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Kaminski M, Brown JI, Seibert SR, Hernández F, Duya MV, Fontanilla IKC, Roshier D, Miles A, Joseph L, Peters JL, Lavretsky P. Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data. Mol Phylogenet Evol 2024; 197:108085. [PMID: 38688441 DOI: 10.1016/j.ympev.2024.108085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
AIM We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LOCATION Oceania, greater Indonesia, and the Philippines. TAXON Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. RESULTS Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. MAIN CONCLUSIONS Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.
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Affiliation(s)
- Marissa Kaminski
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Upper Midwest Environmental Sciences Center, United States Geological Survey, La Crosse, WI, USA.
| | - Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Sara R Seibert
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Melizar V Duya
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Ian Kendrich C Fontanilla
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - David Roshier
- School of Animal and Veterinary Science, University of Adelaide, Roseworthy SA, Australia
| | - Adam Miles
- Department of Marine and Wildlife Resources, Pago Pago, 96799, American Samoa
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
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Lavretsky P, Kraai KJ, Butler D, Morel J, VonBank JA, Marty JR, Musni VM, Collins DP. Human-Induced Range Expansions Result in a Recent Hybrid Zone between Sister Species of Ducks. Genes (Basel) 2024; 15:651. [PMID: 38927587 PMCID: PMC11202560 DOI: 10.3390/genes15060651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Landscapes are consistently under pressure from human-induced ecological change, often resulting in shifting species distributions. For some species, changing the geographical breadth of their niche space results in matching range shifts to regions other than those in which they are formally found. In this study, we employ a population genomics approach to assess potential conservation issues arising from purported range expansions into the south Texas Brush Country of two sister species of ducks: mottled (Anas fulvigula) and Mexican (Anas diazi) ducks. Specifically, despite being non-migratory, both species are increasingly being recorded outside their formal ranges, with the northeastward and westward expansions of Mexican and mottled ducks, respectively, perhaps resulting in secondary contact today. We assessed genetic ancestry using thousands of autosomal loci across the ranges of both species, as well as sampled Mexican- and mottled-like ducks from across overlapping regions of south Texas. First, we confirm that both species are indeed expanding their ranges, with genetically pure Western Gulf Coast mottled ducks confirmed as far west as La Salle county, Texas, while Mexican ducks recorded across Texas counties near the USA-Mexico border. Importantly, the first confirmed Mexican × mottled duck hybrids were found in between these regions, which likely represents a recently established contact zone that is, on average, ~100 km wide. We posit that climate- and land use-associated changes, including coastal habitat degradation coupled with increases in artificial habitats in the interior regions of Texas, are facilitating these range expansions. Consequently, continued monitoring of this recent contact event can serve to understand species' responses in the Anthropocene, but it can also be used to revise operational survey areas for mottled ducks.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79668, USA;
| | - Kevin J. Kraai
- Waterfowl Program, Texas Parks and Wildlife Department, Canyon, TX 79015, USA;
| | - David Butler
- Central Coast Wetland Ecosystem Project, Texas Parks and Wildlife Department, Bay City, TX 77414, USA; (D.B.); (J.M.)
| | - James Morel
- Central Coast Wetland Ecosystem Project, Texas Parks and Wildlife Department, Bay City, TX 77414, USA; (D.B.); (J.M.)
| | - Jay A. VonBank
- Northern Prairie Wildlife Research Center, U.S. Geological Survey, Jamestown, ND 58401, USA;
| | - Joseph R. Marty
- Southwest Region—Texas Chenier Plain NWR Complex, U.S. Fish and Wildlife Service, Anahuac, TX 77514, USA;
| | - Vergie M. Musni
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79668, USA;
| | - Daniel P. Collins
- Southwest Region—Migratory Bird Program, U.S. Fish and Wildlife Service, Albuquerque, NM 87103, USA;
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3
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Wilson RE, Boyd WS, Sonsthagen SA, Ward DH, Clausen P, Dickson KM, Ebbinge BS, Gudmundsson GA, Sage GK, Rearick JR, Derksen DV, Talbot SL. Where east meets west: Phylogeography of the high Arctic North American brant goose. Ecol Evol 2024; 14:e11245. [PMID: 38601857 PMCID: PMC11004662 DOI: 10.1002/ece3.11245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.
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Affiliation(s)
- Robert E. Wilson
- School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Nebraska State MuseumUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - W. Sean Boyd
- Environment and Climate Change CanadaScience and Technology BranchDeltaBritish ColumbiaCanada
| | - Sarah A. Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - David H. Ward
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | | | - Kathryn M. Dickson
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | | | | | - George K. Sage
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
| | | | - Dirk V. Derksen
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | - Sandra L. Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
- Alaska Center for Conservation ScienceUniversity of AlaskaAnchorageAlaskaUSA
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Kuprina K, Smorkatcheva A, Rudyk A, Galkina S. Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus. Mol Biol Rep 2023; 51:36. [PMID: 38157080 PMCID: PMC10756869 DOI: 10.1007/s11033-023-08913-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus. METHODS AND RESULTS PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop. CONCLUSIONS Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.
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Affiliation(s)
- Kristina Kuprina
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald, 17489, Germany.
