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Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Authors

  • BÉNÉDICTE N. PONCET,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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    • The first two authors contributed equally to this paper.

  • DORIS HERRMANN,

    1. WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
    2. Indo-Swiss Collaboration in Biotechnology (ISCB), EPFL AI-VP CO-ISCB, 1015 Lausanne, Switzerland
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    • The first two authors contributed equally to this paper.

  • FELIX GUGERLI,

    1. WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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  • PIERRE TABERLET,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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  • ROLF HOLDEREGGER,

    1. WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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  • LUDOVIC GIELLY,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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  • DELPHINE RIOUX,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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  • WILFRIED THUILLER,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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  • SERGE AUBERT,

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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  • STÉPHANIE MANEL

    1. Laboratoire d’Écologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
    2. Laboratoire Population–Environnement–Développement, UMR 151 UP/IRD, Université de Provence, centre Saint-Charles, Case 10, 3, place Victor-Hugo, 13331 Marseille Cedex 3, France
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S. Manel, Fax: +33 476514279; E-mail: stephanie.manel@ujf-grenoble.fr

Abstract

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.

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