversity}} and {{Loss}}},
  volume = {28},
  doi = {10.1146/annurev.energy.28.050302.105532},
  abstract = {Biodiversity, a central component of Earth's life support systems, is directly relevant to human societies. We examine the dimensions and nature of the Earth's terrestrial biodiversity and review the scientific facts concerning the rate of loss of biodiversity and the drivers of this loss. The estimate for the total number of species of eukaryotic organisms possible lies in the 5\textendash{}15 million range, with a best guess of {$\sim$}7 million. Species diversity is unevenly distributed; the highest concentrations are in tropical ecosystems. Endemisms are concentrated in a few hotspots, which are in turn seriously threatened by habitat destruction\textemdash{}the most prominent driver of biodiversity loss. For the past 300 years, recorded extinctions for a few groups of organisms reveal rates of extinction at least several hundred times the rate expected on the basis of the geological record. The loss of biodiversity is the only truly irreversible global environmental change the Earth faces today.},
  number = {1},
  urldate = {2018-05-08},
  journal = {Annual Review of Environment and Resources},
  url = {https://doi.org/10.1146/annurev.energy.28.050302.105532},
  author = {Dirzo, Rodolfo and Raven, Peter H.},
  year = {2003},
  pages = {137-167},
  file = {/home/mpetersen/bib/storage/LA6RGVNE/Dirzo and Raven - 2003 - Global State of Biodiversity and Loss.pdf}
}

@article{Schipper2008,
  title = {The {{Status}} of the {{World}}'s {{Land}} and {{Marine Mammals}}: {{Diversity}}, {{Threat}}, and {{Knowledge}}},
  volume = {322},
  copyright = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  shorttitle = {The {{Status}} of the {{World}}'s {{Land}} and {{Marine Mammals}}},
  doi = {10.1126/science.1165115},
  abstract = {Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.
A comprehensive assessment of all of Earth's mammals shows that primary productivity drives species richness on land and sea and that 20 to 25 percent of species are under threat.
A comprehensive assessment of all of Earth's mammals shows that primary productivity drives species richness on land and sea and that 20 to 25 percent of species are under threat.},
  language = {en},
  number = {5899},
  urldate = {2018-05-08},
  journal = {Science},
  url = {http://science.sciencemag.org/content/322/5899/225},
  author = {Schipper, Jan and Chanson, Janice S. and Chiozza, Federica and Cox, Neil A. and Hoffmann, Michael and Katariya, Vineet and Lamoreux, John and Rodrigues, Ana S. L. and Stuart, Simon N. and Temple, Helen J. and Baillie, Jonathan and Boitani, Luigi and Lacher, Thomas E. and Mittermeier, Russell A. and Smith, Andrew T. and Absolon, Daniel and Aguiar, John M. and Amori, Giovanni and Bakkour, Noura and Baldi, Ricardo and Berridge, Richard J. and Bielby, Jon and Black, Patricia Ann and Blanc, J. Julian and Brooks, Thomas M. and Burton, James A. and Butynski, Thomas M. and Catullo, Gianluca and Chapman, Roselle and Cokeliss, Zoe and Collen, Ben and Conroy, Jim and Cooke, Justin G. and da Fonseca, Gustavo A. B. and Derocher, Andrew E. and Dublin, Holly T. and Duckworth, J. W. and Emmons, Louise and Emslie, Richard H. and {Festa-Bianchet}, Marco and Foster, Matt and Foster, Sabrina and Garshelis, David L. and Gates, Cormack and {Gimenez-Dixon}, Mariano and Gonzalez, Susana and {Gonzalez-Maya}, Jose Fernando and Good, Tatjana C. and Hammerson, Geoffrey and Hammond, Philip S. and Happold, David and Happold, Meredith and Hare, John and Harris, Richard B. and Hawkins, Clare E. and Haywood, Mandy and Heaney, Lawrence R. and Hedges, Simon and Helgen, Kristofer M. and {Hilton-Taylor}, Craig and Hussain, Syed Ainul and Ishii, Nobuo and Jefferson, Thomas A. and Jenkins, Richard K. B. and Johnston, Charlotte H. and Keith, Mark and Kingdon, Jonathan and Knox, David H. and Kovacs, Kit M. and Langhammer, Penny and Leus, Kristin and Lewison, Rebecca and Lichtenstein, Gabriela and Lowry, Lloyd F. and Macavoy, Zoe and Mace, Georgina M. and Mallon, David P. and Masi, Monica and McKnight, Meghan W. and Medell\'in, Rodrigo A. and Medici, Patricia and Mills, Gus and Moehlman, Patricia D. and Molur, Sanjay and Mora, Arturo and Nowell, Kristin and Oates, John F. and Olech, Wanda and Oliver, William R. L. and Oprea, Monik and Patterson, Bruce D. and Perrin, William F. and Polidoro, Beth A. and Pollock, Caroline and Powel, Abigail and Protas, Yelizaveta and Racey, Paul and Ragle, Jim and Ramani, Pavithra and Rathbun, Galen and Reeves, Randall R. and Reilly, Stephen B. and Reynolds, John E. and Rondinini, Carlo and {Rosell-Ambal}, Ruth Grace and Rulli, Monica and Rylands, Anthony B. and Savini, Simona and Schank, Cody J. and Sechrest, Wes and {Self-Sullivan}, Caryn and Shoemaker, Alan and {Sillero-Zubiri}, Claudio and Silva, Naamal De and Smith, David E. and Srinivasulu, Chelmala and Stephenson, Peter J. and van Strien, Nico and Talukdar, Bibhab Kumar and Taylor, Barbara L. and Timmins, Rob and Tirira, Diego G. and Tognelli, Marcelo F. and Tsytsulina, Katerina and Veiga, Liza M. and Vi\'e, Jean-Christophe and Williamson, Elizabeth A. and Wyatt, Sarah A. and Xie, Yan and Young, Bruce E.},
  month = oct,
  year = {2008},
  pages = {225-230},
  file = {/home/mpetersen/bib/storage/L6KFY9LZ/225.html},
  pmid = {18845749}
}

@article{Burkhead2012,
  title = {Extinction {{Rates}} in {{North American Freshwater Fishes}}, 1900\textendash{}2010},
  volume = {62},
  issn = {0006-3568},
  doi = {10.1525/bio.2012.62.9.5},
  abstract = {Abstract.  Widespread evidence shows that the modern rates of extinction in many plants and animals exceed background rates in the fossil record. In the present},
  language = {en},
  number = {9},
  urldate = {2018-05-08},
  journal = {BioScience},
  url = {https://academic.oup.com/bioscience/article/62/9/798/231282},
  author = {Burkhead, Noel M.},
  month = sep,
  year = {2012},
  pages = {798-808},
  file = {/home/mpetersen/bib/storage/LYDK2A4Y/Burkhead - 2012 - Extinction Rates in North American Freshwater Fish.pdf;/home/mpetersen/bib/storage/EIU738I2/231282.html}
}

@article{Pimm2014,
  title = {The Biodiversity of Species and Their Rates of Extinction, Distribution, and Protection},
  volume = {344},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1246752},
  abstract = {{$<$}h3{$>$}Background{$<$}/h3{$>$} {$<$}p{$>$}A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to ``perform regular and timely assessments of knowledge on biodiversity.'' In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD's Aichi Targets of the Strategic Plan for Biodiversity 2011\textendash{}2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention ``known species''\textemdash{}a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them.{$<$}/p{$><$}p{$>$}\textbf{Different visualizations of species biodiversity.} (\textbf{A}) The distributions of 9927 bird species. (\textbf{B}) The 4964 species with smaller than the median geographical range size. (\textbf{C}) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. (\textbf{D}) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org.{$<$}/p{$><$}h3{$>$}Advances{$<$}/h3{$>$} {$<$}p{$>$}Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity.{$<$}/p{$><$}h3{$>$}Outlook{$<$}/h3{$>$} {$<$}p{$>$}Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species' distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.{$<$}/p{$>$}, {$<$}p{$>$}Recent studies clarify where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. We assess key statistics about species, their distribution, and their status. Most are undescribed. Those we know best have large geographical ranges and are often common within them. Most known species have small ranges. The numbers of small-ranged species are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. Current rates of extinction are about 1000 times the likely background rate of extinction. Future rates depend on many factors and are poised to increase. Although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity.{$<$}/p{$>$}, {$<$}h3{$>$}Maintaining biodiversity: From here to eternity?{$<$}/h3{$>$} {$<$}p{$>$}There has been substantial recent progress in determining the distributions and identity of vulnerable species, and in understanding how (and where) human activity is leading to extinctions. Pimm \emph{et al.} review the current state of knowledge and ask what the future rates of species extinction will be, how well protected areas will slow extinction rates, and how the remaining gaps in knowledge might be filled.{$<$}/p{$><$}p{$>$}\emph{Science}, this issue p. 10.1126/science.1246752{$<$}/p{$>$}},
  language = {en},
  number = {6187},
  urldate = {2018-05-08},
  journal = {Science},
  url = {http://science.sciencemag.org/content/344/6187/1246752},
  author = {Pimm, S. L. and Jenkins, C. N. and Abell, R. and Brooks, T. M. and Gittleman, J. L. and Joppa, L. N. and Raven, P. H. and Roberts, C. M. and Sexton, J. O.},
  month = may,
  year = {2014},
  pages = {1246752},
  file = {/home/mpetersen/bib/storage/EGECVK3W/tab-pdf.html},
  pmid = {24876501}
}

@article{Mooney2001,
  title = {The Evolutionary Impact of Invasive Species},
  volume = {98},
  copyright = {Copyright \textcopyright{} 2001, The National Academy of Sciences},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.091093398},
  abstract = {Since the Age of Exploration began, there has been a drastic breaching of biogeographic barriers that previously had isolated the continental biotas for millions of years. We explore the nature of these recent biotic exchanges and their consequences on evolutionary processes. The direct evidence of evolutionary consequences of the biotic rearrangements is of variable quality, but the results of trajectories are becoming clear as the number of studies increases. There are examples of invasive species altering the evolutionary pathway of native species by competitive exclusion, niche displacement, hybridization, introgression, predation, and ultimately extinction. Invaders themselves evolve in response to their interactions with natives, as well as in response to the new abiotic environment. Flexibility in behavior, and mutualistic interactions, can aid in the success of invaders in their new environment.},
  language = {en},
  number = {10},
  urldate = {2018-05-08},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/98/10/5446},
  author = {Mooney, H. A. and Cleland, E. E.},
  month = may,
  year = {2001},
  pages = {5446-5451},
  file = {/home/mpetersen/bib/storage/3KS3I4ZJ/Mooney and Cleland - 2001 - The evolutionary impact of invasive species.pdf;/home/mpetersen/bib/storage/RQJ4USZL/5446.html},
  pmid = {11344292}
}

@article{Bank2017,
  title = {Transcriptome and Target {{DNA}} Enrichment Sequence Data Provide New Insights into the Phylogeny of Vespid Wasps ({{Hymenoptera}}: {{Aculeata}}: {{Vespidae}})},
  volume = {116},
  issn = {10557903},
  shorttitle = {Transcriptome and Target {{DNA}} Enrichment Sequence Data Provide New Insights into the Phylogeny of Vespid Wasps ({{Hymenoptera}}},
  doi = {10.1016/j.ympev.2017.08.020},
  language = {en},
  urldate = {2018-05-10},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790317303305},
  author = {Bank, Sarah and Sann, Manuela and Mayer, Christoph and Meusemann, Karen and Donath, Alexander and Podsiadlowski, Lars and Kozlov, Alexey and Petersen, Malte and Krogmann, Lars and Meier, Rudolf and Rosa, Paolo and Schmitt, Thomas and Wurdack, Mareike and Liu, Shanlin and Zhou, Xin and Misof, Bernhard and Peters, Ralph S. and Niehuis, Oliver},
  month = nov,
  year = {2017},
  pages = {213-226},
  file = {/home/mpetersen/bib/storage/MUB4AKX7/Bank et al. - 2017 - Transcriptome and target DNA enrichment sequence d.pdf}
}

@inproceedings{Hozza2015,
  series = {Lecture {{Notes}} in {{Computer Science}}},
  title = {How {{Big}} Is That {{Genome}}? {{Estimating Genome Size}} and {{Coverage}} from k-Mer {{Abundance Spectra}}},
  isbn = {978-3-319-23825-8 978-3-319-23826-5},
  shorttitle = {How {{Big}} Is That {{Genome}}?},
  doi = {10.1007/978-3-319-23826-5_20},
  abstract = {Many practical algorithms for sequence alignment, genome assembly and other tasks represent a sequence as a set of k-mers. Here, we address the problems of estimating genome size and sequencing coverage from sequencing reads, without the need for sequence assembly. Our estimates are based on a histogram of k-mer abundance in the input set of sequencing reads and on probabilistic modeling of distribution of k-mer abundance based on parameters related to the coverage, error rate and repeat structure of the genome. Our method provides reliable estimates even at coverage as low as 0.5 or at error rates as high as 10\%.},
  language = {en},
  urldate = {2018-05-11},
  booktitle = {String {{Processing}} and {{Information Retrieval}}},
  publisher = {{Springer, Cham}},
  url = {https://link.springer.com/chapter/10.1007/978-3-319-23826-5_20},
  author = {Hozza, Michal and Vina{\v r}, Tom\'a{\v s} and Brejov\'a, Bro{\v n}a},
  month = sep,
  year = {2015},
  pages = {199-209},
  file = {/home/mpetersen/bib/storage/J7Q9ATPZ/978-3-319-23826-5_20.html;/home/mpetersen/bib/storage/R4ITFJFE/978-3-319-23826-5_20.html}
}

@article{Cameron2012,
  title = {A Mitochondrial Genome Phylogeny of Termites ({{Blattodea}}: {{Termitoidae}}): {{Robust}} Support for Interfamilial Relationships and Molecular Synapomorphies Define Major Clades},
  volume = {65},
  issn = {1055-7903},
  shorttitle = {A Mitochondrial Genome Phylogeny of Termites ({{Blattodea}}},
  doi = {10.1016/j.ympev.2012.05.034},
  abstract = {Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister-group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites+Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus+termites), and a further series of compensatory base changes in this stem-loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae+Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.},
  number = {1},
  urldate = {2018-05-11},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://www.sciencedirect.com/science/article/pii/S1055790312002126},
  author = {Cameron, Stephen L. and Lo, Nathan and Bourguignon, Thomas and Svenson, Gavin J. and Evans, Theodore A.},
  month = oct,
  year = {2012},
  keywords = {Phylogeny,Mitochondrial genomics,Rare genomic changes,Termites},
  pages = {163-173},
  file = {/home/mpetersen/bib/storage/IE5KCVIN/Cameron et al. - 2012 - A mitochondrial genome phylogeny of termites (Blat.pdf;/home/mpetersen/bib/storage/IBXAQBKB/S1055790312002126.html}
}

@article{Wiegmann2011,
  title = {Episodic Radiations in the Fly Tree of Life},
  volume = {108},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1012675108},
  language = {en},
  number = {14},
  urldate = {2018-05-11},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1012675108},
  author = {Wiegmann, B. M. and Trautwein, M. D. and Winkler, I. S. and Barr, N. B. and Kim, J.-W. and Lambkin, C. and Bertone, M. A. and Cassel, B. K. and Bayless, K. M. and Heimberg, A. M. and Wheeler, B. M. and Peterson, K. J. and Pape, T. and Sinclair, B. J. and Skevington, J. H. and Blagoderov, V. and Caravas, J. and Kutty, S. N. and {Schmidt-Ott}, U. and Kampmeier, G. E. and Thompson, F. C. and Grimaldi, D. A. and Beckenbach, A. T. and Courtney, G. W. and Friedrich, M. and Meier, R. and Yeates, D. K.},
  month = apr,
  year = {2011},
  pages = {5690-5695},
  file = {/home/mpetersen/bib/storage/LUUDFDNS/Wiegmann et al. - 2011 - Episodic radiations in the fly tree of life.pdf;/home/mpetersen/bib/storage/MSLH2FE4/Wiegmann et al. - 2011 - Episodic radiations in the fly tree of life.pdf}
}

@article{Breinholt2018,
  title = {Resolving {{Relationships}} among the {{Megadiverse Butterflies}} and {{Moths}} with a {{Novel Pipeline}} for {{Anchored Phylogenomics}}},
  volume = {67},
  issn = {1063-5157},
  doi = {10.1093/sysbio/syx048},
  abstract = {Abstract.  The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid e},
  language = {en},
  number = {1},
  urldate = {2018-05-11},
  journal = {Systematic Biology},
  url = {https://academic.oup.com/sysbio/article/67/1/78/3796843},
  author = {Breinholt, Jesse W. and Earl, Chandra and Lemmon, Alan R. and Lemmon, Emily Moriarty and Xiao, Lei and Kawahara, Akito Y.},
  month = jan,
  year = {2018},
  pages = {78-93},
  file = {/home/mpetersen/bib/storage/JMQAREL9/Breinholt et al. - 2018 - Resolving Relationships among the Megadiverse Butt.pdf;/home/mpetersen/bib/storage/MRGJIA5S/3796843.html}
}

@article{Kawahara2009,
  title = {Phylogeny and {{Biogeography}} of {{Hawkmoths}} ({{Lepidoptera}}: {{Sphingidae}}): {{Evidence}} from {{Five Nuclear Genes}}},
  volume = {4},
  issn = {1932-6203},
  shorttitle = {Phylogeny and {{Biogeography}} of {{Hawkmoths}} ({{Lepidoptera}}},
  doi = {10.1371/journal.pone.0005719},
  abstract = {Background The 1400 species of hawkmoths (Lepidoptera: Sphingidae) comprise one of most conspicuous and well-studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes. Methodology/Principal Findings The data set consisted of 131 sphingid species and 6793 bp of sequence from five protein-coding nuclear genes. Maximum likelihood and parsimony analyses provided strong support for more than two-thirds of all nodes, including strong signal for or against nearly all of the fifteen current subfamily, tribal and sub-tribal groupings. Monophyly was strongly supported for some of these, including Macroglossinae, Sphinginae, Acherontiini, Ambulycini, Philampelini, Choerocampina, and Hemarina. Other groupings proved para- or polyphyletic, and will need significant redefinition; these include Smerinthinae, Smerinthini, Sphingini, Sphingulini, Dilophonotini, Dilophonotina, Macroglossini, and Macroglossina. The basal divergence, strongly supported, is between Macroglossinae and Smerinthinae+Sphinginae. All genes contribute significantly to the signal from the combined data set, and there is little conflict between genes. Ancestral state reconstruction reveals multiple separate origins of New World and Old World radiations. Conclusions/Significance Our study provides the first comprehensive phylogeny of one of the most conspicuous and well-studied insects. The molecular phylogeny challenges current concepts of Sphingidae based on morphology, and provides a foundation for a new classification. While there are multiple independent origins of New World and Old World radiations, we conclude that broad-scale geographic distribution in hawkmoths is more phylogenetically conserved than previously postulated.},
  language = {en},
  number = {5},
  urldate = {2018-05-11},
  journal = {PLOS ONE},
  url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005719},
  author = {Kawahara, Akito Y. and Mignault, Andre A. and Regier, Jerome C. and Kitching, Ian J. and Mitter, Charles},
  month = may,
  year = {2009},
  keywords = {Phylogenetics,Animal phylogenetics,Phylogenetic analysis,Biogeography,Larvae,Moths and butterflies,Nucleic acids,Phylogeography},
  pages = {e5719},
  file = {/home/mpetersen/bib/storage/LX8HEAP3/Kawahara et al. - 2009 - Phylogeny and Biogeography of Hawkmoths (Lepidopte.pdf;/home/mpetersen/bib/storage/AXHTNLGQ/article.html}
}

@article{Mitchell2005,
  title = {Systematics and Evolution of the Cutworm Moths ({{Lepidoptera}}: {{Noctuidae}}): Evidence from Two Protein-Coding Nuclear Genes: {{Molecular}} Systematics of {{Noctuidae}}},
  volume = {31},
  issn = {03076970, 13653113},
  shorttitle = {Systematics and Evolution of the Cutworm Moths ({{Lepidoptera}}},
  doi = {10.1111/j.1365-3113.2005.00306.x},
  language = {en},
  number = {1},
  urldate = {2018-05-11},
  journal = {Systematic Entomology},
  url = {http://doi.wiley.com/10.1111/j.1365-3113.2005.00306.x},
  author = {Mitchell, Andrew and Mitter, Charles and Regier, Jerome C.},
  month = apr,
  year = {2005},
  pages = {21-46}
}

@article{Ratnasingham2007,
  title = {Bold: {{The Barcode}} of {{Life Data System}} ({{http://www.barcodinglife.org)}}},
  volume = {7},
  issn = {1471-8278},
  shorttitle = {Bold},
  doi = {10.1111/j.1471-8286.2007.01678.x},
  abstract = {The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.},
  number = {3},
  urldate = {2018-05-12},
  journal = {Molecular Ecology Notes},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1890991/},
  author = {Ratnasingham, Sujeevan and Hebert, Paul D N},
  month = may,
  year = {2007},
  pages = {355-364},
  file = {/home/mpetersen/bib/storage/K34YXMUM/RATNASINGHAM and HEBERT - 2007 - bold The Barcode of Life Data System (httpwww..pdf;/home/mpetersen/bib/storage/LEQHX44L/RATNASINGHAM and HEBERT - 2007 - bold The Barcode of Life Data System (httpwww..pdf},
  pmid = {18784790},
  pmcid = {PMC1890991}
}

@article{Dolgin2006,
  title = {The {{Fate}} of {{Transposable Elements}} in {{Asexual Populations}}},
  volume = {174},
  copyright = {Copyright \textcopyright{} 2006 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.106.060434},
  abstract = {Sexual reproduction and recombination are important for maintaining a stable copy number of transposable elements (TEs). In sexual populations, elements can be contained by purifying selection against host carriers with higher element copy numbers; however, in the absence of sex and recombination, asexual populations could be driven to extinction by an unchecked proliferation of TEs. Here we provide a theoretical framework for analyzing TE dynamics under asexual reproduction. Analytic results show that, in an infinite asexual population, an equilibrium in copy number is achieved if no element excision is possible, but that all TEs are eliminated if there is some excision. In a finite population, computer simulations demonstrate that small populations are driven to extinction by a Muller's ratchet-like process of element accumulation, but that large populations can be cured of vertically transmitted TEs, even with excision rates well below transposition rates. These results may have important consequences for newly arisen asexual lineages and may account for the lack of deleterious retrotransposons in the putatively ancient asexual bdelloid rotifers.},
  language = {en},
  number = {2},
  urldate = {2018-05-14},
  journal = {Genetics},
  url = {http://www.genetics.org/content/174/2/817},
  author = {Dolgin, Elie S. and Charlesworth, Brian},
  month = oct,
  year = {2006},
  pages = {817-827},
  file = {/home/mpetersen/bib/storage/3PH28K82/Dolgin and Charlesworth - 2006 - The Fate of Transposable Elements in Asexual Popul.pdf;/home/mpetersen/bib/storage/A8UF5IBW/817.html},
  pmid = {16888330}
}

@article{Drosophila12GenomesConsortium2007,
  title = {Evolution of Genes and Genomes on the {{Drosophila}} Phylogeny},
  volume = {450},
  copyright = {2007 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature06341},
  abstract = {Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.},
  language = {en},
  number = {7167},
  urldate = {2018-05-14},
  journal = {Nature},
  url = {https://www.nature.com/articles/nature06341},
  author = {{Drosophila 12 Genomes Consortium}},
  month = nov,
  year = {2007},
  pages = {203-218},
  file = {/home/mpetersen/bib/storage/GAMYKGAF/Consortium - 2007 - Evolution of genes and genomes on the iDrosophil.pdf}
}

@article{Santos2014,
  title = {{The evolution of cichlid fish egg-spots is linked with a cis-regulatory change}},
  volume = {5},
  doi = {10.1038/ncomms6149},
  language = {English (US)},
  urldate = {2017-11-27},
  journal = {Nature Communications},
  url = {https://scholars.opb.msu.edu/en/publications/the-evolution-of-cichlid-fish-egg-spots-is-linked-with-a-cis-regu},
  author = {Santos, M. Em\'ilia and Braasch, Ingo and Boileau, Nicolas and Meyer, Britta S. and Sauteur, Lo\"ic and B\"ohne, Astrid and Belting, Heinz Georg and Affolter, Markus and Salzburger, Walter},
  year = {2014},
  file = {/home/mpetersen/bib/storage/EZSX5R68/the-evolution-of-cichlid-fish-egg-spots-is-linked-with-a-cis-regu.html},
  pmid = {25296686}
}

@article{Chen2015,
  title = {Genome Sequence of the {{Asian Tiger}} Mosquito, {{Aedes}} Albopictus, Reveals Insights into Its Biology, Genetics, and Evolution},
  volume = {112},
  issn = {1091-6490},
  doi = {10.1073/pnas.1516410112},
  abstract = {The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.},
  language = {eng},
  number = {44},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Chen, Xiao-Guang and Jiang, Xuanting and Gu, Jinbao and Xu, Meng and Wu, Yang and Deng, Yuhua and Zhang, Chi and Bonizzoni, Mariangela and Dermauw, Wannes and Vontas, John and Armbruster, Peter and Huang, Xin and Yang, Yulan and Zhang, Hao and He, Weiming and Peng, Hongjuan and Liu, Yongfeng and Wu, Kun and Chen, Jiahua and Lirakis, Manolis and Topalis, Pantelis and Van Leeuwen, Thomas and Hall, Andrew Brantley and Jiang, Xiaofang and Thorpe, Chevon and Mueller, Rachel Lockridge and Sun, Cheng and Waterhouse, Robert Michael and Yan, Guiyun and Tu, Zhijian Jake and Fang, Xiaodong and James, Anthony A.},
  month = nov,
  year = {2015},
  keywords = {Animals,Molecular,Phylogeny,Genome,Evolution,Evolution; Molecular,Genome; Insect,Insect,Aedes,diapause,flavivirus,insecticide resistance,mosquito genome,transposons},
  pages = {E5907-5915},
  pmid = {26483478},
  pmcid = {PMC4640774}
}

@article{Nene2007,
  title = {Genome {{Sequence}} of {{Aedes}} Aegypti, a {{Major Arbovirus Vector}}},
  volume = {316},
  copyright = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1138878},
  abstract = {We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at {$\sim$}1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50\% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of {$\sim$}4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of {$\sim$}2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
The genome of the mosquito that carries dengue and yellow fever consists of almost 50 percent transposable elements and over 15,000 protein-coding genes.
The genome of the mosquito that carries dengue and yellow fever consists of almost 50 percent transposable elements and over 15,000 protein-coding genes.},
  language = {en},
  number = {5832},
  urldate = {2018-05-15},
  journal = {Science},
  url = {http://science.sciencemag.org/content/316/5832/1718},
  author = {Nene, Vishvanath and Wortman, Jennifer R. and Lawson, Daniel and Haas, Brian and Kodira, Chinnappa and Tu, Zhijian (Jake) and Loftus, Brendan and Xi, Zhiyong and Megy, Karyn and Grabherr, Manfred and Ren, Quinghu and Zdobnov, Evgeny M. and Lobo, Neil F. and Campbell, Kathryn S. and Brown, Susan E. and Bonaldo, Maria F. and Zhu, Jingsong and Sinkins, Steven P. and Hogenkamp, David G. and Amedeo, Paolo and Arensburger, Peter and Atkinson, Peter W. and Bidwell, Shelby and Biedler, Jim and Birney, Ewan and Bruggner, Robert V. and Costas, Javier and Coy, Monique R. and Crabtree, Jonathan and Crawford, Matt and {deBruyn}, Becky and DeCaprio, David and Eiglmeier, Karin and Eisenstadt, Eric and {El-Dorry}, Hamza and Gelbart, William M. and Gomes, Suely L. and Hammond, Martin and Hannick, Linda I. and Hogan, James R. and Holmes, Michael H. and Jaffe, David and Johnston, J. Spencer and Kennedy, Ryan C. and Koo, Hean and Kravitz, Saul and Kriventseva, Evgenia V. and Kulp, David and LaButti, Kurt and Lee, Eduardo and Li, Song and Lovin, Diane D. and Mao, Chunhong and Mauceli, Evan and Menck, Carlos F. M. and Miller, Jason R. and Montgomery, Philip and Mori, Akio and Nascimento, Ana L. and Naveira, Horacio F. and Nusbaum, Chad and O'Leary, Sin\'ead and Orvis, Joshua and Pertea, Mihaela and Quesneville, Hadi and Reidenbach, Kyanne R. and Rogers, Yu-Hui and Roth, Charles W. and Schneider, Jennifer R. and Schatz, Michael and Shumway, Martin and Stanke, Mario and Stinson, Eric O. and Tubio, Jose M. C. and VanZee, Janice P. and {Verjovski-Almeida}, Sergio and Werner, Doreen and White, Owen and Wyder, Stefan and Zeng, Qiandong and Zhao, Qi and Zhao, Yongmei and Hill, Catherine A. and Raikhel, Alexander S. and Soares, Marcelo B. and Knudson, Dennis L. and Lee, Norman H. and Galagan, James and Salzberg, Steven L. and Paulsen, Ian T. and Dimopoulos, George and Collins, Frank H. and Birren, Bruce and {Fraser-Liggett}, Claire M. and Severson, David W.},
  month = jun,
  year = {2007},
  pages = {1718-1723},
  file = {/home/mpetersen/bib/storage/DVDNZD86/1718.html;/home/mpetersen/bib/storage/KPMRW9HX/1718.html},
  pmid = {17510324}
}

