Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

Abstract

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 data sets 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 data sets recently published for a nonmodel species, comprising 5662 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 that are 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.

Allele surfing causes maladaptation in a Pacific salmon of conservation concern

“…Previous studies showed that this population is highly divergent from any others [35,36,52] and displayed an increased rate of long runs of homozygosity [38]. It has been subjected to extensive hatchery enhancement (from a single population) to circumvent the decline of Coho salmon in the Thompson drainage [53].…”

“…We further demonstrated that one population, the Salmon River (Thompson R. watershed) displayed an increased fixed load and decreased selection efficacy compared to southern populations. Previous studies showed that this population is highly divergent from any others [35,36,52] and displayed an increased rate of long runs of homozygosity [38]. It has been subjected to extensive hatchery enhancement (from a single population) to circumvent the decline of Coho salmon in the Thompson drainage [53].…”

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

“…The first condition for the protection of natural populations and their proper management is the identification of species’ genetic characteristics of their populations. Molecular markers such as mtDNA, microsatellites and MHC turned out to be sensitive enough to find a population differentiation generally congruent with the genomic methods based on the genotyping of a large number of SNPs in the conservation units of coho salmon ( Oncorhynchus kisutch ) in Canada [ 14 ]. However, the genotyping of many thousands of SNPs has revealed a more detailed structure in some evolutionary and biologically significant units.…”

“…Despite stocking being carried out with material from a well-defined management unit, enhancement leads to a reduction in the diversity of this population compared to other wild populations. This is due to the reduction in the effective population size and the constraints of the gene pool representation [ 14 ]. Nevertheless, fisheries’ overexploitation of many declining populations is mitigated by stocking.…”

“…The main concerns of conservation genetics are defining populations and closely related species, the characterization of their polymorphism and its changes over time, the identification of hybrids in wild populations, the estimation of effective population size, estimation of inbreeding, and understanding the local adaptations and genetic polymorphism at quantitative trait loci in populations. An understanding of the spatial structure of populations enables the delineation of evolutionary conservation units [ 13 , 14 ]. Evolutionary significant units are groups of individuals adapted to the local conditions and reproductively self-maintaining.…”