Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics

Abstract Genomic data can provide valuable insights into the evolutionary history of rapidly diversifying groups and the genetic basis of phenotypic traits. We performed whole-genome resequencing of the warbler genus Myioborus to investigate the dynamics of its recent diversification in Neotropical mountains. Mitochondrial and nuclear DNA produced mostly concordant tree topologies and revealed a pattern of north-to-south and low-to-high elevation colonization. Within a young tropical Andes clade (M. albifrons, M. ornatus, and M. melanocephalus), we found topological incongruence between our phylogenies. In general, relationships coincided with plumage types; however, three taxa with striking plumage differences exhibited low mitochondrial divergence. The hybridizing taxa M. ornatus chrysops and M. melanocephalus bairdi showed very shallow genomic differentiation, with most divergence peaks across the genome shared with other parulid warbler pairs, pointing to shared genomic architecture shaping these regions. However, a unique differentiated region included the gene CCDC91, which is associated with melanin-based plumage differences in other birds. We also identified a large region of elevated differentiation on the Z chromosome showing strong signals of reduced recombination. Together, these results highlight the interplay of deep ancestral divergence, recent hybridization, and shared genomic architecture in shaping the evolution of phenotypic and genomic diversity in Myioborus.