1_Introduction.Rmd

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#Introduction

##Basic Information
Yellowtail Rockfish, *Sebastes flavidus*, occur off the West Coast of the United States from Baja California to the Aleutian Islands.  Yellowtail is a major commercial species, captured mostly in trawls from Central California to British Columbia [@Love2011].  Because it is an aggregating, midwater species it is usually caught in the commercial midwater trawl fishery. In California there is a large recreational fishery as well. The center of Yellowtail Rockfish abundance is from southern Oregon through British Columbia [@Fraidenburg1980].  Yellowtail Rockfish are colloquially known as "greenies", although *flavidus* is Latin for "yellow" [@Love2011].  We briefly summarize Yellowtail Rockfish life history, fisheries, assessment and management here, but in-depth, extensive background information on Yellowtail Rockfish and other managed species is available at [@PFMC2016].  

A number of studies correlate environmental conditions to pelagic juvenile abundance and juvenile recruitment of rockfishes, including Yellowtail Rockfish. Year-class strength is particularly impacted during the early larval phase, and annual pelagic juvenile abundance is correlated with physical conditions, especially upwelling strength along the coast (e.g., [@Field2005], [@Laidig2007], [@Laidig2010], [@Ralston2013]).

A recent genetic study [@Hess2011] indicates that there are in fact two stocks of Yellowtail Rockfish, with a genetic cline at Cape Mendocino, California, roughly $40^\circ 10^\prime$ North Latitude.  This study of 1013 fish from 21 sites along the West Coast from Mexico through Alaska examined two datasets, one of mitochondrial DNA, and one of nuclear DNA microsattelite loci.  Findings in both datasets agreed, and also concur with the findings of Field and Ralston [@Field2005] who looked at differences in recruitment trends related to physical forcing and coherence along the coast, and found the greatest differences among the U.S. and Canadian stocks to be defined by Cape Mendocino.  Neither the genetic study nor the oceanographic studies definitively identify mechanisms of stock isolation, however they suggest that a combination of physical forcing due to offshore advection and differences in available habitat across Cape Mendocino may together account for the differences observed.

The species has never had a full length and age integrated assessment south of Cape Mendocino, mainly due to a lack of fishery-independent data; this assessment represents an initial attempt to do so.

A map showing the scope of the assessment and depicting boundaries for fisheries or data collection strata is provided in Figure \ref{fig:assess_region_map}.

##Life History
Rockfish are in general long-lived and slow-growing, however Yellowtail Rockfish have a high growth rate relative to other rockfish species, reaching a maximum size of about 55 cm in approximately 15 years [@Tagart1991].  Yellowtail are reported to live at least 64 years [@Love2011], however no fish that old occur in data available for this assessment (For the Northern model, the 95th percentile of age is 35 years for females and 45 years for males and for the Southern model, 30 and 40 years respectively for females and males).  The maximum age plausibly observed in the north is 60; in the south, 49.  There were data we considered to be outliers, for example, three fish in the PacFIN data were reported to be 70, 99, and 101.

ellowtail Rockfish are among those that are fertilized internally and release live young.  Spawning aggregations occur in the fall, and parturition in the winter and spring (January-May) [@Eldridge1991].  Young-of-the-year recruit to nearshore waters from April through August, migrating to deeper water in the fall.  Preferred habitat is the midwater over reefs and boulder fields.  

Yellowtail Rockfish are extremely motile, and make rapid and frequent ascents and descents of 40 meters; they also exhibit strong homing tendencies [@Love2011].  They are able to quickly release gas from their swim bladders, perhaps making them less susceptible to barotrauma than similar species [@Eldridge1991].  

Rockfish Conservation Areas (RCAs) have been closed to fishing since 2002.  Following that closure, Yellowtail Rockfish are among the many species that have been seen to increase in both abundance and in average size in Central California  [@Marks2015].

Literature values for von Bertallanfy parameters are $L_\infty = 52.2, k = 0.17, t_0 = -0.75$ for females, $L_\infty = 47.6, k=0.19, t_0 = -1.69$ for males.  Length-Weight parameters are $W = 0.0287L^{2.822}$ for females, $W = 0.0359L^{2.745}$ for males [@Love2011].  See Section \ref{bio-params} for a discussion of the new analysis of the weight-length relationship.  Fecundity is represented in the models as:  $1.1185^{-11}W^{4.59}$.  This is a rescaling of the values provided in [@Dick2017].


##Ecosystem Considerations{-}
Rockfish in general are sensitive to the strength and timing of the upwelling cycle in the Eastern Pacific, which affects where pelagic juveniles settle, and impacts the availability of the zooplankton which the young require.

Yellowtail Rockfish feed mainly on pelagic animals, but are opportunistic, occasionally eating benthic animals as well. Large juveniles and adults eat fish (small Pacific Whiting, Pacific Herring, smelt, anchovies, lanternfishes, and others), along with squid, krill, and other planktonic organisms.  They are prey for Chinook Salmon, Lingcod, Cormorants, Pigeon Guillemots and Rhinoceros Auklets. [@Love2011]


##Fishery and Management History
There has been a commercial fishery in California for Yellowtail Rockfish since at least 1916, the earliest year for which we have data.  Records for recreational fishing start in 1928.  In Washington the Recreational data go back to 1889, however in Washington and Oregon the commercial trawl fishery is many times larger than the recreation fishery.  In California that has not been the case in recent time; the recreational fishery has been larger than the commercial fishery since the late 1990s.

