Land ahead: using genome scans to identify molecular markers of adaptive relevance

Abstract

Adaptation is back on the research schedules of evolutionists and ecologists. This renewed interest is driven by global change, to which species, in particular arctic and alpine ones, either react by migration or adaptation. In this overview, we give a brief introduction to the use of genome scans along with environmental data to identify molecular markers of adaptive relevance. This approach encompasses the sampling of many populations along ecological gradients or from different habitat types combined with genome scans using presumably neutral markers such as amplified fragment length polymorphisms or microsatellites. To identify markers linked to genes under selection, two different methods (besides others) are particularly relevant. (1) One searches for markers exhibiting higher genetic differentiation among populations than expected under neutrality. The frequencies of alleles at such outlier loci can then be related to ecological factors. (2) The other method uses logistic regression between allele presence/absence and ecological factors (i.e. an allele distribution model). It thus directly links marker occurrence with environmental data. We illustrate these two methods with examples from the literature. The strength of genome scans used in parallel with environmental data is that they provide distinct clues for selective forces acting on molecular markers of adaptive relevance in real landscapes. We further discuss limitations of genome scans (e.g. sensitivity to phylogeographic structure and bottlenecks) and of other genomic approaches to detect adaptive molecular markers such as candidate genes, quantitative trait loci or transcription profiling. We stress that the selective advantage of particular alleles has to be proven in selection experiments. We conclude that combining studies on adaptive and neutral molecular markers will largely contribute to our understanding of how species react to global change and will allow us to investigate the ‘migration of adaptation’.