Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

The resiliency of populations and species to environmental change is
dependent on the maintenance of genetic diversity, and as such quantifying
diversity is central to combatting ongoing wide spread reductions in
biodiversity. With the advent of next-generation sequencing, several
methods now exist for resolving fine-scale population structure, but the
comparative performance of these methods for genetic assignment has rarely
been tested. Here we evaluate the performance of sequenced microsatellites
and a single nucleotide polymorphism (SNP) array to resolve fine-scale
population structure in a critically important salmonid in northeastern
Canada, Arctic charr (Salvelinus alpinus). We also assess the utility of
sequenced microsatellites for fisheries applications by quantifying the
spatial scales of movement and exploitation through genetic assignment of
fishery samples to rivers of origin and comparing these results with a
29-year tagging dataset. Self-assignment and simulation-based analyses of
111 genome-wide microsatellite loci and 500 informative SNPs from 28
populations of Arctic charr in northeastern Canada identified largely
river-specific genetic structure. Despite large differences (~4X) in the
number of loci surveyed between panels, mean self-assignment accuracy was
similar with the SNP panel and with the microsatellite loci (>90%).
Subsequent analysis of 996 fishery-collected samples using the
microsatellite panel revealed that larger rivers contribute greater
numbers of individuals to the fishery, and that coastal fisheries largely
exploit individuals originating from nearby rivers, corroborating results
from traditional tagging experiments. Our results demonstrate the efficacy
of sequence-based microsatellite genotyping to advance understanding of
fine-scale population structure and harvest composition in northern and
understudied species.