A new evolutionary unit of <i>Merganetta armata</i> (Torrent Duck) in Patagonia: De-hybridization, phylogeography, and implications for conservation

Abstract Although previous studies have characterized genetic structure throughout much of the range of Merganetta armata (Torrent Duck), Patagonian populations have not been included. This study presents the first genetic analysis of the Patagonian population and situates it within the broader evolutionary context of the species. Here, we identify a divergent Patagonian mitochondrial DNA (mtDNA) lineage distinct from all other known subspecies. Our analyses further reveal that the traditionally recognized berlepschi and garleppi forms are nearly indistinguishable and cluster closely with armata, thereby challenging established taxonomic boundaries. These findings suggest that Patagonian M. armata may constitute an Evolutionarily Significant Unit of conservation concern. Feathers from 41 individuals were sampled across the Southern Andes, including the Yungas, High-Andes headwaters, and Patagonian Forests regions (22–50°S). During this study, we sequenced the mitochondrial control region and estimated population genetic and demographic parameters. In particular, we evaluated structure and connectivity through haplotype networks, principal component analysis, phylogenetic inference, and Bayesian divergence dating. This approach revealed fine-scale structuring and restricted gene flow, as well as unexpected affinities among northern and central lineages. The analyses also underscored the deep isolation and evolutionary distinctiveness of the Patagonian clade. Our mtDNA dataset, augmented with previously published sequences, provides broad geographic coverage across the species' distribution. The results are consistent with hybridization, paraphyly, and riverine connectivity shaping subspecific limits in Merganetta. Pleistocene glacial cycles likely reinforced the isolation of the Patagonian lineage. Together, these insights underscore the importance of integrating phylogeography and ecology to redefine M. armata subspecies and conserve the unique diversity of Andean waterfowl.