Abstract
AimTo 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.LocationPeruvian and Argentine Andes.TaxonTwo subspecies of torrent duck (Merganetta armata).MethodsWe sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. 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. 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.ResultsHaplotype and nucleotide diversities were higher in Peru than Argentina across all markers. 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. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂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 ∂a∂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.Main conclusionsWe 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.
Highlights
Establishing how populations are structured is fundamental for understanding evolutionary processes (Hartl & Clark, 2007; Hey & Machaco, 2003; Ma, Ji, & Zhang, 2015; Wright, 1969)
Main conclusions: We suggest that the South American Arid Diagonal was preexist‐ ing 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
Tajima's D was calculated to test for the departure from neutrality in sce‐ narios characterized by an excess of rare alleles. Negative values for this test statistic may indicate a population evolving under nonran‐ dom processes such as directional selection or recent demographic expansion, whereas positive values may be indicative of popula‐ tion decline or balancing selection
Summary
Establishing how populations are structured is fundamental for understanding evolutionary processes (Hartl & Clark, 2007; Hey & Machaco, 2003; Ma, Ji, & Zhang, 2015; Wright, 1969). As popula‐ tions subdivide through time, variation in the rate of genetic drift and gene flow, as well as selective pressures, will define the ge‐ netic diversity, divergence, or extinction of each species (Bowler & Benton, 2005; Frankham, 2005; Hey, 2010; Lenormand, 2002; Ma et al, 2015; Shaffer, 1981; Slatkin, 1987). Characterizing population structure and the rate of gene flow among populations of habitat specialists is crucial for understanding the ecological and evolutionary processes under‐ pinning population dynamics and historical demography, including speciation and extinction (Hartl & Clark, 2007; Lenormand, 2002; McCauley, 1991; Neigel, 1997; Slatkin, 1993)
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