{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Alza L"],"funding":["Consejo Nacional de Investigaciones Científicas y Técnicas","Agencia Nacional de Promoción Científica y Tecnológica","National Science Foundation"],"pagination":["9961-9976"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6745679"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["9(17)"],"pubmed_abstract":["<h4>Aim</h4>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.<h4>Location</h4>Peruvian and Argentine Andes.<h4>Taxon</h4>Two subspecies of torrent duck (<i>Merganetta armata</i>).<h4>Methods</h4>We sampled 156 individuals in Peru (<i>M. a. leucogenis;</i> Chillón River, <i>n</i> = 57 and Pachachaca River, <i>n</i> = 49) and Argentina (<i>M. a. armata;</i> Arroyo Grande River, <i>n</i> = 33 and Malargüe River, <i>n</i> = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, <i>n</i> = 10 and Argentina, <i>n</i> = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences.<h4>Results</h4>Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species-level differences (Φ<sub>ST</sub> mtDNA = 0.82; Φ<sub>ST</sub> autosomal = 0.30; Φ<sub>ST</sub> Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using <i>∂a∂i</i> (isolation-with-migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal <i>∂a∂i</i> = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well-differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.<h4>Main conclusions</h4>We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure."],"journal":["Ecology and evolution"],"pubmed_title":["Old divergence and restricted gene flow between torrent duck (<i>Merganetta armata</i>) subspecies in the Central and Southern Andes."],"pmcid":["PMC6745679"],"funding_grant_id":["PICT-2016-3712","PIP 112 201301 00803 CO","NSF 0949439","D3657"],"pubmed_authors":["Ceron G","Smith M","Kopuchian C","Lavretsky P","Astie A","McCracken KG","Alza L","Peters JL"],"additional_accession":[]},"is_claimable":false,"name":"Old divergence and restricted gene flow between torrent duck (<i>Merganetta armata</i>) subspecies in the Central and Southern Andes.","description":"<h4>Aim</h4>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.<h4>Location</h4>Peruvian and Argentine Andes.<h4>Taxon</h4>Two subspecies of torrent duck (<i>Merganetta armata</i>).<h4>Methods</h4>We sampled 156 individuals in Peru (<i>M. a. leucogenis;</i> Chillón River, <i>n</i> = 57 and Pachachaca River, <i>n</i> = 49) and Argentina (<i>M. a. armata;</i> Arroyo Grande River, <i>n</i> = 33 and Malargüe River, <i>n</i> = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, <i>n</i> = 10 and Argentina, <i>n</i> = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences.<h4>Results</h4>Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species-level differences (Φ<sub>ST</sub> mtDNA = 0.82; Φ<sub>ST</sub> autosomal = 0.30; Φ<sub>ST</sub> Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using <i>∂a∂i</i> (isolation-with-migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal <i>∂a∂i</i> = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well-differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.<h4>Main conclusions</h4>We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Sep","modification":"2024-11-10T02:55:44.245Z","creation":"2019-09-26T07:06:32Z"},"accession":"S-EPMC6745679","cross_references":{"pubmed":["31534707"],"doi":["10.1002/ece3.5538"]}}