Scripts from: Distinct intraspecific diversification dynamics in Neotropical montane versus lowland canopy birds (Thraupidae: <em>Tangara</em>) revealed by whole-genome comparative phylogeography

Comparing phylogeographic patterns across different biogeographic regions can illuminate how different types of landscapes promote the formation and persistence of incipient species, providing insights into the evolutionary mechanisms underlying broadscale biodiversity gradients. The Neotropics are a global biodiversity hotspot, and the megadiverse Andes-Amazonia system exhibits elevational gradients in both species richness and speciation rates. Using whole genomes from a congeneric set of eight habitat-generalist canopy frugivore birds (Tangara tanagers), we compare the phylogeography of tropical Andean versus lowland Amazonian species to characterize intraspecific diversification dynamics associated with these distinct but adjacent biomes. We found that all species exhibited low genetic structure consistent with their dispersive ecology, but Andean species have relatively greater population genetic structuring across their ranges than Amazonian species. Additionally, populations separated by prominent geoclimatic barriers showed lower gene flow and higher differentiation in montane versus lowland Tangara. Lastly, all Andean species have lower genetic diversity, a proxy of effective population size. Together, these results support greater incipient speciation in the mountains owing to stronger allopatry and smaller populations, while the larger, more diverse, and well-connected populations of the lowlands may foster enhanced persistence. We discuss potential implications for the origin and maintenance of regional biodiversity gradients.