Integrating mitochondrial and ddRADseq data to unravel phylogenetic relationships in Geothlypis warblers

Understanding evolutionary relationships within avian genera remains a central challenge in systematics. The New World yellowthroats (Geothlypis, Parulidae) comprise 14 recognized species whose phylogenetic relationships and species limits remain unresolved. In this study, we combined mitochondrial (ND2) and genome-wide nuclear data (ddRADseq) from 142 individuals of 8 Geothlypis species, with broad geographic sampling from North America to reconstruct phylogenetic relationships and assess population structure across the genus. In general, both datasets recover 4 major clades: (1) G. semiflava and G. aequinoctialis, (2) G. rostrata, (3) eastern G. trichas, and (4) western G. trichas. However, notable mito-nuclear discordance was detected. Genome-wide nuclear data place G. nelsoni as sister to the group composed of G. semiflava and G. aequinoctialis (Central and South American lineage), whereas mitochondrial DNA embeds it within the eastern G. trichas group, suggesting historical introgression or mitochondrial capture. Similarly, G. flavovelata and G. beldingi are monophyletic in nuclear analyses but are embedded within G. trichas groups in the mitochondrial phylogeny. Population genomic analyses reveal strong geographic structure in G. trichas (eastern vs western), G. rostrata (northern vs southern Bahamas), and G. beldingi (northern vs southern Baja California Sur). Our results support the recognition of several independent evolutionary lineages and highlight the polyphyletic nature of the G. trichas complex. This study refines the evolutionary understanding and the systematics of Geothlypis and provides a foundation for future taxonomic and conservation assessments.