An outlier locus relevant in habitat-mediated selection in an alpine plant across independent regional replicates

Abstract

Habitat types can induce genetic responses in species and may drive adaptive differentiation and evolutionary divergence of populations. In this study, we aimed at detecting loci indicative of adaptation for different habitat types in the alpine plant Arabis alpina. We used a dataset consisting of A. alpina plants collected in scree, nutrient-rich and moist habitat types in two independent regional replicates of the European Alps (the Swiss and French Alps). Genome scans resulting in 825 amplified fragment length polymorphisms (AFLPs) followed by outlier analysis, i.e. looking for excessive differentiation between habitat types, after accounting for heterozygosity and population structure, was used to detect loci under divergent selection for habitat type within and across the alpine regions. The outlier analyses resulted in the detection of a consistent single outlier locus, which showed a higher fragment frequency in moist compared to the other habitat types in both alpine regions. In addition, a posteriori tests for hierarchical population structuring in the dataset did not detect signals confounding selection at this locus (i.e. signals of regional population structure). Thus, we consider this locus indicative of habitat-mediated selection, and we subsequently sequence-characterized and compared it to the Arabidopsis genome. The sequence was found to be a putative homologue to the SIT4 phosphatase-associated family protein. The detection of this locus in two alpine regions and the availability of its genome sequence make this locus a strong candidate worth further exploration in the habitat-mediated selection and genetic adaptation of natural populations in the alpine plant A. alpina.