Low Genic Variation between Black Ducks and Mallards

Ankney, C. Davison; Dennis, Darrell G.; Wishard, Lisa N.; Seeb, James E.

doi:10.1093/auk/103.4.701

Cited by 60 publications

(35 citation statements)

References 22 publications

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“…Hybridization leading to the transfer of mtDNA from one species to another can result in a mtDNA tree that is incongruent with the species tree, but it will not necessarily prevent species from being distinguished, unless the mitochondrial transfer is so recent that their sequences have not diverged (Moore 1995). However, recent hybridization will lead species to share COI barcodes, and we expect that more intensive study will reveal such shared sequences in species that are known to hybridize, such as the white-headed gulls (Crochet et al 2003) and Mallard/Black Ducks (Ankney et al 1986; Avise et al 1990). …”

Section: Discussionmentioning

confidence: 99%

Identification of Birds through DNA Barcodes

et al. 2004

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Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10× average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

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Section: Discussionmentioning

confidence: 99%

Identification of Birds through DNA Barcodes

et al. 2004

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“…Despite high rates of observed interspecific interactions between black ducks and mallards in the middle part of the 20th century (Ankney et al, 1986;Avise et al, 1990;Heusmann, 1974;Mank et al, 2004;McAuley, Clugston, & Longcore, 1998;Merendino & Ankney, 1994;Merendino, Ankney, & Dennis, 1993), our results do not support the eastern hybrid swarm hypothesis or predict the subsequent genetic extinction of the black duck (Rhymer, 2006). ADMIXTURE analysis of our dataset suggests a minimum ~25% hybridization rate between mallards and black ducks (Table 1), which is substantially higher than rates between mallards and either Mexican ducks (~2%; Lavretsky, Dacosta et al, 2015) or mottled ducks (~5%; Ford, Selman, & Taylor, 2017;Peters et al, 2016 Alternative to assortative mating limiting gene flow, we hypothesize that the possibility to reestablish the parental lineage through backcrossing in only a few generations may be playing an important role in maintaining black ducks in the face of relative high rates of hybridization.…”

Section: Genomics Of Hybridization and Islands Of Differentiationmentioning

confidence: 99%

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

Lavretsky

Janzen

McCracken

2019

Ecology and Evolution

101

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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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“…Among the monochromatic species, black ducks have the highest rates of hybridization and introgression with mallards (Lavretsky, Janzen, & McCracken, ), and previous studies have suggested either that the two forms are conspecific (Ankney et al, ), or that black ducks have suffered a complete breakdown of their genetic distinctiveness (Mank, Carlson, & Brittingham, ). 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, ).…”

Section: Introductionmentioning

confidence: 99%

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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Low Genic Variation between Black Ducks and Mallards

Cited by 60 publications

References 22 publications

Identification of Birds through DNA Barcodes

Identification of Birds through DNA Barcodes

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

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