Gene Conservation Laboratory
Cook Inlet Coho Salmon Genetic Baseline Project

Coho salmon are harvested in both commercial and sport fisheries in Upper Cook Inlet (UCI), with a 10-year average of 186,655 fish being harvested by commercial fisheries annually (Shields and Dupuis 2013 PDF 2,586 kB). Because coho salmon returns in Northern Cook Inlet (NCI) streams have been on the decline in recent years, there is a management need for the ability to estimate the harvest of these stocks in UCI fisheries. Genetic baselines have been developed for sockeye and Chinook salmon for use in mixed stock analysis (MSA) of harvest samples collected from commercial, sport, and personal use fisheries in UCI; however, a genetic baseline for coho salmon in UCI has not been developed yet. This project will develop a comprehensive coho salmon genetic baseline in Cook Inlet to allow for future MSA of coho salmon harvests in UCI fisheries.

Since 1992, the U.S. Fish and Wildlife Service (USFWS) has collected genetic samples from coho stocks throughout Cook Inlet, with a majority being collected in Kenai and Kasilof rivers. In the early 2000s, the USFWS Conservation Genetics Lab developed a statewide baseline, which included 8 UCI coho salmon populations for 9 microsatellite loci (Olsen et al. 2003). The baseline demonstrated that genetic markers could be used to distinguish coho salmon populations in Alaska, and the possibility for distinguishing stocks within Cook Inlet.

Coho salmon samples have been collected throughout UCI by department staff opportunistically since the early 1990s, with the majority collected between 2006 and 2012. In 2013, the State of Alaska funded a three phase study to develop a Cook Inlet coho salmon single nucleotide polymorphism (SNP) baseline. The first phase was completed in spring of 2013 and involved determining whether sufficient genetic diversity exists in Cook Inlet coho salmon stocks for genetic stock identification using existing samples and genetic markers. Statistical analysis of these data indicated that sufficient variation exists in Cook Inlet coho salmon stocks for genetic stock identification.

This study is in the second phase, which began in summer of 2013. During the 2013 field season, samples of coho salmon were collected by several projects; Susitna Hydroelectric Project, 6 Sport Fish Division NCI weirs, Grant Creek Hydroelectric project, and this project all of which are being processed for statistical analysis this fall.