@article{TheHeliconiusGenomeConsortium2012,
  title = {Butterfly Genome Reveals Promiscuous Exchange of Mimicry Adaptations among Species},
  volume = {487},
  copyright = {2012 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature11041},
  abstract = {The evolutionary importance of hybridization and introgression has long been debated1. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2,3,4,5. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.},
  language = {en},
  number = {7405},
  urldate = {2018-05-15},
  journal = {Nature},
  url = {https://www.nature.com/articles/nature11041},
  author = {{The Heliconius Genome Consortium} and Dasmahapatra, Kanchon K. and Walters, James R. and Briscoe, Adriana D. and Davey, John W. and Whibley, Annabel and Nadeau, Nicola J. and Zimin, Aleksey V. and Hughes, Daniel S. T. and Ferguson, Laura C. and Martin, Simon H. and Salazar, Camilo and Lewis, James J. and Adler, Sebastian and Ahn, Seung-Joon and Baker, Dean A. and Baxter, Simon W. and Chamberlain, Nicola L. and Chauhan, Ritika and Counterman, Brian A. and Dalmay, Tamas and Gilbert, Lawrence E. and Gordon, Karl and Heckel, David G. and Hines, Heather M. and Hoff, Katharina J. and Holland, Peter W. H. and {Jacquin-Joly}, Emmanuelle and Jiggins, Francis M. and Jones, Robert T. and Kapan, Durrell D. and Kersey, Paul and Lamas, Gerardo and Lawson, Daniel and Mapleson, Daniel and Maroja, Luana S. and Martin, Arnaud and Moxon, Simon and Palmer, William J. and Papa, Riccardo and Papanicolaou, Alexie and Pauchet, Yannick and Ray, David A. and Rosser, Neil and Salzberg, Steven L. and Supple, Megan A. and Surridge, Alison and {Tenger-Trolander}, Ayse and Vogel, Heiko and Wilkinson, Paul A. and Wilson, Derek and Yorke, James A. and Yuan, Furong and Balmuth, Alexi L. and Eland, Cathlene and Gharbi, Karim and Thomson, Marian and Gibbs, Richard A. and Han, Yi and Jayaseelan, Joy C. and Kovar, Christie and Mathew, Tittu and Muzny, Donna M. and Ongeri, Fiona and Pu, Ling-Ling and Qu, Jiaxin and Thornton, Rebecca L. and Worley, Kim C. and Wu, Yuan-Qing and Linares, Mauricio and Blaxter, Mark L. and {ffrench-Constant}, Richard H. and Joron, Mathieu and Kronforst, Marcus R. and Mullen, Sean P. and Reed, Robert D. and Scherer, Steven E. and Richards, Stephen and Mallet, James and McMillan, W. Owen and Jiggins, Chris D.},
  month = jul,
  year = {2012},
  pages = {94-98},
  file = {/home/mpetersen/bib/storage/LGVSIPKH/Consortium et al. - 2012 - Butterfly genome reveals promiscuous exchange of m.pdf;/home/mpetersen/bib/storage/CVG5GWYZ/nature11041.html}
}

@article{Cong2016,
  title = {Complete Genomes of {{Hairstreak}} Butterflies, Their Speciation, and Nucleo-Mitochondrial Incongruence},
  volume = {6},
  issn = {2045-2322},
  doi = {10.1038/srep24863},
  abstract = {Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729\,Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30\,years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.},
  language = {eng},
  journal = {Scientific Reports},
  author = {Cong, Qian and Shen, Jinhui and Borek, Dominika and Robbins, Robert K. and Otwinowski, Zbyszek and Grishin, Nick V.},
  month = apr,
  year = {2016},
  keywords = {Animals,Sequence Analysis,DNA,Genome,Genetic Variation,Genes,Sequence Analysis; DNA,Genes; Insect,Genome; Insect,Insect,Biological Variation; Population,Butterflies,Biological Variation,Population},
  pages = {24863},
  pmid = {27120974},
  pmcid = {PMC4848470}
}

@article{Kanost2016,
  title = {Multifaceted Biological Insights from a Draft Genome Sequence of the Tobacco Hornworm Moth, {{Manduca}} Sexta},
  volume = {76},
  issn = {0965-1748},
  doi = {10.1016/j.ibmb.2016.07.005},
  abstract = {Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10~g in the larval stage. M.~sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M.~sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex\_1.0 genome assembly resulted in a total genome size of 419.4~Mbp. Repetitive sequences accounted for 25.8\% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.},
  urldate = {2018-05-15},
  journal = {Insect Biochemistry and Molecular Biology},
  url = {http://www.sciencedirect.com/science/article/pii/S0965174816300947},
  author = {Kanost, Michael R. and Arrese, Estela L. and Cao, Xiaolong and Chen, Yun-Ru and Chellapilla, Sanjay and Goldsmith, Marian R. and {Grosse-Wilde}, Ewald and Heckel, David G. and Herndon, Nicolae and Jiang, Haobo and Papanicolaou, Alexie and Qu, Jiaxin and Soulages, Jose L. and Vogel, Heiko and Walters, James and Waterhouse, Robert M. and Ahn, Seung-Joon and Almeida, Francisca C. and An, Chunju and Aqrawi, Peshtewani and Bretschneider, Anne and Bryant, William B. and Bucks, Sascha and Chao, Hsu and Chevignon, Germain and Christen, Jayne M. and Clarke, David F. and Dittmer, Neal T. and Ferguson, Laura C. F. and Garavelou, Spyridoula and Gordon, Karl H. J. and Gunaratna, Ramesh T. and Han, Yi and Hauser, Frank and He, Yan and {Heidel-Fischer}, Hanna and Hirsh, Ariana and Hu, Yingxia and Jiang, Hongbo and Kalra, Divya and Klinner, Christian and K\"onig, Christopher and Kovar, Christie and Kroll, Ashley R. and Kuwar, Suyog S. and Lee, Sandy L. and Lehman, R\"udiger and Li, Kai and Li, Zhaofei and Liang, Hanquan and Lovelace, Shanna and Lu, Zhiqiang and Mansfield, Jennifer H. and McCulloch, Kyle J. and Mathew, Tittu and Morton, Brian and Muzny, Donna M. and Neunemann, David and Ongeri, Fiona and Pauchet, Yannick and Pu, Ling-Ling and Pyrousis, Ioannis and Rao, Xiang-Jun and Redding, Amanda and Roesel, Charles and {Sanchez-Gracia}, Alejandro and Schaack, Sarah and Shukla, Aditi and Tetreau, Guillaume and Wang, Yang and Xiong, Guang-Hua and Traut, Walther and Walsh, Tom K. and Worley, Kim C. and Wu, Di and Wu, Wenbi and Wu, Yuan-Qing and Zhang, Xiufeng and Zou, Zhen and Zucker, Hannah and Briscoe, Adriana D. and Burmester, Thorsten and Clem, Rollie J. and Feyereisen, Ren\'e and Grimmelikhuijzen, Cornelis J. P. and Hamodrakas, Stavros J. and Hansson, Bill S. and Huguet, Elisabeth and Jermiin, Lars S. and Lan, Que and Lehman, Herman K. and Lorenzen, Marce and Merzendorfer, Hans and Michalopoulos, Ioannis and Morton, David B. and Muthukrishnan, Subbaratnam and Oakeshott, John G. and Palmer, Will and Park, Yoonseong and Passarelli, A. Lorena and Rozas, Julio and Schwartz, Lawrence M. and Smith, Wendy and Southgate, Agnes and Vilcinskas, Andreas and Vogt, Richard and Wang, Ping and Werren, John and Yu, Xiao-Qiang and Zhou, Jing-Jiang and Brown, Susan J. and Scherer, Steven E. and Richards, Stephen and Blissard, Gary W.},
  month = sep,
  year = {2016},
  keywords = {Synteny,Lepidoptera,Insect,Innate immunity,Insect biochemistry,Moth,Tobacco hornworm},
  pages = {118-147},
  file = {/home/mpetersen/bib/storage/7Q7D4HML/Kanost et al. - 2016 - Multifaceted biological insights from a draft geno.pdf;/home/mpetersen/bib/storage/YHAZHDAN/S0965174816300947.html}
}

@article{Cuartas2015,
  title = {The {{Complete Sequence}} of the {{First Spodoptera}} Frugiperda {{Betabaculovirus Genome}}: {{A Natural Multiple Recombinant Virus}}},
  volume = {7},
  issn = {1999-4915},
  shorttitle = {The {{Complete Sequence}} of the {{First Spodoptera}} Frugiperda {{Betabaculovirus Genome}}},
  doi = {10.3390/v7010394},
  abstract = {Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs) and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs), 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.},
  number = {1},
  urldate = {2018-05-15},
  journal = {Viruses},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306845/},
  author = {Cuartas, Paola E. and Barrera, Gloria P. and Belaich, Mariano N. and Barreto, Emiliano and Ghiringhelli, Pablo D. and Villamizar, Laura F.},
  month = jan,
  year = {2015},
  pages = {394-421},
  file = {/home/mpetersen/bib/storage/RMB8549G/Cuartas et al. - 2015 - The Complete Sequence of the First Spodoptera frug.pdf;/home/mpetersen/bib/storage/XE6J7963/Cuartas et al. - 2015 - The Complete Sequence of the First Spodoptera frug.pdf},
  pmid = {25609309},
  pmcid = {PMC4306845}
}

@article{Yin2014,
  title = {{{ChiloDB}}: A Genomic and Transcriptome Database for an Important Rice Insect Pest {{Chilo}} Suppressalis},
  volume = {2014},
  shorttitle = {{{ChiloDB}}},
  doi = {10.1093/database/bau065},
  abstract = {Abstract.  ChiloDB is an integrated resource that will be of use to the rice stem borer research community. The rice striped stem borer (SSB), Chilo suppressali},
  language = {en},
  urldate = {2018-05-15},
  journal = {Database},
  url = {https://academic.oup.com/database/article/doi/10.1093/database/bau065/2634640},
  author = {Yin, Chuanlin and Liu, Ying and Liu, Jinding and Xiao, Huamei and Huang, Shuiqing and Lin, Yongjun and Han, Zhaojun and Li, Fei},
  month = jan,
  year = {2014},
  file = {/home/mpetersen/bib/storage/38NB6ZEE/Yin et al. - 2014 - ChiloDB a genomic and transcriptome database for .pdf;/home/mpetersen/bib/storage/4BLTPHX3/2634640.html}
}

@article{Derks2015,
  title = {The {{Genome}} of {{Winter Moth}} ({{Operophtera}} Brumata) {{Provides}} a {{Genomic Perspective}} on {{Sexual Dimorphism}} and {{Phenology}}},
  volume = {7},
  doi = {10.1093/gbe/evv145},
  abstract = {Abstract.  The winter moth (Operophtera brumata) belongs to one of the most species-rich families in Lepidoptera, the Geometridae (approximately 23,000 species)},
  language = {en},
  number = {8},
  urldate = {2018-05-15},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/7/8/2321/558093},
  author = {Derks, Martijn F. L. and Smit, Sandra and Salis, Lucia and Schijlen, Elio and Bossers, Alex and Mateman, Christa and Pijl, Agata S. and {de Ridder}, Dick and Groenen, Martien A. M. and Visser, Marcel E. and Megens, Hendrik-Jan},
  month = aug,
  year = {2015},
  pages = {2321-2332},
  file = {/home/mpetersen/bib/storage/VAQRK2WG/Derks et al. - 2015 - The Genome of Winter Moth (Operophtera brumata) Pr.pdf;/home/mpetersen/bib/storage/5CAM5SQ2/558093.html}
}

@article{InternationalSilkwormGenomeConsortium2008,
  title = {The Genome of a Lepidopteran Model Insect, the Silkworm {{Bombyx}} Mori},
  volume = {38},
  issn = {1879-0240},
  doi = {10.1016/j.ibmb.2008.11.004},
  abstract = {Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87\% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6\% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.},
  language = {eng},
  number = {12},
  journal = {Insect Biochemistry and Molecular Biology},
  author = {{International Silkworm Genome Consortium}},
  month = dec,
  year = {2008},
  keywords = {Animals,Phylogeny,Genome,Databases,Databases; Factual,Genes,Insect Proteins,Gene Expression Regulation,Genes; Insect,Genome; Insect,Insect,Bombyx,Factual},
  pages = {1036-1045},
  pmid = {19121390}
}

@article{TriboliumGenomeSequencingConsortium2008,
  title = {The Genome of the Model Beetle and Pest {{Tribolium}} Castaneum},
  volume = {452},
  copyright = {2008 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature06784},
  abstract = {Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell\textendash{}cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.},
  language = {en},
  number = {7190},
  urldate = {2018-05-15},
  journal = {Nature},
  url = {https://www.nature.com/articles/nature06784},
  author = {{Tribolium Genome Sequencing Consortium}},
  month = apr,
  year = {2008},
  pages = {949-955},
  file = {/home/mpetersen/bib/storage/HIPWN5F7/Consortium - 2008 - The genome of the model beetle and pest iTriboli.pdf;/home/mpetersen/bib/storage/N4ZDP23B/nature06784.html}
}

@article{Meyer2016,
  title = {Draft {{Genome}} of the {{Scarab Beetle Oryctes}} Borbonicus on {{La R\'eunion Island}}},
  volume = {8},
  doi = {10.1093/gbe/evw133},
  abstract = {Abstract.   Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal model},
  language = {en},
  number = {7},
  urldate = {2018-05-15},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/8/7/2093/2465979},
  author = {Meyer, Jan M. and Markov, Gabriel V. and Baskaran, Praveen and Herrmann, Matthias and Sommer, Ralf J. and R\"odelsperger, Christian},
  month = jul,
  year = {2016},
  pages = {2093-2105},
  file = {/home/mpetersen/bib/storage/9X622F57/Meyer et al. - 2016 - Draft Genome of the Scarab Beetle Oryctes borbonic.pdf;/home/mpetersen/bib/storage/FP6A7SY2/2465979.html}
}

@article{Cunningham2015,
  title = {The {{Genome}} and {{Methylome}} of a {{Beetle}} with {{Complex Social Behavior}}, {{Nicrophorus}} Vespilloides ({{Coleoptera}}: {{Silphidae}})},
  volume = {7},
  shorttitle = {The {{Genome}} and {{Methylome}} of a {{Beetle}} with {{Complex Social Behavior}}, {{Nicrophorus}} Vespilloides ({{Coleoptera}}},
  doi = {10.1093/gbe/evv194},
  abstract = {Abstract.   Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multipl},
  language = {en},
  number = {12},
  urldate = {2018-05-15},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/7/12/3383/2465950},
  author = {Cunningham, Christopher B. and Ji, Lexiang and Wiberg, R. Axel W. and Shelton, Jennifer and McKinney, Elizabeth C. and Parker, Darren J. and Meagher, Richard B. and Benowitz, Kyle M. and {Roy-Zokan}, Eileen M. and Ritchie, Michael G. and Brown, Susan J. and Schmitz, Robert J. and Moore, Allen J.},
  month = dec,
  year = {2015},
  pages = {3383-3396},
  file = {/home/mpetersen/bib/storage/Q89CZWUQ/Cunningham et al. - 2015 - The Genome and Methylome of a Beetle with Complex .pdf;/home/mpetersen/bib/storage/HUBFB8PZ/2465950.html}
}

@article{Sadd2015,
  title = {The Genomes of Two Key Bumblebee Species with Primitive Eusocial Organization},
  volume = {16},
  issn = {1465-6906},
  doi = {10.1186/s13059-015-0623-3},
  abstract = {The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.},
  urldate = {2018-05-15},
  journal = {Genome Biology},
  url = {https://doi.org/10.1186/s13059-015-0623-3},
  author = {Sadd, Ben M. and Barribeau, Seth M. and Bloch, Guy and {de Graaf}, Dirk C. and Dearden, Peter and Elsik, Christine G. and Gadau, J\"urgen and Grimmelikhuijzen, Cornelis JP and Hasselmann, Martin and Lozier, Jeffrey D. and Robertson, Hugh M. and Smagghe, Guy and Stolle, Eckart and Van Vaerenbergh, Matthias and Waterhouse, Robert M. and {Bornberg-Bauer}, Erich and Klasberg, Steffen and Bennett, Anna K. and C\^amara, Francisco and Guig\'o, Roderic and Hoff, Katharina and Mariotti, Marco and {Munoz-Torres}, Monica and Murphy, Terence and Santesmasses, Didac and Amdam, Gro V. and Beckers, Matthew and Beye, Martin and Biewer, Matthias and Bitondi, M\'arcia MG and Blaxter, Mark L. and Bourke, Andrew FG and Brown, Mark JF and Buechel, Severine D. and Cameron, Rossanah and Cappelle, Kaat and Carolan, James C. and Christiaens, Olivier and Ciborowski, Kate L. and Clarke, David F. and Colgan, Thomas J. and Collins, David H. and Cridge, Andrew G. and Dalmay, Tamas and Dreier, Stephanie and {du Plessis}, Louis and Duncan, Elizabeth and Erler, Silvio and Evans, Jay and Falcon, Tiago and Flores, Kevin and Freitas, Fl\'avia CP and Fuchikawa, Taro and Gempe, Tanja and Hartfelder, Klaus and Hauser, Frank and Helbing, Sophie and Humann, Fernanda C. and Irvine, Frano and Jermiin, Lars S. and Johnson, Claire E. and Johnson, Reed M. and Jones, Andrew K. and Kadowaki, Tatsuhiko and Kidner, Jonathan H. and Koch, Vasco and K\"ohler, Arian and Kraus, F. Bernhard and Lattorff, H. Michael G. and Leask, Megan and Lockett, Gabrielle A. and Mallon, Eamonn B. and Antonio, David S. Marco and Marxer, Monika and Meeus, Ivan and Moritz, Robin FA and Nair, Ajay and N\"apflin, Kathrin and Nissen, Inga and Niu, Jinzhi and Nunes, Francis MF and Oakeshott, John G. and Osborne, Amy and Otte, Marianne and Pinheiro, Daniel G. and Rossi\'e, Nina and Rueppell, Olav and Santos, Carolina G. and {Schmid-Hempel}, Regula and Schmitt, Bj\"orn D. and Schulte, Christina and Sim\~oes, Zil\'a LP and Soares, Michelle PM and Swevers, Luc and Winnebeck, Eva C. and Wolschin, Florian and Yu, Na and Zdobnov, Evgeny M. and Aqrawi, Peshtewani K. and Blankenburg, Kerstin P. and Coyle, Marcus and Francisco, Liezl and Hernandez, Alvaro G. and Holder, Michael and Hudson, Matthew E. and Jackson, LaRonda and Jayaseelan, Joy and Joshi, Vandita and Kovar, Christie and Lee, Sandra L. and Mata, Robert and Mathew, Tittu and Newsham, Irene F. and Ngo, Robin and Okwuonu, Geoffrey and Pham, Christopher and Pu, Ling-Ling and Saada, Nehad and Santibanez, Jireh and Simmons, DeNard and Thornton, Rebecca and Venkat, Aarti and Walden, Kimberly KO and Wu, Yuan-Qing and Debyser, Griet and Devreese, Bart and Asher, Claire and Blommaert, Julie and Chipman, Ariel D. and Chittka, Lars and Fouks, Bertrand and Liu, Jisheng and O'Neill, Meaghan P. and Sumner, Seirian and Puiu, Daniela and Qu, Jiaxin and Salzberg, Steven L. and Scherer, Steven E. and Muzny, Donna M. and Richards, Stephen and Robinson, Gene E. and Gibbs, Richard A. and {Schmid-Hempel}, Paul and Worley, Kim C.},
  month = apr,
  year = {2015},
  keywords = {Long Terminal Repeat,Transposable Element,Bumblebee Species,Odorant Receptor,Synteny Block},
  pages = {76},
  file = {/home/mpetersen/bib/storage/9H7BMKNE/Sadd et al. - 2015 - The genomes of two key bumblebee species with prim.pdf;/home/mpetersen/bib/storage/U8GI84R3/s13059-015-0623-3.html}
}

@article{Rosenfeld2016,
  title = {Genome Assembly and Geospatial Phylogenomics of the Bed Bug {{{\emph{Cimex}}}}{\emph{ Lectularius}}},
  volume = {7},
  copyright = {2016 Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/ncomms10164},
  abstract = {The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.},
  language = {en},
  urldate = {2018-05-15},
  journal = {Nature Communications},
  url = {https://www.nature.com/articles/ncomms10164},
  author = {Rosenfeld, Jeffrey A. and Reeves, Darryl and Brugler, Mercer R. and Narechania, Apurva and Simon, Sabrina and Durrett, Russell and Foox, Jonathan and Shianna, Kevin and Schatz, Michael C. and Gandara, Jorge and Afshinnekoo, Ebrahim and Lam, Ernest T. and Hastie, Alex R. and Chan, Saki and Cao, Han and Saghbini, Michael and Kentsis, Alex and Planet, Paul J. and Kholodovych, Vladyslav and Tessler, Michael and Baker, Richard and DeSalle, Rob and Sorkin, Louis N. and Kolokotronis, Sergios-Orestis and Siddall, Mark E. and Amato, George and Mason, Christopher E.},
  month = feb,
  year = {2016},
  pages = {10164},
  file = {/home/mpetersen/bib/storage/KKFVDNW6/Rosenfeld et al. - 2016 - Genome assembly and geospatial phylogenomics of th.pdf;/home/mpetersen/bib/storage/K82UB6FK/ncomms10164.html}
}

@article{Xue2014,
  title = {Genomes of the Rice Pest Brown Planthopper and Its Endosymbionts Reveal Complex Complementary Contributions for Host Adaptation},
  volume = {15},
  issn = {1474-760X},
  doi = {10.1186/s13059-014-0521-0},
  abstract = {The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. To better understand how a monophagous sap-sucking arthropod herbivore has adapted to its exclusive host selection and to provide insights to improve pest control, we analyzed the genomes of the brown planthopper and its two endosymbionts.},
  urldate = {2018-05-15},
  journal = {Genome Biology},
  url = {https://doi.org/10.1186/s13059-014-0521-0},
  author = {Xue, Jian and Zhou, Xin and Zhang, Chuan-Xi and Yu, Li-Li and Fan, Hai-Wei and Wang, Zhuo and Xu, Hai-Jun and Xi, Yu and Zhu, Zeng-Rong and Zhou, Wen-Wu and Pan, Peng-Lu and Li, Bao-Ling and Colbourne, John K. and Noda, Hiroaki and Suetsugu, Yoshitaka and Kobayashi, Tetsuya and Zheng, Yuan and Liu, Shanlin and Zhang, Rui and Liu, Yang and Luo, Ya-Dan and Fang, Dong-Ming and Chen, Yan and Zhan, Dong-Liang and Lv, Xiao-Dan and Cai, Yue and Wang, Zhao-Bao and Huang, Hai-Jian and Cheng, Ruo-Lin and Zhang, Xue-Chao and Lou, Yi-Han and Yu, Bing and Zhuo, Ji-Chong and Ye, Yu-Xuan and Zhang, Wen-Qing and Shen, Zhi-Cheng and Yang, Huan-Ming and Wang, Jian and Wang, Jun and Bao, Yan-Yuan and Cheng, Jia-An},
  month = dec,
  year = {2014},
  keywords = {Brown Planthopper,Fosmid Clone,Fosmid Library,Peritrophic Matrix,Unannotated Gene},
  pages = {521},
  file = {/home/mpetersen/bib/storage/MLTYLMMA/Xue et al. - 2014 - Genomes of the rice pest brown planthopper and its.pdf;/home/mpetersen/bib/storage/KFBN6FWC/s13059-014-0521-0.html}
}

@article{Chipman2014,
  title = {The {{First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content}} and {{Genome Organisation}} in the {{Centipede Strigamia}} Maritima},
  volume = {12},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.1002005},
  abstract = {Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.},
  language = {en},
  number = {11},
  urldate = {2018-05-15},
  journal = {PLOS Biology},
  url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002005},
  author = {Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schr\"oder, Reinhard and {Torres-Oliva}, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and {Capella-Guti\'errez}, Salvador and Coyle, Marcus and Dearden, Peter K. and Pasquier, Louis Du and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabald\'on, Toni and Gillis, William J. and {Goodwin-Horn}, Elizabeth A. and Green, Jack E. and {Griffiths-Jones}, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guig\'o, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, Fran{\c c}ois and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and {S\'anchez-Gracia}, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and {Tessmar-Raible}, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen},
  year = {25-Nov-2014},
  keywords = {Evolutionary genetics,Drosophila melanogaster,Insects,Invertebrate genomics,Homeobox,DNA methylation,Arthropoda,Phylogenetic analysis},
  pages = {e1002005},
  file = {/home/mpetersen/bib/storage/4Q8SJDCT/Chipman et al. - 2014 - The First Myriapod Genome Sequence Reveals Conserv.pdf;/home/mpetersen/bib/storage/YYWLISYD/article.html}
}

@article{Simpson2017,
  title = {The {{Draft Genome}} and {{Transcriptome}} of the {{Atlantic Horseshoe Crab}}, {{Limulus}} Polyphemus},
  doi = {10.1155/2017/7636513},
  abstract = {The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in contigs with N50 of 4,736, while the transcriptome assembly resulted in contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate the Limulus clock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.},
  language = {en},
  urldate = {2018-05-15},
  journal = {International Journal of Genomics},
  url = {https://www.hindawi.com/journals/ijg/2017/7636513/},
  author = {Simpson, Stephen D. and Ramsdell, Jordan S. and Iii, Watson and H, Winsor and Chabot, Christopher C.},
  year = {2017},
  file = {/home/mpetersen/bib/storage/AWGXIE3T/Simpson et al. - 2017 - The Draft Genome and Transcriptome of the Atlantic.pdf;/home/mpetersen/bib/storage/GRGXHWUF/7636513.html}
}

@article{Ahola2017,
  title = {Butterfly {{Genomics}}: {{Insights}} from the {{Genome}} of {{{\emph{Melitaea}}}}{\emph{ Cinxia}}},
  volume = {54},
  issn = {0003-455X, 1797-2450},
  shorttitle = {Butterfly {{Genomics}}},
  doi = {10.5735/086.054.0123},
  language = {en},
  number = {1-4},
  urldate = {2018-05-15},
  journal = {Annales Zoologici Fennici},
  url = {http://www.bioone.org/doi/10.5735/086.054.0123},
  author = {Ahola, Virpi and Wahlberg, Niklas and Frilander, Mikko J.},
  month = apr,
  year = {2017},
  pages = {275-291},
  file = {/home/mpetersen/bib/storage/ACAJV9ZC/086.054.html;/home/mpetersen/bib/storage/AMDMCEY4/086.054.html;/home/mpetersen/bib/storage/J6YJZ5CA/086.054.html;/home/mpetersen/bib/storage/PPV9R6SI/086.054.html}
}

@article{Ahola2014,
  title = {The {{Glanville}} Fritillary Genome Retains an Ancient Karyotype and Reveals Selective Chromosomal Fusions in {{Lepidoptera}}},
  volume = {5},
  issn = {2041-1723},
  doi = {10.1038/ncomms5737},
  urldate = {2018-05-15},
  journal = {Nature Communications},
  url = {http://www.nature.com/doifinder/10.1038/ncomms5737},
  author = {Ahola, Virpi and Lehtonen, Rainer and Somervuo, Panu and Salmela, Leena and Koskinen, Patrik and Rastas, Pasi and V\"alim\"aki, Niko and Paulin, Lars and Kvist, Jouni and Wahlberg, Niklas and Tanskanen, Jaakko and Hornett, Emily A. and Ferguson, Laura C. and Luo, Shiqi and Cao, Zijuan and {de Jong}, Maaike A. and Duplouy, Anne and Smolander, Olli-Pekka and Vogel, Heiko and McCoy, Rajiv C. and Qian, Kui and Chong, Wong Swee and Zhang, Qin and Ahmad, Freed and Haukka, Jani K. and Joshi, Aruj and Saloj\"arvi, Jarkko and Wheat, Christopher W. and {Grosse-Wilde}, Ewald and Hughes, Daniel and Katainen, Riku and Pitk\"anen, Esa and Ylinen, Johannes and Waterhouse, Robert M. and Turunen, Mikko and V\"ah\"arautio, Anna and Ojanen, Sami P. and Schulman, Alan H. and Taipale, Minna and Lawson, Daniel and Ukkonen, Esko and M\"akinen, Veli and Goldsmith, Marian R. and Holm, Liisa and Auvinen, Petri and Frilander, Mikko J. and Hanski, Ilkka},
  month = sep,
  year = {2014},
  pages = {4737}
}

@article{Shen2016,
  title = {Complete Genome of {{Pieris}} Rapae, a Resilient Alien, a Cabbage Pest, and a Source of Anti-Cancer Proteins},
  volume = {5},
  issn = {2046-1402},
  doi = {10.12688/f1000research.9765.1},
  language = {en},
  urldate = {2018-05-15},
  journal = {F1000Research},
  url = {https://f1000research.com/articles/5-2631/v1},
  author = {Shen, Jinhui and Cong, Qian and Kinch, Lisa N. and Borek, Dominika and Otwinowski, Zbyszek and Grishin, Nick V.},
  month = nov,
  year = {2016},
  pages = {2631},
  file = {/home/mpetersen/bib/storage/2VLQFZ9M/v1.html;/home/mpetersen/bib/storage/CRQRAP7C/v1.html}
}