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia.
| | - Antonina Smorkatcheva
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| | - Anna Rudyk
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| | - Svetlana Galkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
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Lavretsky P, Mohl JE, Söderquist P, Kraus RHS, Schummer ML, Brown JI. The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards. Commun Biol 2023; 6:819. [PMID: 37543640 PMCID: PMC10404241 DOI: 10.1038/s42003-023-05170-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/24/2023] [Indexed: 08/07/2023] Open
Abstract
The translocation of individuals around the world is leading to rising incidences of anthropogenic hybridization, particularly between domestic and wild congeners. We apply a landscape genomics approach for thousands of mallard (Anas platyrhynchos) samples across continental and island populations to determine the result of over a century of supplementation practices. We establish that a single domestic game-farm mallard breed is the source for contemporary release programs in Eurasia and North America, as well as for established feral populations in New Zealand and Hawaii. In particular, we identify central Europe and eastern North America as epicenters of ongoing anthropogenic hybridization, and conclude that the release of game-farm mallards continues to affect the genetic integrity of wild mallards. Conversely, self-sustaining feral populations in New Zealand and Hawaii not only show strong differentiation from their original stock, but also signatures of local adaptation occurring in less than a half-century since game-farm mallard releases have ceased. We conclude that 'wild' is not singular, and that even feral populations are capable of responding to natural processes. Although considered paradoxical to biological conservation, understanding the capacity for wildness among feral and feral admixed populations in human landscapes is critical as such interactions increase in the Anthropocene.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA.
| | - Jonathon E Mohl
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Pär Söderquist
- Faculty of Natural Sciences, Kristianstad University, SE- 291 88, Kristianstad, Sweden
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, 78315, Radolfzell, Germany
| | - Michael L Schummer
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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6
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Lavretsky P, Hoyt A, Musni VM, Howell D, Williams CK. Frequency and types of alternative breeding strategies employed by nesting American black ducks in North Carolina. PLoS One 2023; 18:e0278905. [PMID: 36809383 PMCID: PMC9942969 DOI: 10.1371/journal.pone.0278905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/27/2022] [Indexed: 02/23/2023] Open
Abstract
Although most birds are considered to be at least partially monogamous, molecular evidence continues to uncover that many species can have multiple sexual mates. Many species of Waterfowl (Order Anseriformes) consistently deploy alternative breeding strategies, and although cavity nesting species have been well studied, few attempts to understand rates of alternative breeding strategies exist in the Anatini tribe. Here, we assay mitochondrial DNA and thousands of nuclear markers across 20 broods of American black ducks (Anas rubripes; "black duck") that included 19 females and 172 offspring to study population structure as well as types and rates of secondary breeding strategies in coastal North Carolina. First, we report high levels of relatedness among nesting black ducks and offspring and while 17 (of 19) females were of pure black duck descent, three were found to be black duck x mallard (A. platyrhynchos) hybrids. Next, we evaluated for mismatched mitochondrial DNA and paternity identities across each female's clutch to determine types and frequency of alternative or secondary breeding strategies. Although we report that nest parasitism occurred in two nests, 37% (7 of 19) of the sampled nests were multi-paternal as a result of extra-pair copulation. In addition to being part of a mix of strategies used to increase fecundity by successfully breeding females, we posit nest densities providing easier alternative mate access for males also explains high rates of extra-pair copulation among our sampled black ducks. Ultimately, however, while some proportion of females of many species engage in forms of secondary breeding strategies, we conclude that the decision to do so appears to be seasonally flexible for each individual.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
- * E-mail:
| | - Amanda Hoyt
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, United States of America
| | - Vergie M. Musni
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Doug Howell
- North Carolina Wildlife Resources Commission, Edenton, North Carolina, United States of America
| | - Christopher K. Williams
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, United States of America
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7
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Jia Y, Qiu G, Cao C, Wang X, Jiang L, Zhang T, Geng Z, Jin S. Mitochondrial genome and phylogenetic analysis of Chaohu duck. Gene 2022; 851:147018. [DOI: 10.1016/j.gene.2022.147018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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Rohwer S, Wood CS, Peters JL, Miller ET, Cagley D, Butcher BG, Epperly KL, Campagna L. Interspecific forced copulations generate most hybrids in broadly sympatric ducks. PLoS One 2022; 17:e0274059. [PMID: 36126057 PMCID: PMC9488771 DOI: 10.1371/journal.pone.0274059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022] Open
Abstract
Although rare, hybrids are more common in broadly sympatric waterfowl than in any other avian family; yet, the behavioral ecology explaining their generation has remained controversial. Leading hypotheses are forced interspecific copulations, mis-imprinting caused by mixed broods, and scarcity of conspecific mates. Using a large sample of hybrid ducks solicited from North American hunters we evaluated these hypotheses by genetically determining the mother and father species of F1 hybrids. Based on abundances in areas where their breeding ranges overlap, the frequency of hybrids varied greatly from expectations, with hybrids between species within recently derived clades being much more frequent than those between more divergent clades. Forced copulations, as measured by large phallus-length asymmetries between parentals, strongly predicted the father species of most F1 hybrids. Thus, most Anas acuta x A. platyrhynchos (Northern Pintail x Mallard) F1s were sired by A. acuta, and most A. platyrhynchos x Mareca strepera (Mallard x Gadwall) F1s were sired by A. platyrhynchos. Siring asymmetries were consistent with phallus length asymmetries in five additional parental combinations, but none had samples large enough to be individually statistically significant. The exception to this trend was our sample of nine A. platyrhynchos x Mareca americana (Mallard x Gadwall) F1s, for which a large phallus asymmetry failed to predict the father species. Hybrids were rare in brood parasitic species, suggesting mis-imprinting to be an unlikely cause of most hybrids; however, our samples of hybrids from regular brood parasites were inadequate to strongly address this hypothesis. We could test the scarcity of mates hypothesis for only a single hybrid combination and it contradicted our prediction: most F1M. Penelope x M. americana (Eurasian x American Wigeon) were sired by M. penelope, strongly contradicting our prediction that female M. penelope wintering in enormous flocks of M. americana (American Wigeon) on the west coast of North America would have difficulty finding conspecific mates. In general, our results support interspecific forced copulations as the predominant behavioral mechanism generating hybrids in North temperate waterfowl.
