Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Marion Sinclair-Waters; Paul Bentzen; Corey J. Morris; Daniel E. Ruzzante; Matthew P. Kent; SigbjØrn Lien; Ian R. Bradbury

doi:10.1139/cjfas-2017-0254

Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Marion Sinclair-Waters, Paul Bentzen, Corey J. Morris, Daniel E. Ruzzante, Matthew P. Kent, SigbjØrn Lien, Ian R. Bradbury

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15 Citas (Scopus)

Resumen

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using F_ST rankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

Idioma original	English
Páginas (desde-hasta)	1915-1925
Número de páginas	11
Publicación	Canadian Journal of Fisheries and Aquatic Sciences
Volumen	75
N.º	11
DOI	https://doi.org/10.1139/cjfas-2017-0254
Estado	Published - 2018

Nota bibliográfica

Funding Information:
We thank Fisheries and Oceans Canada, NunatuKavut Community Council, J. Green, C. Pennell, and G. Rowe for sample collection and providing valuable local knowledge. We also thank L. Hamilton for assisting with DNA extractions and R. Waples for providing consultation on estimating effective population size. Thank you to L. Hauser and C. Herbinger for providing valuable comments on an earlier version of the manuscript. Funding was provided by a strategic project grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) led by P. Bentzen and a Nova Scotia Graduate Scholarship awarded to M. Sinclair-Waters. The Genomics Research and Development Initiative of Fisheries and Oceans Canada also helped cover genotyp-ing costs. We are also grateful for the analytical assistance provided by N. Jeffery, R. Stanley, E. Sylvester, and B. Wringe.

Publisher Copyright:
© 2018, Published by NRC Research Press.

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Aquatic Science

ODS de las Naciones Unidas

Este resultado contribuye a los siguientes Objetivos de Desarrollo Sostenible

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title = "Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area",

abstract = "Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FST rankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.",

author = "Marion Sinclair-Waters and Paul Bentzen and Morris, {Corey J.} and Ruzzante, {Daniel E.} and Kent, {Matthew P.} and Sigbj{\O}rn Lien and Bradbury, {Ian R.}",

note = "Funding Information: We thank Fisheries and Oceans Canada, NunatuKavut Community Council, J. Green, C. Pennell, and G. Rowe for sample collection and providing valuable local knowledge. We also thank L. Hamilton for assisting with DNA extractions and R. Waples for providing consultation on estimating effective population size. Thank you to L. Hauser and C. Herbinger for providing valuable comments on an earlier version of the manuscript. Funding was provided by a strategic project grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) led by P. Bentzen and a Nova Scotia Graduate Scholarship awarded to M. Sinclair-Waters. The Genomics Research and Development Initiative of Fisheries and Oceans Canada also helped cover genotyp-ing costs. We are also grateful for the analytical assistance provided by N. Jeffery, R. Stanley, E. Sylvester, and B. Wringe. Publisher Copyright: {\textcopyright} 2018, Published by NRC Research Press.",

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AU - Kent, Matthew P.

AU - Lien, SigbjØrn

AU - Bradbury, Ian R.

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PY - 2018

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N2 - Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FST rankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

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Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Resumen

Nota bibliográfica

ASJC Scopus Subject Areas

ODS de las Naciones Unidas

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