@article{Gouin2017,
  title = {Two Genomes of Highly Polyphagous Lepidopteran Pests ( {{Spodoptera}} Frugiperda , {{Noctuidae}}) with Different Host-Plant Ranges},
  volume = {7},
  copyright = {2017 The Author(s)},
  issn = {2045-2322},
  doi = {10.1038/s41598-017-10461-4},
  abstract = {Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20\% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (``C'' and ``R'') that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.},
  language = {en},
  number = {1},
  urldate = {2018-05-15},
  journal = {Scientific Reports},
  url = {https://www.nature.com/articles/s41598-017-10461-4},
  author = {Gouin, Ana\"is and Bretaudeau, Anthony and Nam, Kiwoong and Gimenez, Sylvie and Aury, Jean-Marc and Duvic, Bernard and Hilliou, Fr\'ed\'erique and Durand, Nicolas and Montagn\'e, Nicolas and Darboux, Isabelle and Kuwar, Suyog and Chertemps, Thomas and Siaussat, David and Bretschneider, Anne and Mon\'e, Yves and Ahn, Seung-Joon and H\"anniger, Sabine and Grenet, Anne-Sophie Gosselin and Neunemann, David and Maumus, Florian and Luyten, Isabelle and Labadie, Karine and Xu, Wei and Koutroumpa, Fotini and Escoubas, Jean-Michel and Llopis, Angel and {Ma\"ib\`eche-Coisne}, Martine and Salasc, Fanny and Tomar, Archana and Anderson, Alisha R. and Khan, Sher Afzal and Dumas, Pascaline and Orsucci, Marion and Guy, Julie and Belser, Caroline and Alberti, Adriana and Noel, Benjamin and Couloux, Arnaud and Mercier, Jonathan and Nidelet, Sabine and Dubois, Emeric and Liu, Nai-Yong and Boulogne, Isabelle and Mirabeau, Olivier and Goff, Gaelle and Gordon, Karl and Oakeshott, John and Consoli, Fernando L. and Volkoff, Anne-Nathalie and Fescemyer, Howard W. and Marden, James H. and Luthe, Dawn S. and Herrero, Salvador and Heckel, David G. and Wincker, Patrick and Kergoat, Gael J. and Amselem, Joelle and Quesneville, Hadi and Groot, Astrid T. and {Jacquin-Joly}, Emmanuelle and N\`egre, Nicolas and Lemaitre, Claire and Legeai, Fabrice and {d'Alen{\c c}on}, Emmanuelle and Fournier, Philippe},
  month = sep,
  year = {2017},
  pages = {11816},
  file = {/home/mpetersen/bib/storage/84RMSMK6/Gouin et al. - 2017 - Two genomes of highly polyphagous lepidopteran pes.pdf;/home/mpetersen/bib/storage/EKBYE8YS/s41598-017-10461-4.html}
}

@article{Dolezel2003,
  title = {Letter to the Editor},
  volume = {51A},
  copyright = {Copyright \textcopyright{} 2003 Wiley-Liss, Inc.},
  issn = {1552-4930},
  doi = {10.1002/cyto.a.10013},
  language = {en},
  number = {2},
  urldate = {2018-05-16},
  journal = {Cytometry Part A},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cyto.a.10013},
  author = {Dole{\v z}el, J. and Barto{\v s}, J. and Voglmayr, H. and Greilhuber, J.},
  month = feb,
  year = {2003},
  pages = {127-128},
  file = {/home/mpetersen/bib/storage/XS4ZT5GI/Doležel et al. - 2003 - Letter to the editor.pdf;/home/mpetersen/bib/storage/93252IF5/cyto.a.html}
}

@article{Huerta-Cepas2016,
  title = {{{ETE}} 3: {{Reconstruction}}, {{Analysis}}, and {{Visualization}} of {{Phylogenomic Data}}},
  volume = {33},
  issn = {0737-4038, 1537-1719},
  shorttitle = {{{ETE}} 3},
  doi = {10.1093/molbev/msw046},
  language = {en},
  number = {6},
  urldate = {2018-05-16},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msw046},
  author = {{Huerta-Cepas}, Jaime and Serra, Fran{\c c}ois and Bork, Peer},
  month = jun,
  year = {2016},
  pages = {1635-1638}
}

@article{Letsch2016,
  title = {Not Going with the Flow: A Comprehensive Time-Calibrated Phylogeny of Dragonflies ({{Anisoptera}}: {{Odonata}}: {{Insecta}}) Provides Evidence for the Role of Lentic Habitats on Diversification},
  volume = {25},
  issn = {09621083},
  shorttitle = {Not Going with the Flow},
  doi = {10.1111/mec.13562},
  language = {en},
  number = {6},
  urldate = {2018-05-17},
  journal = {Molecular Ecology},
  url = {http://doi.wiley.com/10.1111/mec.13562},
  author = {Letsch, Harald and Gottsberger, Brigitte and Ware, Jessica L.},
  month = mar,
  year = {2016},
  pages = {1340-1353},
  file = {/home/mpetersen/bib/storage/6F2W2UMD/Letsch et al. - 2016 - Not going with the flow a comprehensive time-cali.pdf;/home/mpetersen/bib/storage/RUSG4LCN/Letsch et al. - 2016 - Not going with the flow a comprehensive time-cali.pdf}
}

@article{Revell2012,
  title = {Phytools: An {{R}} Package for Phylogenetic Comparative Biology (and Other Things): Phytools: {{R}} Package},
  volume = {3},
  issn = {2041210X},
  shorttitle = {Phytools},
  doi = {10.1111/j.2041-210X.2011.00169.x},
  language = {en},
  number = {2},
  urldate = {2018-05-21},
  journal = {Methods in Ecology and Evolution},
  url = {http://doi.wiley.com/10.1111/j.2041-210X.2011.00169.x},
  author = {Revell, Liam J.},
  month = apr,
  year = {2012},
  pages = {217-223}
}

@article{Provataris2018,
  title = {Signatures of {{DNA Methylation}} across {{Insects Suggest Reduced DNA Methylation Levels}} in {{Holometabola}}},
  volume = {10},
  doi = {10.1093/gbe/evy066},
  abstract = {Abstract.  It has been experimentally shown that DNA methylation is involved in the regulation of gene expression and the silencing of transposable element acti},
  language = {en},
  number = {4},
  urldate = {2018-05-22},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/10/4/1185/4943971},
  author = {Provataris, Panagiotis and Meusemann, Karen and Niehuis, Oliver and Grath, Sonja and Misof, Bernhard and Wagner, Gunter},
  month = apr,
  year = {2018},
  pages = {1185-1197},
  file = {/home/mpetersen/bib/storage/2E7PWLD2/Provataris et al. - 2018 - Signatures of DNA Methylation across Insects Sugge.pdf;/home/mpetersen/bib/storage/VKD3J67Q/4943971.html}
}

@article{Hanrahan2011,
  title = {New Genome Size Estimates of 134 Species of Arthropods},
  volume = {19},
  issn = {0967-3849, 1573-6849},
  doi = {10.1007/s10577-011-9231-6},
  language = {en},
  number = {6},
  urldate = {2018-05-22},
  journal = {Chromosome Research},
  url = {http://link.springer.com/10.1007/s10577-011-9231-6},
  author = {Hanrahan, Shawn Jason and Johnston, J. Spencer},
  month = aug,
  year = {2011},
  keywords = {Animal Genetics and Genomics,arthropods,Cell Biology,DNA flow cytometry,evolutionary genomics,genome size,Human Genetics,Plant Genetics \& Genomics},
  pages = {809-823},
  file = {/home/mpetersen/bib/storage/47WF6QKZ/Hanrahan and Johnston - 2011 - New genome size estimates of 134 species of arthro.pdf;/home/mpetersen/bib/storage/S2LA5BIE/Hanrahan and Johnston - 2011 - New genome size estimates of 134 species of arthro.pdf}
}

@article{Branstetter2017,
  title = {Phylogenomic {{Insights}} into the {{Evolution}} of {{Stinging Wasps}} and the {{Origins}} of {{Ants}} and {{Bees}}},
  volume = {27},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2017.03.027},
  abstract = {Summary
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae), and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing the phylogenetic affinities of ants and bees helps us understand and reconstruct patterns of social evolution as well as fully appreciate the biological implications of the switch from carnivory to pollen feeding (pollenivory). Despite recent advancements in aculeate phylogeny [4\textendash{}11], considerable uncertainty remains regarding higher-level relationships within Aculeata, including the phylogenetic affinities of ants and bees [5\textendash{}7]. We used ultraconserved element (UCE) phylogenomics [7, 12] to resolve relationships among stinging-wasp families, gathering sequence data from {$>$}800~UCE loci and 187 samples, including 30 out of 31 aculeate families. We analyzed the 187-taxon dataset using multiple analytical approaches, and we evaluated several alternative taxon sets. We also tested alternative hypotheses for the phylogenetic positions of ants and bees. Our results present a highly supported phylogeny of the stinging wasps. Most importantly, we find unequivocal evidence that ants are the sister group to bees+apoid wasps (Apoidea) and that bees are nested within a~paraphyletic Crabronidae. We also demonstrate that taxon choice can fundamentally impact tree topology and clade support in phylogenomic inference.},
  number = {7},
  urldate = {2018-05-25},
  journal = {Current Biology},
  url = {http://www.sciencedirect.com/science/article/pii/S0960982217303251},
  author = {Branstetter, Michael G. and Danforth, Bryan N. and Pitts, James P. and Faircloth, Brant C. and Ward, Philip S. and Buffington, Matthew L. and Gates, Michael W. and Kula, Robert R. and Brady, Se\'an G.},
  month = apr,
  year = {2017},
  keywords = {Hymenoptera,phylogenomics,social insects,Aculeata,molecular systematics,next-generation sequencing,taxon sampling,ultraconserved elements},
  pages = {1019-1025},
  file = {/home/mpetersen/bib/storage/DA9UVQUW/1-s2.0-S0960982217303251-mmc1.pdf;/home/mpetersen/bib/storage/I38JY8V8/Branstetter et al. - 2017 - Phylogenomic Insights into the Evolution of Stingi.pdf;/home/mpetersen/bib/storage/8HMX8RXD/S0960982217303251.html}
}

@article{Ward2015,
  title = {The Evolution of Myrmicine Ants: Phylogeny and Biogeography of a Hyperdiverse Ant Clade ({{Hymenoptera}}: {{Formicidae}}): {{Phylogeny}} and Evolution of Myrmicine Ants},
  volume = {40},
  issn = {03076970},
  shorttitle = {The Evolution of Myrmicine Ants},
  doi = {10.1111/syen.12090},
  language = {en},
  number = {1},
  urldate = {2018-05-25},
  journal = {Systematic Entomology},
  url = {http://doi.wiley.com/10.1111/syen.12090},
  author = {Ward, Philip S. and Brady, Se\'aN G. and Fisher, Brian L. and Schultz, Ted R.},
  month = jan,
  year = {2015},
  pages = {61-81},
  file = {/home/mpetersen/bib/storage/WZACTXAC/Ward et al. - 2015 - The evolution of myrmicine ants phylogeny and bio.pdf;/home/mpetersen/bib/storage/YJHL8M8E/Ward et al. - 2015 - The evolution of myrmicine ants phylogeny and bio.pdf}
}

@article{McKenna2009,
  title = {Temporal Lags and Overlap in the Diversification of Weevils and Flowering Plants},
  volume = {106},
  issn = {1091-6490},
  doi = {10.1073/pnas.0810618106},
  abstract = {The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on approximately 8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning approximately 166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca. 112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.},
  language = {eng},
  number = {17},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {McKenna, Duane D. and Sequeira, Andrea S. and Marvaldi, Adriana E. and Farrell, Brian D.},
  month = apr,
  year = {2009},
  keywords = {Animals,Phylogeny,Molecular Sequence Data,Time Factors,Asteraceae,Flowers,Population Dynamics,Weevils},
  pages = {7083-7088},
  file = {/home/mpetersen/bib/storage/EQ75CEFA/McKenna et al. - 2009 - Temporal lags and overlap in the diversification o.pdf;/home/mpetersen/bib/storage/HLKCMYA7/McKenna et al. - 2009 - Temporal lags and overlap in the diversification o.pdf},
  pmid = {19365072},
  pmcid = {PMC2678426}
}

@article{Cranston2011,
  title = {A Dated Molecular Phylogeny for the {{Chironomidae}} ({{Diptera}})},
  volume = {37},
  copyright = {\textcopyright{} 2011 The Authors. Systematic Entomology \textcopyright{} 2011 The Royal Entomological Society},
  issn = {1365-3113},
  doi = {10.1111/j.1365-3113.2011.00603.x},
  abstract = {We provide the first highly sampled phylogeny estimate for the dipteran family Chironomidae using molecular data from fragments of two ribosomal genes (18S and 28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed-model Bayesian and maximum likelihood inference methods. The most recently described subfamilies Chilenomyiinae and Usambaromyiinae proved elusive, and are unsampled. We confirm monophyly of all sampled subfamilies except Prodiamesinae, which contains Propsilocerus Kieffer, previously in Orthocladiinae. The semifamily Chironomoinae is confirmed only if Telmatogetoninae is included, which is closer to Brundin's original suggestion. Buchonomyiinae is excluded from Chironomoinae: it is a sister group to all remaining Chironomidae, conforming more to Murray and Ashe's argumentation. Semifamily Tanypodoinae is a grade and unsupported as monophyletic: the austral Aphroteniinae alone is sister to all Chironomidae (less Buchonomyiinae). Podonominae is weakly supported as the next sister group, in contrast to some estimates that place this subfamily as sister group to Tanypodinae alone. In Diamesinae, the southern African Harrisonini is confirmed as a member, but embedded within austral tribe Heptagiini, which is confirmed as sister to the undersampled Diamesini. Tribe Pentaneurini and `non-Pentaneurini' taxa are reciprocally monophyletic in Tanypodinae. Recent molecular findings concerning Podonominae are substantiated, with a monophyletic tribe Podonomini, Boreochlini forming a grade and Lasiodiamesa Kieffer placed as sister to all other Podonominae, but with uncertainty. In Orthocladiinae, a postulated two-tribe system of Orthocladiini and Metriocnemini can be supported after exclusion of a Corynoneura group and a Brillia group, which is revealed as sister to Stictocladius Edwards. The marine Clunio Haliday and Thalassosmittia Strenzke \& Remmert (given high rank in the past) are clearly embedded deep in Orthocladiinae. The finding of Shangomyia S\ae{}ther \& Wang + Xyiaomyia S\ae{}ther \& Wang as sister group to all other Chironominae justifies high rank, as their authors suggested. Pseudochironomini (untested by sampling shortfall) is sister to a monophyletic Tanytarsini (with a weakly supported inclusion of the enigmatic Nandeva Wiedenbrug, Reiss \& Fittkau). The tribe Chironomini can be supported only by excluding Shangomyia + Xyiaomyia, and a postulated monophyletic clade comprising several taxa such as Microtendipes Kieffer, with six-segmented larval antennae and alternate Lauterborn organs, that is sister group to Pseudochironomini + Tanytarsini. The tempo of diversification of the family, deduced by divergence time analysis (beast), shows Permian origination with subfamily stem-group origination from the mid\textendash{}late Triassic to the early Cretaceous. Crown-group origination ranged from Podonominae on a short stem originating in the mid Jurassic to long-stemmed Aphroteninae from the late Cretaceous. Node dates allow inference of some vicariance via Gondwanan fragmentation, including certain nodes involving southern Africa.},
  language = {en},
  number = {1},
  urldate = {2018-06-05},
  journal = {Systematic Entomology},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3113.2011.00603.x},
  author = {Cranston, Peter S. and Hardy, Nate B. and Morse, Geoffrey E.},
  year = {2011},
  pages = {172-188},
  file = {/home/mpetersen/bib/storage/VQCPXJ3M/Cranston et al. - A dated molecular phylogeny for the Chironomidae (.pdf;/home/mpetersen/bib/storage/3W83DP2J/j.1365-3113.2011.00603.html}
}

@article{Hundsdoerfer2009,
  title = {Towards the Phylogeny of the {{Curculionoidea}} ({{Coleoptera}}): {{Reconstructions}} from Mitochondrial and Nuclear Ribosomal {{DNA}} Sequences},
  volume = {248},
  issn = {0044-5231},
  shorttitle = {Towards the Phylogeny of the {{Curculionoidea}} ({{Coleoptera}})},
  doi = {10.1016/j.jcz.2008.09.001},
  abstract = {With about 60,000 described species, Curculionoidea represent the most species-rich superfamily in the animal kingdom. The immense diversity apparently creates difficulties in the reconstruction of the phylogenetic relationships. Independent morphological studies have led to very different classifications. This study is based on molecular data from two independent molecular sources, the 16S and 18S rDNA. Sensitivity analyses were conducted for the sequence alignment (gap costs were varied) as well as the phylogenetic reconstruction algorithms and some of their parameters. The higher-level relationships reconstructed within Curculionoidea are sensitive to alignment and reconstruction method. Nemonychidae or Oxycorynidae+Belidae were found to be sister to all remaining Curculionoidea in many analyses. The 16S rDNA sequence data (obtained from 157 species) corroborate many tribes and genera as monophyletic. It is observed that the phylogenetic reconstruction of genera with specific genetic features such as polyploidy and parthenogenetic reproduction is difficult in weevils. The curculionid subfamily Lixinae appears monophyletic. A new monophylum consisting of Entiminae, Hyperinae, Cyclominae, Myllorhinus plus possibly the Cossoninae is distinguished and we call it Entiminae s.l. For most other subfamilies and families homoplasy concealed the phylogenetic signal (due to saturation of the 16S sequences), or the species sampling was insufficient, although our sampling scheme was rather broad. We observed that although data from one source can easily be misleading (16S) or hardly informative (18S), the combination of the two independent data sets can result in useful information for such a speciose group of organisms. Our study represents the most thorough analysis of molecular sequence data of the Curculionoidea to date and although the phylogenetic results appear less stable than expected, they reflect the information content of these sequence data realistically and thus contribute to the total knowledge about the phylogeny of the Curculionoidea.},
  number = {1},
  urldate = {2018-06-05},
  journal = {Zoologischer Anzeiger - A Journal of Comparative Zoology},
  url = {http://www.sciencedirect.com/science/article/pii/S0044523108000533},
  author = {Hundsdoerfer, Anna K. and Rheinheimer, Joachim and Wink, Michael},
  month = mar,
  year = {2009},
  keywords = {Molecular phylogeny,16S and 18S rDNA,Bayesian inference,Curculionoidea,POY,Sensitivity analysis},
  pages = {9-31},
  file = {/home/mpetersen/bib/storage/QG5H9VEV/Hundsdoerfer et al. - 2009 - Towards the phylogeny of the Curculionoidea (Coleo.pdf;/home/mpetersen/bib/storage/W252A2GR/S0044523108000533.html}
}

@article{Pohl2005,
  title = {The Phylogeny of {{Strepsiptera}} ({{Hexapoda}})},
  volume = {21},
  issn = {1096-0031},
  doi = {10.1111/j.1096-0031.2005.00074.x},
  language = {en},
  number = {4},
  urldate = {2018-06-05},
  journal = {Cladistics},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2005.00074.x},
  author = {Pohl, Hans and Beutel, Rolf Georg},
  month = oct,
  year = {2005},
  pages = {328-374},
  file = {/home/mpetersen/bib/storage/T83RXMDZ/Pohl and Beutel - 2005 - The phylogeny of Strepsiptera (Hexapoda).pdf;/home/mpetersen/bib/storage/T4T6BDMZ/j.1096-0031.2005.00074.html}
}

@article{Abraham2001,
  title = {Molecular {{Phylogeny}} of the {{Subfamilies}} in {{Geometridae}} ({{Geometroidea}}: {{Lepidoptera}})},
  volume = {20},
  issn = {10557903},
  shorttitle = {Molecular {{Phylogeny}} of the {{Subfamilies}} in {{Geometridae}} ({{Geometroidea}}},
  doi = {10.1006/mpev.2001.0949},
  language = {en},
  number = {1},
  urldate = {2018-06-05},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790301909492},
  author = {Abraham, David and Ryrholm, Nils and Wittzell, H\aa{}kan and Holloway, Jeremy D. and Scoble, Malcolm J. and L\"ofstedt, Christer},
  month = jul,
  year = {2001},
  pages = {65-77},
  file = {/home/mpetersen/bib/storage/8CK6WJBG/Abraham et al. - 2001 - Molecular Phylogeny of the Subfamilies in Geometri.pdf;/home/mpetersen/bib/storage/UYLB9MR7/Abraham et al. - 2001 - Molecular Phylogeny of the Subfamilies in Geometri.pdf}
}

@article{Regier2013,
  title = {A {{Large}}-{{Scale}}, {{Higher}}-{{Level}}, {{Molecular Phylogenetic Study}} of the {{Insect Order Lepidoptera}} ({{Moths}} and {{Butterflies}})},
  volume = {8},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0058568},
  abstract = {Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. Conclusions / Significance Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.},
  language = {en},
  number = {3},
  urldate = {2018-06-05},
  journal = {PLOS ONE},
  url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058568},
  author = {Regier, Jerome C. and Mitter, Charles and Zwick, Andreas and Bazinet, Adam L. and Cummings, Michael P. and Kawahara, Akito Y. and Sohn, Jae-Cheon and Zwickl, Derrick J. and Cho, Soowon and Davis, Donald R. and Baixeras, Joaquin and Brown, John and Parr, Cynthia and Weller, Susan and Lees, David C. and Mitter, Kim T.},
  year = {12-Mar-2013},
  keywords = {Phylogenetics,Taxonomy,Sequence assembly tools,Animal phylogenetics,Phylogenetic analysis,Sequence alignment,Moths and butterflies,Paleogenetics},
  pages = {e58568},
  file = {/home/mpetersen/bib/storage/3ZIFARKV/Regier et al. - 2013 - A Large-Scale, Higher-Level, Molecular Phylogeneti.pdf;/home/mpetersen/bib/storage/K4TPIGXT/article.html}
}

@article{Miller2018,
  title = {High-Quality Genome Assemblies of 15 {{Drosophila}} Species Generated Using {{Nanopore}} Sequencing},
  doi = {10.1101/267393},
  abstract = {The
            
            genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species,
            
            , many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million of years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present high-quality genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (
            
            ,
            
            ,
            
            ,
            
            ,
            
            ,
            
            ,
            
            ,
            
            ,
            
            , and
            
            ), as well as five additional species that also had previously reported assemblies (
            
            ,
            
            ,
            
            ,
            
            , and
            
            ). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close nearly 60\% of gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately \$1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.},
  urldate = {2018-06-19},
  url = {http://biorxiv.org/lookup/doi/10.1101/267393},
  author = {Miller, Danny E. and Staber, Cynthia and Zeitlinger, Julia and Hawley, R. Scott},
  month = jun,
  year = {2018}
}

@article{Reinhold2002,
  title = {Energetically Costly Behaviour and the Evolution of Resting Metabolic Rate in Insects},
  volume = {13},
  issn = {0269-8463, 1365-2435},
  doi = {10.1046/j.1365-2435.1999.00300.x},
  language = {en},
  number = {2},
  urldate = {2018-06-19},
  journal = {Functional Ecology},
  url = {http://doi.wiley.com/10.1046/j.1365-2435.1999.00300.x},
  author = {Reinhold, K.},
  year = {2002},
  pages = {217-224}
}

@article{Speakman2005,
  title = {Body Size, Energy Metabolism and Lifespan},
  volume = {208},
  issn = {0022-0949, 1477-9145},
  doi = {10.1242/jeb.01556},
  language = {en},
  number = {9},
  urldate = {2018-06-19},
  journal = {Journal of Experimental Biology},
  url = {http://jeb.biologists.org/cgi/doi/10.1242/jeb.01556},
  author = {Speakman, J. R.},
  month = may,
  year = {2005},
  pages = {1717-1730}
}

@article{Alekseeva2001,
  title = {Standard {{Metabolism}} and {{Macrotaxonomy}} of {{Crustaceans}}},
  volume = {28},
  issn = {1062-3590, 1608-3059},
  doi = {10.1023/A:1009415032315},
  abstract = {The influence of temperature and other environmental factors on the rate of oxygen consumption has been studied in adult crustaceans. The allometric relationship between respiration and body weight...},
  language = {en},
  number = {2},
  urldate = {2018-06-19},
  journal = {Biology Bulletin of the Russian Academy of Sciences},
  url = {https://link.springer.com/article/10.1023/A:1009415032315},
  author = {Alekseeva, T. A. and Zotin, A. I.},
  month = mar,
  year = {2001},
  pages = {157-162},
  file = {/home/mpetersen/bib/storage/G8PFBZC8/10.html}
}

@book{Kolbert2014,
  address = {New York},
  edition = {First edition},
  title = {The Sixth Extinction: An Unnatural History},
  isbn = {978-0-8050-9299-8},
  lccn = {QE721.2.E97 K65 2014},
  shorttitle = {The Sixth Extinction},
  publisher = {{Henry Holt and Company}},
  author = {Kolbert, Elizabeth},
  year = {2014},
  keywords = {Environmental disasters,Extinction (Biology),Mass extinctions,SCIENCE / Environmental Science,SCIENCE / Life Sciences / Evolution}
}

@article{Hallmann2017,
  title = {More than 75 Percent Decline over 27 Years in Total Flying Insect Biomass in Protected Areas},
  volume = {12},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0185809},
  abstract = {Global declines in insects have sparked wide interest among scientists, politicians, and the general public. Loss of insect diversity and abundance is expected to provoke cascading effects on food webs and to jeopardize ecosystem services. Our understanding of the extent and underlying causes of this decline is based on the abundance of single species or taxonomic groups only, rather than changes in insect biomass which is more relevant for ecological functioning. Here, we used a standardized protocol to measure total insect biomass using Malaise traps, deployed over 27 years in 63 nature protection areas in Germany (96 unique location-year combinations) to infer on the status and trend of local entomofauna. Our analysis estimates a seasonal decline of 76\%, and mid-summer decline of 82\% in flying insect biomass over the 27 years of study. We show that this decline is apparent regardless of habitat type, while changes in weather, land use, and habitat characteristics cannot explain this overall decline. This yet unrecognized loss of insect biomass must be taken into account in evaluating declines in abundance of species depending on insects as a food source, and ecosystem functioning in the European landscape.},
  language = {en},
  number = {10},
  urldate = {2018-06-22},
  journal = {PLOS ONE},
  url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185809},
  author = {Hallmann, Caspar A. and Sorg, Martin and Jongejans, Eelke and Siepel, Henk and Hofland, Nick and Schwan, Heinz and Stenmans, Werner and M\"uller, Andreas and Sumser, Hubert and H\"orren, Thomas and Goulson, Dave and de Kroon, Hans},
  year = {18-Oct-2017},
  keywords = {Insects,Biomass (ecology),Conservation science,Grasslands,Herbs,Land use,Seasons,Species diversity},
  pages = {e0185809},
  file = {/home/mpetersen/bib/storage/SU6CKKT2/Hallmann et al. - 2017 - More than 75 percent decline over 27 years in tota.pdf;/home/mpetersen/bib/storage/FX4S4QIJ/article.html}
}

@article{Newbold2016,
  title = {Has Land Use Pushed Terrestrial Biodiversity beyond the Planetary Boundary? {{A}} Global Assessment},
  volume = {353},
  copyright = {Copyright \textcopyright{} 2016, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  shorttitle = {Has Land Use Pushed Terrestrial Biodiversity beyond the Planetary Boundary?},
  doi = {10.1126/science.aaf2201},
  abstract = {Crossing ``safe'' limits for biodiversity loss
The planetary boundaries framework attempts to set limits for biodiversity loss within which ecological function is relatively unaffected. Newbold et al. present a quantitative global analysis of the extent to which the proposed planetary boundary has been crossed (see the Perspective by Oliver). Using over 2 million records for nearly 40,000 terrestrial species, they modeled the response of biodiversity to land use and related pressures and then estimated, at a spatial resolution of {$\sim$}1 km2, the extent and spatial patterns of changes in local biodiversity. Across 65\% of the terrestrial surface, land use and related pressures have caused biotic intactness to decline beyond 10\%, the proposed ``safe'' planetary boundary. Changes have been most pronounced in grassland biomes and biodiversity hotspots.
Science, this issue p. 288; see also p. 220
Land use and related pressures have reduced local terrestrial biodiversity, but it is unclear how the magnitude of change relates to the recently proposed planetary boundary (``safe limit''). We estimate that land use and related pressures have already reduced local biodiversity intactness\textemdash{}the average proportion of natural biodiversity remaining in local ecosystems\textemdash{}beyond its recently proposed planetary boundary across 58.1\% of the world's land surface, where 71.4\% of the human population live. Biodiversity intactness within most biomes (especially grassland biomes), most biodiversity hotspots, and even some wilderness areas is inferred to be beyond the boundary. Such widespread transgression of safe limits suggests that biodiversity loss, if unchecked, will undermine efforts toward long-term sustainable development.
Land use has reduced biosphere intactness below safe limits across 65\% of Earth's terrestrial surface, especially in grasslands.
Land use has reduced biosphere intactness below safe limits across 65\% of Earth's terrestrial surface, especially in grasslands.},
  language = {en},
  number = {6296},
  urldate = {2018-06-22},
  journal = {Science},
  url = {http://science.sciencemag.org/content/353/6296/288},
  author = {Newbold, Tim and Hudson, Lawrence N. and Arnell, Andrew P. and Contu, Sara and Palma, Adriana De and Ferrier, Simon and Hill, Samantha L. L. and Hoskins, Andrew J. and Lysenko, Igor and Phillips, Helen R. P. and Burton, Victoria J. and Chng, Charlotte W. T. and Emerson, Susan and Gao, Di and {Pask-Hale}, Gwilym and Hutton, Jon and Jung, Martin and {Sanchez-Ortiz}, Katia and Simmons, Benno I. and Whitmee, Sarah and Zhang, Hanbin and Scharlemann, J\"orn P. W. and Purvis, Andy},
  month = jul,
  year = {2016},
  pages = {288-291},
  file = {/home/mpetersen/bib/storage/PDJZHVZB/288.html},
  pmid = {27418509}
}

