Distinct intraspecific diversification dynamics in Neotropical montane versus lowland birds revealed by whole-genome comparative phylogeography

Comparing phylogeographic patterns across different biogeographic regions can illuminate how different types of landscapes promote the formation 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 has elevational gradients in both species richness and speciation rates. Here, we compare the phylogeographic dynamics of birds in the tropical Andes mountains versus the Amazonian lowlands using whole genomes from a congeneric set of colorful canopy frugivores (Tangara tanagers). We first show that Andean species have greater population structuring across their geographic ranges than Amazonian species. Next, we evaluated whether differences in geographic barrier efficacy and range size drive this elevated population-level divergence in the mountains. We find greater population differentiation and reduced gene flow across individual geographic barriers in the Andes. Furthermore, Andean species have consistently lower genetic diversity and smaller effective population sizes. Together, these results support a model of Neotropical diversification whereby incipient species form more readily in the mountains than the lowlands owing to more effective geographic barriers and smaller populations. These different phylogeographic processes across the Andes-Amazonia system carry implications for our understanding of the origin and maintenance of regional biodiversity gradients.