Phylogenomics of the American robin ( <i>Turdus migratorius</i> ) reveals hidden lineages and introgression

Abstract Many bird species with broad geographic distributions show complex patterns of lineage divergence shaped by historical isolation, migration, and gene flow. The American robin, Turdus migratorius , is found throughout North America and includes seven described subspecies that differ in plumage and migratory behavior; yet, their evolutionary relationships remain uncertain. Here, we used genome‐wide SNP data, population structure analyses, phylogenomic inference, divergence time estimation, and D‐statistics to reconstruct relationships within the T. migratorius complex and evaluate patterns of lineage divergence and introgression. Our analyses consistently recovered four principal genomic lineages that do not correspond to currently recognized subspecies: (1) T. m. confinis from Baja California Sur, (2) a Mexican lineage, (3) western North America, and (4) boreal eastern North America. Time‐calibrated analyses indicate a deep late‐Miocene divergence (~8 Ma) separating T. m. confinis from all other lineages, followed by Pleistocene diversification among the remaining groups. Genome‐wide differentiation and long‐term isolation support the recognition of T. m. confinis as an independently evolving lineage consistent with species‐level status. In contrast, Turdus rufitorques , which is traditionally considered the sister species of T. migratorius , was nested within the Mexican lineage. Significant D ‐statistics revealed excess allele sharing between the Mexican lineage and T. rufitorques , supporting a history of introgression. This study refines species limits within the American robin complex and highlights the importance of genome‐wide data for resolving evolutionary independence in widespread migratory birds.