Data and R code accompanying:

Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef

Authors: Danielle C. Claar, Kristina L. Tietjen, Kieran D. Cox, Ruth D. Gates, Julia K. Baum

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Structure of files and folders within this repo

main folder

Files

KI_Compartment.Rproj : RProject file for this project
ITS2db_trimmed_derep_data.fasta : ITS2 database used in bioinformatic pipeline

data

Scripts

Coralphoto__Metadata/process_coral_metadata.R : append coral photo metadata to mapping file
INPUT Coral Photo Metadata: data/Coralphoto__Metadata/KI_Coralphoto_Metadata_Jan_to_Apr_2017_23March.csv
INPUT Mapping File: data/mapping_file_dada.txt
OUTPUT data/Coralphoto__Metadata/KI_Compartment_metadata.csv
OUTPUT data/Coralphoto__Metadata/KI_Compartment_metadata.csv

export_physeq_objects.R : extract taxa table and otu tables
INPUT analyses/KI_Compartment.RData
OUTPUT Taxa table: data/tax_table.txt
OUTPUT OTU table: data/otu_table.txt

count_water_sediment_samples.R : count number of samples
INPUT data/KI_Compartment_f_coral_grouped.RData
OUTPUT manually extract sample sizes

Files

KI_Compartment_f_coral_grouped.RData : all objects created after filtering dataset
KI_Compartment_phyASVfcp.RData : only phyASVfcp after filtering dataset
KI_env_all_KI_Compartment.csv : Environmental parameters from Kiritimati field monitoring program
mapping_file_dada.txt : mapping file for dada2 bioinformatics pipeline

Folders

tree/ contains distance matrices, sequences for each genus, and aligne sequences for each genus, as well as the 'uber.tree' which is produced by analyses/dada2/KI_Compartment_filter_samples_dada.R

analyses

Scripts

dada2/dada2.R : Dada2 bioinformatic pipeline. Runs the following -

• cutadapt to remove primers
• full dada2 pipeline
  INPUT data/Bioinf/sequences/DClaar_2-34439409_seqs_KI_Compartment : original sequences (download from Zenodo to run this script)
  INPUT ITS2db_trimmed_derep_dada.fasta : reference ITS2 database
  INPUT data/mapping_file_dada.txt : mapping file for sequences
  OUTPUT analyses/dada2/KI_Compartment_dada.RData

dada2/KI_Compartment_filter_samples_dada.R

• filters samples
• defines site names/disturbance levels
• make phylogenetic tree
• transform to proportional abundances
• count number of sequences
• subset phyloseqs by compartment/field season
  INPUT analyses/dada2/KI_Compartment_dada.RData
  OUTPUT data/Bioinf/tree/uber.tre : phylogenetic tree
  OUTPUT data/KI_Compartment_f_coral_grouped.RData : all objects created in this script
  OUTPUT data/KI_Compartment_phyASVfcp.RData : only phyASVfcp

environmental_parameters/env_summ.R : summarize environmental parameters from field surveys and satellite data
INPUT data/KI_env_all_KI_Compartment.csv
OUTPUT analyses/env_summ.csv

count_seqs.R : count number of sequences (total, and by compartment)

count_taxa.R : count number of taxa by coral species

KI_Compartment_colors.R : creates colors for plots
OUTPUT KI_Compartment_colors.RData

balance_sensitivity.R : sensitivity analysis for Disturbance, to see if PERMANOVA results remain significant if dataset is pared down to a balanced design (see methods for justification)

balance_sensitivity_field_season.R : sensitivity analysis for Field Season, to see if PERMANOVA results remain significant if dataset is pared down to a balanced design (see methods for justification)

permanova_betadisper_sensitivity.R : calculate number of samples to pare down to for "balance_sensitivity*.R" scripts

Files

environmental_parameters/env_summ.csv : summary of environmental parameters
KI_Compartment_colors.RData : colors for plots dada2/KI_Compartment_dada.RData : data after dada2 pipeline, but before additional filtering

Folders

refseqs/ : dominant sequences in .fasta format for blasting. Also includes refseq_blast_IDs.xlsx, with blast information

figures

Folders

Each figure folder contains the script to produce the figure, the final figure, and any intermediate files

Figure_1
Figure_2
Figure_3
Figure_4
Figure_5
Figure_S1
Figure_S2
Figure_S3
Figure_S4
Figure_S5
Figure_S6

Files

KI_Compartment_Table_S1.docx
SupplementaryTable3.xlsx