DOI: 10.5061/dryad.r4xgxd2gx
title: Re-evaluating coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

description: Conservation units (CUs) are important tools for supporting the
 implementation of standardized management practices for exploited species.
 Following the adoption of the Wild Salmon Policy in Canada, CUs were
 defined for Pacific salmon based on characteristics related to ecotype,
 life history, and genetic variation using microsatellite markers as
 indirect measures of local adaptation. Genomic datasets have the potential
 to improve the definition of CUs by reducing variance around estimates of
 population genetic parameters, thereby increasing the power to detect more
 subtle patterns of population genetic structure and by providing an
 opportunity to incorporate adaptive information more directly with the
 identification of variants putatively under selection. We used one of the
 largest genomic datasets recently published for a non-model species,
 comprising 5,662 individual Coho salmon (Oncorhynchus kisutch) from 149
 sampling locations and a total of 24,542 high-quality SNPs obtained using
 genotyping-by-sequencing and mapped to the Coho salmon reference genome to
 1) evaluate the current delineation of CUs for Coho in Canada and 2)
 compare patterns of population structure observed using neutral and
 outlier loci from genotype-environment association analyses to determine
 whether separate CUs that capture adaptive diversity are needed. Our
 results reflected CU boundaries on the whole, with the majority of
 sampling locations managed in the same CU clustering together within
 genetic groups. However, additional groups not currently represented by
 CUs were also uncovered. We observed considerable overlap in the genetic
 clusters identified using neutral or candidate loci, indicating a general
 congruence in patterns of genetic variation driven by local adaptation and
 gene flow in this species. Consequently, we suggest that the current CU
 boundaries for Coho salmon are largely well-suited for meeting the
 Canadian Wild Salmon Policy’s objective of defining biologically distinct
 groups, but we highlight specific areas where CU boundaries may be
 refined.
description: Samples were collected from
 5,662 individual Coho salmon from 149 locations in British Columbia (BC),
 Canada, located within 35
 of the 44 established CUs. DNA was extracted from all individuals and
 libraries were prepared for genotyping by sequencing (GBS) on the Ion
 Proton P1v2 chip (Université Laval). Raw sequencing reads were processed
 using the Stacks v2 pipeline (Catchen et al., 2013) with the updated Coho
 salmon reference genome. Raw sequencing data are deposited on NCBI,
 project PRJNA647050. These are the filtered .vcf files, and
 additional data files used to run all analyses. To generate filtered vcf
 files, we: 1) excluded loci that were
 not present in at least 60% of all populations and in 60% of individuals
 within each population, and loci for which the rare allele was not present
 in at least 5 samples, 2) retained one SNP per RAD locus (i.e., the one
 with the highest minor allele frequency), 3) removed duplicated, diverged,
 and low-confidence loci using the method implemented in stacks_workflow
 (https://github.com/enormandeau/stacks_workflow), 4) removed SNPs with a read depth greater than 10 and less than 120 and with a minor allele count (MAC) &gt; 15, and 5) retained SNPs that were not missing in at least 95% of the dataset. See publication for full details. For each of the two regions (BC and Thompson) .vcf files for each SNP subset (i.e., neutral SNPs or outlier SNPs identified using genotype-environment association analyses) are also available.