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Affiliation(s)
- Sievert Rohwer
- Department of Biology and Burke Museum, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Christopher S. Wood
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Jefferey L. Peters
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America
| | | | - David Cagley
- Independent Researcher, Myrtle Point, Oregon, United States of America
| | - Bronwyn G. Butcher
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, United States of America
| | - Kevin L. Epperly
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, United States of America
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
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Brown JI, Hernández F, Engilis A, Hernández-Baños BE, Collins D, Lavretsky P. Genomic and morphological data shed light on the complexities of shared ancestry between closely related duck species. Sci Rep 2022; 12:10212. [PMID: 35715515 PMCID: PMC9205961 DOI: 10.1038/s41598-022-14270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Causes for genomic and morphological similarities among recently radiated species are often multifaceted and are further convoluted among species that readily interbreed. Here, we couple genomic and morphological trait comparisons to test the extent that ancestry and gene flow explain the retention of mallard-like traits within a sister species, the Mexican duck. First, we confirm that these taxa remain genetically structured, and that Mexican ducks exhibit an isolation-by-distance pattern. Despite the assumption of wide-spread hybridization, we found only a few late-stage hybrids, all from the southwestern USA. Next, assessing 23 morphological traits, we developed a genetically-vetted morphological key that is > 97% accurate in distinguishing across sex-age cohorts of Mexican ducks, mallards, and hybrids. During key development, we determined that 25% of genetically pure, immature male Mexican ducks of the northern population naturally displayed mallard-like traits in their formative plumage. In fact, applying this key to 55 museum specimens, we identified that only four of the 14 specimens originally classified as phenotypic hybrids were truly hybrids. We discuss how genomic and morphological comparisons shed light into the mechanism(s) underlying the evolution of complex phenotypic traits in recent radiations, and how misunderstanding the true morphological diversity within Mexican ducks resulted in taxonomic revisions that hindered conservation efforts.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA.
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Andrew Engilis
- Museum of Wildlife and Fish Biology, Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.,Department of Wildlife, Fish and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Distrito Federal, Mexico
| | - Dan Collins
- U.S. Fish and Wildlife Service - Region 2 Migratory Bird Program, Albuquerque, NM, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79968, USA
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10
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Harvey K, Lavretsky P, Foth J, Williams CK. Nest parasitism, promiscuity, and relatedness among wood ducks. PLoS One 2021; 16:e0257105. [PMID: 34855769 PMCID: PMC8639054 DOI: 10.1371/journal.pone.0257105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/23/2021] [Indexed: 11/19/2022] Open
Abstract
Nest parasitism is a common reproductive strategy used by many species of cavity nesting birds. Among these, the wood duck (Aix sponsa) is known to have evolved very specific strategies of when and whom to parasitize that is often based on population and/or environmental queues. Here, we investigated the genetic relationship of two female wood ducks competing over an artificial nesting box in Delaware, including the continued incubation of one female despite the death and body remains of the other female throughout the incubation process. We test whether such an extreme case of nest parasitism can be explained by relatedness, egg lineage composition, or a combination of other factors. To do so, we extracted genomic DNA from blood and tissue of the females, as well as chorioallantoic membranes of all viable and inviable eggs. Subsequently, we assessed relatedness among females and eggs based on hundreds of nuclear loci and the mitochondrial control region. We concluded that (1) the two incubating females were entirely unrelated, (2) the single clutch is in fact represented by a minimum of four unrelated females, and (3) a single female can lay eggs sired by different males. The latter finding is the first direct evidence for successful extra-pair copulation in wood ducks. With decreasing costs and increasing effectiveness, genomic methods have the potential to provide important insights into more complex ecological and evolutionary tactics of such populations.
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Affiliation(s)
- Kayla Harvey
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
- Delaware Department of Natural Resources and Environmental Control–Division of Fish & Wildlife, Dover, Delaware, United States of America
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Justyn Foth
- Delaware Department of Natural Resources and Environmental Control–Division of Fish & Wildlife, Dover, Delaware, United States of America
- Division of Bird Habitat Conservation, United States Fish and Wildlife Service, Falls Church, Virginia, United States of America
| | - Christopher K. Williams
- Delaware Department of Natural Resources and Environmental Control–Division of Fish & Wildlife, Dover, Delaware, United States of America
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, United States of America
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11
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Chow S, Yanagimoto T, Takeyama H. Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus. Sci Rep 2021; 11:21780. [PMID: 34741113 PMCID: PMC8571370 DOI: 10.1038/s41598-021-01346-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169-23.880% for COI, 1.336-23.434% for 12S, and 7.897-71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.
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Affiliation(s)
- Seinen Chow
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
| | - Takashi Yanagimoto
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Yokohama, Kanagawa, 236-8648, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu cho, Shinjuku, Tokyo, 162-8480, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan.
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12
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Sangster G, Luksenburg JA. Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies. Genome Biol Evol 2021; 13:evab210. [PMID: 34505894 PMCID: PMC8462277 DOI: 10.1093/gbe/evab210] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 02/06/2023] Open
Abstract
Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.
