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Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

Authors

  • MORTEN T. LIMBORG,

    1. National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
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    • Joint first authors.

  • SARAH J. HELYAR,

    1. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK
    2. Matís, Vínlandsleið 12, 113 Reykjavík, Iceland
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    • Joint first authors.

  • MARK De BRUYN,

    1. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK
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  • MARTIN I. TAYLOR,

    1. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK
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  • EINAR E. NIELSEN,

    1. National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
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  • ROB OGDEN,

    1. TRACE Wildlife Forensics Network, Royal Zoological Society of Scotland, Corstorphine Road, Edinburgh EH12 6TS, UK
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  • GARY R. CARVALHO,

    1. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK
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  • FPT Consortium,

  • DORTE BEKKEVOLD

    1. National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
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Errata

This article is corrected by:

  1. Errata: Corrigendum Volume 22, Issue 8, 2355–2356, Article first published online: 7 February 2013

Morten T. Limborg, Fax: +45 35 88 31 50; E-mail: mol@aqua.dtu.dk

Abstract

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5–12 °C) and two salinity clines (5–35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic–North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

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