Diversification and coexistence amid widespread and persistent gene flow in Andean trees

Hybridization and introgression are increasingly recognized as important in plant evolution, yet their prevalence and consequences remain poorly understood in tropical Andean trees, where species coexist at low densities and turn over rapidly across elevation gradients. Here, we investigate whether species boundaries are maintained among 10 congeneric Andean Prunus L. species distributed across the Andes-Amazon elevational gradient by reconstructing phylogenetic relationships, divergence times, and patterns of historical and recent gene flow. We find that Andean Prunus diversified during the Miocene, likely in response to novel habitat opportunities resulting from mountain uplift, combined with allopatric processes. Despite this evolutionary divergence, these species show extensive ancient introgression and recent admixture, indicating that species boundaries remain permeable across both ecological and phylogenetic distance. Together, these results suggest that Andean Prunus comprise distinct but evolutionarily connected lineages that retain morphological identity while potentially functioning as a long-lived syngameon, with implications for understanding the origin and maintenance of tropical tree diversity and future response to global change.