@article{Kusmanoff2017,
  title = {Decline of `Biodiversity' in Conservation Policy Discourse in {{Australia}}},
  volume = {77},
  issn = {1462-9011},
  doi = {10.1016/j.envsci.2017.08.016},
  abstract = {Market-based instruments along with conceptualizing the environment as a collection of `ecosystem services' has become increasingly common within environmental and conservation policy. This kind of thinking is also increasingly prominent in the public discourse surrounding environment and conservation policy, particularly in the context of communicating the importance of policy measures. Language used in public discourse can have a powerful influence on how people engage with policy issues, and changes within the biodiversity and conservation discourse may have consequences for public engagement in conservation. We explored how these factors are changing with time by documenting the use of the terms `bio' and the prevalence of economic language in the text of 3553 media releases between 2003 and 2014 from the Australian Government environment portfolio, and 1064 media releases from the Australian Conservation Foundation (ACF). Results show that in the last decade, the term `biodiversity' has become less prevalent whilst economic language has increased in both Australian Government and ACF communication. A further content analysis in a subsample of 745 media releases explored the prevalence of ecosystem services framing, results indicating that it has become a mainstream concept. While this may reflect a strategic response by these agencies to better engage with both the general public and decision makers within what is an increasingly dominant neoliberal paradigm, we argue it may also have unintended (possibly adverse) impacts on how people think about and engage with biodiversity conservation.},
  urldate = {2018-06-22},
  journal = {Environmental Science \& Policy},
  url = {http://www.sciencedirect.com/science/article/pii/S1462901116309510},
  author = {Kusmanoff, Alexander M. and Fidler, Fiona and Gordon, Ascelin and Bekessy, Sarah A.},
  month = nov,
  year = {2017},
  keywords = {Biodiversity,Discourse,Environment policy,Framing,Public policy},
  pages = {160-165},
  file = {/home/mpetersen/bib/storage/4MZDW4QK/Kusmanoff et al. - 2017 - Decline of ‘biodiversity’ in conservation policy d.pdf;/home/mpetersen/bib/storage/WLUN5935/S1462901116309510.html}
}

@misc{Puntaru2017,
  title = {The Politics of Biodiversity Conservation},
  abstract = {As biodiversity conservation projects have increased significantly in recent decades aiming to protect the environment from degradation, the trend has spread unevenly across the globe, with some re\ldots{}},
  language = {en},
  urldate = {2018-06-22},
  journal = {Cristina Puntaru},
  url = {https://cristinapuntaru.wordpress.com/2017/04/28/the-politics-of-biodiversity-conservation/},
  author = {Puntaru, Cristina},
  month = apr,
  year = {2017},
  file = {/home/mpetersen/bib/storage/SH93RW54/the-politics-of-biodiversity-conservation.html}
}

@article{Ceballos2017,
  title = {Biological Annihilation via the Ongoing Sixth Mass Extinction Signaled by Vertebrate Population Losses and Declines},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1704949114},
  language = {en},
  urldate = {2018-06-23},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1704949114},
  author = {Ceballos, Gerardo and Ehrlich, Paul R. and Dirzo, Rodolfo},
  month = jul,
  year = {2017},
  pages = {201704949}
}

@article{Makalowski2001,
  title = {The Human Genome Structure and Organization},
  volume = {48},
  issn = {0001-527X},
  abstract = {Genetic information of human is encoded in two genomes: nuclear and mitochondrial. Both of them reflect molecular evolution of human starting from the beginning of life (about 4.5 billion years ago) until the origin of Homo sapiens species about 100,000 years ago. From this reason human genome contains some features that are common for different groups of organisms and some features that are unique for Homo sapiens. 3.2 x 10(9) base pairs of human nuclear genome are packed into 23 chromosomes of different size. The smallest chromosome - 21st contains 5 x 10(7) base pairs while the biggest one -1st contains 2.63 x 10(8) base pairs. Despite the fact that the nucleotide sequence of all chromosomes is established, the organisation of nuclear genome put still questions: for example: the exact number of genes encoded by the human genome is still unknown giving estimations from 30 to 150 thousand genes. Coding sequences represent a few percent of human nuclear genome. The majority of the genome is represented by repetitiVe sequences (about 50\%) and noncoding unique sequences. This part of the genome is frequently wrongly called "junk DNA". The distribution of genes on chromosomes is irregular, DNA fragments containing low percentage of GC pairs code lower number of genes than the fragments of high percentage of GC pairs.},
  language = {eng},
  number = {3},
  journal = {Acta Biochimica Polonica},
  author = {Maka\l{}owski, W.},
  year = {2001},
  keywords = {Animals,Humans,Phylogeny,Genome,Nucleic Acid,Multigene Family,Gene Duplication,Genome; Human,Repetitive Sequences; Nucleic Acid,Exons,Gene Order,Retroelements,Repetitive Sequences,Human},
  pages = {587-598},
  pmid = {11833767}
}

@incollection{Seuanez1979,
  address = {Berlin, Heidelberg},
  title = {Composition of the {{Human Genome}}},
  isbn = {978-3-540-09303-9 978-3-642-67260-6},
  language = {en},
  urldate = {2018-06-23},
  booktitle = {The {{Phylogeny}} of {{Human Chromosomes}}},
  publisher = {{Springer Berlin Heidelberg}},
  url = {http://www.springerlink.com/index/10.1007/978-3-642-67260-6_9},
  author = {Seu\'anez, H\'ector N.},
  collaborator = {Seu\'anez, H\'ector N.},
  year = {1979},
  pages = {87-94},
  doi = {10.1007/978-3-642-67260-6_9}
}

@article{Gregory2004,
  title = {Macroevolution, Hierarchy Theory, and the {{C}}-Value Enigma},
  volume = {30},
  issn = {0094-8373, 1938-5331},
  doi = {10.1666/0094-8373(2004)030<0179:MHTATC>2.0.CO;2},
  language = {en},
  number = {2},
  urldate = {2018-06-26},
  journal = {Paleobiology},
  url = {http://www.bioone.org/doi/abs/10.1666/0094-8373\%282004\%29030\%3C0179\%3AMHTATC\%3E2.0.CO\%3B2},
  author = {Gregory, T. Ryan},
  month = jun,
  year = {2004},
  pages = {179-202},
  file = {/home/mpetersen/bib/storage/EFEAUAAE/Gregory - 2004 - Macroevolution, hierarchy theory, and the C-value .pdf}
}

@article{Parfrey2008,
  title = {The Dynamic Nature of Eukaryotic Genomes},
  volume = {25},
  issn = {1537-1719},
  doi = {10.1093/molbev/msn032},
  abstract = {Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in the life cycle of some members of the "radiolaria," ploidy increases from haploid (N) to approximately 1,000N, whereas intrapopulation variability of the enteric parasite Entamoeba ranges from 4N to 40N. Variation has also been found within our own species, with substantial differences in both gene content and chromosome lengths between individuals. Data on the dynamic nature of genomes shift the perception of the genome from being fixed and characteristic of a species (typological) to plastic due to variation within and between species.},
  language = {eng},
  number = {4},
  journal = {Molecular Biology and Evolution},
  author = {Parfrey, Laura Wegener and Lahr, Daniel J. G. and Katz, Laura A.},
  month = apr,
  year = {2008},
  keywords = {Animals,DNA,Eukaryotic Cells,Genome,Genetic Variation,Species Specificity,Cell Nucleus},
  pages = {787-794},
  pmid = {18258610},
  pmcid = {PMC2933061}
}

@article{Wielgoss2011,
  title = {Mutation {{Rate Inferred From Synonymous Substitutions}} in a {{Long}}-{{Term Evolution Experiment With Escherichia}} Coli},
  volume = {1},
  issn = {2160-1836},
  doi = {10.1534/g3.111.000406},
  abstract = {The quantification of spontaneous mutation rates is crucial for a mechanistic understanding of the evolutionary process. In bacteria, traditional estimates using experimental or comparative genetic methods are prone to statistical uncertainty and consequently estimates vary by over one order of magnitude. With the advent of next-generation sequencing, more accurate estimates are now possible. We sequenced 19 Escherichia coli genomes from a 40,000-generation evolution experiment and directly inferred the point-mutation rate based on the accumulation of synonymous substitutions. The resulting estimate was 8.9 \texttimes{} 10(-11) per base-pair per generation, and there was a significant bias toward increased AT-content. We also compared our results with published genome sequence datasets for other bacterial evolution experiments. Given the power of our approach, our estimate represents the most accurate measure of bacterial base-substitution rates available to date.},
  language = {eng},
  number = {3},
  journal = {G3 (Bethesda, Md.)},
  author = {Wielgoss, S\'ebastien and Barrick, Jeffrey E. and Tenaillon, Olivier and Cruveiller, St\'ephane and {Chane-Woon-Ming}, B\'eatrice and M\'edigue, Claudine and Lenski, Richard E. and Schneider, Dominique},
  month = aug,
  year = {2011},
  pages = {183-186},
  file = {/home/mpetersen/bib/storage/JU7D3NC9/Wielgoss et al. - 2011 - Mutation Rate Inferred From Synonymous Substitutio.pdf},
  pmid = {22207905},
  pmcid = {PMC3246271}
}

@article{Gregory2007,
  title = {Coincidence, Coevolution, or Causation? {{DNA}} Content, Cellsize, and the {{C}}-Value Enigma},
  volume = {76},
  issn = {14647931},
  shorttitle = {Coincidence, Coevolution, or Causation?},
  doi = {10.1111/j.1469-185X.2000.tb00059.x},
  language = {en},
  number = {1},
  urldate = {2018-06-26},
  journal = {Biological Reviews},
  url = {http://doi.wiley.com/10.1111/j.1469-185X.2000.tb00059.x},
  author = {Gregory, T. Ryan},
  month = jan,
  year = {2007},
  pages = {65-101}
}

@article{Grime1983,
  title = {Prediction of Weed and Crop Response to Climate Based upon Measurements of Nuclear {{DNA}} Content},
  volume = {4},
  journal = {Aspects of Applied Biology},
  author = {Grime, JP},
  year = {1983},
  pages = {87-98}
}

@article{Horner1983,
  title = {C Value and Cell Volume: Their Significance in the Evolution and Development of Amphibians},
  volume = {63},
  journal = {Journal of Cell Science},
  url = {http://jcs.biologists.org/content/63/1/135.long},
  author = {Horner, AH and Macgregor, Herbert},
  month = oct,
  year = {1983},
  pages = {135-46}
}

@article{Olmo1982,
  title = {Relationships between {{DNA}} Content and Cell Morphometric Parameters in Reptiles},
  volume = {26},
  issn = {0391-7258},
  abstract = {The relationships between the genome size and various cellular morphometric parameters have been, studied in 38 reptilian species. The nuclear volume, the cell volume and the cell surface area show a direct, linear and statistically significant correlation with the nuclear DNA content; the cell surface/cell volume ratio tends to decrease as DNA increases. The results are similar to those previously observed in Amphibia, which suggests, that at least in poikilothermic vertebrates, the correlations between DNA amounts and cell sizes are controlled by substantially similar mechanisms. A comparison of the average variations of the various morphometric parameters among each other and with the average variation of the genome size suggests that these parameters are not regulated all in the same way.},
  language = {eng},
  number = {1},
  journal = {Basic and Applied Histochemistry},
  author = {Olmo, E. and Odierna, G.},
  year = {1982},
  keywords = {Animals,DNA,Genes,Cell Nucleus,Cell Membrane,Erythrocytes,Reptiles},
  pages = {27-34},
  pmid = {7082266}
}

@article{Gregory2000,
  title = {Nucleotypic Effects without Nuclei: {{Genome}} Size and Erythrocyte Size in Mammals},
  volume = {43},
  issn = {0831-2796, 1480-3321},
  shorttitle = {Nucleotypic Effects without Nuclei},
  doi = {10.1139/g00-069},
  language = {en},
  number = {5},
  urldate = {2018-06-26},
  journal = {Genome},
  url = {http://www.nrcresearchpress.com/doi/10.1139/g00-069},
  author = {Gregory, T Ryan},
  month = oct,
  year = {2000},
  pages = {895-901}
}

@article{Vinogradov1997,
  title = {Nucleotypic {{Effect}} in {{Homeotherms}}: {{Body}}-{{Mass Independent Resting Metabolic Rate}} of {{Passerine Birds}} Is {{Related}} to {{Genome Size}}},
  volume = {51},
  issn = {00143820},
  shorttitle = {{{NUCLEOTYPIC EFFECT IN HOMEOTHERMS}}},
  doi = {10.1111/j.1558-5646.1997.tb02403.x},
  language = {en},
  number = {1},
  urldate = {2018-06-26},
  journal = {Evolution},
  url = {http://doi.wiley.com/10.1111/j.1558-5646.1997.tb02403.x},
  author = {Vinogradov, Alexander E.},
  month = feb,
  year = {1997},
  pages = {220-225}
}

@article{Lisch2009,
  title = {Epigenetic {{Regulation}} of {{Transposable Elements}} in {{Plants}}},
  volume = {60},
  issn = {1543-5008, 1545-2123},
  doi = {10.1146/annurev.arplant.59.032607.092744},
  language = {en},
  number = {1},
  urldate = {2018-06-27},
  journal = {Annual Review of Plant Biology},
  url = {http://www.annualreviews.org/doi/10.1146/annurev.arplant.59.032607.092744},
  author = {Lisch, Damon},
  month = jun,
  year = {2009},
  pages = {43-66}
}

@article{Kazazian1988,
  title = {Haemophilia {{A}} Resulting from de Novo Insertion of {{L1}} Sequences Represents a Novel Mechanism for Mutation in Man},
  volume = {332},
  copyright = {1988 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/332164a0},
  abstract = {L1 sequences are a human-specific family of long, interspersed, repetitive elements, present as {$\sim$}105 copies dispersed throughout the genome1. The full-length L1 sequence is 6.1 kilobases, but the majority of L1 elements are truncated at the 5' end, resulting in a fivefold higher copy number of 3' sequences1. The nucleotide sequence of L1 elements includes an A-rich 3' end and two long open reading frames (orf-1 and orf-2), the second of which encodes a potential polypeptide having sequence homology with the reverse transcriptases1–4. This structure suggests that L1 elements represent a class of non-viral retrotransposons1,2. A number of L1 complementary DNAs, including a nearly full-length element, have been isolated from an undifferentiated teratocarcinoma cell line5. We now report insertions of L1 elements into exon 14 of the factor VIII gene in two of 240 unrelated patients with haemophilia A. Both of these insertions (3.8 and 2.3 kilobases respectively) contain 3' portions of the L1 sequence, including the poly (A) tract, and create target site duplications of at least 12 and 13 nucleotides of the factor VIII gene. In addition, their 3'-trailer sequences following orf-2 are nearly identical to the consensus sequence of L1 cDNAs (ref. 6). These results indicate that certain L1 sequences in man can be dispersed, presumably by an RNA intermediate, and cause disease by insertional mutation.},
  language = {en},
  number = {6160},
  urldate = {2018-06-27},
  journal = {Nature},
  url = {https://www.nature.com/articles/332164a0},
  author = {Kazazian, Haig H. and Wong, Corinne and Youssoufian, Hagop and Scott, Alan F. and Phillips, Deborah G. and Antonarakis, Stylianos E.},
  month = mar,
  year = {1988},
  pages = {164-166},
  file = {/home/mpetersen/bib/storage/9DEG3KDB/332164a0.html}
}

@article{Aminetzach2005,
  title = {Pesticide {{Resistance}} via {{Transposition}}-{{Mediated Adaptive Gene Truncation}} in {{Drosophila}}},
  volume = {309},
  copyright = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1112699},
  abstract = {To study adaptation, it is essential to identify multiple adaptive mutations and to characterize their molecular, phenotypic, selective, and ecological consequences. Here we describe a genomic screen for adaptive insertions of transposable elements in Drosophila. Using a pilot application of this screen, we have identified an adaptive transposable element insertion, which truncates a gene and apparently generates a functional protein in the process. The insertion of this transposable element confers increased resistance to an organophosphate pesticide and has spread in D. melanogaster recently.
A transposable element that confers resistance to organophosphate insecticides evolved rapidly through the world's population of fruit flies in the last 250 years.
A transposable element that confers resistance to organophosphate insecticides evolved rapidly through the world's population of fruit flies in the last 250 years.},
  language = {en},
  number = {5735},
  urldate = {2018-06-27},
  journal = {Science},
  url = {http://science.sciencemag.org/content/309/5735/764},
  author = {Aminetzach, Yael T. and Macpherson, J. Michael and Petrov, Dmitri A.},
  month = jul,
  year = {2005},
  pages = {764-767},
  file = {/home/mpetersen/bib/storage/F3A7TKC8/764.html},
  pmid = {16051794}
}

@article{Daborn2002,
  title = {A {{Single P450 Allele Associated}} with {{Insecticide Resistance}} in {{Drosophila}}},
  volume = {297},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1074170},
  abstract = {Insecticide resistance is one of the most widespread genetic changes caused by human activity, but we still understand little about the origins and spread of resistant alleles in global populations of insects. Here, via microarray analysis of all P450s in Drosophila melanogaster, we show that DDT-R, a gene conferring resistance to DDT, is associated with overtranscription of a single cytochrome P450 gene, Cyp6g1. Transgenic analysis ofCyp6g1 shows that overtranscription of this gene alone is both necessary and sufficient for resistance. Resistance and up-regulation in Drosophila populations are associated with a single Cyp6g1 allele that has spread globally. This allele is characterized by the insertion of an Accord transposable element into the 5{${'}$} end of the Cyp6g1 gene.},
  language = {en},
  number = {5590},
  urldate = {2018-06-27},
  journal = {Science},
  url = {http://science.sciencemag.org/content/297/5590/2253},
  author = {Daborn, P. J. and Yen, J. L. and Bogwitz, M. R. and Goff, G. Le and Feil, E. and Jeffers, S. and Tijet, N. and Perry, T. and Heckel, D. and Batterham, P. and Feyereisen, R. and Wilson, T. G. and {ffrench-Constant}, R. H.},
  month = sep,
  year = {2002},
  pages = {2253-2256},
  file = {/home/mpetersen/bib/storage/85DM3LFZ/2253.html},
  pmid = {12351787}
}

@article{Mathiopoulos1998,
  title = {Cloning of Inversion Breakpoints in the {{Anopheles}} Gambiae Complex Traces a Transposable Element at the Inversion Junction},
  volume = {95},
  copyright = {Copyright \textcopyright{} 1998, The National Academy of Sciences},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.95.21.12444},
  abstract = {Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd{${'}$} of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd{${'}$} suggests that the inversion may be the result of the transposable element's activity. Characteristics of Odysseus' terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.},
  language = {en},
  number = {21},
  urldate = {2018-06-27},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/95/21/12444},
  author = {Mathiopoulos, Kostas D. and della Torre, Alessandra and Predazzi, Valentina and Petrarca, Vincenzo and Coluzzi, Mario},
  month = oct,
  year = {1998},
  keywords = {Anopheles arabiensis/malaria/sub-saharan Africa/chromosomal rearrangements},
  pages = {12444-12449},
  file = {/home/mpetersen/bib/storage/JZY3JEME/Mathiopoulos et al. - 1998 - Cloning of inversion breakpoints in the Anopheles .pdf;/home/mpetersen/bib/storage/9QTGMZDP/12444.html},
  pmid = {9770505}
}

@article{Remnant2013,
  title = {Gene Duplication in the Major Insecticide Target Site, {{Rdl}}, in {{Drosophila}} Melanogaster},
  volume = {110},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1311341110},
  abstract = {The Resistance to Dieldrin gene, Rdl, encodes a GABA-gated chloride channel subunit that is targeted by cyclodiene and phenylpyrazole insecticides. The gene was first characterized in Drosophila melanogaster by genetic mapping of resistance to the cyclodiene dieldrin. The 4,000-fold resistance observed was due to a single amino acid replacement, Ala301 to Ser. The equivalent change was subsequently identified in Rdl orthologs of a large range of resistant insect species. Here, we report identification of a duplication at the Rdl locus in D. melanogaster. The 113-kb duplication contains one WT copy of Rdl and a second copy with two point mutations: an Ala301 to Ser resistance mutation and Met360 to Ile replacement. Individuals with this duplication exhibit intermediate dieldrin resistance compared with single copy Ser301 homozygotes, reduced temperature sensitivity, and altered RNA editing associated with the resistant allele. Ectopic recombination between Roo transposable elements is involved in generating this genomic rearrangement. The duplication phenotypes were confirmed by construction of a transgenic, artificial duplication integrating the 55.7-kb Rdl locus with a Ser301 change into an Ala301 background. Gene duplications can contribute significantly to the evolution of insecticide resistance, most commonly by increasing the amount of gene product produced. Here however, duplication of the Rdl target site creates permanent heterozygosity, providing unique potential for adaptive mutations to accrue in one copy, without abolishing the endogenous role of an essential gene.},
  language = {en},
  number = {36},
  urldate = {2018-06-27},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/110/36/14705},
  author = {Remnant, Emily J. and Good, Robert T. and Schmidt, Joshua M. and Lumb, Christopher and Robin, Charles and Daborn, Phillip J. and Batterham, Philip},
  month = sep,
  year = {2013},
  pages = {14705-14710},
  file = {/home/mpetersen/bib/storage/DSVDVF4V/Remnant et al. - 2013 - Gene duplication in the major insecticide target s.pdf;/home/mpetersen/bib/storage/Z3RHXWXZ/14705.html},
  pmid = {23959864}
}

@article{Fiston-Lavier2007,
  title = {A Model of Segmental Duplication Formation in {{Drosophila}} Melanogaster},
  volume = {17},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.6208307},
  abstract = {Segmental duplications (SDs) are low-copy repeats of DNA segments that have long been recognized to be involved in genome organization and evolution. But, to date, the mechanism of their formation remains obscure. We propose a model for SD formation that we name ``duplication-dependent strand annealing'' (DDSA). This model is a variant of the synthesis-dependent strand annealing (SDSA) model\textemdash{}a double-strand break (DSB) homologous repair model. DSB repair in Drosophila melanogaster genome usually occurs primarily through homologous repair, more preferentially through the SDSA model. The DDSA model predicts that after a DSB, the search for an ectopic homologous region\textemdash{}here a repeat\textemdash{}initiates the repair. As expected by the model, the analysis of SDs detected by a computational analysis of the D. melanogaster genome indicates a high enrichment in transposable elements at SD ends. It shows moreover a preferential location of SDs in heterochromatic regions. The model has the advantage of also predicting specific traces left during synthesis. The observed traces support the DDSA model as one model of formation of SDs in D. melanogaster genome. The analysis of these DDSA signatures suggests moreover a sequestration of the dissociated strand in the repair complex.},
  language = {en},
  number = {10},
  urldate = {2018-06-27},
  journal = {Genome Research},
  url = {http://genome.cshlp.org/content/17/10/1458},
  author = {{Fiston-Lavier}, Anna-Sophie and Anxolabehere, Dominique and Quesneville, Hadi},
  month = jan,
  year = {2007},
  pages = {1458-1470},
  file = {/home/mpetersen/bib/storage/HN8P7PNW/Fiston-Lavier et al. - 2007 - A model of segmental duplication formation in Dros.pdf;/home/mpetersen/bib/storage/QCQF7R8N/1458.html},
  pmid = {17726166}
}

@article{Lim1988,
  title = {Intrachromosomal Rearrangements Mediated by Hobo Transposons in {{Drosophila}} Melanogaster},
  volume = {85},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.85.23.9153},
  abstract = {The recurring intrachromosomal rearrangements observed in an unstable X chromosome, designated Uc, of Drosophila melanogaster are shown to be mediated by hobo transposable elements. Each of 29 chromosome rearrangement breakpoints in 16 gross aberrations detected in the Uc-derived X chromosomes had a hobo element. In one particular unstable X chromosome line selected for detailed studies, a hobo element was found in each of the five hot spots for rearrangements. Furthermore, hobo elements at deletion hot spots were found to lie in the same orientation, whereas those hobo elements at inversion hot spots were in the opposite orientation. The restriction maps of two phage lambda clones containing rearrangement breakpoints indicated that a hobo element was inserted exactly at the breakpoints. Pairing of hobo elements in the same chromosome followed by recombination between the paired hobo elements is suggested as the explanation for the intrachromosomal aberrations observed in the Uc X chromosomes. A clear qualitative difference among the hobo elements in their ability to participate in rearrangement formation was noted. It was also found that each of the 11 recessive lethal mutations mapped in the 6F1-2 doublet had a hobo element in the doublet, whereas none of the 16 independent revertants of the mutation had a hobo element in the site. This observation indicates that hobo movement is responsible for production and subsequent instability of recessive lethal mutations in the 6F region of the Uc X chromosomes.},
  language = {en},
  number = {23},
  urldate = {2018-06-27},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/85/23/9153},
  author = {Lim, J. K.},
  month = dec,
  year = {1988},
  pages = {9153-9157},
  file = {/home/mpetersen/bib/storage/E76GAYN2/Lim - 1988 - Intrachromosomal rearrangements mediated by hobo t.pdf;/home/mpetersen/bib/storage/RLUDC8DE/9153.html},
  pmid = {2848256}
}

@article{Warnefors2010,
  title = {Transposable {{Elements}}: {{Insertion Pattern}} and {{Impact}} on {{Gene Expression Evolution}} in {{Hominids}}},
  volume = {27},
  issn = {0737-4038},
  shorttitle = {Transposable {{Elements}}},
  doi = {10.1093/molbev/msq084},
  abstract = {Abstract.  Transposable elements (TEs) can affect the regulation of nearby genes through several mechanisms. Here, we examine to what extent recent TE insertion},
  language = {en},
  number = {8},
  urldate = {2018-06-27},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article/27/8/1955/989395},
  author = {Warnefors, Maria and Pereira, Vini and {Eyre-Walker}, Adam},
  month = aug,
  year = {2010},
  pages = {1955-1962},
  file = {/home/mpetersen/bib/storage/SZX49KD9/Warnefors et al. - 2010 - Transposable Elements Insertion Pattern and Impac.pdf;/home/mpetersen/bib/storage/RMRAZCYG/989395.html}
}

@incollection{Bernstein1987,
  series = {Molecular {{Genetics}} of {{Development}}},
  title = {The {{Molecular Basis}} of the {{Evolution}} of {{Sex}}},
  volume = {24},
  abstract = {Traditionally, sexual reproduction has been explained as an adaptation for producing genetic variation through allelic recombination. A recent informational approach has led to the view that the two fundamental aspects of sex\textemdash{}recombination and outcrossing\textemdash{}are adaptive responses to the two major sources of noise in transmitting genetic information\textemdash{}DNA damage and replication errors. This view is referred to as ``the repair hypothesis.'' In the repair hypothesis, recombination is a process for repairing damaged DNA. In dealing with damage, recombination produces a form of informational noise, allelic recombination, as a by-product. Recombinational repair is the only repair process known that can overcome double-strand damages in DNA, and such damages are common in nature. Recombinational repair is prevalent from the simplest to the most complex organisms. It is effective against many different types of DNA-damaging agents and, in particular, is highly efficient in overcoming double-strand damages.},
  urldate = {2018-06-27},
  booktitle = {Advances in {{Genetics}}},
  publisher = {{Academic Press}},
  url = {http://www.sciencedirect.com/science/article/pii/S0065266008600127},
  author = {Bernstein, H. and Hopf, F. A. and Michod, R. E.},
  editor = {Scandalios, John G. and Caspari, E. W.},
  month = jan,
  year = {1987},
  pages = {323-370},
  file = {/home/mpetersen/bib/storage/7UZDRZSJ/S0065266008600127.html},
  doi = {10.1016/S0065-2660(08)60012-7}
}

@article{Altenberg2011,
  title = {An {{Evolutionary Reduction Principle}} for {{Mutation Rates}} at {{Multiple Loci}}},
  volume = {73},
  issn = {0092-8240, 1522-9602},
  doi = {10.1007/s11538-010-9557-9},
  abstract = {A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin (Evolutionary Biology, vol. 14, pp. 61\textendash{}204, 1982) that overcome the weak selection constraints needed for tractability in prior studies of multilocus event models.A multivariate form of the reduction principle is found: reduction results at individual loci combine topologically to produce a surface of mutation rate alterations that are neutral for a new modifier allele. New mutation rates survive if and only if they fall below this surface\textemdash{}a generalization of the hyperplane found by Zhivotovsky et al. (Proc. Natl. Acad. Sci. USA 91, 1079\textendash{}1083, 1994) for a multilocus recombination modifier. Increases in mutation rates at some loci may evolve if compensated for by decreases at other loci. The strength of selection on the modifier scales in proportion to the number of germline cell divisions, and increases with the number of loci affected. Loci that do not make a difference to marginal fitnesses at equilibrium are not subject to the reduction principle, and under fine tuning of mutation rates would be expected to have higher mutation rates than loci in mutation-selection balance.Other results include the nonexistence of `viability analogous, Hardy\textendash{}Weinberg' modifier polymorphisms under multiplicative mutation, and the sufficiency of average transmission rates to encapsulate the effect of modifier polymorphisms on the transmission of loci under selection. A conjecture is offered regarding situations, like recombination in the presence of mutation, that exhibit departures from the reduction principle. Constraints for tractability are: tight linkage of all loci, initial fixation at the modifier locus, and mutation distributions comprising transition probabilities of reversible Markov chains.},
  language = {en},
  number = {6},
  urldate = {2018-06-27},
  journal = {Bulletin of Mathematical Biology},
  url = {https://link.springer.com/article/10.1007/s11538-010-9557-9},
  author = {Altenberg, Lee},
  month = jun,
  year = {2011},
  pages = {1227-1270},
  file = {/home/mpetersen/bib/storage/4U49DVUB/10.html}
}

