Peruvian and Argentine subspecies showed concordant species-level differences (ΦST mtDNA = 0.82 ΦST autosomal = 0.30 ΦST Z chromosome = 0.45), including no shared mtDNA haplotypes. Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences. armata Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. leucogenis Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. Two subspecies of torrent duck (Merganetta armata). To investigate the structure and rate of gene flow among populations of habitat-specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.
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