Genomic signatures and correlates of widespread population declines in salmon

S. J. Lehnert; T. Kess; P. Bentzen; M. P. Kent; S. Lien; J. Gilbey; M. Clément; N. W. Jeffery; R. S. Waples; I. R. Bradbury

doi:10.1038/s41467-019-10972-w

Genomic signatures and correlates of widespread population declines in salmon

S. J. Lehnert, T. Kess, P. Bentzen, M. P. Kent, S. Lien, J. Gilbey, M. Clément, N. W. Jeffery, R. S. Waples, I. R. Bradbury

Research output: Contribution to journal › Article › peer-review

55 Citations (Scopus)

Abstract

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (N_e) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, N_e has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.

Original language	English
Article number	2996
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-10972-w
Publication status	Published - Dec 1 2019

Bibliographical note

Funding Information:
We thank the Centre for Integrative Genetics (CIGENE) for genotyping the range-wide data used in the present study. We thank E. Sylvester, K. Wellband and C. Hollenbeck for advice and assistance on statistical analyses. Funding was provided through the Genomics Research and Development Initiative, and the International Governance Strategy of Fisheries and Oceans Canada, as well as a Strategic Project Grant from National Sciences and Engineering Research Council of Canada.

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus Subject Areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

PubMed: MeSH publication types

Journal Article
Research Support, Non-U.S. Gov't

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10.1038/s41467-019-10972-w

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title = "Genomic signatures and correlates of widespread population declines in salmon",

abstract = "Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.",

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note = "Funding Information: We thank the Centre for Integrative Genetics (CIGENE) for genotyping the range-wide data used in the present study. We thank E. Sylvester, K. Wellband and C. Hollenbeck for advice and assistance on statistical analyses. Funding was provided through the Genomics Research and Development Initiative, and the International Governance Strategy of Fisheries and Oceans Canada, as well as a Strategic Project Grant from National Sciences and Engineering Research Council of Canada. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

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AU - Lehnert, S. J.

AU - Kess, T.

AU - Bentzen, P.

AU - Kent, M. P.

AU - Lien, S.

AU - Gilbey, J.

AU - Clément, M.

AU - Jeffery, N. W.

AU - Waples, R. S.

AU - Bradbury, I. R.

N1 - Funding Information: We thank the Centre for Integrative Genetics (CIGENE) for genotyping the range-wide data used in the present study. We thank E. Sylvester, K. Wellband and C. Hollenbeck for advice and assistance on statistical analyses. Funding was provided through the Genomics Research and Development Initiative, and the International Governance Strategy of Fisheries and Oceans Canada, as well as a Strategic Project Grant from National Sciences and Engineering Research Council of Canada. Publisher Copyright: © 2019, The Author(s).

PY - 2019/12/1

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N2 - Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.

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Genomic signatures and correlates of widespread population declines in salmon

Abstract

Bibliographical note

ASJC Scopus Subject Areas

PubMed: MeSH publication types

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