@article{Zaher2009,
  title = {Fidelity at the Molecular Level: Lessons from Protein Synthesis},
  volume = {136},
  issn = {1097-4172},
  shorttitle = {Fidelity at the Molecular Level},
  doi = {10.1016/j.cell.2009.01.036},
  abstract = {The faithful and rapid translation of genetic information into peptide sequences is an indispensable property of the ribosome. The mechanistic understanding of strategies used by the ribosome to achieve both speed and fidelity during translation results from nearly a half century of biochemical and structural studies. Emerging from these studies is the common theme that the ribosome uses local as well as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon recognition during both tRNA selection and translation termination.},
  language = {eng},
  number = {4},
  journal = {Cell},
  author = {Zaher, Hani S. and Green, Rachel},
  month = feb,
  year = {2009},
  keywords = {Escherichia coli,Codon,RNA; Bacterial,Protein Biosynthesis,Ribosomes,RNA; Transfer},
  pages = {746-762},
  pmid = {19239893},
  pmcid = {PMC3691815}
}

@article{Slotkin2007,
  title = {Transposable Elements and the Epigenetic Regulation of the Genome},
  volume = {8},
  issn = {1471-0056, 1471-0064},
  doi = {10.1038/nrg2072},
  language = {en},
  number = {4},
  urldate = {2018-06-28},
  journal = {Nature Reviews Genetics},
  url = {http://www.nature.com/articles/nrg2072},
  author = {Slotkin, R. Keith and Martienssen, Robert},
  month = apr,
  year = {2007},
  pages = {272-285},
  file = {/home/mpetersen/bib/storage/J8PVSUFU/Slotkin and Martienssen - 2007 - Transposable elements and the epigenetic regulatio.pdf}
}

@article{Vieira1999,
  title = {Wake up of Transposable Elements Following {{Drosophila}} Simulans Worldwide Colonization.},
  volume = {16},
  issn = {0737-4038},
  doi = {10.1093/oxfordjournals.molbev.a026215},
  abstract = {Transposable elements (TEs) make up around 10\%-15\% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as},
  language = {en},
  number = {9},
  urldate = {2018-06-28},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article/16/9/1251/2925525},
  author = {Vieira, C. and Lepetit, D. and Dumont, S. and Bi\'emont, C.},
  month = sep,
  year = {1999},
  pages = {1251-1255},
  file = {/home/mpetersen/bib/storage/L5XN54JU/Vieira et al. - 1999 - Wake up of transposable elements following Drosoph.pdf;/home/mpetersen/bib/storage/BZCPDJYJ/2925525.html}
}

@article{Zilberman2007,
  title = {Genome-Wide Analysis of {{Arabidopsis}} Thaliana {{DNA}} Methylation Uncovers an Interdependence between Methylation and Transcription},
  volume = {39},
  copyright = {2006 Nature Publishing Group},
  issn = {1546-1718},
  doi = {10.1038/ng1929},
  abstract = {Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.},
  language = {en},
  number = {1},
  urldate = {2018-06-28},
  journal = {Nature Genetics},
  url = {https://www.nature.com/articles/ng1929},
  author = {Zilberman, Daniel and Gehring, Mary and Tran, Robert K. and Ballinger, Tracy and Henikoff, Steven},
  month = jan,
  year = {2007},
  pages = {61-69},
  file = {/home/mpetersen/bib/storage/S3FIDWCR/Zilberman et al. - 2007 - Genome-wide analysis of iArabidopsis thalianai.pdf}
}

@article{Siomi2011,
  title = {{{PIWI}}-Interacting Small {{RNAs}}: The Vanguard of Genome Defence},
  volume = {12},
  copyright = {2011 Nature Publishing Group},
  issn = {1471-0080},
  shorttitle = {{{PIWI}}-Interacting Small {{RNAs}}},
  doi = {10.1038/nrm3089},
  abstract = {PIWI-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs that form the piRNA-induced silencing complex (piRISC) in the germ line of many animal species. The piRISC protects the integrity of the genome from invasion by 'genomic parasites' \textemdash{} transposable elements \textemdash{} by silencing them. Owing to their limited expression in gonads and their sequence diversity, piRNAs have been the most mysterious class of small non-coding RNAs regulating RNA silencing. Now, much progress is being made into our understanding of their biogenesis and molecular functions, including the specific subcellular compartmentalization of the piRNA pathway in granular cytoplasmic bodies.},
  language = {en},
  number = {4},
  urldate = {2018-06-28},
  journal = {Nature Reviews Molecular Cell Biology},
  url = {https://www.nature.com/articles/nrm3089},
  author = {Siomi, Mikiko C. and Sato, Kaoru and Pezic, Dubravka and Aravin, Alexei A.},
  month = apr,
  year = {2011},
  pages = {246-258}
}

@article{Zeng2011,
  title = {Structural Insights into {{piRNA}} Recognition by the Human {{PIWI}}-like 1 {{PAZ}} Domain},
  volume = {79},
  copyright = {Copyright \textcopyright{} 2011 Wiley-Liss, Inc.},
  issn = {1097-0134},
  doi = {10.1002/prot.23003},
  language = {en},
  number = {6},
  urldate = {2018-06-28},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.23003},
  author = {Zeng, Lei and Zhang, Qiang and Yan, Kelley and Zhou, Ming-Ming},
  year = {2011},
  keywords = {PAZ,piRNA,PIWI,ssRNA},
  pages = {2004-2009},
  file = {/home/mpetersen/bib/storage/A837FIRA/prot.html}
}

@article{Kofler2012,
  title = {Sequencing of {{Pooled DNA Samples}} ({{Pool}}-{{Seq}}) {{Uncovers Complex Dynamics}} of {{Transposable Element Insertions}} in {{Drosophila}} Melanogaster},
  volume = {8},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1002487},
  language = {en},
  number = {1},
  urldate = {2018-07-01},
  journal = {PLoS Genetics},
  url = {http://dx.plos.org/10.1371/journal.pgen.1002487},
  author = {Kofler, Robert and Betancourt, Andrea J. and Schl\"otterer, Christian},
  editor = {Begun, David J.},
  month = jan,
  year = {2012},
  pages = {e1002487}
}

@article{Schubeler2015,
  title = {Function and Information Content of {{DNA}} Methylation},
  volume = {517},
  doi = {10.1038/nature14192},
  urldate = {2018-07-01},
  journal = {Nature},
  url = {http://www.nature.com/articles/nature14192},
  author = {Sch\"ubeler, Dirk},
  month = jan,
  year = {2015},
  pages = {321-326}
}

@article{Petersen2019a,
  title = {Dynamics of Genome Size Evolution in Insects},
  journal = {In prep.},
  author = {Petersen, Malte and Nottebrock, Gaby and Misof, Bernhard},
  year = {2019}
}

@article{Bertone2016,
  title = {Arthropods of the Great Indoors: Characterizing Diversity inside Urban and Suburban Homes},
  volume = {4},
  issn = {2167-8359},
  shorttitle = {Arthropods of the Great Indoors},
  doi = {10.7717/peerj.1582},
  abstract = {Although humans and arthropods have been living and evolving together for all of our history, we know very little about the arthropods we share our homes with apart from major pest groups. Here we surveyed, for the first time, the complete arthropod fauna of the indoor biome in 50 houses (located in and around Raleigh, North Carolina, USA). We discovered high diversity, with a conservative estimate range of 32\textendash{}211 morphospecies, and 24\textendash{}128 distinct arthropod families per house. The majority of this indoor diversity (73\%) was made up of true flies (Diptera), spiders (Araneae), beetles (Coleoptera), and wasps and kin (Hymenoptera, especially ants: Formicidae). Much of the arthropod diversity within houses did not consist of synanthropic species, but instead included arthropods that were filtered from the surrounding landscape. As such, common pest species were found less frequently than benign species. Some of the most frequently found arthropods in houses, such as gall midges (Cecidomyiidae) and book lice (Liposcelididae), are unfamiliar to the general public despite their ubiquity. These findings present a new understanding of the diversity, prevalence, and distribution of the arthropods in our daily lives. Considering their impact as household pests, disease vectors, generators of allergens, and facilitators of the indoor microbiome, advancing our knowledge of the ecology and evolution of arthropods in homes has major economic and human health implications.},
  language = {en},
  urldate = {2018-07-04},
  journal = {PeerJ},
  url = {https://peerj.com/articles/1582},
  author = {Bertone, Matthew A. and Leong, Misha and Bayless, Keith M. and Malow, Tara L. F. and Dunn, Robert R. and Trautwein, Michelle D.},
  month = jan,
  year = {2016},
  pages = {e1582},
  file = {/home/mpetersen/bib/storage/IYILZ9YM/Bertone et al. - 2016 - Arthropods of the great indoors characterizing di.pdf;/home/mpetersen/bib/storage/ARZ6P6M9/1582.html}
}

@article{Mural2002,
  title = {{A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome}},
  volume = {296},
  issn = {0036-8075},
  doi = {10.1126/science.1069193},
  language = {English (US)},
  number = {5573},
  urldate = {2018-07-05},
  journal = {Science},
  url = {https://mayoclinic.pure.elsevier.com/en/publications/a-comparison-of-whole-genome-shotgun-derived-mouse-chromosome-16-},
  author = {Mural, R. J. and Adams, M. D. and Myers, E. W. and Smith, H. O. and Miklos, G. L. Gabor and Wides, R. and Halpern, A. and Li, P. W. and Sutton, G. G. and Nadeau, J. and Salzberg, S. L. and Holt, R. A. and Kodira, C. D. and Lu, F. and Chen, L. and Deng, Z. and Evangelista, C. C. and Gan, W. and Heiman, T. J. and Li, J. and Li, Z. and Merkulov, G. V. and Milshina, N. V. and Naik, A. K. and Qi, R. and Shue, B. Chris and Wang, A. and Wang, J. and Wang, X. and Yan, X. and Ye, J. and Yooseph, S. and Zhao, Q. and Zheng, L. and Zhu, S. C. and Biddick, K. and Bolanos, R. and Delcher, A. L. and Dew, I. M. and Fasulo, D. and Flanigan, M. J. and Huson, D. H. and Kravitz, S. A. and Miller, J. R. and Mobarry, C. M. and Reinert, K. and Remington, K. A. and Zhang, Q. and Zheng, X. H. and Nusskern, D. R. and Lai, Z. and Lei, Y. and Zhong, W. and Yao, A. and Guan, P. and Ji, R. R. and Gu, Z. and Wang, Z. Y. and Zhong, F. and Xiao, C. and Chiang, C. C. and Yandell, M. and Wortman, J. R. and Amanatides, P. G. and Hladun, S. L. and Pratts, E. C. and Johnson, J. E. and Dodson, K. L. and Woodford, K. J. and Evans, C. A. and Gropman, B. and Rusch, D. B. and Venter, E. and Wang, M. and Smith, T. J. and Houck, J. T. and Tompkins, D. E. and Haynes, C. and Jacob, D. and Chin, S. H. and Allen, D. R. and Dahlke, C. E. and Sanders, R. and Li, K. and Liu, X. and Levitsky, A. A. and Majoros, W. H. and Chen, Q. and Xia, A. C. and Lopez, J. R. and Donnelly, M. T. and Newman, M. H. and Glodek, A. and Kraft, C. L. and Nodell, M. and Ali, F. and An, H. J. and {Baldwin-Pitts}, D. and Beeson, K. Y. and Cai, S. and Carnes, M. and Carver, A. and Caulk, P. M. and Center, A. and Chen, Y. H. and Cheng, M. L. and Coyne, M. D. and Crowder, M. and Danaher, S. and Davenport, L. B. and Desilets, R. and Dietz, S. M. and Doup, L. and Dullaghan, P. and Ferriera, S. and Fosler, C. R. and Gire, H. C. and Gluecksmann, A. and Gocayne, J. D. and Gray, J. and Hart, B. and Haynes, J. and Hoover, J. and Howland, T. and Ibegwam, C. and Jalali, M. and Johns, D. and Kline, L. and Ma, D. S. and MacCawley, S. and Magoon, A. and Mann, F. and May, D. and McIntosh, T. C. and Mehta, S. and Moy, L. and Moy, M. C. and Murphy, B. J. and Murphy, S. D. and Nelson, K. A. and Nuri, Z. and Parker, K. A. and Prudhomme, A. C. and Puri, V. N. and Qureshi, H. and Raley, J. C. and Reardon, M. S. and Regier, M. A. and Rogers, Yu H. C. and Romblad, D. L. and Schutz, J. and Scott, J. L. and Scott, R. and Sitter, C. D. and Smallwood, M. and Sprague, A. C. and Stewart, E. and Strong, R. V. and Suh, E. and Sylvester, K. and Thomas, R. and Tint, N. Ni and Tsonis, C. and Wang, G. and Wang, G. and Williams, M. S. and Williams, S. M. and Windsor, S. M. and Wolfe, K. and Wu, M. M. and Zaveri, J. and Chaturvedi, K. and Gabrielian, A. E. and Ke, Z. and Sun, J. and Subramanian, G. and Venter, J. Craig},
  month = may,
  year = {2002},
  pages = {1661-1671},
  file = {/home/mpetersen/bib/storage/VXSBKEUQ/a-comparison-of-whole-genome-shotgun-derived-mouse-chromosome-16-.html},
  pmid = {12040188}
}

@book{DeMaddalena2008,
  address = {Auckland Park, South Africa},
  title = {Sharks: The Perfect Predators},
  isbn = {978-1-77009-559-5},
  lccn = {QL638.9 .D454 2008},
  shorttitle = {Sharks},
  publisher = {{Jacana Media}},
  author = {De Maddalena, Alessandro and Gabriotti, Vittorio and Heim, Walter},
  year = {2008},
  keywords = {Predatory animals,Sharks},
  note = {OCLC: ocn256666681}
}

@article{Linnell2011,
  title = {Can We Separate the Sinners from the Scapegoats?},
  volume = {14},
  copyright = {\textcopyright{} 2011 The Author. Animal Conservation \textcopyright{} 2011 The Zoological Society of London},
  issn = {1469-1795},
  doi = {10.1111/j.1469-1795.2011.00510.x},
  language = {en},
  number = {6},
  urldate = {2018-07-06},
  journal = {Animal Conservation},
  url = {https://zslpublications.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-1795.2011.00510.x},
  author = {Linnell, J. D. C.},
  year = {2011},
  pages = {602-603},
  file = {/home/mpetersen/bib/storage/654NGC6B/Linnell - Can we separate the sinners from the scapegoats.pdf;/home/mpetersen/bib/storage/9KDYUMQ8/j.1469-1795.2011.00510.html}
}

@article{Packer2005,
  title = {Conservation Biology: {{Lion}} Attacks on Humans in {{Tanzania}}},
  volume = {436},
  copyright = {2005 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {Conservation Biology},
  doi = {10.1038/436927a},
  abstract = {Large carnivores inspire opposition to conservation efforts1,2 owing to their impact on livestock3,4,5 and human safety6,7. Here we analyse the pattern of lion attacks over the past 15 years on humans in Tanzania, which has the largest population of lions in Africa8,9, and find that they have killed more than 563 Tanzanians since 1990 and injured at least 308. Attacks have increased dramatically during this time: they peak at harvest time each year and are most frequent in areas with few prey apart from bush pigs (Potamochoerus larvatus), the most common nocturnal crop pest. Our findings provide an important starting point for devising strategies to reduce the risk to rural Tanzanians of lion attacks.},
  language = {en},
  number = {7053},
  urldate = {2018-07-06},
  journal = {Nature},
  url = {https://www.nature.com/articles/436927a},
  author = {Packer, Craig and Ikanda, Dennis and Kissui, Bernard and Kushnir, Hadas},
  month = aug,
  year = {2005},
  pages = {927-928},
  file = {/home/mpetersen/bib/storage/MMKPVFSM/Packer et al. - 2005 - Conservation biology Lion attacks on humans in Ta.pdf;/home/mpetersen/bib/storage/3QP29QQN/436927a.html}
}

@article{Kasturiratne2008,
  title = {The {{Global Burden}} of {{Snakebite}}: {{A Literature Analysis}} and {{Modelling Based}} on {{Regional Estimates}} of {{Envenoming}} and {{Deaths}}},
  volume = {5},
  issn = {1549-1676},
  shorttitle = {The {{Global Burden}} of {{Snakebite}}},
  doi = {10.1371/journal.pmed.0050218},
  abstract = {Background Envenoming resulting from snakebites is an important public health problem in many tropical and subtropical countries. Few attempts have been made to quantify the burden, and recent estimates all suffer from the lack of an objective and reproducible methodology. In an attempt to provide an accurate, up-to-date estimate of the scale of the global problem, we developed a new method to estimate the disease burden due to snakebites. Methods and Findings The global estimates were based on regional estimates that were, in turn, derived from data available for countries within a defined region. Three main strategies were used to obtain primary data: electronic searching for publications on snakebite, extraction of relevant country-specific mortality data from databases maintained by United Nations organizations, and identification of grey literature by discussion with key informants. Countries were grouped into 21 distinct geographic regions that are as epidemiologically homogenous as possible, in line with the Global Burden of Disease 2005 study (Global Burden Project of the World Bank). Incidence rates for envenoming were extracted from publications and used to estimate the number of envenomings for individual countries; if no data were available for a particular country, the lowest incidence rate within a neighbouring country was used. Where death registration data were reliable, reported deaths from snakebite were used; in other countries, deaths were estimated on the basis of observed mortality rates and the at-risk population. We estimate that, globally, at least 421,000 envenomings and 20,000 deaths occur each year due to snakebite. These figures may be as high as 1,841,000 envenomings and 94,000 deaths. Based on the fact that envenoming occurs in about one in every four snakebites, between 1.2 million and 5.5 million snakebites could occur annually. Conclusions Snakebites cause considerable morbidity and mortality worldwide. The highest burden exists in South Asia, Southeast Asia, and sub-Saharan Africa.},
  language = {en},
  number = {11},
  urldate = {2018-07-06},
  journal = {PLOS Medicine},
  url = {http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0050218},
  author = {Kasturiratne, Anuradhani and Wickremasinghe, A. Rajitha and de Silva, Nilanthi and Gunawardena, N. Kithsiri and Pathmeswaran, Arunasalam and Premaratna, Ranjan and Savioli, Lorenzo and Lalloo, David G. and de Silva, H. Janaka},
  year = {04-Nov-2008},
  keywords = {Africa,Asia,Death rates,Global health,India,Public and occupational health,Snakebite,Snakes},
  pages = {e218},
  file = {/home/mpetersen/bib/storage/GCAJF94L/Kasturiratne et al. - 2008 - The Global Burden of Snakebite A Literature Analy.pdf;/home/mpetersen/bib/storage/UEXDYVKG/article.html}
}

@book{Lamarque2009,
  address = {Rome},
  series = {{{FAO}} Forestry Paper},
  title = {Human-Wildlife Conflict in {{Africa}}: Causes, Consequences and Management Strategies},
  isbn = {978-92-5-106372-9},
  shorttitle = {Human-Wildlife Conflict in {{Africa}}},
  language = {eng},
  number = {157},
  publisher = {{Food and Agriculture Organization of the United Nations}},
  editor = {Lamarque, F.},
  year = {2009},
  file = {/home/mpetersen/bib/storage/PVTPWZHZ/Lamarque - 2009 - Human-wildlife conflict in Africa causes, consequ.pdf},
  note = {OCLC: 837661033}
}

@techreport{WHO2017,
  type = {Fact Sheet},
  title = {Vector-Borne Diseases},
  urldate = {2018-07-06},
  institution = {{WHO}},
  url = {http://www.who.int/en/news-room/fact-sheets/detail/vector-borne-diseases},
  author = {{WHO}},
  year = {2017}
}

@article{Oliveira2014,
  title = {Crop Losses and the Economic Impact of Insect Pests on {{Brazilian}} Agriculture},
  volume = {56},
  issn = {0261-2194},
  doi = {10.1016/j.cropro.2013.10.022},
  abstract = {Among the various sectors of the Brazilian economy, agriculture plays a prominent role, generating jobs and income for the country. However, the agricultural sector faces systematic annual losses due to pests and diseases. The damage caused by insect pests is one of the primary factors leading to the reduced production of major crops. The study presented here estimates the production losses of major crops caused by insects and the economic impact related to the direct damage caused by insects, to the purchase of insecticides, and to medical treatment for humans poisoned by insecticides. The results indicate that insect pests cause an average annual loss of 7.7\% in production in Brazil, which is a reduction of approximately 25~million~tons of food, fiber, and biofuels. The total annual economic losses reach approximately US\$ 17.7 billion. These results are important for government policies in the agricultural sector, as well as indicate the need for updated data regarding the losses caused by insects in Brazil and the need for systematic monitoring of these losses.},
  urldate = {2018-07-06},
  journal = {Crop Protection},
  url = {http://www.sciencedirect.com/science/article/pii/S026121941300269X},
  author = {Oliveira, C. M. and Auad, A. M. and Mendes, S. M. and Frizzas, M. R.},
  month = feb,
  year = {2014},
  keywords = {Brazil,Brazilian agribusiness,Damages,Estimated losses,Insecta,Social and environmental cost},
  pages = {50-54},
  file = {/home/mpetersen/bib/storage/P3XXUBCJ/S026121941300269X.html}
}

@article{Vogel2017,
  title = {Where Have All the Insects Gone?},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.aal1160},
  urldate = {2018-07-06},
  journal = {Science},
  url = {http://www.sciencemag.org/news/2017/05/where-have-all-insects-gone},
  author = {Vogel, Gretchen},
  month = may,
  year = {2017}
}

@article{Behjati2013,
  title = {What Is next Generation Sequencing?},
  volume = {98},
  issn = {1743-0585},
  doi = {10.1136/archdischild-2013-304340},
  abstract = {Next generation sequencing (NGS), massively parallel or deep sequencing are related terms that describe a DNA sequencing technology which has revolutionised genomic research. Using NGS an entire human genome can be sequenced within a single day. In contrast, the previous Sanger sequencing technology, used to decipher the human genome, required over a decade to deliver the final draft. Although in genome research NGS has mostly superseded conventional Sanger sequencing, it has not yet translated into routine clinical practice. The aim of this article is to review the potential applications of NGS in paediatrics.},
  number = {6},
  urldate = {2018-07-08},
  journal = {Archives of Disease in Childhood. Education and Practice Edition},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841808/},
  author = {Behjati, Sam and Tarpey, Patrick S},
  month = dec,
  year = {2013},
  pages = {236-238},
  file = {/home/mpetersen/bib/storage/IDJWLPF5/Behjati and Tarpey - 2013 - What is next generation sequencing.pdf},
  pmid = {23986538},
  pmcid = {PMC3841808}
}

@article{OLeary2016,
  title = {Reference Sequence ({{RefSeq}}) Database at {{NCBI}}: Current Status, Taxonomic Expansion, and Functional Annotation},
  volume = {44},
  issn = {1362-4962},
  shorttitle = {Reference Sequence ({{RefSeq}}) Database at {{NCBI}}},
  doi = {10.1093/nar/gkv1189},
  abstract = {The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms ({$>$}4800 viruses, {$>$}40,000 prokaryotes and {$>$}10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.},
  language = {eng},
  number = {D1},
  journal = {Nucleic Acids Research},
  author = {O'Leary, Nuala A. and Wright, Mathew W. and Brister, J. Rodney and Ciufo, Stacy and Haddad, Diana and McVeigh, Rich and Rajput, Bhanu and Robbertse, Barbara and {Smith-White}, Brian and {Ako-Adjei}, Danso and Astashyn, Alexander and Badretdin, Azat and Bao, Yiming and Blinkova, Olga and Brover, Vyacheslav and Chetvernin, Vyacheslav and Choi, Jinna and Cox, Eric and Ermolaeva, Olga and Farrell, Catherine M. and Goldfarb, Tamara and Gupta, Tripti and Haft, Daniel and Hatcher, Eneida and Hlavina, Wratko and Joardar, Vinita S. and Kodali, Vamsi K. and Li, Wenjun and Maglott, Donna and Masterson, Patrick and McGarvey, Kelly M. and Murphy, Michael R. and O'Neill, Kathleen and Pujar, Shashikant and Rangwala, Sanjida H. and Rausch, Daniel and Riddick, Lillian D. and Schoch, Conrad and Shkeda, Andrei and Storz, Susan S. and Sun, Hanzhen and {Thibaud-Nissen}, Francoise and Tolstoy, Igor and Tully, Raymond E. and Vatsan, Anjana R. and Wallin, Craig and Webb, David and Wu, Wendy and Landrum, Melissa J. and Kimchi, Avi and Tatusova, Tatiana and DiCuccio, Michael and Kitts, Paul and Murphy, Terence D. and Pruitt, Kim D.},
  month = jan,
  year = {2016},
  keywords = {Animals,Humans,Phylogeny,Genomics,Databases; Genetic,Invertebrates,Genome; Fungal,Mice,Molecular Sequence Annotation,Genome; Human,Sequence Analysis; Protein,Genome; Plant,Gene Expression Profiling,Vertebrates,Sequence Analysis; RNA,Nematoda,Cattle,Genome; Microbial,Genome; Viral,Rats,Reference Standards,RNA; Long Noncoding},
  pages = {D733-745},
  pmid = {26553804},
  pmcid = {PMC4702849}
}

@article{Gillung2018,
  title = {Bias in Big-Data Phylogenetics: Anchored Phylogenomics Unravels the Evolution of Spider Flies ({{Acroceridae}}) and Reveals Discordance between Nucleotides and Amino Acids},
  abstract = {The onset of phylogenomics has resolved some of the most challenging evolutionary questions while giving us a new perspective on biodiversity. However, it has become clear that analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we investigate the evolution of spider flies (Acroceridae) to understand the basis for incongruence among phylogenomic trees, and to explore the effectiveness of amino acids and nucleotides in resolving relatively old divergences in the Diptera tree of life. Our study constitutes the first phylogenomic scale study of dipteran parasitoids, built upon anchored hybrid enrichment and transcriptomic data of 240 loci from 43 ingroup and seven outgroup taxa. We performed multiple analyses to test the robustness of our phylogenetic inferences to permutations of the data and phylogenetic methods, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, homogeneous versus heterogeneous models, and alternative data and taxon sets. Importantly, resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant. Our results indicate that the analysis based on amino acids was more affected by biases in our dataset than trees generated at the nucleotide level. We also take advantage of the recent advances in divergence time dating, including the fossilized birth-death process, to propose a new hypothesis for the timing of spider fly evolution.},
  journal = {Molecular Biology and Evolution},
  author = {Gillung, Jessica P and Winterton, Shaun L and Bayless, Keith M. and Khouri, Ziad and Borowiec, Marek L. and Yeates, David K and Kimsey, Lynn S and Meusemann, Karen and Misof, Bernhard and Shin, Seunggwan and Zhou, Xin and Mayer, Christoph and Petersen, Malte and Wiegmann, Brian M},
  year = {2018}
}

@article{Wang2009,
  title = {{{RNA}}-{{Seq}}: A Revolutionary Tool for Transcriptomics},
  volume = {10},
  issn = {1471-0064},
  shorttitle = {{{RNA}}-{{Seq}}},
  doi = {10.1038/nrg2484},
  abstract = {RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.},
  language = {eng},
  number = {1},
  journal = {Nature Reviews. Genetics},
  author = {Wang, Zhong and Gerstein, Mark and Snyder, Michael},
  month = jan,
  year = {2009},
  keywords = {Animals,Humans,Base Sequence,Chromosome Mapping,Molecular Sequence Data,RNA,Models; Genetic,Gene Expression Profiling,Exons,Sequence Analysis; RNA,Transcription; Genetic},
  pages = {57-63},
  pmid = {19015660},
  pmcid = {PMC2949280}
}

@article{Wiens2006,
  series = {Phylogenetic {{Inferencing}}: {{Beyond Biology}}},
  title = {Missing Data and the Design of Phylogenetic Analyses},
  volume = {39},
  issn = {1532-0464},
  doi = {10.1016/j.jbi.2005.04.001},
  abstract = {Concerns about the deleterious effects of missing data may often determine which characters and taxa are included in phylogenetic analyses. For example, researchers may exclude taxa lacking data for some genes or exclude a gene lacking data in some taxa. Yet, there may be very little evidence to support these decisions. In this paper, I review the effects of missing data on phylogenetic analyses. Recent simulations suggest that highly incomplete taxa can be accurately placed in phylogenies, as long as many characters have been sampled overall. Furthermore, adding incomplete taxa can dramatically improve results in some cases by subdividing misleading long branches. Adding characters with missing data can also improve accuracy, although there is a risk of long-branch attraction in some cases. Consideration of how missing data does (or does not) affect phylogenetic analyses may allow researchers to design studies that can reconstruct large phylogenies quickly, economically, and accurately.},
  number = {1},
  urldate = {2018-07-09},
  journal = {Journal of Biomedical Informatics},
  url = {http://www.sciencedirect.com/science/article/pii/S1532046405000341},
  author = {Wiens, John J.},
  month = feb,
  year = {2006},
  keywords = {Phylogeny,Maximum likelihood,Accuracy,Bayesian analysis,Missing data,Neighbor-joining,Parsimony,Phylogenetic method,Systematics},
  pages = {34-42},
  file = {/home/mpetersen/bib/storage/5QJKJ2ND/Wiens - 2006 - Missing data and the design of phylogenetic analys.pdf;/home/mpetersen/bib/storage/7SY8AH56/S1532046405000341.html}
}

@misc{1KITE2018,
  title = {{{1KITE}} - {{1K Insect Transcriptome Evolution}}},
  shorttitle = {{{1KITE}}},
  abstract = {Insects are one of the most species-rich groups of metazoan organisms. They play a pivotal role in most non-marine ecosystems and many insect species are of enormous economical and medical importance. Unravelling the evolution of insects is essential for understanding how life in terrestrial and limnic environments evolved. The 1KITE (1K Insect Transcriptome Evolution) project aims to study the transcriptomes (that is the entirety of expressed genes) of more than 1,000 insect species encompassing all recognized insect orders. For each species, so-called ESTs (Expressed Sequence Tags) will be produced using next generation sequencing techniques (NGS). Sequencing and sequence assembly have been completed for more than 1,200 species. The expected data will allow inferring robust phylogenetic backbone trees of insects. Furthermore, the project includes the development of new software for data quality assessment and analysis.

