Herbarium-based phylogenomics sheds light on the evolutionary history of mesoamerican tropical forests: annonaceae as a case study
The tropical forests of Mesoamerica, stretching from Mexico to northern Colombia, represent one of the most diverse biotas on Earth. Yet their evolutionary history and the processes that shape their assembly remain poorly understood, often leading to their treatment as a single biotic unit. In this study, we use the family Annonaceae as a model lineage to reconstruct the region’s evolutionary trajectories, integrating hundreds of nuclear markers derived from both historical and contemporary herbarium specimens. This high-resolution phylogenomic framework, encompassing more than 80 % of the ~2,500 species in the family, reveals consistent patterns of floristic and evolutionary differentiation, as well as sharp contrasts between northern Mesoamerica (MegaMexico 2 and the Caribbean) and the southern regions. Northern areas exhibit deeper phylogenetic diversity despite lower species richness, reflecting prolonged isolation and greater environmental heterogeneity. In contrast, the south shows high species richness but phylogenetic redundancy, driven by recent colonizations and climatic filters. Divergence times highlight the central role of Miocene-Pliocene climatic oscillations and more recent orogenic activity in shaping Mesoamerican forests: dry forests emerge as evolutionary refugia and center of radiation. In contrast, wet forests consistently harbor younger lineages. Taken together, these findings challenge the view of Mesoamerica as a single evolutionary unit and demonstrate that its tropical forests are dynamic systems, repeatedly molded by cycles of climatic change and geographic isolation.