Abstract
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next‐generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation‐based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.
Highlights
A variety of genomic tools exist for population resolution and assignment, but increasingly applications are favoring the use of single nucleotide polymorphisms (SNPs) over microsatellite loci (Guichoux et al, 2011; Putman & Carbone, 2014)
As information content is in part a function of the number of alleles measured, on a per-amplicon basis, the use of microsatellite loci with their multi-allelic nature should in some contexts provide greater population resolution relative to biallelic SNPs
We show that next-generation sequencing of genome-wide microsatellite loci allows large numbers of alleles to be genotyped and scored quickly and cheaply, presenting new opportunities for individual assignment and genetic mixed-stock analysis in Atlantic salmon and other exploited species
Summary
The maintenance of intraspecific diversity has been linked to both species and fishery persistence and stability (Hilborn, Quinn, Schindler, & Rogers, 2003; Schindler et al, 2010), and as such is central to successful wildlife and fisheries management (Funk, McKay, Hohenlohe, & Allendorf, 2012). Microsatellite and SNP-based examinations have identified 13–20 regional groups in the northwest Atlantic for assignment and mixed-stock application (Bradbury et al, 2015; Gauthier-Ouellet, Dionne, Caron, King, & Bernatchez, 2009; Moore et al, 2014). Of these groups, the northern range limit in Labrador is perhaps least well defined with only three regional groups across 700 km of coastline, and most of the region comprised of a single reporting group. We show that next-generation sequencing of genome-wide microsatellite loci allows large numbers of alleles to be genotyped and scored quickly and cheaply, presenting new opportunities for individual assignment and genetic mixed-stock analysis in Atlantic salmon and other exploited species
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