Genomic structure, phenotypic variation and drivers of diversification in <i>Euphonia hirundinacea</i> (Aves: Fringilidae)

The evolutionary drivers of genetic and phenotypic diversity in widespread Neotropical birds remain poorly understood, particularly in species with high dispersal capabilities. In this study, we examine the population genetic structure, demographic history, and phenotypic variation of Euphonia hirundinacea across its Mesoamerican range using NextRad genomic data, as well as geographic and phenotypic variables. A maximum-likelihood phylogeny confirmed the monophyly of E. hirundinacea , with two well-supported clades corresponding to geographically segregated populations that align with the subspecies E. h. hirundinacea and E. h. gnatho . Our findings indicate moderate genetic differentiation partially shaped by isolation by distance (IBD), with the Nicaragua Depression acting as a semi-permeable barrier that allows limited gene flow. Most phenotypic traits did not correlate with genetic divergence, geographic distance, or environmental variables. However, in females, wing chord and throat coloration were significantly associated with both genetic and geographic distances. Demographic analyses support a scenario of divergence initiated during Pleistocene climatic fluctuations (∼2,668,739.13 years ago), followed by population expansion during Holocene (∼20,000 years ago) and secondary contact, supported by ecological niche models. The species’ ecological flexibility and high vagility likely mitigated long-term isolation and facilitated rapid post-glacial recolonization. Overall, our findings highlight the roles of isolation by distance, Pleistocene climatic dynamics, geographic barriers, and sex-specific traits in shaping diversification in a highly mobile Neotropical bird.