Data from: Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could have also promoted interspecific divergence through ecological speciation. In this study, we examined genetic variation within and between two closely related pine species, Pinus massoniana and Pinus hwangshanensis. These two species occur in Southeast China and exhibit contrasting ecological preferences, although hybrids are formed where their distributions overlap. We sampled 26 populations of the two species across their distributional ranges and sequenced 25 climate-related candidate genes and 12 reference loci, assumed not to be related to climatic selection. More than half of the 25 candidate genes (17) showed signals of recent and/or ancient selection, as indicated by one or several robust tests at different evolutionary timescales, while selection signals were only detected at three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared history. We compared intra- and interspecific genetic differentiation of loci detected under recent selection (selected loci) with those showing no signals of recent selection (unselected loci). Intraspecific differentiation was reduced, but interspecific differentiation was elevated for selected loci. Under the Isolation with Migration model, climate-related candidate genes had earlier divergence time estimates and more restricted levels of migration in both directions between the two species than reference loci. Taken together, our results suggested that climate-related candidate genes might be commonly shaped by climatic selection and recent divergent selection might have counteracted interspecific gene flow and play an important role during ecological divergence of these two closely related pine species.