DOI: 10.5061/dryad.402sb71
title: Data from: Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

description: The discernment of populations as management units is a fundamental
 prerequisite for sustainable exploitation of species. A lack of clear
 stock boundaries complicates not only the identification of spatial
 management units, but also the assessment of mixed fisheries by population
 assignment and mixed stock analysis. Many marine species, such as Pacific
 cod, are characterized by isolation-by-distance, showing significant
 differentiation but no clear stock boundaries. Here, we used
 restriction-site associated DNA (RAD) sequencing to investigate population
 structure and assess power to genetically assign Pacific cod to putative
 populations of origin. Samples were collected across the species range in
 the Eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A
 total of 6,425 putative biallelic single nucleotide polymorphisms were
 identified from 276 individuals. We found a strong isolation-by-distance
 signal along coastlines that mirrored previous microsatellite results, and
 pronounced genetic differentiation between coastal samples and those from
 the inland waters of the Salish Sea with no evidence for hybridization
 between these two populations. Individual assignment success based on two
 methods was high overall (≥ 84%) but decreased from south to north.
 Assignment to geographic location of origin also was successful, with
 average distance between capture and assignment location of 220 km.
 Outlier analyses identified more loci potentially under selection along
 the coast than between Salish Sea and coast samples, suggesting more
 diverse adaptation to latitudinal environmental factors than inshore vs
 offshore environments. Our results confirm previous observations of sharp
 genetic differentiation of the Salish Sea population and
 isolation-by-distance along the coast, but also highlight the feasibility
 of using modern genomic techniques to inform stock boundaries and
 fisheries management in a low FST marine species.
description: Genepop file of RAD SNP
 genotypesPcodGenepop.genPacific cod scriptsScripts for Stacks, Perl and R. Details within the fileSequences for loci in Genepop fileThis fasta file contains the consensus sequences for all of the loci in the genepop file. The locus name in this file corresponds to locus names in the genepop file, which also gives the position of the SNP.genepop_loci_sequences.faIndividual barcodes of RAD sequences used in StacksThis text file is a combination of the barcodes file and the "population map" file for the program stacks. Each line consists of (1) the individual barcode, (2) the sample ID, and (3) a numeric designation for the sampling site (putative population) to which the individuals belongs. Copying the first two columns into a separate text file will provide the barcodes.txt file used in stacks to demultiplex raw data. Copying the second two columns into a separate text file will provide the population map file used in the stacks function `populations` to call genotypes.barcodes_populations.txtNCBI accession numbersThis text file contains specific accession numbers of individual samples. The accession number for the study is SRA accession SRP137021. Link: https://www.ncbi.nlm.nih.gov/sra/SRP137021