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Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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13
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Lavretsky P, Duenez E, Kneece M, Kaminski RM. Population Genetics of a Translocated Population of Mottled Ducks and Allies. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences University of Texas at El Paso El Paso TX 79668 USA
| | - Esmeralda Duenez
- Department of Biological Sciences University of Texas at El Paso El Paso TX 79668 USA
| | - Molly Kneece
- South Carolina Department of Natural Resources Georgetown SC 29440 USA
| | - Richard M. Kaminski
- Clemson University's James C. Kennedy Waterfowl and Wetlands Conservation Center Georgetown SC 29442 USA
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14
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Lawson DM, Williams CK, Lavretsky P, Howell DL, Fuller JC. Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Daniel M. Lawson
- University of Delaware, 531 South College Avenue Newark DE 19716 USA
| | | | - Philip Lavretsky
- University of Texas at El Paso, 500 W University Avenue El Paso TX 79968 USA
| | - Douglas L. Howell
- North Carolina Wildlife Resources Commission 132 Marine Drive Edenton NC 27699 USA
| | - Joseph C. Fuller
- North Carolina Wildlife Resources Commission 132 Marine Drive Edenton NC 27699 USA
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15
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Pereira MC, Coelho T, Werther K, Andreazzi RB, Morales AC. Genetic structure and diversity in Neochen jubata (Aves: Anatidae) from the Araguaia River, GO, Brazil. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2020-1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: The Orinoco Goose (Neochen jubata) is a few-known and endemic Anatidae to South America, inhabiting sandy beaches along medium and large rivers, with a well-developed riparian forest and in swamp savannas and large freshwater baths. Recent data indicate the presence of longitudinal migratory behavior, and despite them, there are no records on the genetic profile of this species. The Araguaia River region, in the municipality of Luiz Alves, Goiás, receives an undetermined number of ducks seasonally, and there is little information about the individuals who visit this place, constituting the ideal scenario for a study able to offer a genetic overview perspective of this species and to understand the relationship between these individuals better. For this, we genetically characterized 61 individuals sampled in three distinct years of collection using microsatellite molecular markers and mitochondrial DNA. Genetic diversity analyses revealed low levels of heterozygosity for all sampled groups. However, they are within the equilibrium proposed by Hardy-Weinberg (HWE), as inbreeding or drift are not acting in these groups. The parentage analysis supports it, showing a high number of unrelated individuals over the years. AMOVA showed a significant difference among groups. These results may reflect the structure of this migratory species in that region, with the paired differentiation test of individuals from 2013 and 2014 being more similar to each other than those from other years, indicating a possible genetic structure diagnosed by the years of capture. However, there is a high allelic sharing among the three sampled groups, suggesting that these individuals are a population that connects over time and that they have a philopatric relationship with the location. The results found in this study constitute an initial milestone for the genetic knowledge of the mallard duck that should be raised in many other genetic studies.
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Affiliation(s)
| | - Thaís Coelho
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
| | - Karin Werther
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
| | | | - Adriana Coletto Morales
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
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16
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Jha A, Vasudevan K. Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’sDand Fu’sFsand small positive value of Ramos-Onsins and Rozas’R2suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.
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Affiliation(s)
- A Jha
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500048, India
| | - K Vasudevan
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500048, India
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17
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Scattolini MC, Lira-Noriega A, Confalonieri VA, Pietrokovsky S, Cigliano MM. Biogeographical patterns and processes in the genus group Scotussae (Acrididae: Melanoplinae): an integrative approach. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
A biogeographical study of the genus group Scotussae, a clade of grasshoppers endemic to the subtropical temperate region of the La Plata Basin, South America, was performed within a phylogenetic context to test whether wing reduction reflects evolutionary and ecological processes within the clade. We used an integrative biogeographical approach to determine the role of geohistorical events, geography, ecology and phylogenetic niche conservatism on the distribution and diversification processes of the group. We performed a total evidence phylogenetic analysis and tested the phylogenetic signal of ecological niche traits (niche optimum and niche breadth). We also assessed the degree to which phylogenetic distance is correlated with geographical and ecological niche traits and we used BioGeoBEARS to estimate ancestral ranges. The results provided evidence for phylogenetic niche conservatism as well as a significant association between phylogeny and both geographical and, more strongly, ecological traits. Two main clades were clearly associated with wing development, and evidence points to the evolutionary and ecological processes within these two groups being different. The Brachypterous clade shows evidence that allopatric speciation was the main source of diversification, while for the Macropterous clade sympatric speciation seems more likely.
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Affiliation(s)
- María Celeste Scattolini
- Centro de Estudios Parasitológicos y de Vectores, CEPAVE, CONICET-CCT La Plata, Argentina
- Museo de La Plata, División Entomología, FCNyM-UNLP, La Plata, Argentina
| | - Andrés Lira-Noriega
- Catedrático CONACyT, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Veracruz, Xalapa, México
| | - Viviana Andrea Confalonieri
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (EGE–FCEN–UBA) and IEGEBA (UBA–CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvia Pietrokovsky
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (EGE–FCEN–UBA) and IEGEBA (UBA–CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Marta Cigliano
- Centro de Estudios Parasitológicos y de Vectores, CEPAVE, CONICET-CCT La Plata, Argentina
- Museo de La Plata, División Entomología, FCNyM-UNLP, La Plata, Argentina
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18
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Dawson NJ, Alza L, Nandal G, Scott GR, McCracken KG. Convergent changes in muscle metabolism depend on duration of high-altitude ancestry across Andean waterfowl. eLife 2020; 9:e56259. [PMID: 32729830 PMCID: PMC7494360 DOI: 10.7554/elife.56259] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023] Open
Abstract
High-altitude environments require that animals meet the metabolic O2 demands for locomotion and thermogenesis in O2-thin air, but the degree to which convergent metabolic changes have arisen across independent high-altitude lineages or the speed at which such changes arise is unclear. We examined seven high-altitude waterfowl that have inhabited the Andes (3812-4806 m elevation) over varying evolutionary time scales, to elucidate changes in biochemical pathways of energy metabolism in flight muscle relative to low-altitude sister taxa. Convergent changes across high-altitude taxa included increased hydroxyacyl-coA dehydrogenase and succinate dehydrogenase activities, decreased lactate dehydrogenase, pyruvate kinase, creatine kinase, and cytochrome c oxidase activities, and increased myoglobin content. ATP synthase activity increased in only the longest established high-altitude taxa, whereas hexokinase activity increased in only newly established taxa. Therefore, changes in pathways of lipid oxidation, glycolysis, and mitochondrial oxidative phosphorylation are common strategies to cope with high-altitude hypoxia, but some changes require longer evolutionary time to arise.
