The tangled evolutionary history of a long-debated Mesoamerican taxon: The Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae)

[Display omitted] •The Velazquez Woodpecker (Melanerpes santacruzi) is a polytypic taxon whose taxonomy and evolutionary history have been historically controversial due to complex distribution patterns of morphologically differentiated populations, and the lack of phylogeographic structure among them.•Genomic data provided good resolution for detecting population structure within the Velazquez Woodpecker, which is consistent with some major geographical features in southeastern Mexico and only partially congruent with previous grouping hypotheses.•Populations of M. santacruzi diverged recently and show genetic admixture among them, but also with the Golden-Fronted Woodpecker (M. aurifrons), although each one maintains its own morphological and evolutionary identity.•Ecological niche models support the genetic differentiation of M. santacruzi populations and suggest intermittent areas of sympatry since Last Interglacial. The Velazquez Woodpecker Melanerpes santacruzi is a highly polytypic species distributed from east-central Mexico to northern Nicaragua. The ample variation in body size, barring of the plumage, and the coloration of nasal tufts, neck, and belly have fueled debates about the taxonomy and evolutionary history of the species; however, the processes generating these patterns of variation and the underlying population dynamics throughout the species’ distribution remain poorly understood. Here, we employed reduced representation genome sequencing (NextRAD) and Ecological Niche Modeling methods to test the distinctiveness of the Velazquez Woodpecker based on this new set of genomic data and analyze the correspondence of the genetic structure and ecological differentiation with phenotypic variation and geographic distribution. From phylogenetic and demographic analyses including the Golden-Fronted (M. aurifrons) and Red-bellied Woodpecker (M. carolinus), we obtained results congruent with previous molecular phylogenies. The clades of M. santacruzi and M. carolinus-M. aurifrons are reciprocally monophyletic, although the sister group relationship of M. aurifrons is ambiguous. Using genetic and ecological analyses, we found that the species is structured into three genetically and ecologically differentiated groups comprising the subspecies (1) M. s. santacruzi, (2) M. s. dubius and (3) M. s. grateloupensis-polygrammus-veraecrucis. These groups diverged recently, with two splits between 250,000 and 150,000 years ago, and show a significant genetic