Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

Next-generation sequencing yields high-resolution information to infer population structure, genetic diversity, local adaptation, and effective population size (Ne), necessary for conservation and management of exploited species. Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing in order to elucidate patterns of neutral and adaptive variation in this species with high gene flow. A total of 4,104 single-nucleotide polymorphisms (SNPs) were discovered across the genome; with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar but provided greater resolution of stocks compared with a putative neutral panel of 3,911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel but not in the neutral markers (SNPs or microsatellites) which may indicate divergent selective pressures in differing estuary environments between regional eulachon populations. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provides higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlight the importance of integrating both neutral and adaptive genetic variation from the genome for applications of conservation and management.