Chum salmon baseline for the Western Alaska Salmon Stock Identification Program

Uncertainty about the magnitude, frequency, location, and timing of the nonlocal harvest of sockeye and chum salmon was the impetus for the Western Alaska Salmon Stock Identification Program. The program was designed to use genetic data in mixed stock analysis to reduce this uncertainty. A baseline of allele frequencies in spawning populations is required for use in mixed-stock analysis to estimate the stock of origin of harvested fish. This report describes the methodology used to understand the population genetic structure among chum salmon populations and to build and test a baseline for use in mixed stock analysis of chum salmon. Of the 35,921 fish from 434 collections selected to be genotyped, the final baseline was composed of 32,817 fish from 402 collections representing 310 populations. Average population sample size was 106 fish. Reporting groups were determined through a combination of stakeholder needs and identifiability using genetic information, as measured using proof tes..., Tissue Sampling
Baseline collections
Baseline samples were collected from spawning populations of chum salmon ranging from Korea to the State of Washington (Table 2). Tissue samples were collected by ADF&G and collaborators. In some cases, only DNA extracts were available, especially for collections from Asia. Target sample size for baseline populations was 95 individuals to achieve acceptable precision for estimating allele frequencies (Allendorf and Phelps 1981; Waples 1990a) and to accommodate our SNP genotyping platform. It was evident early on that a sample size of 95 fish was not possible for some collections.
Selection of baseline collections to genotype
We selected a subset of collections to include in the WASSIP baseline to represent 1) population abundance, 2) genetic diversity, 3) geographic coverage, and 4) among-year variation of allele frequencies within populations. We attempted to find the greatest representative value by balancing maximum representation and the high..., Genepop and rubias.