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

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dc.contributor.authorLayton, Kara K. S.
dc.contributor.authorDempson, Brian
dc.contributor.authorSnelgrove, Paul V. R.
dc.contributor.authorDuffy, Steven J.
dc.contributor.authorMessmer, Amber M.
dc.contributor.authorPaterson, Ian G.
dc.contributor.authorJeffrey, Nicholas W.
dc.contributor.authorKess, Tony
dc.contributor.authorHorne, John B.
dc.contributor.authorSalisbury, Sarah J.
dc.contributor.authorRuzzante, Daniel E.
dc.contributor.authorBentzen, Paul
dc.contributor.authorCôte, David
dc.contributor.authorNugent, Cameron M.
dc.contributor.authorFerguson, Moira M.
dc.contributor.authorLeong, John S.
dc.contributor.authorKoop, Ben F.
dc.contributor.authorBradbury, Ian R.
dc.date.accessioned2020-06-18T23:26:59Z
dc.date.available2020-06-18T23:26:59Z
dc.date.copyright2020en_US
dc.date.issued2020
dc.description.abstractThe resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread 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 north eastern 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 north‐eastern 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 microsatellite loci and the SNP panel (>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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThe authors thank staff of the Newfoundland DFO Salmonids section, Parks Canada, the Nunatsiavut Government, the NunatuKavut Community Council, the Sivunivut Inuit Community Corporation, the Innu Nation, the Labrador Hunting and Fishing Association and fishers for their support, participation and tissue collections and the staff of the Aquatic Biotechnology Lab at the Bedford Institute of Oceanography for DNA extractions. We also thank the Marine Gene Probe Laboratory for genotyping the data used in the present study. We also thank Sarah Lehnert for comments on an earlier version of this manuscript. This study was supported by the Ocean Frontier Institute, a Genomics Research and Development Initiative (GRDI) Grant, a Natural Sciences and Engineering Research Council (NSERC) Discovery Grant and Strategic Project Grant to IRB, the Weston Family Award for research at the Torngat Mountains Base Camp, an Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grant allocated to the Labrador Institute (MC).en_US
dc.identifier.citationLayton, K. K. S., Dempson, B., Snelgrove, P. V. R., Duffy, S. J., Messmer, A. M., Paterson, I. G., … Bradbury, I. R. (2020). Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evolutionary Applications, 13(5), 1055-1068. https://doi.org/10.1111/eva.12922.en_US
dc.identifier.urihttps://doi.org/10.1111/eva.12922
dc.identifier.urihttp://hdl.handle.net/1828/11861
dc.language.isoenen_US
dc.publisherEvolutionary Applicationsen_US
dc.subjectgenetic assignment
dc.subjectgenome-wide polymorphisms
dc.subjectmixed stock analysis
dc.subjectSalvelinus alpinus
dc.subjectsequenced microsatellites
dc.subjecttagging
dc.subjectCentre for Biomedical Research
dc.subject.departmentDepartment of Biology
dc.titleResolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fishen_US
dc.typeArticleen_US

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