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Affiliation(s)
- Neal J Dawson
- Department of Biology, McMaster UniversityHamiltonCanada
- Department of Biology University of MiamiCoral GablesUnited States
| | - Luis Alza
- Department of Biology University of MiamiCoral GablesUnited States
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
- Centro de Ornitología y Biodiversidad - CORBIDILimaPeru
| | | | - Graham R Scott
- Department of Biology, McMaster UniversityHamiltonCanada
| | - Kevin G McCracken
- Department of Biology University of MiamiCoral GablesUnited States
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
- Centro de Ornitología y Biodiversidad - CORBIDILimaPeru
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of MiamiMiamiUnited States
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of MedicineMiamiUnited States
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19
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Lavretsky P, McInerney NR, Mohl JE, Brown JI, James HF, McCracken KG, Fleischer RC. Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks. Mol Ecol 2020; 29:578-595. [PMID: 31872482 DOI: 10.1111/mec.15343] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Jonathon E Mohl
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Joshua I Brown
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin G McCracken
- Department of Biology, University of Miami, Coral Gables, FL, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.,Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Institute of Arctic Biology, University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
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20
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Wells CP, Lavretsky P, Sorenson MD, Peters JL, DaCosta JM, Turnbull S, Uyehara KJ, Malachowski CP, Dugger BD, Eadie JM, Engilis A. Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands. Mol Ecol 2019; 28:5203-5216. [DOI: 10.1111/mec.15286] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Caitlin P. Wells
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
| | - Philip Lavretsky
- Department of Biological Sciences University of Texas El Paso TX USA
| | | | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton OH USA
| | | | - Stephen Turnbull
- Division of Forestry and Wildlife Department of Land and Natural Resources Honolulu HI USA
| | - Kimberly J. Uyehara
- Kauaʻi National Wildlife Refuge Complex U.S. Fish and Wildlife Service Kīlauea HI USA
| | | | - Bruce D. Dugger
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - John M. Eadie
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
| | - Andrew Engilis
- Department of Wildlife, Fish, and Conservation Biology University of California Davis CA USA
- Museum of Wildlife and Fish Biology University of California Davis CA USA
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21
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Gutiérrez‐Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, Cadena CD. Molecular and morphological differentiation among Torrent Duck (
Merganetta armata
) populations in the Andes. ZOOL SCR 2019. [DOI: 10.1111/zsc.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natalia Gutiérrez‐Pinto
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- School of Biological Sciences University of Nebraska Lincoln Nebraska
| | - Kevin G. McCracken
- Department of Biology University of Miami Coral Gables Florida
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences Miami Florida
- Institute of Arctic Biology University of Alaska Museum Fairbanks Alaska
- Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks Alaska
| | - Pablo Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET) Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CONICET‐CCT Mendoza) Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
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22
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Kulikova IV, Zhuravlev YN, Korobitsyn IG, Nemkova GA, McCracken KG, Peters JL. Holarctic phylogeographic structure of Eurasian wigeon (Mareca penelope). Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Eurasian wigeon (Mareca penelope) is one of the most numerous migrant species of waterfowl in the Palearctic. Annually, significant part of the world’s wigeon population makes seasonal flights over distances from tens to thousands or more kilometers. According to different estimates based on banding data, five geographic populations of the species were described in the Palearctic. However, distinct borders between the populations have not been identified. At the same time, no phylogeographic studies have been carried out for the complete native range of wigeon so far. In addition to the fundamental importance of such a study, knowledge of the genetic structure of populations is necessary for the development of measures to increase the number of and preserve this valuable game species. The aim of our work was a phylogeographic analysis of the wigeon across its vast native range in the Palearctic including ducks wintering in North America. We examined genetic diversity and differentiation of wigeon populations identified with banding data, phylogenetic relationships of mtDNA haplotypes and demographic history of populations and species as a whole by sequencing a 661 base-pair 5’-fragment of the mitochondrial control region from 195 individual ducks collected throughout the Palearctic and Nearctic. Genetic diversity was high in all studied populations. A reconstruction of haplotypes phylogeny revealed the absence of geographic structure in the data. Nonetheless, analysis of molecular variance (AMOVA) identified two groups of populations: EuropeanSiberian and East Asian. The former included wigeons from Europe, Siberia and the Atlantic coast of North America, and the latter comprised ducks from Russian Far East, Kamchatka Peninsula, Chukotka Autonomous District, the Aleutian Islands, Alaska, and the Pacific coast of North America.