1KITE has brought together internationally recognized experts in molecular biology, morphology, palaeontology, embryology, bioinformatics, and scientific computing in a yet unparalleled way. Overall, scientists from eleven nations (Australia, Austria, China, France, Germany, Japan, Mexico, The Netherlands, New Zealand, UK and the US) are tightly collaborating in the 1KITE project.},
  language = {en},
  urldate = {2018-07-10},
  journal = {1KITE - 1K Insect Transcriptome Evolution},
  url = {http://1kite.org/},
  author = {{1KITE}},
  month = may,
  year = {2018},
  file = {/home/mpetersen/bib/storage/VPLXVCBW/1kite.org.html}
}

@article{Mora2011,
  title = {How {{Many Species Are There}} on {{Earth}} and in the {{Ocean}}?},
  volume = {9},
  issn = {1544-9173},
  doi = {10.1371/journal.pbio.1001127},
  abstract = {The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science. Yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. Here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. This approach was validated against well-known taxa, and when applied to all domains of life, it predicts {$\sim$}8.7 million ({$\pm$}1.3 million SE) eukaryotic species globally, of which {$\sim$}2.2 million ({$\pm$}0.18 million SE) are marine. In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86\% of existing species on Earth and 91\% of species in the ocean still await description. Renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on Earth is to be closed., Knowing the number of species on Earth is one of the most basic yet elusive questions in science. Unfortunately, obtaining an accurate number is constrained by the fact that most species remain to be described and because indirect attempts to answer this question have been highly controversial. Here, we document that the taxonomic classification of species into higher taxonomic groups (from genera to phyla) follows a consistent pattern from which the total number of species in any taxonomic group can be predicted. Assessment of this pattern for all kingdoms of life on Earth predicts {$\sim$}8.7 million ({$\pm$}1.3 million SE) species globally, of which {$\sim$}2.2 million ({$\pm$}0.18 million SE) are marine. Our results suggest that some 86\% of the species on Earth, and 91\% in the ocean, still await description. Closing this knowledge gap will require a renewed interest in exploration and taxonomy, and a continuing effort to catalogue existing biodiversity data in publicly available databases.},
  number = {8},
  urldate = {2018-07-12},
  journal = {PLoS Biology},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160336/},
  author = {Mora, Camilo and Tittensor, Derek P. and Adl, Sina and Simpson, Alastair G. B. and Worm, Boris},
  month = aug,
  year = {2011},
  file = {/home/mpetersen/bib/storage/CYKV55PK/Mora et al. - 2011 - How Many Species Are There on Earth and in the Oce.pdf},
  pmid = {21886479},
  pmcid = {PMC3160336}
}

@techreport{IUCN2018,
  title = {The {{IUCN Red List}} of {{Threatened Species}}},
  number = {2018-1},
  urldate = {2018-07-12},
  institution = {{IUCN}},
  url = {http://www.iucnredlist.org/},
  author = {{IUCN}},
  year = {2018}
}

@book{Baillie2010,
  title = {Evolution Lost: Status and Trends of the World's Vertebrates},
  isbn = {978-0-900881-40-4 978-0-900881-41-1},
  shorttitle = {Evolution Lost},
  language = {English},
  author = {Baillie, Jonathan and Griffiths, Janine and Turvey, Sam and Loh, Jonathan and Collen, Ben and Mace, G. M and Stuart, S. N},
  year = {2010},
  note = {OCLC: 815968534}
}

@article{Felsenstein1985,
  title = {Phylogenies and the {{Comparative Method}}},
  volume = {125},
  issn = {0003-0147, 1537-5323},
  doi = {10.1086/284325},
  language = {English},
  number = {1},
  journal = {The American Naturalist},
  author = {Felsenstein, Joseph},
  month = jan,
  year = {1985},
  pages = {1-15}
}

@article{Schachat1974,
  title = {Repetitive {{Sequences}} in {{Isolated Thomas Circles}} from {{Drosophila}} Melanogaster},
  volume = {38},
  doi = {10.1101/sqb.1974.038.01.040},
  number = {0},
  journal = {Cold Spring Harbor Symposia on Quantitative Biology},
  url = {http://dx.doi.org/10.1101/sqb.1974.038.01.040},
  author = {Schachat, F. H. and Hogness, D. S.},
  month = jan,
  year = {1974},
  pages = {371-381},
  publisher = {{Cold Spring Harbor Laboratory Press}}
}

@article{Schmid1975,
  title = {Inverted Repeat Sequences in the Drosophila Genome},
  volume = {5},
  doi = {10.1016/0092-8674(75)90024-0},
  number = {2},
  journal = {Cell},
  url = {http://dx.doi.org/10.1016/0092-8674(75)90024-0},
  author = {Schmid, Carl W. and Manning, Jerry E. and Davidson, Norman},
  month = jun,
  year = {1975},
  pages = {159-172},
  publisher = {{Elsevier BV}}
}

@article{SanMiguel1996,
  title = {Nested {{Retrotransposons}} in the {{Intergenic Regions}} of the {{Maize Genome}}},
  volume = {274},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.274.5288.765},
  language = {English},
  number = {5288},
  urldate = {2016-08-26},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.274.5288.765},
  author = {SanMiguel, P. and Tikhonov, A. and Jin, Y.-K. and Motchoulskaia, N. and Zakharov, D. and {Melake-Berhan}, A. and Springer, P. S. and Edwards, K. J. and Lee, M. and Avramova, Z. and Bennetzen, J. L.},
  month = nov,
  year = {1996},
  pages = {765-768}
}

@article{Sessegolo2016,
  title = {Strong {{Phylogenetic Inertia}} on {{Genome Size}} and {{Transposable Element Content}} among 26 {{Species}} of {{Flies}}},
  volume = {12},
  issn = {1744-9561, 1744-957X},
  doi = {10.1098/rsbl.2016.0407},
  language = {English},
  number = {8},
  urldate = {2016-09-07},
  journal = {Biology Letters},
  url = {http://rsbl.royalsocietypublishing.org/lookup/doi/10.1098/rsbl.2016.0407},
  author = {Sessegolo, Camille and Burlet, Nelly and Haudry, Annabelle},
  month = aug,
  year = {2016},
  pages = {20160407}
}

@article{Flavell1992,
  title = {Ty1-Copia Group Retrotransposons and the Evolution of Retroelements in the Eukaryotes},
  volume = {86},
  doi = {10.1007/bf00133721},
  number = {1-3},
  journal = {Genetica},
  url = {http://dx.doi.org/10.1007/bf00133721},
  author = {Flavell, A. J.},
  year = {1992},
  pages = {203-214},
  publisher = {{Springer Science Business Media}}
}

@article{Tsutsui2008,
  title = {The Evolution of Genome Size in Ants},
  volume = {8},
  doi = {10.1186/1471-2148-8-64},
  number = {1},
  journal = {BMC Evol Biol},
  url = {http://dx.doi.org/10.1186/1471-2148-8-64},
  author = {Tsutsui, Neil D and Suarez, Andrew V and Spagna, Joseph C and Johnston, J Spencer},
  year = {2008},
  pages = {64},
  publisher = {{Springer Nature}}
}

@article{Joly-Lopez2014,
  title = {Diversity and Evolution of Transposable Elements in {{Arabidopsis}}},
  volume = {22},
  doi = {10.1007/s10577-014-9418-8},
  number = {2},
  journal = {Chromosome Research},
  url = {http://dx.doi.org/10.1007/s10577-014-9418-8},
  author = {{Joly-Lopez}, Zo\'e and Bureau, Thomas E.},
  month = may,
  year = {2014},
  pages = {203-216},
  publisher = {{Springer Science Business Media}}
}

@article{Diaz-Uriarte1998,
  title = {Effects of {{Branch Length Errors}} on the {{Performance}} of {{Phylogenetically Independent Contrasts}}},
  volume = {47},
  doi = {10.1080/106351598260653},
  number = {4},
  journal = {Systematic Biology},
  url = {http://dx.doi.org/10.1080/106351598260653},
  author = {{D\'iaz-Uriarte}, Ramon},
  month = dec,
  year = {1998},
  pages = {654-672},
  publisher = {{Oxford University Press (OUP)}}
}

@article{Agren2011,
  title = {Co-Evolution between Transposable Elements and Their Hosts: A Major Factor in Genome Size Evolution?},
  volume = {19},
  doi = {10.1007/s10577-011-9229-0},
  number = {6},
  journal = {Chromosome Research},
  url = {http://dx.doi.org/10.1007/s10577-011-9229-0},
  author = {\AA{}gren, J. Arvid and Wright, Stephen I.},
  month = aug,
  year = {2011},
  pages = {777-786},
  publisher = {{Springer Nature}}
}

@article{Vieira2002,
  title = {Evolution of {{Genome Size}} in {{Drosophila}}. {{Is}} the {{Invader}}'s {{Genome Being Invaded}} by {{Transposable Elements}}?},
  volume = {19},
  doi = {10.1093/oxfordjournals.molbev.a004173},
  number = {7},
  journal = {Molecular Biology and Evolution},
  url = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a004173},
  author = {Vieira, C. and Nardon, C. and Arpin, C. and Lepetit, D. and Biemont, C.},
  month = jul,
  year = {2002},
  pages = {1154-1161},
  publisher = {{Oxford University Press (OUP)}}
}

@article{Kidwell2000,
  title = {Transposable Elements and Host Genome Evolution},
  volume = {15},
  doi = {10.1016/s0169-5347(99)01817-0},
  number = {3},
  journal = {Trends in Ecology \& Evolution},
  url = {http://dx.doi.org/10.1016/s0169-5347(99)01817-0},
  author = {Kidwell, Margaret G and Lisch, Damon R},
  month = mar,
  year = {2000},
  pages = {95-99},
  publisher = {{Elsevier BV}}
}

@article{Bosco2007,
  title = {Analysis of {{Drosophila Species Genome Size}} and {{Satellite DNA Content Reveals Significant Differences Among Strains}} as {{Well}} as {{Between Species}}},
  volume = {177},
  doi = {10.1534/genetics.107.075069},
  number = {3},
  journal = {Genetics},
  url = {http://dx.doi.org/10.1534/genetics.107.075069},
  author = {Bosco, G. and Campbell, P. and {Leiva-Neto}, J. T. and Markow, T. A.},
  month = nov,
  year = {2007},
  pages = {1277-1290},
  publisher = {{Genetics Society of America}}
}

@incollection{LeRouzic2006,
  title = {Theoretical {{Approaches}} to the {{Dynamics}} of {{Transposable Elements}} in {{Genomes Populations}}, and {{Species}}},
  booktitle = {Transposons and the {{Dynamic Genome}}},
  publisher = {{Springer Science Business Media}},
  url = {http://dx.doi.org/10.1007/7050_017},
  author = {Le Rouzic, Arnaud and Capy, Pierre},
  year = {2006},
  pages = {1-19},
  doi = {10.1007/7050_017}
}

@article{Sun2011,
  title = {{{LTR Retrotransposons Contribute}} to {{Genomic Gigantism}} in {{Plethodontid Salamanders}}},
  volume = {4},
  doi = {10.1093/gbe/evr139},
  number = {2},
  journal = {Genome Biology and Evolution},
  url = {http://dx.doi.org/10.1093/gbe/evr139},
  author = {Sun, C. and Shepard, D. B. and Chong, R. A. and Arriaza, J. Lopez and Hall, K. and Castoe, T. A. and Feschotte, C. and Pollock, D. D. and Mueller, R. L.},
  month = dec,
  year = {2011},
  pages = {168-183},
  publisher = {{Oxford University Press (OUP)}}
}

@article{Sormacheva2012,
  title = {Vertical {{Evolution}} and {{Horizontal Transfer}} of {{CR1 Non}}-{{LTR Retrotransposons}} and {{Tc1}}/Mariner {{DNA Transposons}} in {{Lepidoptera Species}}},
  volume = {29},
  doi = {10.1093/molbev/mss181},
  number = {12},
  journal = {Molecular Biology and Evolution},
  url = {http://dx.doi.org/10.1093/molbev/mss181},
  author = {Sormacheva, I. and Smyshlyaev, G. and Mayorov, V. and Blinov, A. and Novikov, A. and Novikova, O.},
  month = jul,
  year = {2012},
  pages = {3685-3702},
  publisher = {{Oxford University Press (OUP)}}
}

@article{Syvanen2012,
  title = {Evolutionary {{Implications}} of {{Horizontal Gene Transfer}}},
  volume = {46},
  doi = {10.1146/annurev-genet-110711-155529},
  number = {1},
  journal = {Annu. Rev. Genet.},
  url = {http://dx.doi.org/10.1146/annurev-genet-110711-155529},
  author = {Syvanen, Michael},
  month = dec,
  year = {2012},
  pages = {341-358},
  publisher = {{Annual Reviews}}
}

@incollection{Lynch2003a,
  title = {The Evolutionary Demography of Duplicate Genes},
  booktitle = {Genome {{Evolution}}},
  publisher = {{Springer Nature}},
  url = {http://dx.doi.org/10.1007/978-94-010-0263-9_4},
  author = {Lynch, Michael and Conery, John S.},
  year = {2003},
  pages = {35-44},
  doi = {10.1007/978-94-010-0263-9_4}
}

@article{Kriegs2007,
  title = {Evolutionary History of {{7SL RNA}}-Derived {{SINEs}} in {{Supraprimates}}},
  volume = {23},
  doi = {10.1016/j.tig.2007.02.002},
  number = {4},
  journal = {Trends in Genetics},
  url = {https://doi.org/10.1016\%2Fj.tig.2007.02.002},
  author = {Kriegs, Jan Ole and Churakov, Gennady and Jurka, Jerzy and Brosius, J\"urgen and Schmitz, J\"urgen},
  month = apr,
  year = {2007},
  pages = {158-161},
  publisher = {{Elsevier BV}}
}

@article{Liu2003,
  title = {Analysis of {{Primate Genomic Variation Reveals}} a {{Repeat}}-{{Driven Expansion}} of the {{Human Genome}}},
  volume = {13},
  doi = {10.1101/gr.923303},
  number = {3},
  journal = {Genome Research},
  url = {https://doi.org/10.1101\%2Fgr.923303},
  author = {Liu, G.},
  month = mar,
  year = {2003},
  pages = {358-368},
  publisher = {{Cold Spring Harbor Laboratory Press}}
}

@article{Cambareri1994,
  title = {Tadl-1 an Active {{LINE}}-like Element of {{Neurospora}} Crassa},
  volume = {242},
  doi = {10.1007/bf00283420},
  number = {6},
  journal = {MGG Molecular \& General Genetics},
  url = {https://doi.org/10.1007\%2Fbf00283420},
  author = {Cambareri, EdwardB. and Helber, Jennifer and Kinsey, JohnA.},
  year = {1994},
  publisher = {{Springer Nature}}
}

@article{Schatz2010,
  title = {Assembly of Large Genomes Using Second-Generation Sequencing.},
  volume = {20},
  journal = {Genome Res},
  author = {Schatz, MC and Delcher, AL and Salzberg, SL},
  month = sep,
  year = {2010},
  pages = {1165-73},
  source = {Genome Res},
  authors = {Schatz, MC and Delcher, AL and Salzberg, SL},
  pubmed_id = {20508146}
}

@article{Kidwell2002,
  title = {Transposable Elements and the Evolution of Genome Size in Eukaryotes},
  volume = {115},
  issn = {0016-6707, 1573-6857},
  doi = {10.1023/A:1016072014259},
  abstract = {It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.},
  language = {en},
  number = {1},
  urldate = {2018-07-18},
  journal = {Genetica},
  url = {https://link.springer.com/article/10.1023/A:1016072014259},
  author = {Kidwell, Margaret G.},
  month = may,
  year = {2002},
  pages = {49-63},
  file = {/home/mpetersen/bib/storage/D9XCU32Y/10.html}
}

@phdthesis{Reinar2016,
  address = {Oslo},
  type = {{{PhD}} Thesis},
  title = {In Silico Explorations of {{TE}} Activity, Diversity and Abundance across 74 Teleost Fish Genomes},
  language = {English},
  school = {University of Oslo},
  author = {Reinar, William Brynildsen},
  year = {2016}
}

@article{Coates2015,
  title = {Horizontal Transfer of a Non-Autonomous {{Helitron}} among Insect and Viral Genomes},
  volume = {16},
  issn = {1471-2164},
  doi = {10.1186/s12864-015-1318-6},
  language = {en},
  number = {1},
  urldate = {2018-08-05},
  journal = {BMC Genomics},
  url = {http://www.biomedcentral.com/1471-2164/16/137},
  author = {Coates, Brad S},
  year = {2015},
  pages = {137},
  file = {/home/mpetersen/bib/storage/GEV2L64P/Coates - 2015 - Horizontal transfer of a non-autonomous Helitron a.pdf}
}

@article{Chuong2016,
  title = {Regulatory Activities of Transposable Elements: From Conflicts to Benefits},
  volume = {18},
  copyright = {2016 Nature Publishing Group},
  issn = {1471-0064},
  shorttitle = {Regulatory Activities of Transposable Elements},
  doi = {10.1038/nrg.2016.139},
  abstract = {Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs. Many recent studies reinvigorate the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and the conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes. We review recent findings supporting the long-standing hypothesis that the waves of TE invasions endured by organisms for eons have catalysed the evolution of gene-regulatory networks. We also discuss the challenges of dissecting and interpreting the phenotypic effect of regulatory activities encoded by TEs in health and disease.},
  language = {en},
  number = {2},
  urldate = {2018-08-05},
  journal = {Nature Reviews Genetics},
  url = {https://www.nature.com/articles/nrg.2016.139},
  author = {Chuong, Edward B. and Elde, Nels C. and Feschotte, C\'edric},
  month = nov,
  year = {2016},
  pages = {71-86},
  file = {/home/mpetersen/bib/storage/WZ4EAEJQ/Chuong et al. - 2017 - Regulatory activities of transposable elements fr.pdf;/home/mpetersen/bib/storage/3UNAEFGY/nrg.2016.html;/home/mpetersen/bib/storage/E9NJHQ9K/nrg.2016.html}
}

@article{Czech2008,
  title = {An Endogenous Small Interfering {{RNA}} Pathway in {{Drosophila}}},
  volume = {453},
  issn = {0028-0836},
  doi = {10.1038/nature07007},
  abstract = {Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of \textasciitilde{}22 nucleotides in length, which arise from structured precursors through the action of Drosha\textendash{}Pasha and Dicer-1\textendash{}Loquacious complexes\textendash. These join Argonaute-1 to regulate gene expression,. A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons,. Piwi-interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi-catalysed cleavage of single-stranded RNAs,. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer-2, but a subset depends preferentially on Loquacious,, rather than the canonical Dicer-2 partner, R2D2 (ref. ). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue-specific fashion. They predominantly join Argonaute-2 and have the capacity, as a class, to target both protein-coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles.},
  number = {7196},
  urldate = {2018-08-05},
  journal = {Nature},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895258/},
  author = {Czech, Benjamin and Malone, Colin D. and Zhou, Rui and Stark, Alexander and Schlingeheyde, Catherine and Dus, Monica and Perrimon, Norbert and Kellis, Manolis and Wohlschlegel, James A. and Sachidanandam, Ravi and Hannon, Gregory J. and Brennecke, Julius},
  month = jun,
  year = {2008},
  pages = {798-802},
  file = {/home/mpetersen/bib/storage/YZXCHTQV/Czech et al. - 2008 - An endogenous small interfering RNA pathway in Dro.pdf},
  pmid = {18463631},
  pmcid = {PMC2895258}
}

@article{Ibarra-Laclette2013,
  title = {Architecture and Evolution of a Minute Plant Genome},
  volume = {498},
  copyright = {2013 Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature12132},
  abstract = {It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.},
  language = {en},
  number = {7452},
  urldate = {2018-08-06},
  journal = {Nature},
  url = {https://www.nature.com/articles/nature12132},
  author = {{Ibarra-Laclette}, Enrique and Lyons, Eric and {Hern\'andez-Guzm\'an}, Gustavo and {P\'erez-Torres}, Claudia Anah\'i and {Carretero-Paulet}, Lorenzo and Chang, Tien-Hao and Lan, Tianying and Welch, Andreanna J. and Ju\'arez, Mar\'ia Jazm\'in Abraham and Simpson, June and {Fern\'andez-Cort\'es}, Araceli and {Arteaga-V\'azquez}, Mario and {G\'ongora-Castillo}, Elsa and {Acevedo-Hern\'andez}, Gustavo and Schuster, Stephan C. and Himmelbauer, Heinz and Minoche, Andr\'e E. and Xu, Sen and Lynch, Michael and {Oropeza-Aburto}, Araceli and {Cervantes-P\'erez}, Sergio Alan and {Ortega-Estrada}, Mar\'ia de Jes\'us and {Cervantes-Luevano}, Jacob Israel and Michael, Todd P. and Mockler, Todd and Bryant, Douglas and {Herrera-Estrella}, Alfredo and Albert, Victor A. and {Herrera-Estrella}, Luis},
  month = jun,
  year = {2013},
  pages = {94-98},
  file = {/home/mpetersen/bib/storage/7ACP6VY6/Ibarra-Laclette et al. - 2013 - Architecture and evolution of a minute plant genom.pdf;/home/mpetersen/bib/storage/MB63282U/nature12132.html}
}

@article{Burke2015,
  title = {The Plant Parasite {{Pratylenchus}} Coffeaecarries a Minimal Nematode Genome},
  volume = {17},
  issn = {1568-5411},
  doi = {10.1163/15685411-00002901},
  abstract = {Here we report the genome sequence of the lesion nematode, Pratylenchus coffeae, a significant pest of banana and other staple crops in tropical and sub-tropical regions worldwide. Initial analysis of the 19.67 Mb genome reveals 6712 protein encoding genes, the smallest number found in a metazoan, although sufficient to make a nematode. Significantly, no developmental or physiological pathways are obviously missing when compared to the model free-living nematode Caenorhabditis elegans, which possesses approximately 21 000 genes. The highly streamlined P. coffeaegenome may reveal a remarkable functional plasticity in nematode genomes and may also indicate evolutionary routes to increased specialisation in other nematode genera. In addition, the P. coffeaegenome may begin to reveal the core set of genes necessary to make a multicellular animal. Nematodes exhibit striking diversity in the niches they occupy, and the sequence of P. coffeaeis a tool to begin to unravel the mechanisms that enable the extraordinary success of this phylum as both free-living and parasitic forms. Unlike the sedentary endoparasitic root-knot nematodes ( Meloidogynespp.), P. coffeaeis a root-lesion nematode that does not establish a feeding site within the root. Because the P. coffeaenematode genome encodes fewer than half the number of genes found in the genomes of root-knot nematodes, comparative analysis to determine genes P. coffeaedoes not carry may help to define development of more sophisticated forms of nematode-plant interactions. The P. coffeaegenome sequence may help to define timelines related to evolution of parasitism amongst nematodes. The genome of P. coffeaeis a significant new tool to understand not only nematode evolution but animal biology in general.},
  language = {en},
  number = {6},
  urldate = {2018-08-06},
  journal = {Nematology},
  url = {http://booksandjournals.brillonline.com/content/journals/10.1163/15685411-00002901},
  author = {Burke, Mark and Scholl, Elizabeth H. and Bird, David McK and Schaff, Jennifer E. and Colman, Steven D. and Crowell, Randy and Diener, Stephen and Gordon, Oksana and Graham, Steven and Wang, Xinguo and Windham, Eric and Wright, Garron M. and Opperman, Charles H.},
  month = jul,
  year = {2015},
  keywords = {Caenorhabditis elegans,lesion nematode,Meloidogyne hapla,migratory endoparasitic nematodes,nematode evolution,protein encoding genes},
  pages = {621-637},
  file = {/home/mpetersen/bib/storage/EF7INEHP/NEMY__Plant_Parasite_Pratylenchus_Coffeae_-_DHMRI.pdf;/home/mpetersen/bib/storage/B5LFYUKE/15685411-00002901.html}
}

@article{Schrader2018,
  title = {The Impact of Transposable Elements in Adaptive Evolution},
  issn = {09621083},
  doi = {10.1111/mec.14794},
  language = {en},
  urldate = {2018-08-06},
  journal = {Molecular Ecology},
  url = {http://doi.wiley.com/10.1111/mec.14794},
  author = {Schrader, Lukas and Schmitz, J\"urgen},
  month = jul,
  year = {2018},
  file = {/home/mpetersen/bib/storage/6X5HZW7S/Schrader and Schmitz - 2018 - The impact of transposable elements in adaptive ev.pdf}
}

@article{Kutty2018,
  title = {A Phylogenomic Analysis of {{Culicomorpha}} ({{Diptera}}) Resolves the Relationships among the Eight Constituent Families},
  volume = {43},
  copyright = {\textcopyright{} 2018 The Royal Entomological Society},
  issn = {1365-3113},
  doi = {10.1111/syen.12285},
  abstract = {Culicomorpha is a particularly species-rich clade within Diptera (true flies) that comprises c. 10\% of the described diversity, including many medically important flies. Morphological studies \textendash{} even when all life stages are included \textendash{} yield relationships different from those derived from molecular data, notably with regard to the position of Chironomidae. Congruence amongst molecular studies has been weak due to limitations in gene- and family-level taxon coverage. Here we use a whole-transcriptome shotgun phylogenomic approach to clarify the relationships among all families of Culicomorpha. The dataset comprised 30 species (27 ingroup) and 364 888 amino acid residues for 1233 single-copy protein-encoding genes. Likelihood and parsimony analyses produce robust and highly congruent phylogenetic trees, with only one node in conflict. The superfamily Culicoidea is well supported and comprises Dixidae + [Corethrellidae + (Chaoboridae + Culicidae)]. As suggested previously, Chironomoidea is not monophyletic. The well supported Thaumaleidae + Simuliidae is sister group to Culicoidea, with the weakly supported Chironomidae + Ceratopogonidae probably being the sister group of all remaining Culicomorpha. We used random addition concatenation analysis (RADICAL) and four-cluster likelihood mapping (FcLM) to assess the strengths of nodal support. The sister-group relationship between Chironomidae + Ceratopogonidae is consistent with the FcLM results but support for this relationship emerges only when 1150 of the 1233 loci are analysed. We discuss briefly nodes that remain poorly supported even with thousands of genes and mention problems with vouchering in transcriptomic studies.},
  language = {en},
  number = {3},
  urldate = {2018-08-08},
  journal = {Systematic Entomology},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/syen.12285},
  author = {Kutty, Sujatha Narayanan and Wong, Wing Hing and Meusemann, Karen and Meier, Rudolf and Cranston, Peter S.},
  month = jul,
  year = {2018},
  pages = {434-446},
  file = {/home/mpetersen/bib/storage/DKAAMWPI/syen.html}
}

@article{Simon2018,
  series = {Wings and {{Powered Flight}}: {{Core Novelties}} in {{Insect Evolution}}},
  title = {Reanalyzing the {{Palaeoptera}} Problem \textendash{} {{The}} Origin of Insect Flight Remains Obscure},
  volume = {47},
  issn = {1467-8039},
  doi = {10.1016/j.asd.2018.05.002},
  abstract = {The phylogenetic relationships of the winged insect lineages \textendash{} mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) \textendash{} are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.},
  number = {4},
  urldate = {2018-08-08},
  journal = {Arthropod Structure \& Development},
  url = {http://www.sciencedirect.com/science/article/pii/S1467803918300550},
  author = {Simon, Sabrina and Blanke, Alexander and Meusemann, Karen},
  month = jul,
  year = {2018},
  keywords = {Palaeoptera,Phylogenomics,Chiastomyaria,Homologization,Metapterygota,Transcriptomics},
  pages = {328-338},
  file = {/home/mpetersen/bib/storage/A2CAH9JD/S1467803918300550.html}
}

