Chinook Salmon in Upper Cook Inlet, Alaska: Using Genetic Data to Protect Vulnerable Stocks While Targeting Abundant Stocks

Chinook salmon, Oncorhynchus tshawytscha provide important commercial, sport, and personal use fisheries in Upper Cook Inlet, Alaska with annual harvests greater than 25,000 fish.  Many populations of salmon contribute to the catch and some of these populations have seen large declines in returns in recent years.  In particular, the Susitna River populations have declined to the point that they collectively are considered a stock of concern.  Since most of the harvests are from mixtures of stocks, the exploitation and productivity of any given stock is not well known.  This lack of knowledge compromises both stock protection from over harvest and attempts to utilize fish in excess of spawning needs.  Genetic analysis using single nucleotide polymorphism (SNP) technology holds promise in successfully discriminating among discrete fish stocks in fishery samples.  A new baseline will be presented that doubles the number of populations and increases the geographic coverage relative to prior baseline.  Chinook salmon genetic samples were collected throughout Upper Cook Inlet from 2008–2010.  Here we examine the genetic variation in the baseline and compare it to the life history and geographic distribution of the populations.   We evaluate the baseline for use in mixed stock analysis with and test the model with mixtures of fish of know origin that are not in the baseline.