Population genomic data delineate conservation units in mottled ducks (Anas fulvigula)

Peters, Jeffrey L.; Lavretsky, Philip; DaCosta, Jeffrey M.; Bielefeld, Ronald R.; Feddersen, Jamie C.; Sorenson, Michael D.

doi:10.1016/j.biocon.2016.10.003

Cited by 43 publications

(48 citation statements)

References 82 publications

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“…admixture results suggest that several individuals among the monochromatic taxa show some evidence of mixed ancestry, but only one mottled duck from Florida showed evidence of elevated coancestry with mallards in the fineRADstructure analysis (Figures and ). Given the greater sensitivity of fineRADstructure to recent ancestry (Malinsky, Trucchi, et al, ), we conclude that putative signals of admixture in the admixture analysis are likely due to shared ancestral variation (i.e., ILS), and that the occurrence of hybrid individuals in our data set is low, consistent with other recent analyses of the NW “mallards” (Ford, Selman, & Taylor, ; Lavretsky et al, ; Peters et al, ). We note, however, that we intentionally avoided sampling in geographic regions where mallards and Mexican ducks come into contact, and Peters et al () only examined mottled ducks that were phenotypically “pure,” though this sampling protocol would not necessarily exclude subsequent generation backcrosses.…”

Section: Discussionsupporting

confidence: 90%

“…In this study, the thousands of loci recovered using ddRAD‐seq did not include any perfectly diagnostic SNPs, but did include a sufficient number of loci with differences in allele frequencies to allow multi‐locus assignment of individuals to populations. Importantly, complementing recent studies showing multi‐locus genetic discrimination of mallards and Mexican ducks (Lavretsky et al, ) and the two mottled duck subspecies (Peters et al, ), respectively, we demonstrate that mallards and black ducks are also distinguishable using ddRAD‐seq data (Figures and ).…”

Section: Discussionsupporting

confidence: 87%

“…Whereas TreeMix identified gene flow from mallards into either Mexican ducks or black ducks in two different data partitions (Figure ; Table ), f 4‐statistics were equivocal with respect to rejecting a null hypothesis of no gene flow involving mallards (Table ). In addition, other recent studies have detected a relatively low frequency of hybrids and/or recent backcrosses—for example, between mallards and either mottled ducks (~5%; Peters et al, ; Ford et al, ) or Mexican ducks (~2%; Lavretsky et al, ). Thus, although hybridization is known to occur between mallards and each of the monochromatic species, our results suggest that contemporary gene flow and introgression may be lower than assumed.…”

Section: Discussionmentioning

confidence: 98%

“…Although the frequency of mixed pairs and hybrid individuals remains uncertain (Heusmann, ; Johnsgard, ; Kirby, Reed, Dupuis, Obrecht, & Quist, ), black ducks and mallards are genetically indistinguishable based on allozymes (Ankney et al, ), microsatellites (Mank et al, ), and sequence data from a limited number of mitochondrial and nuclear genes (Johnson & Sorenson, ; Lavretsky, Hernández Baños, & Peters, ; Lavretsky, McCracken, et al, ; McCracken et al, ). ddRAD‐seq methods, however, have provided sufficient genomic coverage and allele frequency differences to identify population structure, hybrid individuals, founder events, and genomic regions putatively under divergent selection between mallards and Mexican ducks (Lavretsky et al, ), between the two mottled duck subspecies (Peters et al, ), and more recently between mallards and black ducks (Lavretsky et al, ). Regardless, assessing the relative roles of gene flow and ILS in explaining the genetic similarity across New World (NW) mallard taxa remains difficult.…”

Section: Introductionmentioning

confidence: 99%

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ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

et al. 2019

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Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes that may have been involved in the diversification of species in this recent radiation.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

et al. 2019

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“…In fact, torrent ducks from Peru had values of mtDNA diversity more similar to those found in other ducks with Ne several orders of magnitude larger Ne (e.g., mallards; Lavretsky et al, 2015). In contrast to mtDNA, diversity estimates from nuclear DNA for the two torrent duck subspecies were lower compared to other waterfowl species (Lavretsky et al, 2015;Lavretsky et al, 2016;Peters et al, 2016;Wilson et al, 2012). In contrast to mtDNA, diversity estimates from nuclear DNA for the two torrent duck subspecies were lower compared to other waterfowl species (Lavretsky et al, 2015;Lavretsky et al, 2016;Peters et al, 2016;Wilson et al, 2012).…”

Section: Genetic Diversity and Small Effective Population Sizementioning

confidence: 73%

Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes

Alza

Lavretsky

Peters

et al. 2019

Ecology and Evolution

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Aim 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. Location Peruvian and Argentine Andes. Taxon Two subspecies of torrent duck (Merganetta armata). Methods We 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. Results Haplotype 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 conclusions 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.

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Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America

Lavretsky

Janzen

McCracken

2019

Ecology and Evolution

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Resolving evolutionary relationships and establishing population structure depends on molecular diagnosability that is often limited for closely related taxa. Here, we use 3,200 ddRAD‐seq loci across 290 mallards, American black ducks, and putative hybrids to establish population structure and estimate hybridization rates. We test between traditional assignment probability and accumulated recombination events based analyses to assign hybrids to generational classes. For hybrid identification, we report the distribution of recombination events complements ADMIXTURE simulation by extending resolution past F4 hybrid status; however, caution against hybrid assignment based on accumulated recombination events due to an inability to resolve F1 hybrids. Nevertheless, both analyses suggest that there are relatively few backcrossed stages before a lineage's hybrid ancestry is lost and the offspring are effectively parental again. We conclude that despite high rates of observed interspecific hybridization between mallards and black ducks in the middle part of the 20th century, our results do not support the predicted hybrid swarm. Conversely, we report that mallard samples genetically assigned to western and non‐western clusters. We indicate that these non‐western mallards likely originated from game‐farm stock, suggesting landscape level gene flow between domestic and wild conspecifics.

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Population genomic data delineate conservation units in mottled ducks (Anas fulvigula)

Cited by 43 publications

References 82 publications

ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes

Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America

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