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Affiliation(s)
- I. V. Kulikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | - Y. N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | | | - G. A. Nemkova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | - K. G. McCracken
- Department of Biology, University of Miami; Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami; Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
| | - J. L. Peters
- Department of Biological Sciences, Wright State University
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23
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Lavretsky P, Janzen T, McCracken KG. Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America. Ecol Evol 2019; 9:3470-3490. [PMID: 30962906 PMCID: PMC6434578 DOI: 10.1002/ece3.4981] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 01/04/2023] Open
Abstract
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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Affiliation(s)
- Philip Lavretsky
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTexas
- Department of BiologyUniversity of MiamiCoral GablesFlorida
| | - Thijs Janzen
- Department of Ecological Genomics, Institute for Biology and Environmental SciencesCarl von Ossietzky Universität OldenburgOldenburgGermany
| | - Kevin G. McCracken
- Department of BiologyUniversity of MiamiCoral GablesFlorida
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFlorida
- Human Genetics and GenomicsHussman Institute for Human Genomics, University of Miami Miller School of MedicineMiamiFlorida
- Institute of Arctic Biology and University of Alaska MuseumUniversity of Alaska FairbanksFairbanksAlaska
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24
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Bulgarella M, Quenu M, Shepherd LD, Morgan-Richards M. The ectoparasites of hybrid ducks in New Zealand (Mallard x Grey Duck). INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:335-342. [PMID: 30258780 PMCID: PMC6154467 DOI: 10.1016/j.ijppaw.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 11/26/2022]
Abstract
We studied the population genetics of one population sample of hybrid Mallard x Grey Ducks and their lice in New Zealand. We aimed to document the relationship between ectoparasite load and host phenotype, and test for an association between the mtDNA diversity of the lice and their hosts, which is predicted based on maternal care. We found three feather lice species previously described for these hosts: Anaticola crassicornis (wing louse), Anatoecus dentatus (head louse), and Trinoton querquedulae (body louse). No new or rare lice species were uncovered. Most ducks in our sample were more Mallard-like than Grey Duck-like hybrids for the five colour and plumage traits examined. We confirm that based solely on phenotypic characters it is difficult to distinguish between Mallards, hybrids and Grey Ducks. We detected no association between the number of lice and host phenotype for two of the three louse species (while controlling for bird size). However, the Grey Duck-like hybrids had fewer head lice (A. dentatus) than their Mallard-like counterparts. Only three of the 40 hosts had mtDNA haplotypes that characterise Grey Ducks. We present the first genetic data of Anaticola crassicornis, Anatoecus dentatus and Trinoton querquedulae from New Zealand waterfowl. We found that the lice mtDNA had greater sequence diversity than the homologous gene for the ducks. A mitochondrial phylogeny for A. crassicornis collected from hosts worldwide has been previously published, and we added our novel data to infer evolutionary relationships among worldwide populations of this louse. None of the three lice species showed a close association of parasite and host mtDNA lineage despite lack of paternal care in these duck species. We studied population genetics of hybrid Mallard x Grey Ducks and their lice in New Zealand. We found three feather lice species previously described for these hosts. Most ducks were more Mallard-like than Grey Duck-like hybrids for the traits examined. Only three of the forty hosts had mtDNA haplotypes that characterise Grey Ducks. We present the first genetic data for the three lice species from New Zealand.
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Affiliation(s)
- Mariana Bulgarella
- Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington, 6140, New Zealand
| | - Mathieu Quenu
- Ecology, College of Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington, 6140, New Zealand
| | - Mary Morgan-Richards
- Ecology, College of Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
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Wilson RE, Ely CR, Talbot SL. Flyway structure in the circumpolar greater white-fronted goose. Ecol Evol 2018; 8:8490-8507. [PMID: 30250718 PMCID: PMC6144976 DOI: 10.1002/ece3.4345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/28/2018] [Accepted: 06/04/2018] [Indexed: 11/06/2022] Open
Abstract
Dispersal and migratory behavior are influential factors in determining how genetic diversity is distributed across the landscape. In migratory species, genetic structure can be promoted via several mechanisms including fidelity to distinct migratory routes. Particularly within North America, waterfowl management units have been delineated according to distinct longitudinal migratory flyways supported by banding data and other direct evidence. The greater white-fronted goose (Anser albifrons) is a migratory waterfowl species with a largely circumpolar distribution consisting of up to six subspecies roughly corresponding to phenotypic variation. We examined the rangewide population genetic structure of greater white-fronted geese using mtDNA control region sequence data and microsatellite loci from 23 locales across North America and Eurasia. We found significant differentiation in mtDNA between sampling locales with flyway delineation explaining a significant portion of the observed genetic variation (~12%). This is concordant with band recovery data which shows little interflyway or intercontinental movements. However, microsatellite loci revealed little genetic structure suggesting a panmictic population across most of the Arctic. As with many high-latitude species, Beringia appears to have played a role in the diversification of this species. A common Beringian origin of North America and Asian populations and a recent divergence could at least partly explain the general lack of structure at nuclear markers. Further, our results do not provide strong support for the various taxonomic proposals for this species except for supporting the distinctness of two isolated breeding populations within Cook Inlet, Alaska (A. a. elgasi) and Greenland (A. a. flavirostris), consistent with their subspecies status.
