Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.
Candy, John R., Fisheries and Oceans Canada
Campbell, Nathan R., Columbia River Inter-Tribal Fish Commission
Beacham, Terry D., Fisheries and Oceans Canada
Grinnell, Matthew H., Fisheries and Oceans Canada
Narum, Shawn R., Columbia River Inter-Tribal Fish Commission
Larson, Wesley A., University of Washington
Published Mar 03, 2015 on Dryad.
Cite this dataset
Candy, John R. et al. (2015). Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt. [Dataset]. Dryad. https://doi.org/10.5061/dryad.1797v
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.
Thaleichthys pacificus, Osmeridae RAD sequences for putative neutral SNP loci
File consists of loci name, loci sequence, and SNP location in comma delimited file.
Thaleichthys pacificus, Osmeridae RAD sequences from putative adaptive SNP loci
File consists of loci name, loci sequence and SNP location in comma delimited format
Thaleichthys pacificus, Osmeridae putative adaptive SNP loci
This file in genpop format and contains 193 SNPs per sample
Thaleichthys pacificus, Osmeridae putative neutral loci
This file is in genpop format and contains 3,911 SNPS per sample
Paired-end extended sequences for eulachon
R 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.
R script to calculate effective population size with an R2 value
R script to impute missing loci by population
Thaleichthys pacificus, Osmeridae key file for NCBI SRA database
This file contains: sample name, sample number, biosample account, library ID, and barcode.