The first two authors contributed equally to this paper.
Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina
Article first published online: 1 JUL 2010
© 2010 Blackwell Publishing Ltd
Volume 19, Issue 14, pages 2896–2907, July 2010
How to Cite
PONCET, B. N., HERRMANN, D., GUGERLI, F., TABERLET, P., HOLDEREGGER, R., GIELLY, L., RIOUX, D., THUILLER, W., AUBERT, S. and MANEL, S. (2010), Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Molecular Ecology, 19: 2896–2907. doi: 10.1111/j.1365-294X.2010.04696.x
- Issue published online: 12 JUL 2010
- Article first published online: 1 JUL 2010
- Received 15 January 2010; revision received 22 March 2010; accepted 26 April 2010
- adaptive genetic variation;
- amplified fragment length polymorphism;
- generalized estimating equations;
- landscape genomics;
- local adaptation
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.