DOI: 10.5061/dryad.1797v
title: Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

description: 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 to elucidate patterns of neutral and adaptive variation in this
 high geneflow species. A total of 4104 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 putatively neutral panel of
 3911 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). This may indicate divergent selective pressures in
 differing freshwater and marine environments between regional eulachon
 populations and that these adaptive diversity patterns not seen with
 neutral markers could be a consideration when determining genetic
 boundaries for conservation purposes. 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 provided 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 highlighted the importance of
 integrating genome-wide neutral and adaptive genetic variation for the
 applications of conservation and management.
description: Thaleichthys pacificus,
 Osmeridae RAD sequences for putative neutral SNP lociFile consists of loci
 name, loci sequence, and SNP location in comma delimited
 file.Eulachon_NeutralRADs.csvThaleichthys pacificus, Osmeridae RAD sequences from putative adaptive SNP lociFile consists of loci name, loci sequence and SNP location in comma delimited formatEulachon_AdaptiveRADS.csvThaleichthys pacificus, Osmeridae putative adaptive SNP lociThis file in genpop format and contains 193 SNPs per sample1_EulachonSig.genThaleichthys pacificus, Osmeridae putative neutral lociThis file is in genpop format and contains 3,911 SNPS per sample2_EulachonNonSig.genPaired-end extended sequences for eulachonR code to Impute missing SNP data.This code was developed by Matt Grinnell to impute missing SNPs from the eulachon datasets so it could be used by ONCOR for assignment testing.ImputeMissing.RR script to calculate effective population size with an R2 valueR script to impute missing loci by populationThaleichthys pacificus, Osmeridae key file for NCBI SRA databaseThis file contains: sample name, sample number, biosample account, library ID, and barcode.Eulachon_Key.txt