The rockfish fishery off the U.S. Pacific coast first developed off California in the late 19th century as a hook-and-line fishery [@Love2002].  The rockfish trawl fishery was established in the early 1940s, when the United States became involved in World War II and wartime shortage of red meat created an increased demand for other sources of protein [@Alverson1964; @Harry1961; @Miller2014].

Until late 2002, Yellowtail Rockfish were harvested as part of a directed mid-water trawl fishery, with fairly high landings in the 1980s and 1990s.  Yellowtail commonly co-occur with Canary, Widow Rockfish and several other rockfishes [@Tagart1988]; [@Rogers1992]. Association with these and other rockfish species has substantially altered fishing opportunity for Yellowtail Rockfish since Canary Rockfish stocks were declared overfished by National Marine Fisheries service in 2000. In order to achieve the necessary reduction in the catch of Canary Rockfish, Widow Rockfish and other overfished species, stringent management measures were adopted, limiting harvest of Yellowtail Rockfish as well as other co-occurring species.

Beginning in 2000, shelf rockfish species could no longer be retained by vessels using bottom trawl footropes with a diameter greater than 8 inches. The use of small footrope gear increases the risk of gear loss in rocky areas. This restriction was intended to provide an incentive for fishers to avoid high-relief, rocky habitat, thus reducing the exposure of many depleted species to trawling. This was reinforced through reductions in landing limits for most shelf rockfish species.

Since September 2002, Rockfish Conservation Areas (RCAs, areas known to be critical habitat) have been closed to fishing.  Alongside these closures, limits on landings have been put in place that were designed so as to accommodate incidental bycatch only.  These eliminated directed mid-water fishing opportunities for Yellowtail Rockfish in non-tribal trawl fisheries. A somewhat greater opportunity to target Yellowtail Rockfish in the trawl fishery has been available since 2011 under the trawl rationalization program, however quotas for Widow and Canary Rockfish continue to constrain targeting of Yellowtail Rockfish.  With the recent improved status of constraining stocks, the industry is developing strategies to better attain allocations of Yellowtail Rockfish and Widow Rockfish. 

Yellowtail Rockfish are currently managed with stock-specific harvest specifications north of $40^\circ 10^\prime$ N. latitude, and as part of the Southern Shelf Rockfish complex south of $40^\circ 10^\prime$ N. latitude. The Over Fishing Limit (OFL) contribution of Yellowtail Rockfish to the Southern Shelf Rockfish complex is based on a data-poor analysis [@Dick2010].

Total catch (including landings and discards) in  both areas has remained well below the management limits and harvest specifications in recent years (Tables \ref{tab:mnmgt_perform.N} and \ref{tab:mnmgt_perform.S})

##Assessment History
Early studies of Yellowtail Rockfish stocks on the U.S. West Coast north of  $40^\circ 10^\prime$ N. latitude (Cape Mendocino, northern California) began in the 1980s with observational surveys.  Statistical assessments of Yellowtail Rockfish  were conducted in 1982 [@Tagart1982], 1988 [@Tagart1988], 1996 [@Tagart1997], and 1997 [@Tagart1997] to determine harvest specifications for the stock. These early assessments employed a variety of statistical methods, for example, the 1997 assessment used cohort analysis and dynamic pool modeling.  Figure \ref{fig:assessment_history}shows the timeseries of age 4+ biomass for Yellowtail Rockfish across past assessments.

The Yellowtail Rockfish assessment in 2000 [@Tagart2000] was the first that estimated stock status, with an estimated depletion of 60.5 percent at the start of 2000. Lai et al. [@Lai2003] updated the 2000 assessment and estimated that stock depletion was 46 percent at the start of 2003. A second assessment update was prepared in 2005 [@Wallace2005] with an estimated depletion of 55 percent at the start of 2005.  The 2000 assessment and updates were age-structured assessments conducted using AD Model Builder as the software platform for nonlinear optimization [@Fournier2012].

A data-moderate assessment of Yellowtail Rockfish south of $40^\circ 10^\prime$ N. latitude was conducted in 2013 [@Cope2013]. This assessment estimated depletion at the start of 2013 at 67 percent, and estimated the spawning biomass at 50,043 mt. This was a large biomass increase relative to previous estimates and may be attributed to the low removals over the previous decade.

The data-poor assessment method, Depletion-Based Stock Reduction Analysis [@Dick2011] was applied to the Southern stock in 2011 [@Dick2010]. This method does not estimate biomass, but did provide the estimate of the OFL contribution for the southern stock to the complex in which it is managed.


##Fisheries off Canada, Alaska, and/or Mexico
Yellowtail Rockfish are a target species in Canada with catches between 4000-6000 mt since the late 1980s. It has the second largest single-species Total Allowable Catch (TAC) among rockfish species under quota management for the Canadian Pacific Coast. In Canada it is caught in similar amounts by bottom and midwater trawl gear. A 2015 Stock Assessment conducted by the Fisheries and Oceans Canada found the stock to be at 50\% of unfished spawning biomass, in the "healthy" range [@DFO2015].

The Alaska Fisheries Science Center assesses Yellowtail Rockfish as one of 25 species in the "Other Rockfish" complex in the Gulf of Alaska.  The 2015 full assessment of this complex found no evidence of overfishing, which is confirmed in the 2016 SAFE document[@AFSC2016].

Limited catches of Yellowtail are reported as far south as Baja California[@Love2011].