DOI: 10.5061/dryad.j0zpc86fm
title: Stock composition of subsistence harvests and total return of sockeye salmon from the Kvichak River

description: This project will reconstruct the total return of sockeye salmon to the
 Kvichak River to identify: 1) which of four stocks are most utilized by
 subsistence fisheries; 2) when these stocks migrate through the commercial
 fishery and escapement monitoring tower; and 3) if there are temporal
 trends in migration that may allow commercial fisheries managers to
 protect stocks important to subsistence fisheries. In addition, by
 building upon existing smolt stock composition data, this project will
 evaluate survival and productivity of brood years 2012–2015 at smolt and
 returning adult life stages.
description: Objective 1:<br> Subsistence sampling by Local
 Research Assistants<br> In each of the 5 study
 communities, 2 local research assistants (LRA’s) were hired to assist with
 genetic and ASL sampling effort. Project staff worked with the local
 tribal councils and other knowledgeable community members to identify
 potential LRA’s who would be interested in developing sockeye salmon
 sampling skills. Mr. Dann and Ms. Jones traveled to each community before
 the sockeye salmon season to conduct outreach and work closely with
 selected LRA’s to provide technical training and experience. LRA sampling
 began in 2017 and continue through 2019, although sampling of Nondalton
 and Pedro Bay harvests in 2017 was not successful. 
 Sampling for age, sex and length<br>
 During commercial and escapement sampling, scales were removed from the
 preferred area of each fish and placed on an adhesive-coated card for
 subsequent ageing (Clutter and Whitesel 1956; Welander 1940). Otoliths
 were collected from subsistence harvests to determine age after reading by
 the Mark, Tag and Age Lab in Juneau, AK. Sex was identified from external
 morphometric characteristics (i.e., protruding ovipositor on females or a
 developing kype on males) or during salmon processing. Mid-eye to tail
 fork (METF) length will be measured to the nearest millimeter. Sockeye
 salmon were sampled for ASL composition without regard to size, sex,
 length, or location. ASL composition data wererecorded on data sheets and
 paired with tissue samples. Tissue Sampling
 for MSA<br> All fish sampled for ASL were also sampled for
 tissues suitable for genetic analysis. A 1 ½ cm (half-inch) piece of the
 axillary process was removed from each fish and placed on a tissue card to
 be dried. Each tissue card was paired with a scale card; each had 48 gird
 spaces, holding up to 48 axillary fins, and the girds were sequentially
 numbered and gird numbers recorded on data sheets. All tissue cards were
 collected by the Commercial Fisheries and Subsistence division staff post
 season and provided to the ADF&G Gene Conservation Laboratory in
 Anchorage for analysis. Objectives 2 and 3: <br>
 Laboratory Analysis<br> Mixed stock analysis by
 the ADF&G Gene Conservation Laboratory followed standardized
 procedures similar to those previously applied in similar studies (Dann et
 al. 2012). The experimental design of the study analyzed mixtures of
 escapement and commercial and subsistence harvests in strata of 190 fish
 (Table 1). The design allowed for four temporal strata within the
 Naknek-Kvichak District plus one stratum to analyze the Kvichak Section
 setnet harvest separately in each year; this design parallels past MSA of
 commercial harvests and is appropriate for characterizing temporal changes
 in a large, temporally compressed harvest. Three temporal strata
 characterized temporal trends in escapement past the counting tower at
 Iguigig, while each village center was analyzed separately
 (Iliamna-Newhalen harvests combined as in Division of Subsistence
 studies). Samples of subsistence harvests were unavailable for
 2016. Table 1: Experimental design of proposed project
 to identify the stock composition of: subsistence fisheries in five
 village centers, the commercial harvest in five temporal strata in each
 year, and the escapement to the Kvichak River in three temporal strata in
 each year. Numbers represent the numbers of strata (before X) and
 individuals in each stratum (after X) for each analysis category in each
 of four years. Note that subsistence samples will be unavailable from 2016
 but can be sampled from commercial harvest and escapement from existing
 sampling platforms.<br> Year    Escapement    Commercial   
  Subsistence    Total<br> 2016          3 X 190         
  5 X 190    Unavailable    1,520<br> 2017          3 X 190         
  5 X 190          5 X 190    2,470<br> 2018          3 X 190       
    5 X 190          5 X 190    2,470<br> 2019          3 X
 190           5 X 190          5 X 190    2,470<br> Total 
             2,280               3,800             2,850    8,930
 Genomic DNA was extracted from tissue samples using a NucleoSpin®
 96 Tissue Kit by Macherey-Nagel (Düren, Germany). DNA was screened for 96
 SNPs using a Fluidigm® platform. When necessary, SNPs were rescreened on
 an Applied Biosystems® platform as a backup method for assaying genotypes.
 Approximately 8% of individuals analyzed for this project were
 re-extracted and genotyped as a quality control measure to identify
 laboratory errors and to measure the background discrepancy rate of the
 genotyping process. Genotypes were imported and archived in the Gene
 Conservation Laboratory Oracle database, LOKI.
 Statistical Analysis<br> Only
 individuals with high-quality data were included in MSA. Data quality
 control included identifying and removing individuals missing &gt;20%
 genotypic data, duplicate individuals, and non-sockeye salmon. Stock
 composition for each stratum was estimated using the software package
 BAYES (Pella and Masuda 2001). A series of independent Markov Chain Monte
 Carlo (MCMC) chains with different starting values for each population was
 combined to form the posterior distribution describing the stock
 composition of each sample from a location-by-time strata. The analysis
 tabulated summary statistics from these distributions to describe stock
 compositions. Stock composition estimates of commercial
 harvest and escapements were applied to observed harvest and escapement
 numbers to quantify stock-specific harvests and escapements through time
 within each season (2016–2019). Visualization of these abundances through
 time and simple time series models such as AR-1 were fit to observed
 stock-specific abundances in each location to characterize temporal trends
 in stock-specific abundances within seasons.
description: Please see associated "KvichakSockeyeReturnsreadme.txt"
 file for additional usage details.