title: Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina.
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.
authors.affiliation: Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France.
authors.forename: Bénédicte N
authors.initials: BN
authors.lastname: Poncet
authors.forename: Doris
authors.initials: D
authors.lastname: Herrmann
authors.forename: Felix
authors.initials: F
authors.lastname: Gugerli
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.forename: Rolf
authors.initials: R
authors.lastname: Holderegger
authors.forename: Ludovic
authors.initials: L
authors.lastname: Gielly
authors.forename: Delphine
authors.initials: D
authors.lastname: Rioux
authors.forename: Wilfried
authors.initials: W
authors.lastname: Thuiller
authors.forename: Serge
authors.initials: S
authors.lastname: Aubert
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Manel
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D054458:Amplified Fragment Length Polymorphism Analysis; D031214:Arabis / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D004777:Environment; D005602:France; D005828:Genetics, Population; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D015233:Models, Statistical; D013557:Switzerland
chemical_list: D018744:DNA, Plant