@article{Shin2018,
  title = {Phylogenomic {{Data Yield New}} and {{Robust Insights}} into the {{Phylogeny}} and {{Evolution}} of {{Weevils}}},
  volume = {35},
  issn = {0737-4038},
  doi = {10.1093/molbev/msx324},
  abstract = {Abstract.  The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in th},
  language = {en},
  number = {4},
  urldate = {2018-08-08},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article/35/4/823/4765916},
  author = {Shin, Seunggwan and Clarke, Dave J. and Lemmon, Alan R. and Moriarty Lemmon, Emily and Aitken, Alexander L. and Haddad, Stephanie and Farrell, Brian D. and Marvaldi, Adriana E. and Oberprieler, Rolf G. and McKenna, Duane D.},
  month = apr,
  year = {2018},
  pages = {823-836},
  file = {/home/mpetersen/bib/storage/MDI5E6QP/Shin et al. - 2018 - Phylogenomic Data Yield New and Robust Insights in.pdf;/home/mpetersen/bib/storage/FZLE9Q3Z/4765916.html}
}

@article{Sann2018,
  title = {Phylogenomic Analysis of {{Apoidea}} Sheds New Light on the Sister Group of Bees},
  volume = {18},
  issn = {1471-2148},
  doi = {10.1186/s12862-018-1155-8},
  abstract = {Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families.},
  number = {1},
  urldate = {2018-08-08},
  journal = {BMC Evolutionary Biology},
  url = {https://doi.org/10.1186/s12862-018-1155-8},
  author = {Sann, Manuela and Niehuis, Oliver and Peters, Ralph S. and Mayer, Christoph and Kozlov, Alexey and Podsiadlowski, Lars and Bank, Sarah and Meusemann, Karen and Misof, Bernhard and Bleidorn, Christoph and Ohl, Michael},
  month = may,
  year = {2018},
  pages = {71},
  file = {/home/mpetersen/bib/storage/M7GIWEY4/Sann et al. - 2018 - Phylogenomic analysis of Apoidea sheds new light o.pdf;/home/mpetersen/bib/storage/NFUMZDQF/s12862-018-1155-8.html}
}

@article{Zeh2009,
  title = {Transposable Elements and an Epigenetic Basis for Punctuated Equilibria},
  volume = {31},
  copyright = {Copyright \textcopyright{} 2009 Wiley Periodicals, Inc.},
  issn = {1521-1878},
  doi = {10.1002/bies.200900026},
  abstract = {Evolution is frequently concentrated in bursts of rapid morphological change and speciation followed by long-term stasis. We propose that this pattern of punctuated equilibria results from an evolutionary tug-of-war between host genomes and transposable elements (TEs) mediated through the epigenome. According to this hypothesis, epigenetic regulatory mechanisms (RNA interference, DNA methylation and histone modifications) maintain stasis by suppressing TE mobilization. However, physiological stress, induced by climate change or invasion of new habitats, disrupts epigenetic regulation and unleashes TEs. With their capacity to drive non-adaptive host evolution, mobilized TEs can restructure the genome and displace populations from adaptive peaks, thus providing an escape from stasis and generating genetic innovations required for rapid diversification. This ``epi-transposon hypothesis'' can not only explain macroevolutionary tempo and mode, but may also resolve other long-standing controversies, such as Wright's shifting balance theory, Mayr's peripheral isolates model, and McClintock's view of genome restructuring as an adaptive response to challenge.},
  language = {en},
  number = {7},
  urldate = {2018-08-11},
  journal = {BioEssays},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.200900026},
  author = {Zeh, David W. and Zeh, Jeanne A. and Ishida, Yoichi},
  month = jul,
  year = {2009},
  keywords = {transposable elements,epigenetics,fitness landscape,punctuated equilibria,stress},
  pages = {715-726},
  file = {/home/mpetersen/bib/storage/JYIK9I3W/Zeh et al. - 2009 - Transposable elements and an epigenetic basis for .pdf;/home/mpetersen/bib/storage/QB63AXGK/bies.html}
}

@article{Rebollo2010,
  title = {Jumping Genes and Epigenetics: {{Towards}} New Species},
  volume = {454},
  issn = {1879-0038},
  shorttitle = {Jumping Genes and Epigenetics},
  doi = {10.1016/j.gene.2010.01.003},
  abstract = {Transposable elements (TEs) are responsible for rapid genome remodelling by the creation of new regulatory gene networks and chromosome restructuring. TEs are often regulated by the host through epigenetic systems, but environmental changes can lead to physiological and, therefore, epigenetic stress, which disrupt the tight control of TEs. The resulting TE mobilization drives genome restructuring that may sometimes provide the host with an innovative genetic escape route. We suggest that macroevolution and speciation might therefore originate when the host relaxes its epigenetic control of TEs. To understand the impact of TEs and their importance in host genome evolution, it is essential to study TE epigenetic variation in natural populations. We propose to focus on recent data that demonstrate the correlation between changes in the epigenetic control of TEs in species/populations and genome evolution.},
  language = {eng},
  number = {1-2},
  journal = {Gene},
  author = {Rebollo, Rita and Horard, B\'eatrice and Hubert, Benjamin and Vieira, Cristina},
  month = apr,
  year = {2010},
  keywords = {Genome,Genetic Variation,Evolution; Molecular,DNA Transposable Elements,Epigenesis; Genetic,Chromosomes},
  pages = {1-7},
  pmid = {20102733}
}

@article{Horvath2017a,
  title = {The {{Role}} of {{Small RNA}}-{{Based Epigenetic Silencing}} for {{Purifying Selection}} on {{Transposable Elements}} in {{Capsella}} Grandiflora},
  volume = {9},
  doi = {10.1093/gbe/evx206},
  abstract = {Abstract.  To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-d},
  language = {en},
  number = {10},
  urldate = {2018-08-11},
  journal = {Genome Biology and Evolution},
  url = {https://academic.oup.com/gbe/article/9/10/2911/4259792},
  author = {Horvath, Robert and Slotte, Tanja},
  month = oct,
  year = {2017},
  pages = {2911-2920},
  file = {/home/mpetersen/bib/storage/HD4Z87NI/Horvath and Slotte - 2017 - The Role of Small RNA-Based Epigenetic Silencing f.pdf;/home/mpetersen/bib/storage/45XZDY9D/4259792.html}
}

@article{Akagi2013,
  title = {How Do Mammalian Transposons Induce Genetic Variation? {{A}} Conceptual Framework: The Age, Structure, Allele Frequency, and Genome Context of Transposable Elements May Define Their Wide-Ranging Biological Impacts},
  volume = {35},
  issn = {1521-1878},
  shorttitle = {How Do Mammalian Transposons Induce Genetic Variation?},
  doi = {10.1002/bies.201200133},
  abstract = {In this essay, we discuss new insights into the wide-ranging impacts of mammalian transposable elements (TE) on gene expression and function. Nearly half of each mammalian genome is comprised of these mobile, repetitive elements. While most TEs are ancient relics, certain classes can move from one chromosomal location to another even now. Indeed, striking recent data show that extensive transposition occurs not only in the germline over evolutionary time, but also in developing somatic tissues and particular human cancers. While occasional germline TE insertions may contribute to genetic variation, many other, similar TEs appear to have little or no impact on neighboring genes. However, the effects of somatic insertions on gene expression and function remain almost completely unknown. We present a conceptual framework to understand how the ages, allele frequencies, molecular structures, and especially the genomic context of mammalian TEs each can influence their various possible functional consequences.},
  language = {eng},
  number = {4},
  journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology},
  author = {Akagi, Keiko and Li, Jingfeng and Symer, David E.},
  month = apr,
  year = {2013},
  keywords = {Animals,Humans,Genetic Variation,Evolution; Molecular,DNA Transposable Elements,Gene Expression Regulation,Neoplasms,Alleles,Gene Expression,Gene Frequency},
  pages = {397-407},
  pmid = {23319453},
  pmcid = {PMC4270750}
}

@article{Oliver2012,
  title = {Transposable Elements and Viruses as Factors in Adaptation and Evolution: An Expansion and Strengthening of the {{TE}}-{{Thrust}} Hypothesis},
  volume = {2},
  copyright = {\textcopyright{} 2012 The Authors.           Ecology and Evolution published by Blackwell Publishing Ltd.},
  issn = {2045-7758},
  shorttitle = {Transposable Elements and Viruses as Factors in Adaptation and Evolution},
  doi = {10.1002/ece3.400},
  abstract = {In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. ``Adaptive potential'' and ``evolutionary potential'' are proposed as the extremes of a continuum of ``intra-genomic potential'' due to TE-Thrust. Specific data is given, indicating ``adaptive potential'' being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of ``evolutionary potential'' is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.},
  language = {en},
  number = {11},
  urldate = {2018-08-11},
  journal = {Ecology and Evolution},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.400},
  author = {Oliver, Keith R. and Greene, Wayne K.},
  month = nov,
  year = {2012},
  keywords = {transposable element,Adaptive Potential,evolutionary potential,holobiont,symbiosis,TE-Thrust},
  pages = {2912-2933},
  file = {/home/mpetersen/bib/storage/N4EEM3T7/Oliver and Greene - 2012 - Transposable elements and viruses as factors in ad.pdf;/home/mpetersen/bib/storage/SXW8E8PX/ece3.html}
}

@article{Bachtrog2008,
  title = {Similar Rates of Protein Adaptation in {{Drosophila}} Miranda and {{D}}. Melanogaster, Two Species with Different Current Effective Population Sizes},
  volume = {8},
  issn = {1471-2148},
  doi = {10.1186/1471-2148-8-334},
  abstract = {Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of Nes \textasciitilde{} 5 in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations.},
  number = {1},
  urldate = {2018-08-11},
  journal = {BMC Evolutionary Biology},
  url = {https://doi.org/10.1186/1471-2148-8-334},
  author = {Bachtrog, Doris},
  month = dec,
  year = {2008},
  pages = {334},
  file = {/home/mpetersen/bib/storage/3W9UPRLQ/Bachtrog - 2008 - Similar rates of protein adaptation in Drosophila .pdf;/home/mpetersen/bib/storage/H4MFVH87/1471-2148-8-334.html}
}

@article{Waxman2012,
  title = {Population {{Growth Enhances}} the {{Mean Fixation Time}} of {{Neutral Mutations}} and the {{Persistence}} of {{Neutral Variation}}},
  volume = {191},
  issn = {0016-6731},
  doi = {10.1534/genetics.112.139220},
  abstract = {A fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of {$\sim$}4Ne generations, where Ne is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4Ne,0 generations, where Ne,0 is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.},
  number = {2},
  urldate = {2018-08-11},
  journal = {Genetics},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374318/},
  author = {Waxman, D.},
  month = jun,
  year = {2012},
  pages = {561-577},
  file = {/home/mpetersen/bib/storage/4NU2P2YA/Waxman - 2012 - Population Growth Enhances the Mean Fixation Time .pdf},
  pmid = {22426878},
  pmcid = {PMC3374318}
}

@article{Kimura1969,
  title = {The {{Average Number}} of {{Generations}} until {{Fixation}} of a {{Mutant Gene}} in a {{Finite Population}}},
  volume = {61},
  issn = {0016-6731},
  number = {3},
  urldate = {2018-08-11},
  journal = {Genetics},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1212239/},
  author = {Kimura, Motoo and Ohta, Tomoko},
  month = mar,
  year = {1969},
  pages = {763-771},
  file = {/home/mpetersen/bib/storage/5P38WXC8/Kimura and Ohta - 1969 - The Average Number of Generations until Fixation o.pdf},
  pmid = {17248440},
  pmcid = {PMC1212239}
}

@article{Kapitonov2007,
  title = {Helitrons on a Roll: Eukaryotic Rolling-Circle Transposons},
  volume = {23},
  issn = {01689525},
  shorttitle = {Helitrons on a Roll},
  doi = {10.1016/j.tig.2007.08.004},
  language = {en},
  number = {10},
  urldate = {2018-08-13},
  journal = {Trends in Genetics},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952507002703},
  author = {Kapitonov, Vladimir V. and Jurka, Jerzy},
  month = oct,
  year = {2007},
  pages = {521-529},
  file = {/home/mpetersen/bib/storage/U2X5HXVU/Kapitonov and Jurka - 2007 - Helitrons on a roll eukaryotic rolling-circle tra.pdf}
}

@article{Pasyukova2004,
  title = {Accumulation of {{Transposable Elements}} in the {{Genome}} of {{Drosophila}} Melanogaster Is {{Associated}} with a {{Decrease}} in {{Fitness}}},
  volume = {95},
  doi = {10.1093/jhered/esh050},
  number = {4},
  journal = {Journal of Heredity},
  url = {https://doi.org/10.1093\%2Fjhered\%2Fesh050},
  author = {Pasyukova, E. G.},
  month = jul,
  year = {2004},
  pages = {284-290},
  publisher = {{Oxford University Press (OUP)}}
}

@incollection{Bennetzen2000a,
  title = {Transposable Element Contributions to Plant Gene and Genome Evolution},
  booktitle = {Plant {{Molecular Evolution}}},
  publisher = {{Springer Science Business Media}},
  url = {http://dx.doi.org/10.1007/978-94-011-4221-2_13},
  author = {Bennetzen, Jeffrey L.},
  year = {2000},
  pages = {251-269},
  doi = {10.1007/978-94-011-4221-2_13}
}

@article{Finston1995,
  title = {Genome Size Variation in Aphids},
  volume = {25},
  doi = {10.1016/0965-1748(94)00050-r},
  number = {2},
  journal = {Insect Biochemistry and Molecular Biology},
  url = {http://dx.doi.org/10.1016/0965-1748(94)00050-r},
  author = {Finston, Terrie L. and Hebert, Paul D.N. and Foottit, Robert B.},
  month = feb,
  year = {1995},
  pages = {189-196},
  publisher = {{Elsevier BV}}
}

@article{Bull1985,
  title = {Evolution of {{Sex Determining Mechanisms}}},
  volume = {49},
  doi = {10.1111/j.1469-1809.1985.tb01679.x},
  number = {1},
  journal = {Annals of Human Genetics},
  url = {https://doi.org/10.1111\%2Fj.1469-1809.1985.tb01679.x},
  author = {Bull, JJ},
  month = jan,
  year = {1985},
  pages = {85-86}
}

@article{Peona2018,
  title = {How Complete Are ``Complete'' Genome Assemblies?-{{An}} Avian Perspective},
  doi = {10.1111/1755-0998.12933},
  journal = {Molecular Ecology Resources},
  url = {https://doi.org/10.1111\%2F1755-0998.12933},
  author = {Peona, Valentina and Weissensteiner, Matthias H. and Suh, Alexander},
  month = aug,
  year = {2018},
  keywords = {long reads,repeats,birds,genomics,hybrid assembly,multiplatform sequencing},
  file = {/home/mpetersen/bib/storage/5UIIBTW3/Peona et al. - How complete are “complete” genome assemblies—An .pdf;/home/mpetersen/bib/storage/DC7PYESS/1755-0998.html},
  publisher = {{Wiley}}
}

@article{Zhang2018,
  title = {The {{piRNA}} Targeting Rules and the Resistance to {{piRNA}} Silencing in Endogenous Genes},
  volume = {359},
  issn = {0036-8075},
  doi = {10.1126/science.aao2840},
  abstract = {piRNAs silence transposons to safeguard genome integrity in animals. However, the functions of the many piRNAs that do not map to transposons remain unknown. Here we showed that piRNA targeting in C. elegans can tolerate a few mismatches but prefer perfect pairing at the seed region. The broad targeting capacity of piRNAs underlies the germline silencing of transgenes in C. elegans. Transgenes engineered to avoid piRNA recognition are stably expressed. Interestingly, many endogenous germline-expressed genes also contain predicted piRNA targeting sites, and periodic An/Tn clusters (PATCs) are an intrinsic signal that provides resistance to piRNA silencing. Together, our study revealed the piRNA targeting rules and highlights a unique strategy that C. elegans uses to distinguish endogenous from foreign nucleic acids.},
  number = {6375},
  urldate = {2018-08-15},
  journal = {Science (New York, N.Y.)},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939965/},
  author = {Zhang, Donglei and Tu, Shikui and Stubna, Michael and Wu, Wei-Sheng and Huang, Wei-Che and Weng, Zhiping and Lee, Heng-Chi},
  month = feb,
  year = {2018},
  pages = {587-592},
  file = {/home/mpetersen/bib/storage/IUM4XZVT/Zhang et al. - 2018 - The piRNA targeting rules and the resistance to pi.pdf},
  pmid = {29420292},
  pmcid = {PMC5939965}
}

@article{Yamashiro2017,
  title = {{{PIWI}}-{{Interacting RNA}} in {{Drosophila}}: {{Biogenesis Transposon Regulation}}, and {{Beyond}}},
  volume = {118},
  doi = {10.1021/acs.chemrev.7b00393},
  number = {8},
  journal = {Chemical Reviews},
  url = {https://doi.org/10.1021\%2Facs.chemrev.7b00393},
  author = {Yamashiro, Haruna and Siomi, Mikiko C.},
  month = dec,
  year = {2017},
  pages = {4404-4421},
  file = {/home/mpetersen/bib/storage/F9FTB4I2/Yamashiro and Siomi - 2018 - PIWI-Interacting RNA in iDrosophilai  Biogen.pdf},
  publisher = {{American Chemical Society (ACS)}}
}

@article{Bouallegue2017,
  title = {Diversity and Evolution of Mariner-like Elements in Aphid Genomes},
  volume = {18},
  doi = {10.1186/s12864-017-3856-6},
  number = {1},
  journal = {BMC Genomics},
  url = {https://doi.org/10.1186\%2Fs12864-017-3856-6},
  author = {Bouall\`egue, Maryem and Fil\'ee, Jonathan and Kharrat, Imen and {Mezghani-Khemakhem}, Maha and Rouault, Jacques-Deric and Makni, Mohamed and Capy, Pierre},
  month = jun,
  year = {2017},
  publisher = {{Springer Nature}}
}

@incollection{Toth2016,
  address = {Dordrecht},
  title = {The {{piRNA Pathway Guards}} the {{Germline Genome Against Transposable Elements}}},
  volume = {886},
  isbn = {978-94-017-7415-4 978-94-017-7417-8},
  urldate = {2018-08-15},
  booktitle = {Non-Coding {{RNA}} and the {{Reproductive System}}},
  publisher = {{Springer Netherlands}},
  url = {http://link.springer.com/10.1007/978-94-017-7417-8_4},
  author = {T\'oth, Katalin Fejes and Pezic, Dubravka and Stuwe, Evelyn and Webster, Alexandre},
  editor = {Wilhelm, Dagmar and Bernard, Pascal},
  year = {2016},
  pages = {51-77},
  file = {/home/mpetersen/bib/storage/MXXXNLZI/Tóth et al. - 2016 - The piRNA Pathway Guards the Germline Genome Again.pdf},
  doi = {10.1007/978-94-017-7417-8_4}
}

@article{Matsumoto2016,
  title = {Crystal {{Structure}} of {{Silkworm PIWI}}-{{Clade Argonaute Siwi Bound}} to {{piRNA}}},
  volume = {167},
  doi = {10.1016/j.cell.2016.09.002},
  number = {2},
  journal = {Cell},
  url = {https://doi.org/10.1016\%2Fj.cell.2016.09.002},
  author = {Matsumoto, Naoki and Nishimasu, Hiroshi and Sakakibara, Kazuhiro and Nishida, Kazumichi M. and Hirano, Takamasa and Ishitani, Ryuichiro and Siomi, Haruhiko and Siomi, Mikiko C. and Nureki, Osamu},
  month = oct,
  year = {2016},
  pages = {484-497.e9},
  publisher = {{Elsevier BV}}
}

@article{Krupovic2016,
  title = {Self-Synthesizing Transposons: Unexpected Key Players in the Evolution of Viruses and Defense Systems},
  volume = {31},
  issn = {13695274},
  shorttitle = {Self-Synthesizing Transposons},
  doi = {10.1016/j.mib.2016.01.006},
  language = {en},
  urldate = {2018-08-13},
  journal = {Current Opinion in Microbiology},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1369527416000084},
  author = {Krupovic, Mart and Koonin, Eugene V},
  month = jun,
  year = {2016},
  pages = {25-33},
  file = {/home/mpetersen/bib/storage/QXKKFX2S/Krupovic and Koonin - 2016 - Self-synthesizing transposons unexpected key play.pdf}
}

@article{Chaisson2015,
  title = {Genetic Variation and the de Novo Assembly of Human Genomes},
  volume = {16},
  issn = {1471-0056, 1471-0064},
  doi = {10.1038/nrg3933},
  language = {en},
  number = {11},
  urldate = {2018-08-15},
  journal = {Nature Reviews Genetics},
  url = {http://www.nature.com/articles/nrg3933},
  author = {Chaisson, Mark J. P. and Wilson, Richard K. and Eichler, Evan E.},
  month = nov,
  year = {2015},
  pages = {627-640}
}

@phdthesis{Sambaturu2014,
  address = {Singapore},
  title = {Towards {{Handling Repeats}} in {{Genome Assembly}}},
  language = {en},
  school = {National University of Singapore},
  author = {Sambaturu, Narmada},
  year = {2014},
  doi = {10.13140/2.1.1482.3207}
}

@article{Li2018,
  title = {Multiple Large-Scale Gene and Genome Duplications during the Evolution of Hexapods},
  volume = {115},
  copyright = {\textcopyright{} 2018 . Published under the PNAS license.},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1710791115},
  abstract = {Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.},
  language = {en},
  number = {18},
  urldate = {2018-08-17},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/content/115/18/4713},
  author = {Li, Zheng and Tiley, George P. and Galuska, Sally R. and Reardon, Chris R. and Kidder, Thomas I. and Rundell, Rebecca J. and Barker, Michael S.},
  month = may,
  year = {2018},
  keywords = {polyploidy,genomics,genome duplication,hexapods,insects},
  pages = {4713-4718},
  file = {/home/mpetersen/bib/storage/INDSRJHX/4713.html},
  pmid = {29674453}
}

@misc{Smit2015,
  title = {{{RepeatMasker Open}}-4.0},
  url = {http://www.repeatmasker.org},
  author = {Smit, AFA and Hubley, R and Green, P},
  year = {2015}
}

@article{Werren2010a,
  title = {Functional and {{Evolutionary Insights}} from the {{Genomes}} of {{Three Parasitoid Nasonia Species}}},
  volume = {327},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1178028},
  language = {English},
  number = {5963},
  urldate = {2014-10-23},
  journal = {Science},
  url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1178028},
  author = {Werren, J. H. and Richards, S. and Desjardins, C. A. and Niehuis, O. and Gadau, J. and Colbourne, J. K. and {The Nasonia Genome Working Group} and Beukeboom, L. W. and Desplan, C. and Elsik, C. G. and Grimmelikhuijzen, C. J. P. and Kitts, P. and Lynch, J. A. and Murphy, T. and Oliveira, D. C. S. G. and Smith, C. D. and {v. d. Zande}, L. and Worley, K. C. and Zdobnov, E. M. and Aerts, M. and Albert, S. and Anaya, V. H. and Anzola, J. M. and Barchuk, A. R. and Behura, S. K. and Bera, A. N. and Berenbaum, M. R. and Bertossa, R. C. and Bitondi, M. M. G. and Bordenstein, S. R. and Bork, P. and {Bornberg-Bauer}, E. and Brunain, M. and Cazzamali, G. and Chaboub, L. and Chacko, J. and Chavez, D. and Childers, C. P. and Choi, J.-H. and Clark, M. E. and Claudianos, C. and Clinton, R. A. and Cree, A. G. and Cristino, A. S. and Dang, P. M. and Darby, A. C. and {de Graaf}, D. C. and Devreese, B. and Dinh, H. H. and Edwards, R. and Elango, N. and Elhaik, E. and Ermolaeva, O. and Evans, J. D. and Foret, S. and Fowler, G. R. and Gerlach, D. and Gibson, J. D. and Gilbert, D. G. and Graur, D. and Grunder, S. and Hagen, D. E. and Han, Y. and Hauser, F. and Hultmark, D. and Hunter, H. C. and Hurst, G. D. D. and Jhangian, S. N. and Jiang, H. and Johnson, R. M. and Jones, A. K. and Junier, T. and Kadowaki, T. and Kamping, A. and Kapustin, Y. and Kechavarzi, B. and Kim, J. and Kim, J. and Kiryutin, B. and Koevoets, T. and Kovar, C. L. and Kriventseva, E. V. and Kucharski, R. and Lee, H. and Lee, S. L. and Lees, K. and Lewis, L. R. and Loehlin, D. W. and Logsdon, J. M. and Lopez, J. A. and Lozado, R. J. and Maglott, D. and Maleszka, R. and Mayampurath, A. and Mazur, D. J. and McClure, M. A. and Moore, A. D. and Morgan, M. B. and Muller, J. and {Munoz-Torres}, M. C. and Muzny, D. M. and Nazareth, L. V. and Neupert, S. and Nguyen, N. B. and Nunes, F. M. F. and Oakeshott, J. G. and Okwuonu, G. O. and Pannebakker, B. A. and Pejaver, V. R. and Peng, Z. and Pratt, S. C. and Predel, R. and Pu, L.-L. and Ranson, H. and Raychoudhury, R. and Rechtsteiner, A. and Reid, J. G. and Riddle, M. and {Romero-Severson}, J. and Rosenberg, M. and Sackton, T. B. and Sattelle, D. B. and Schluns, H. and Schmitt, T. and Schneider, M. and Schuler, A. and Schurko, A. M. and Shuker, D. M. and Simoes, Z. L. P. and Sinha, S. and Smith, Z. and Souvorov, A. and Springauf, A. and Stafflinger, E. and Stage, D. E. and Stanke, M. and Tanaka, Y. and Telschow, A. and Trent, C. and Vattathil, S. and Viljakainen, L. and Wanner, K. W. and Waterhouse, R. M. and Whitfield, J. B. and Wilkes, T. E. and Williamson, M. and Willis, J. H. and Wolschin, F. and Wyder, S. and Yamada, T. and Yi, S. V. and Zecher, C. N. and Zhang, L. and Gibbs, R. A.},
  month = jan,
  year = {2010},
  keywords = {Animals,Sequence Analysis,DNA,Genetic Speciation,Genome,Genetic,Genetic Variation,Molecular Sequence Data,Genes,Insect Proteins,Biological Evolution,Arthropods,Quantitative Trait Loci,nasonia,wasp,Male,DNA Transposable Elements,Female,DNA Methylation,Host-Parasite Interactions,Insect Viruses,Insects,Wasp Venoms,Wasps,Wolbachia,Insect,Gene Transfer,Horizontal,Recombination},
  pages = {343-348}
}

@article{Smit2015c,
  title = {{{RepeatMasker Open}}-4.0},
  url = {http://www.repeatmasker.org},
  author = {Smit, AFA and Hubley, R and Green, P},
  year = {2015}
}

@article{Smit2015b,
  title = {{{RepeatModeler Open}}-1.0},
  url = {http://www.repeatmasker.org},
  author = {Smit, AFA and Hubley, R},
  year = {2015}
}

@article{Maumus2015,
  title = {Impact of {{Transposable Elements}} on {{Insect Genomes}} and {{Biology}}},
  volume = {7},
  doi = {10.1016/j.cois.2015.01.001},
  journal = {Current Opinion in Insect Science},
  url = {http://dx.doi.org/10.1016/j.cois.2015.01.001},
  author = {Maumus, Florian and {Fiston-Lavier}, Anna-Sophie and Quesneville, Hadi},
  month = feb,
  year = {2015},
  pages = {30-36},
  file = {/home/mpetersen/bib/storage/7W97ZJDT/1-s2.0-S2214574515000048-main.pdf;/home/mpetersen/bib/storage/RWAPYVWF/1-s2.0-S2214574515000048-main.pdf}
}

@article{Kelley2014,
  title = {Compact {{Genome}} of the {{Antarctic Midge Is Likely}} an {{Adaptation}} to an {{Extreme Environment}}},
  volume = {5},
  issn = {2041-1723},
  doi = {10.1038/ncomms5611},
  urldate = {2014-08-27},
  journal = {Nature Communications},
  url = {http://www.nature.com/doifinder/10.1038/ncomms5611},
  author = {Kelley, Joanna L. and Peyton, Justin T. and {Fiston-Lavier}, Anna-Sophie and Teets, Nicholas M. and Yee, Muh-Ching and Johnston, J. Spencer and Bustamante, Carlos D. and Lee, Richard E. and Denlinger, David L.},
  month = aug,
  year = {2014}
}

@article{Wang2014,
  title = {The {{Locust Genome Provides Insight}} into {{Swarm Formation}} and {{Long}}-{{Distance Flight}}},
  volume = {5},
  issn = {2041-1723},
  doi = {10.1038/ncomms3957},
  urldate = {2014-09-18},
  journal = {Nature Communications},
  url = {http://www.nature.com/doifinder/10.1038/ncomms3957},
  author = {Wang, Xianhui and Fang, Xiaodong and Yang, Pengcheng and Jiang, Xuanting and Jiang, Feng and Zhao, Dejian and Li, Bolei and Cui, Feng and Wei, Jianing and Ma, Chuan and Wang, Yundan and He, Jing and Luo, Yuan and Wang, Zhifeng and Guo, Xiaojiao and Guo, Wei and Wang, Xuesong and Zhang, Yi and Yang, Meiling and Hao, Shuguang and Chen, Bing and Ma, Zongyuan and Yu, Dan and Xiong, Zhiqiang and Zhu, Yabing and Fan, Dingding and Han, Lijuan and Wang, Bo and Chen, Yuanxin and Wang, Junwen and Yang, Lan and Zhao, Wei and Feng, Yue and Chen, Guanxing and Lian, Jinmin and Li, Qiye and Huang, Zhiyong and Yao, Xiaoming and Lv, Na and Zhang, Guojie and Li, Yingrui and Wang, Jian and Wang, Jun and Zhu, Baoli and Kang, Le},
  month = jan,
  year = {2014},
  keywords = {Genome,Evolution,locusta migratoria,genetics,Biological sciences},
  file = {/home/mpetersen/bib/storage/DP8D8KTD/Locust_ncomms3957.pdf;/home/mpetersen/bib/storage/ESTR3DRT/Locust_ncomms3957.pdf}
}

