Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson, Paul Bentzen

Producción científica: Contribución a una revistaArtículorevisión exhaustiva

54 Citas (Scopus)

Resumen

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.

Idioma originalEnglish
Páginas (desde-hasta)918-930
Número de páginas13
PublicaciónEvolutionary Applications
Volumen11
N.º6
DOI
EstadoPublished - jul. 2018

Nota bibliográfica

Funding Information:
The authors thank staff of the Newfoundland DFO Salmonids section, Jonathan Pearce, Judith Savoie, Lianna Rice, and Joshua Adams, the Nunatsiavut Government, the NunatuKavut Community Council, the Sivunivut Inuit Community Corporation, the Innu Nation, the Labrador Hunting and Fishing Association and fishers for tissue collections and the staff of the Aquatic Biotechnology Lab at the Bedford Institute of Oceanography DNA extractions. We also thank the Marine Gene Probe Laboratory for genotyping the data used in the present study. This study was supported by a Genomics Research and Development Initiative (GRDI) Grant, a National Sciences and Engineering Research Council (NSERC) Discovery Grant and Strategic Project Grant to IRB and a National Sciences and Engineering Research Council Strategic Project Grant to PB, Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grants allocated to the Labrador Institute (MC), Atlantic Salmon Conservation Foundation grant allocated to the Nunatsiavut Government, Torngat Wildlife, Plants, and Fisheries Secretariat grant allocated to MC, Atlantic Salmon Federation Olin Fellowship allocated to Jonathan Pearce.

Funding Information:
Genomics Research and Development Initiative (GRDI); National Sciences and Engineering Research Council (NSERC) Discovery; National Sciences and Engineering Research Council Strategic Project; Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grants allocated to the Labrador Institute (MC); Atlantic Salmon Conservation Foundation; Torngat Wildlife, Plants, and Fisheries Secretariat; Atlantic Salmon Federation Olin

Publisher Copyright:
© 2018 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd

ASJC Scopus Subject Areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • General Agricultural and Biological Sciences

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