Range-wide regional assignment of Atlantic salmon (Salmo salar) using genome wide single-nucleotide polymorphisms

作者: Nicholas W. Jeffery , Brendan F. Wringe , Meghan C. McBride , Lorraine C. Hamilton , Ryan R.E. Stanley

DOI: 10.1016/J.FISHRES.2018.05.017

关键词: Fish migrationStock (geology)FisheryPeninsulaGenomeFisheries managementSalmoGeographySingle-nucleotide polymorphismBiodiversity

摘要: Abstract The estimation of stock specific exploitation is imperative to fisheries management and the conservation biodiversity, particularly in instances where simultaneously exploit mixtures stocks. Mixed harvests are common species that have extensive marine migrations, such as Atlantic Pacific salmon. Here we develop a range-wide genetic baseline for salmon (Salmo salar) from North American European rivers allow regional assignment individuals targeted international mixed fisheries. A combination published data additional genotyping was used assemble dataset 96 SNPs 285 populations assignment. Clustering samples identified 20 eight reporting groups with mean individual accuracy 90% (range 70–100%). This applied disentangle composition subset West Greenland fishery. Genetic mixture analysis revealed both originated multiple regions, 92% originating United Kingdom Ireland, three regions; Gulf St. Lawrence (28%), Gaspe Peninsula (23%), coastal Labrador (21%). represents significant resource quantification migration patterns at sea.

参考文章(68)
L. L. Cavalli-Sforza, A. W. F. Edwards, Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics. ,vol. 19, pp. 233- 257 ,(1967)
IAN R. BRADBURY, SOPHIE HUBERT, BRENT HIGGINS, SHAREN BOWMAN, IAN G. PATERSON, PAUL V. R. SNELGROVE, COREY J. MORRIS, ROBERT S. GREGORY, DAVID C. HARDIE, TUDOR BORZA, PAUL BENTZEN, Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua Molecular Ecology Resources. ,vol. 11, pp. 218- 225 ,(2011) , 10.1111/J.1755-0998.2010.02949.X
Mark D. Shriver, Joshua M. Akey, Ranjan Deka, Robert E. Ferrell, Michael W. Smith, Amy Marcini, Li Jin, Ethnic-affiliation estimation by use of population-specific DNA markers. American Journal of Human Genetics. ,vol. 60, pp. 957- 964 ,(1997)
Wesley A Larson, James E Seeb, Carita E Pascal, William D Templin, Lisa W Seeb, E Taylor, Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska Canadian Journal of Fisheries and Aquatic Sciences. ,vol. 71, pp. 698- 708 ,(2014) , 10.1139/CJFAS-2013-0502
Ian R. Bradbury, Lorraine C. Hamilton, Sara Rafferty, David Meerburg, Rebecca Poole, J. Brian Dempson, Martha J. Robertson, David G. Reddin, Vincent Bourret, Mélanie Dionne, Gerald Chaput, Timothy F. Sheehan, Timothy L. King, John R. Candy, Louis Bernatchez, Genetic evidence of local exploitation of Atlantic salmon in a coastal subsistence fishery in the Northwest Atlantic Canadian Journal of Fisheries and Aquatic Sciences. ,vol. 72, pp. 83- 95 ,(2015) , 10.1139/CJFAS-2014-0058
Ian R. Bradbury, Lorraine C. Hamilton, Gerald Chaput, Martha J. Robertson, Herlé Goraguer, Arthur Walsh, Vicki Morris, David Reddin, J. Brian Dempson, Timothy F. Sheehan, Timothy King, Louis Bernatchez, Genetic mixed stock analysis of an interceptory Atlantic salmon fishery in the Northwest Atlantic Fisheries Research. ,vol. 174, pp. 234- 244 ,(2016) , 10.1016/J.FISHRES.2015.10.009
Bourret Vincent, Mélanie Dionne, Matthew P. Kent, Sigbjørn Lien, Louis Bernatchez, Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation. Evolution. ,vol. 67, pp. 3469- 3487 ,(2013) , 10.1111/EVO.12139
STEN KARLSSON, THOMAS MOEN, SIGBJØRN LIEN, KEVIN A. GLOVER, KJETIL HINDAR, Generic genetic differences between farmed and wild Atlantic Salmon identified from a 7K SNP-chip Molecular Ecology Resources. ,vol. 11, pp. 247- 253 ,(2011) , 10.1111/J.1755-0998.2010.02959.X
L. W. SEEB, W. D. TEMPLIN, S. SATO, S. ABE, K. WARHEIT, J. Y. PARK, J. E. SEEB, Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon. Molecular Ecology Resources. ,vol. 11, pp. 195- 217 ,(2011) , 10.1111/J.1755-0998.2010.02966.X