@article{Misof2014,
  title = {Phylogenomics {{Resolves}} the {{Timing}} and {{Pattern}} of {{Insect Evolution}}.},
  volume = {346},
  doi = {10.1126/science.1257570},
  journal = {Science},
  author = {Misof, B and Liu, S and Meusemann, K and Peters, RS and Donath, A and Mayer, C and Frandsen, PB and Ware, J and Flouri, T and Beutel, RG and Niehuis, O and Petersen, M and {Izquierdo-Carrasco}, F and Wappler, T and Rust, J and Aberer, AJ and Asp\"ock, U and Asp\"ock, H and Bartel, D and Blanke, A and Berger, S and B\"ohm, A and Buckley, TR and Calcott, B and Chen, J and Friedrich, F and Fukui, M and Fujita, M and Greve, C and Grobe, P and Gu, S and Huang, Y and Jermiin, LS and Kawahara, AY and Krogmann, L and Kubiak, M and Lanfear, R and Letsch, H and Li, Y and Li, Z and Li, J and Lu, H and Machida, R and Mashimo, Y and Kapli, P and McKenna, DD and Meng, G and Nakagaki, Y and {Navarrete-Heredia}, JL and Ott, M and Ou, Y and Pass, G and Podsiadlowski, L and Pohl, H and {von}, Reumont BM and Sch\"utte, K and Sekiya, K and Shimizu, S and Slipinski, A and Stamatakis, A and Song, W and Su, X and Szucsich, NU and Tan, M and Tan, X and Tang, M and Tang, J and Timelthaler, G and Tomizuka, S and Trautwein, M and Tong, X and Uchifune, T and Walzl, MG and Wiegmann, BM and Wilbrandt, J and Wipfler, B and Wong, TK and Wu, Q and Wu, G and Xie, Y and Yang, S and Yang, Q and Yeates, DK and Yoshizawa, K and Zhang, Q and Zhang, R and Zhang, W and Zhang, Y and Zhao, J and Zhou, C and Zhou, L and Ziesmann, T and Zou, S and Li, Y and Xu, X and Zhang, Y and Yang, H and Wang, J and Wang, J and Kjer, KM and Zhou, X},
  year = {2014},
  pages = {763-7},
  file = {/home/mpetersen/bib/storage/2CNATZJQ/Science-2014-Misof-763-7.pdf;/home/mpetersen/bib/storage/TRD9WSRU/1257570.Misof.SM.pdf},
  source = {Science},
  authors = {Misof, B and Liu, S and Meusemann, K and Peters, RS and Donath, A and Mayer, C and Frandsen, PB and Ware, J and Flouri, T and Beutel, RG and Niehuis, O and Petersen, M and Izquierdo-Carrasco, F and Wappler, T and Rust, J and Aberer, AJ and Aspöck, U and Aspöck, H and Bartel, D and Blanke, A and Berger, S and Böhm, A and Buckley, TR and Calcott, B and Chen, J and Friedrich, F and Fukui, M and Fujita, M and Greve, C and Grobe, P and Gu, S and Huang, Y and Jermiin, LS and Kawahara, AY and Krogmann, L and Kubiak, M and Lanfear, R and Letsch, H and Li, Y and Li, Z and Li, J and Lu, H and Machida, R and Mashimo, Y and Kapli, P and McKenna, DD and Meng, G and Nakagaki, Y and Navarrete-Heredia, JL and Ott, M and Ou, Y and Pass, G and Podsiadlowski, L and Pohl, H and von, Reumont BM and Schütte, K and Sekiya, K and Shimizu, S and Slipinski, A and Stamatakis, A and Song, W and Su, X and Szucsich, NU and Tan, M and Tan, X and Tang, M and Tang, J and Timelthaler, G and Tomizuka, S and Trautwein, M and Tong, X and Uchifune, T and Walzl, MG and Wiegmann, BM and Wilbrandt, J and Wipfler, B and Wong, TK and Wu, Q and Wu, G and Xie, Y and Yang, S and Yang, Q and Yeates, DK and Yoshizawa, K and Zhang, Q and Zhang, R and Zhang, W and Zhang, Y and Zhao, J and Zhou, C and Zhou, L and Ziesmann, T and Zou, S and Li, Y and Xu, X and Zhang, Y and Yang, H and Wang, J and Wang, J and Kjer, KM and Zhou, X},
  pubmed_id = {25378627}
}

@article{Niehuis2012,
  title = {Genomic and {{Morphological Evidence Converge}} to {{Resolve}} the {{Enigma}} of {{Strepsiptera}}},
  volume = {22},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2012.05.018},
  abstract = {Summary The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention [1\textendash{}3]. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate [1,~2,~4\textendash{}11]. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct~(hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects [1, 12, 13]. Here we report the sequencing of~a Strepsiptera genome and show that the analysis of sequence-based genomic data (comprising more than 18 million nucleotides from nearly 4,500 genes obtained from a total of 13 insect genomes), along with genomic metacharacters, clarifies the phylogenetic origin of Strepsiptera and~sheds light on~the evolution of holometabolous insect development. Our results provide overwhelming support for Strepsiptera as the closest living relatives of beetles (Coleoptera). They~demonstrate that the larval developmental features of Strepsiptera, reminiscent of those of hemimetabolous insects, are the result of convergence. Our analyses solve the long-standing enigma of the evolutionary roots of Strepsiptera and reveal that the holometabolous mode of insect development is more malleable than previously thought.},
  number = {14},
  urldate = {2017-10-16},
  journal = {Current Biology},
  url = {http://www.sciencedirect.com/science/article/pii/S0960982212005714},
  author = {Niehuis, Oliver and Hartig, Gerrit and Grath, Sonja and Pohl, Hans and Lehmann, J\"org and Tafer, Hakim and Donath, Alexander and Krauss, Veiko and Eisenhardt, Carina and Hertel, Jana and Petersen, Malte and Mayer, Christoph and Meusemann, Karen and Peters, Ralph S. and Stadler, Peter F. and Beutel, Rolf G. and {Bornberg-Bauer}, Erich and McKenna, Duane D. and Misof, Bernhard},
  month = jul,
  year = {2012},
  pages = {1309-1313},
  file = {/home/mpetersen/bib/storage/WXKC6CPS/Niehuis et al. - 2012 - Genomic and Morphological Evidence Converge to Res.pdf;/home/mpetersen/bib/storage/ZEHFPENW/S0960982212005714.html}
}

@article{Gregory2018a,
  title = {Animal {{Genome Size Database}}},
  url = {http://www.genomesize.com},
  author = {Gregory, T. Ryan},
  year = {2018}
}

@article{Dufresne2011a,
  title = {A {{Guided Tour}} of {{Large Genome Size}} in {{Animals}}: {{What We Know}} and {{Where We Are Heading}}},
  volume = {19},
  issn = {0967-3849, 1573-6849},
  shorttitle = {A {{Guided Tour}} of {{Large Genome Size}} in {{Animals}}},
  doi = {10.1007/s10577-011-9248-x},
  language = {English},
  number = {7},
  urldate = {2018-02-27},
  journal = {Chromosome Research},
  url = {http://link.springer.com/10.1007/s10577-011-9248-x},
  author = {Dufresne, France and Jeffery, Nicholas},
  month = oct,
  year = {2011},
  pages = {925-938}
}

@article{Gregory2008,
  title = {Genome {{Size Diversity}} in the {{Family Drosophilidae}}},
  volume = {101},
  issn = {0018-067X, 1365-2540},
  doi = {10.1038/hdy.2008.49},
  language = {English},
  number = {3},
  urldate = {2018-02-27},
  journal = {Heredity},
  url = {http://www.nature.com/articles/hdy200849},
  author = {Gregory, T R and Johnston, J S},
  month = sep,
  year = {2008},
  keywords = {Drosophila,transposable elements,C value,developmental rate,flow cytometry,satellite DNA},
  pages = {228-238}
}

@article{Sato2010a,
  title = {Teleost {{Fish}} with {{Specific Genome Duplication}} as {{Unique Models}} of {{Vertebrate Evolution}}},
  volume = {88},
  issn = {0378-1909, 1573-5133},
  doi = {10.1007/s10641-010-9628-7},
  abstract = {Whole-genome duplication (WGD) is believed to be one of the major evolutionary events that shaped the genome organization of vertebrates. Here, we review recent research on vertebrate genome evolution, specifically on WGD and its consequences for gene and genome evolution in teleost fishes. Recent genome analyses confirmed that all vertebrates experienced two rounds of WGD early in their evolution, and that teleosts experienced a subsequent additional third-round (3R)-WGD. The 3R-WGD was estimated to have occurred 320\textendash{}400 million years ago in a teleost ancestor, but after its divergence from a common ancestor with living non-teleost actinopterygians (Bichir, Sturgeon, Bowfin, and Gar) based on the analyses of teleost-specific duplicate genes. This 3R-WGD was confirmed by synteny analysis and ancestral karyotype inference using the genome sequences of Tetraodon and medaka. Most of the tetrapods, on the other hand, have not experienced an additional WGD; however, they have experienced repeated chromosomal rearrangements throughout the whole genome. Therefore, different types of chromosomal events have characterized the genomes of teleosts and tetrapods, respectively. The 3R-WGD is useful to investigate the consequences of WGD because it is an evolutionarily recent WGD and thus teleost genomes retain many more WGD-derived duplicates and ``traces'' of their evolution. In addition, the remarkable morphological, physiological, and ecological diversity of teleosts may facilitate understanding of macrophenotypic evolution on the basis of genetic/genomic information. We highlight the teleosts with 3R-WGD as unique models for future studies on ecology and evolution taking advantage of emerging genomics technologies and systems biology environments.},
  language = {English},
  number = {2},
  urldate = {2018-04-10},
  journal = {Environmental Biology of Fishes},
  url = {https://link.springer.com/article/10.1007/s10641-010-9628-7},
  author = {Sato, Yukuto and Nishida, Mutsumi},
  month = jun,
  year = {2010},
  pages = {169-188}
}

@article{Blanco-Bercial2011a,
  title = {Molecular {{Phylogeny}} of the {{Calanoida}} ({{Crustacea}}: {{Copepoda}})},
  volume = {59},
  issn = {1055-7903},
  shorttitle = {Molecular {{Phylogeny}} of the {{Calanoida}} ({{Crustacea}}},
  doi = {10.1016/j.ympev.2011.01.008},
  abstract = {The order Calanoida includes some of the most successful planktonic groups in both marine and freshwater environments. Due to the morphological complexity of the taxonomic characters in this group, subdivision and phylogenies have been complex and problematic. This study establishes a multi-gene molecular phylogeny of the calanoid copepods based upon small (18S) and large (28S) subunits of nuclear ribosomal RNA genes and mitochondrial encoded cytochrome b and cytochrome c oxidase subunit-I genes, including 29 families from 7 superfamilies of the order. This analysis is more comprehensive than earlier studies in terms of number of families, range of molecular markers, and breadth of taxonomic levels resolved. Patterns of divergence of ribosomal RNA genes are shown to be significantly heterogeneous among superfamilies, providing a likely explanation for disparate results of previous studies. The multi-gene phylogeny recovers a monophyletic Calanoida, as well as the superfamilies Augaptiloidea, Centropagoidea, Bathypontioidea, Eucalanoidea, Spinocalanoidea and Clausocalanoidea. The phylogeny largely agrees with previously-published morphological phylogenies, including e.g., enlargement of the Bathypontioidea to include the Fosshageniidae.},
  number = {1},
  urldate = {2018-04-17},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://www.sciencedirect.com/science/article/pii/S105579031100025X},
  author = {{Blanco-Bercial}, Leocadio and {Bradford-Grieve}, Janet and Bucklin, Ann},
  month = apr,
  year = {2011},
  keywords = {18S,28S,Calanoid copepods,COI,Cyt,Molecular phylogeny},
  pages = {103-113}
}

@article{Eyun2017a,
  title = {Phylogenomic {{Analysis}} of {{Copepoda}} ({{Arthropoda}}, {{Crustacea}}) {{Reveals Unexpected Similarities}} with {{Earlier Proposed Morphological Phylogenies}}},
  volume = {17},
  issn = {1471-2148},
  doi = {10.1186/s12862-017-0883-5},
  abstract = {Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.},
  urldate = {2018-04-17},
  journal = {BMC Evolutionary Biology},
  url = {https://doi.org/10.1186/s12862-017-0883-5},
  author = {Eyun, Seong-il},
  month = jan,
  year = {2017},
  keywords = {Phylogeny,Phylogenomics,Arthropoda,Copepoda,Crustacea,Divergence time},
  pages = {23},
  file = {/home/mpetersen/bib/storage/IBLMY3WF/Eyun - 2017 - Phylogenomic analysis of Copepoda (Arthropoda, Cru.pdf;/home/mpetersen/bib/storage/W7XXEY6H/s12862-017-0883-5.html}
}

@article{Figueroa2011a,
  title = {Phylogenetic {{Analysis}} of {{Ridgewayia}} ({{Copepoda}}: {{Calanoida}}) from the {{Galapagos}} and of a {{New Species}} from the {{Florida Keys With}} a {{Reevaluation}} of the {{Phylogeny}} of {{Calanoida}}},
  volume = {31},
  issn = {0278-0372, 1937-240X},
  shorttitle = {Phylogenetic {{Analysis}} of {{Ridgewayia}} ({{Copepoda}}},
  doi = {10.1651/10-3341.1},
  language = {English},
  number = {1},
  urldate = {2018-04-18},
  journal = {Journal of Crustacean Biology},
  url = {https://academic.oup.com/jcb/article-lookup/doi/10.1651/10-3341.1},
  author = {Figueroa, Diego F.},
  month = feb,
  year = {2011},
  pages = {153-165}
}

@article{Ortiz-Rivas2010a,
  title = {Combination of {{Molecular Data Support}} the {{Existence}} of {{Three Main Lineages}} in the {{Phylogeny}} of {{Aphids}} ({{Hemiptera}}: {{Aphididae}}) and the {{Basal Position}} of the {{Subfamily Lachninae}}},
  volume = {55},
  issn = {10557903},
  shorttitle = {Combination of {{Molecular Data Support}} the {{Existence}} of {{Three Main Lineages}} in the {{Phylogeny}} of {{Aphids}} ({{Hemiptera}}},
  doi = {10.1016/j.ympev.2009.12.005},
  language = {English},
  number = {1},
  urldate = {2018-04-24},
  journal = {Molecular Phylogenetics and Evolution},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790309005119},
  author = {{Ortiz-Rivas}, Benjam\'in and {Mart\'inez-Torres}, David},
  month = apr,
  year = {2010},
  pages = {305-317}
}

@article{Zhang2013a,
  title = {The {{Phylogeny}} of the {{Orthoptera}} ({{Insecta}}) as {{Deduced}} from {{Mitogenomic Gene Sequences}}},
  volume = {52},
  issn = {1810-522X},
  doi = {10.1186/1810-522X-52-37},
  abstract = {The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.},
  urldate = {2018-05-11},
  journal = {Zoological Studies},
  url = {https://doi.org/10.1186/1810-522X-52-37},
  author = {Zhang, Hong-Li and Huang, Yuan and Lin, Li-Liang and Wang, Xiao-Yang and Zheng, Zhe-Min},
  month = oct,
  year = {2013},
  keywords = {Phylogeny,Protein-coding genes,Acrididae,Orthoptera,Ribosomal RNA},
  pages = {37},
  file = {/home/mpetersen/bib/storage/GWNFWF4Y/Zhang et al. - 2013 - The phylogeny of the Orthoptera (Insecta) as deduc.pdf;/home/mpetersen/bib/storage/MYTLSF87/1810-522X-52-37.html}
}

@article{Hanrahan2011a,
  title = {New {{Genome Size Estimates}} of 134 {{Species}} of {{Arthropods}}},
  volume = {19},
  issn = {0967-3849, 1573-6849},
  doi = {10.1007/s10577-011-9231-6},
  language = {English},
  number = {6},
  urldate = {2018-05-22},
  journal = {Chromosome Research},
  url = {http://link.springer.com/10.1007/s10577-011-9231-6},
  author = {Hanrahan, Shawn Jason and Johnston, J. Spencer},
  month = aug,
  year = {2011},
  pages = {809-823}
}

@article{Cranston2011a,
  title = {A {{Dated Molecular Phylogeny}} for the {{Chironomidae}} ({{Diptera}})},
  volume = {37},
  issn = {1365-3113},
  doi = {10.1111/j.1365-3113.2011.00603.x},
  abstract = {We provide the first highly sampled phylogeny estimate for the dipteran family Chironomidae using molecular data from fragments of two ribosomal genes (18S and 28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed-model Bayesian and maximum likelihood inference methods. The most recently described subfamilies Chilenomyiinae and Usambaromyiinae proved elusive, and are unsampled. We confirm monophyly of all sampled subfamilies except Prodiamesinae, which contains Propsilocerus Kieffer, previously in Orthocladiinae. The semifamily Chironomoinae is confirmed only if Telmatogetoninae is included, which is closer to Brundin's original suggestion. Buchonomyiinae is excluded from Chironomoinae: it is a sister group to all remaining Chironomidae, conforming more to Murray and Ashe's argumentation. Semifamily Tanypodoinae is a grade and unsupported as monophyletic: the austral Aphroteniinae alone is sister to all Chironomidae (less Buchonomyiinae). Podonominae is weakly supported as the next sister group, in contrast to some estimates that place this subfamily as sister group to Tanypodinae alone. In Diamesinae, the southern African Harrisonini is confirmed as a member, but embedded within austral tribe Heptagiini, which is confirmed as sister to the undersampled Diamesini. Tribe Pentaneurini and `non-Pentaneurini' taxa are reciprocally monophyletic in Tanypodinae. Recent molecular findings concerning Podonominae are substantiated, with a monophyletic tribe Podonomini, Boreochlini forming a grade and Lasiodiamesa Kieffer placed as sister to all other Podonominae, but with uncertainty. In Orthocladiinae, a postulated two-tribe system of Orthocladiini and Metriocnemini can be supported after exclusion of a Corynoneura group and a Brillia group, which is revealed as sister to Stictocladius Edwards. The marine Clunio Haliday and Thalassosmittia Strenzke \& Remmert (given high rank in the past) are clearly embedded deep in Orthocladiinae. The finding of Shangomyia S\ae{}ther \& Wang + Xyiaomyia S\ae{}ther \& Wang as sister group to all other Chironominae justifies high rank, as their authors suggested. Pseudochironomini (untested by sampling shortfall) is sister to a monophyletic Tanytarsini (with a weakly supported inclusion of the enigmatic Nandeva Wiedenbrug, Reiss \& Fittkau). The tribe Chironomini can be supported only by excluding Shangomyia + Xyiaomyia, and a postulated monophyletic clade comprising several taxa such as Microtendipes Kieffer, with six-segmented larval antennae and alternate Lauterborn organs, that is sister group to Pseudochironomini + Tanytarsini. The tempo of diversification of the family, deduced by divergence time analysis (beast), shows Permian origination with subfamily stem-group origination from the mid\textendash{}late Triassic to the early Cretaceous. Crown-group origination ranged from Podonominae on a short stem originating in the mid Jurassic to long-stemmed Aphroteninae from the late Cretaceous. Node dates allow inference of some vicariance via Gondwanan fragmentation, including certain nodes involving southern Africa.},
  language = {English},
  number = {1},
  urldate = {2018-06-05},
  journal = {Systematic Entomology},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3113.2011.00603.x},
  author = {Cranston, Peter S. and Hardy, Nate B. and Morse, Geoffrey E.},
  year = {2011},
  pages = {172-188},
  copyright = {© 2011 The Authors. Systematic Entomology © 2011 The Royal Entomological Society}
}

@article{Waterhouse2011a,
  title = {{{OrthoDB}}: The Hierarchical Catalog of Eukaryotic Orthologs in 2011},
  volume = {39},
  issn = {1362-4962},
  shorttitle = {{{OrthoDB}}},
  doi = {10.1093/nar/gkq930},
  abstract = {The concept of homology drives speculation on a gene's function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation homologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scale delineation of gene genealogies is a challenging task, and the numerous approaches to the problem reflect the importance of the concept of orthology as a cornerstone for comparative studies. Here, we present the updated OrthoDB catalog of eukaryotic orthologs delineated at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi (including the metazoa level). New database features include functional annotations, and quantification of evolutionary divergence and relations among orthologous groups. The interface features extended phyletic profile querying and enhanced text-based searches. The ever-increasing sampling of sequenced eukaryotic genomes brings a clearer account of the majority of gene genealogies that will facilitate informed hypotheses of gene function in newly sequenced genomes. Furthermore, uniform analysis across lineages as different as vertebrates, arthropods and fungi with divergence levels varying from several to hundreds of millions of years will provide essential data for uncovering and quantifying long-term trends of gene evolution. OrthoDB is freely accessible from http://cegg.unige.ch/orthodb.},
  language = {eng},
  number = {Database issue},
  journal = {Nucleic Acids Research},
  author = {Waterhouse, Robert M. and Zdobnov, Evgeny M. and Tegenfeldt, Fredrik and Li, Jia and Kriventseva, Evgenia V.},
  month = jan,
  year = {2011},
  keywords = {Animals,Phylogeny,Genomics,Fungi,Genes,Proteins,Saccharomyces cerevisiae,Databases; Genetic,Evolution; Molecular,Mice,Protein Structure; Tertiary,Molecular Sequence Annotation,Sequence Homology; Amino Acid,Arthropods,Drosophila melanogaster,Vertebrates},
  pages = {D283-288},
  pmid = {20972218},
  pmcid = {PMC3013786}
}

@article{Gillung2018a,
  title = {Anchored Phylogenomics Unravels the Evolution of Spider Flies ({{Diptera}}, {{Acroceridae}}) and Reveals Discordance between Nucleotides and Amino Acids},
  volume = {128},
  issn = {10557903},
  doi = {10.1016/j.ympev.2018.08.007},
  language = {en},
  urldate = {2018-09-06},
  journal = {Molecular Phylogenetics and Evolution},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S1055790318302239},
  author = {Gillung, Jessica P. and Winterton, Shaun L. and Bayless, Keith M. and Khouri, Ziad and Borowiec, Marek L. and Yeates, David and Kimsey, Lynn S. and Misof, Bernhard and Shin, Seunggwan and Zhou, Xin and Mayer, Christoph and Petersen, Malte and Wiegmann, Brian M.},
  month = nov,
  year = {2018},
  pages = {233-245}
}

@article{Johnson2018,
  title = {Phylogenomics and the Evolution of Hemipteroid Insects},
  volume = {115},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1815820115},
  language = {en},
  number = {50},
  urldate = {2018-12-17},
  journal = {Proceedings of the National Academy of Sciences},
  url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1815820115},
  author = {Johnson, Kevin P. and Dietrich, Christopher H. and Friedrich, Frank and Beutel, Rolf G. and Wipfler, Benjamin and Peters, Ralph S. and Allen, Julie M. and Petersen, Malte and Donath, Alexander and Walden, Kimberly K. O. and Kozlov, Alexey M. and Podsiadlowski, Lars and Mayer, Christoph and Meusemann, Karen and Vasilikopoulos, Alexandros and Waterhouse, Robert M. and Cameron, Stephen L. and Weirauch, Christiane and Swanson, Daniel R. and Percy, Diana M. and Hardy, Nate B. and Terry, Irene and Liu, Shanlin and Zhou, Xin and Misof, Bernhard and Robertson, Hugh M. and Yoshizawa, Kazunori},
  month = dec,
  year = {2018},
  pages = {12775-12780}
}

@article{Petersen2019,
  title = {Diversity and Evolution of the Transposable Element Repertoire in Arthropods with Particular Reference to Insects},
  volume = {19},
  issn = {1471-2148},
  doi = {10.1186/s12862-018-1324-9},
  language = {en},
  number = {1},
  urldate = {2019-01-15},
  journal = {BMC Evolutionary Biology},
  url = {https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-018-1324-9},
  author = {Petersen, Malte and Armis\'en, David and Gibbs, Richard A. and Hering, Lars and Khila, Abderrahman and Mayer, Georg and Richards, Stephen and Niehuis, Oliver and Misof, Bernhard},
  month = dec,
  year = {2019},
  file = {/home/mpetersen/bib/storage/7EKCHFDJ/s12862-018-1324-9}
}

@article{Wipfler2019,
  title = {Evolutionary History of {{Polyneoptera}} and Its Implications for Our Understanding of Early Winged Insects},
  copyright = {\textcopyright{} 2019 . Published under the PNAS license.},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1817794116},
  abstract = {Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.},
  language = {en},
  urldate = {2019-01-20},
  journal = {Proceedings of the National Academy of Sciences},
  url = {https://www.pnas.org/content/early/2019/01/08/1817794116},
  author = {Wipfler, Benjamin and Letsch, Harald and Frandsen, Paul B. and Kapli, Paschalia and Mayer, Christoph and Bartel, Daniela and Buckley, Thomas R. and Donath, Alexander and {Edgerly-Rooks}, Janice S. and Fujita, Mari and Liu, Shanlin and Machida, Ryuichiro and Mashimo, Yuta and Misof, Bernhard and Niehuis, Oliver and Peters, Ralph S. and Petersen, Malte and Podsiadlowski, Lars and Sch\"utte, Kai and Shimizu, Shota and Uchifune, Toshiki and Wilbrandt, Jeanne and Yan, Evgeny and Zhou, Xin and Simon, Sabrina},
  month = jan,
  year = {2019},
  keywords = {phylogenomics,lower winged insects,Neoptera,Polyneoptera,Pterygota},
  pages = {201817794},
  file = {/home/mpetersen/bib/storage/FW4RY2V3/1817794116.html},
  pmid = {30642969}
}

@article{Evans2018,
  title = {Genome of the Small Hive Beetle ({{Aethina}} Tumida, {{Coleoptera}}: {{Nitidulidae}}), a Worldwide Parasite of Social Bee Colonies, Provides Insights into Detoxification and Herbivory},
  volume = {7},
  shorttitle = {Genome of the Small Hive Beetle ({{Aethina}} Tumida, {{Coleoptera}}},
  doi = {10.1093/gigascience/giy138},
  abstract = {AbstractBackground.  The small hive beetle (Aethina tumida; ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, fa},
  language = {en},
  number = {12},
  urldate = {2019-03-28},
  journal = {GigaScience},
  url = {https://academic.oup.com/gigascience/article/7/12/giy138/5232982},
  author = {Evans, Jay D. and McKenna, Duane and Scully, Erin and Cook, Steven C. and Dainat, Benjamin and Egekwu, Noble and Grubbs, Nathaniel and Lopez, Dawn and Lorenzen, Marc\'e D. and Reyna, Steven M. and Rinkevich, Frank D. and Neumann, Peter and Huang, Qiang},
  month = dec,
  year = {2018},
  file = {/home/mpetersen/bib/storage/SZHUNJ9L/Evans et al. - 2018 - Genome of the small hive beetle (Aethina tumida, C.pdf;/home/mpetersen/bib/storage/H9YQHIVK/5232982.html}
}

@article{Paterson2017,
  title = {Plodia Interpunctella Strain {{Dundee}}, Whole Genome Shotgun Sequencing Project},
  copyright = {Public domain},
  lccn = {FXST00000000.1},
  language = {en-US},
  urldate = {2019-03-28},
  journal = {NCBI nucleotide database},
  url = {http://www.ncbi.nlm.nih.gov/nuccore/FXST00000000.1},
  author = {Paterson, Steve},
  month = may,
  year = {2017},
  keywords = {dna,Indianmeal moth,insd},
  note = {\{:itemType: dataset\}}
}

@article{Arkhipova2018,
  title = {Neutral {{Theory}}, {{Transposable Elements}}, and {{Eukaryotic Genome Evolution}}},
  volume = {35},
  issn = {0737-4038},
  doi = {10.1093/molbev/msy083},
  abstract = {Abstract.  Among the multitude of papers published yearly in scientific journals, precious few publications may be worth looking back in half a century to appre},
  language = {en},
  number = {6},
  urldate = {2019-03-28},
  journal = {Molecular Biology and Evolution},
  url = {https://academic.oup.com/mbe/article/35/6/1332/4983858},
  author = {Arkhipova, Irina R.},
  month = jun,
  year = {2018},
  pages = {1332-1337},
  file = {/home/mpetersen/bib/storage/D2TBUJJA/Arkhipova - 2018 - Neutral Theory, Transposable Elements, and Eukaryo.pdf;/home/mpetersen/bib/storage/M7KG9LZ7/4983858.html}
}

@article{Robinson2014,
  title = {Megachile Rotundata, Whole Genome Shotgun Sequencing Project},
  copyright = {Public domain},
  lccn = {AFJA00000000.1},
  language = {en-US},
  urldate = {2019-03-28},
  journal = {NCBI nucleotide database},
  url = {http://www.ncbi.nlm.nih.gov/nuccore/AFJA00000000.1},
  author = {Robinson, GE and Robertson, HM and Hudson, ME and Walden, K and Fischman, BJ and {Pitts-Singer}, T and James, R and Salzberg, SL and Puiu, D and Magoc, T and Kelley, D and Zimin, AV},
  month = aug,
  year = {2014},
  keywords = {dna,insd,alfalfa leafcutting bee},
  note = {\{:itemType: dataset\}}
}