Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Abstract

Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometres, have become increasingly valuable in the presence of climate change, increasing hatchery production and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive data sets from spawning populations originating from across the species' range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multinational applications because they are easily shared, require little interlaboratory standardization and can be assayed through increasingly efficient technologies. Here, we discuss the development of a data set for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A data set spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the data set, variable linkage relationships between SNPs associated with ancestral groupings and outlier loci with alleles associated with latitude.