Upslope diversification and gene flow among congeneric Andean trees

The high biodiversity of tropical Andean forests is characterized by many closely related species which turnover rapidly across elevation and environmental gradients. Yet, the eco-evolutionary relationships among these congeneric species remain poorly understood – specifically, how they diversify, sort into their elevational niches, and the extent to which species boundaries are maintained through time. In this study, we use the genus Prunus (cherries) as a model to investigate these processes by (1) reconstructing the phylogenetic relationships and timing of divergence among sympatric species and (2) assessing inter-specific gene flow and its correspondence to evolutionary and ecological distance. Extensive population-level sampling was conducted for species which co-occur along an elevational gradient in Manu National Park, Peru. Additional samples were included for species which co-occur across a gradient in Madidi National Park, Bolivia. Phylogenetic relationships reconstructed a pattern of upslope adaptive diversification concurrent with Andean orogeny during the Miocene. However, despite these ancient diversification events, gene flow analyses found species are not reproductively isolated, and gene flow has occurred through time. Additionally, gene flow is widespread and does not appear to be constrained by evolutionary or ecological distance. Together, these findings provide insight into the processes that have shaped tree diversity in the tropical Andes and suggest that during adaptive radiations, observable ecological, and morphological differences may emerge long before complete phylogenomic isolation, even amid ongoing gene flow.