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Affiliation(s)
- Robert E. Wilson
- Alaska Science CenterU. S. Geological SurveyAnchorageAlaska
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAlaska
| | - Craig R. Ely
- Alaska Science CenterU. S. Geological SurveyAnchorageAlaska
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Molecular and Morphological Phylogenetic Analysis of Naupactus Dejean (Curculionidae: Entiminae) and Allied Genera: The Dilemma of Classification. DIVERSITY 2018. [DOI: 10.3390/d10030059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Valentin RE, Lockwood JL, Mathys BA, Fonseca DM. Influence of invasion history on rapid morphological divergence across island populations of an exotic bird. Ecol Evol 2018; 8:5291-5302. [PMID: 29938053 PMCID: PMC6010901 DOI: 10.1002/ece3.4021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/25/2018] [Indexed: 11/07/2022] Open
Abstract
There is increasing evidence that exotic populations may rapidly differentiate from those in their native range and that differences also arise among populations within the exotic range. Using morphological and DNA-based analyses, we document the extent of trait divergence among native North American and exotic Hawaiian populations of northern cardinal (Cardinalis cardinalis). Furthermore, using a combination of historical records and DNA-based analyses, we evaluate the role of founder effects in producing observed trait differences. We measured and compared key morphological traits across northern cardinal populations in the native and exotic ranges to assess whether trait divergence across the Hawaiian Islands, where this species was introduced between 1929 and 1931, reflected observed variation across native phylogeographic clades in its native North America. We used and added to prior phylogenetic analyses based on a mitochondrial locus to identify the most likely native source clade(s) for the Hawaiian cardinal populations. We then used Approximate Bayesian Computation (ABC) to evaluate the role of founder effects in producing the observed differences in body size and bill morphology across native and exotic populations. We found cardinal populations on the Hawaiian Islands had morphological traits that diverged substantially across islands and overlapped the trait space of all measured native North American clades. The phylogeographic analysis identified the eastern North American clade (C. cardinalis cardinalis) as the most likely and sole native source for all the Hawaiian cardinal populations. The ABC analyses supported written accounts of the cardinal's introduction that indicate the original 300 cardinals shipped to Hawaii were simultaneously and evenly released across Hawaii, Kauai, and Oahu. Populations on each island likely experienced bottlenecks followed by expansion, with cardinals from the island of Hawaii eventually colonizing Maui unaided. Overall, our results suggest that founder effects had limited impact on morphological trait divergence of exotic cardinal populations in the Hawaiian archipelago, which instead reflect postintroduction events.
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Affiliation(s)
- Rafael E. Valentin
- Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickNJUSA
| | - Julie L. Lockwood
- Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickNJUSA
| | - Blake A. Mathys
- Division of Mathematics, Computer and Natural SciencesOhio Dominican UniversityColumbusOHUSA
| | - Dina M. Fonseca
- Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickNJUSA
- Department of EntomologyRutgers UniversityNew BrunswickNJUSA
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Scattolini MC, Confalonieri V, Lira-Noriega A, Pietrokovsky S, Cigliano MM. Diversification mechanisms in the Andean grasshopper genus Orotettix (Orthoptera: Acrididae): ecological niches and evolutionary history. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- María Celeste Scattolini
- Centro de Estudios Parasitologicos y de Vectores, CEPAVE, CONICET-CCT La Plata, Argentina
- Museo de La Plata, División Entomología; FCNyM-UNLP, La Plata, Argentina
| | - Viviana Confalonieri
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (EGE–FCEN–UBA) and IEGEBA (UBA–CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrés Lira-Noriega
- Catedrático CONACyT, Instituto de Ecologia, A.C., Red de Estudios Moleculares Avanzados, Veracruz, Xalapa, Mexico
| | - Silvia Pietrokovsky
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (EGE–FCEN–UBA) and IEGEBA (UBA–CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Marta Cigliano
- Centro de Estudios Parasitologicos y de Vectores, CEPAVE, CONICET-CCT La Plata, Argentina
- Museo de La Plata, División Entomología; FCNyM-UNLP, La Plata, Argentina
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29
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Improved genotyping and sequencing success rates for North American river otter (Lontra canadensis). EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1177-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Shi H, Xing Y, Mao X. The little brown bat nuclear genome contains an entire mitochondrial genome: Real or artifact? Gene 2017; 629:64-67. [PMID: 28754635 DOI: 10.1016/j.gene.2017.07.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 07/11/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
Nuclear mitochondrial DNA sequences (NUMTs) have been documented in almost all eukaryotic genomes studied. Recently, with the number of sequenced genomes increasing, extremely large NUMTs, even a nearly entire mitochondrial genome, have been reported in some plants and animals. However, few such studies provided strong experimental evidences for these important discoveries. In this study using a computer-based search method an entire mitochondrial genome (NUMT-1) was found in the nuclear genome of a bat species (Myotis lucifugus). This super-large NUMT shared a same scaffold with a 754bp nuclear genomic sequence and a second NUMT (NUMT-2, 3292bp). If NUMT-1 was real, it will be the largest NUMT found in animals and this finding will provide valuable insights into the mode of generation of NUMTs in the nuclear genome. Unfortunately, although the initial sequencing technology of the published M. lucifugus genome makes the possibility of artifact less likely, our results from both the PCR amplification followed by Sanger sequencing and mapping method based on the whole-genome resequencing datasets suggested that the scaffold containing the entire mitochondrial genome was artifact possibly due to a misassembly of mitochondrial and the nuclear DNA sequences. Our current study highlights the necessity to validate the authenticity of extremely large NUMTs identified in previous searches on whole-genome sequence assemblies.
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Affiliation(s)
- Huizhen Shi
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Yutong Xing
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.
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31
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Ely CR, Wilson RE, Talbot SL. Genetic structure among greater white-fronted goose populations of the Pacific Flyway. Ecol Evol 2017; 7:2956-2968. [PMID: 28479995 PMCID: PMC5415542 DOI: 10.1002/ece3.2934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/23/2017] [Accepted: 03/03/2017] [Indexed: 01/13/2023] Open
Abstract
An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.
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Affiliation(s)
- Craig R. Ely
- U.S. Geological SurveyAlaska Science CenterAnchorageAKUSA
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32
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Wang N, Liang B, Wang J, Yeh CF, Liu Y, Liu Y, Liang W, Yao CT, Li SH. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves). Mol Phylogenet Evol 2016; 102:62-73. [PMID: 27233437 DOI: 10.1016/j.ympev.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/26/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Abstract
Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.
