Late M iocene lineage divergence and ecological differentiation of rare endemic J uniperus blancoi : clues for the diversification of N orth A merican conifers

Summary Western N orth A merica and M exico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late T ertiary and Q uaternary. In this study, we focus on the evolutionary history of J uniperus blancoi , in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J . blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J . blancoi are differentiated into three lineages that correspond to low‐, mid‐ and high‐altitude populations. The three groups diversified in the late M iocene, early P liocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the P leistocene that could be linked to climate changes. Populations of J . blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.