Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies

Abstract

Most information about Chinook salmon genetic diversity and life history originates from studies from the West Coast USA, western Canada and southeast Alaska; less is known about Chinook salmon from western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving these populations. We assembled a comprehensive, open-access baseline of 45 single nucleotide polymorphisms (SNPs) from 172 populations ranging from Russia to California. We compare SNP data from representative populations throughout the range with particular emphasis on western and southcentral Alaska. We grouped populations into major lineages based upon genetic and geographic characteristics, evaluated the resolution for identifying the composition of admixtures and performed mixed stock analysis on Chinook salmon caught incidentally in the walleye pollock fishery in the Bering Sea. SNP data reveal complex genetic structure within Alaska and can be used in applications to address not only regional issues, but also migration pathways, bycatch studies on the high seas, and potential changes in the range of the species in response to climate change.

Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current large marine ecosystem

“…1). Relationships are in strong agreement with expectations that were based on geography and previous studies (Waples et al, 2004;Beacham et al, 2006;Templin et al, 2011;Moran et al, 2013); populations generally are organized north to south along the main branch, and populations from within the same drainage usually cluster together.…”

“…Templin et al (2011) described a 45 SNP locus baseline for populations in the northern and western parts of the Chinook Salmon range, designed primarily for GSI of populations from western and southcentral Alaska. This same baseline was used also to probe the seasonal distribution and migration pattern of Chinook Salmon in the Bering Sea and North Pacifi c Ocean (Larson et al, 2013).…”

“…Additionally, it now has been demonstrated that SNPs, despite typically having only 2 alleles per locus, do have suffi cient power to be employed successfully in a GSI context with a modest number of genetic markers Narum et al, 2008;Templin et al, 2011;Larson et al, 2013). Early simulation studies indicated that the bi-allelic nature of SNPs would make them less useful than highly polymorphic microsatellites for population discrimination (Bernatchez and Duchesne, 2000;Kalinowski, 2004).…”

The invasion of an Atlantic Ocean river basin in Patagonia by Chinook salmon: new insights from SNPs

“…For example, SNP data is used on a regular basis to predict the stock composition of the world's largest salmon fishery, for sockeye salmon (O. nerka) migrating into Bristol Bay (Habicht et al 2010). The ability of GSI with SNPs to resolve both broad-and fine-scale population structure for ChS across its native range (Clemento et al 2011;Hess et al 2011;Templin et al 2011), as well as to identify the composition of ocean mixtures (Habicht et al 2010;Larson et al 2012;Satterthwaite et al 2014), has been well documented. In this paper, we use GSI to identify the origin of ChS spawning in the Santa Cruz River Basin in Argentina.…”

Single-nucleotide polymorphisms reveal distribution and migration of Chinook salmon (Oncorhynchus tshawytscha) in the Bering Sea and North Pacific Ocean

“…This study applies the species-wide SNP baseline of Templin et al (2011 ; Table 1; Fig. 1) to estimate distributions and migrations of Chinook salmon sampled in the Bering Sea and the North Pacific Ocean.…”