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Affiliation(s)
- Ning Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bin Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yang Liu
- State Key Laboratory of BioControl, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanlin Liu
- Institute of Forestry Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Cheng-Te Yao
- High-Altitude Experimental Station, Taiwan Endemic Species Research Institute, Chi-chi 55244, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
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Shi H, Dong J, Irwin DM, Zhang S, Mao X. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera). Gene 2016; 581:161-9. [DOI: 10.1016/j.gene.2016.01.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 10/22/2022]
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34
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Sultana H, Seo DW, Bhuiyan MSA, Choi NR, Hoque MR, Heo KN, Lee JH. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1688-1695. [PMID: 27004808 PMCID: PMC5088415 DOI: 10.5713/ajas.15.1017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/22/2016] [Accepted: 03/21/2016] [Indexed: 11/27/2022]
Abstract
The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.
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Affiliation(s)
- H Sultana
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - D W Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - M S A Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - N R Choi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - M R Hoque
- Genetbio Inc., Daejeon, 305-500, Korea
| | - K N Heo
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan 331-801, Korea
| | - J H Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
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Lavretsky P, Peters JL, Winker K, Bahn V, Kulikova I, Zhuravlev YN, Wilson RE, Barger C, Gurney K, McCracken KG. Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations. Mol Ecol 2016; 25:661-74. [DOI: 10.1111/mec.13487] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Philip Lavretsky
- Department of Biology and Department of Marine Biology and Ecology; Rosenstiel School of Marine and Atmospheric Sciences; University of Miami; Coral Gables FL 33146 USA
| | - Jeffrey L. Peters
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
| | - Kevin Winker
- Institute of Arctic Biology and University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
| | - Volker Bahn
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
| | - Irina Kulikova
- Institute of Biology and Soil Science FEB RAS; 159 Stoletiya Ave 690022 Vladivostok Russia
| | - Yuri N. Zhuravlev
- Institute of Biology and Soil Science FEB RAS; 159 Stoletiya Ave 690022 Vladivostok Russia
| | - Robert E. Wilson
- Institute of Arctic Biology and University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
| | - Chris Barger
- Institute of Arctic Biology and University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
- Alaska Department of Fish and Game; 1300 College Road Fairbanks AK 99701 USA
| | - Kirsty Gurney
- Department of Biology; University of Saskatchewan; 112 Science Place Saskatoon Saskatchewan Canada S7N 5E2
| | - Kevin G. McCracken
- Department of Biology and Department of Marine Biology and Ecology; Rosenstiel School of Marine and Atmospheric Sciences; University of Miami; Coral Gables FL 33146 USA
- Institute of Arctic Biology and University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
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Lavretsky P, Dacosta JM, Hernández-Baños BE, Engilis A, Sorenson MD, Peters JL. Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards. Mol Ecol 2015; 24:5364-78. [DOI: 10.1111/mec.13402] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
| | | | - Blanca E. Hernández-Baños
- Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México; México Distrito Federal México
| | - Andrew Engilis
- Museum of Wildlife and Fish Biology; Department of Wildlife, Fish, and Conservation Biology; University of California, Davis; One Shields Avenue Davis CA 95616 USA
- Department of Wildlife, Fish and Conservation Biology; University of California, Davis; One Shields Avenue Davis CA 95616 USA
| | | | - Jeffrey L. Peters
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
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Mao X, Dong J, Hua P, He G, Zhang S, Rossiter SJ. Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex. PLoS One 2014; 9:e98035. [PMID: 24842827 PMCID: PMC4026475 DOI: 10.1371/journal.pone.0098035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.
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Affiliation(s)
- Xiuguang Mao
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ji Dong
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Panyu Hua
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Guimei He
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
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Lavretsky P, McCracken KG, Peters JL. Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): Inferences from a genomic transect and the multispecies coalescent. Mol Phylogenet Evol 2014; 70:402-11. [DOI: 10.1016/j.ympev.2013.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/05/2013] [Accepted: 08/15/2013] [Indexed: 10/26/2022]
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Welch AJ, Olson SL, Fleischer RC. Phylogenetic relationships of the extinct St Helena petrel,Pterodroma rupinarum Olson, 1975 (Procellariiformes: Procellariidae), based on ancient DNA. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Andreanna J. Welch
- Department of Biological Sciences; University at Buffalo; Buffalo NY 14260 USA
| | - Storrs L. Olson
- Department of Vertebrate Zoology, National Museum of Natural History; Smithsonian Institution; Washington DC 20013 USA
| | - Robert C. Fleischer
- Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics; National Zoological Park; Washington DC 20013 USA
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Shen F, Huang W, Qi JH, Yuan BF, Huang JT, Zhou X, Feng YQ, Liu YJ, Liu SM. Association of 5-methylcytosine and 5-hydroxymethylcytosine with mitochondrial DNA content and clinical and biochemical parameters in hepatocellular carcinoma. PLoS One 2013; 8:e76967. [PMID: 24143196 PMCID: PMC3797098 DOI: 10.1371/journal.pone.0076967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/30/2013] [Indexed: 01/24/2023] Open
Abstract
Increasing epidemiological evidence has indicated that inherited variations of mitochondrial DNA (mtDNA) copy number affect the genetic susceptibility of many malignancies in a tumour-specific manner and that DNA methylation also plays an important role in controlling gene expression during the differentiation and development of hepatocellular carcinoma (HCC). Our previous study demonstrated that HCC tissues showed a lower 5-hydroxymethylcytosine (5-hmC) content when compared to tumour-adjacent tissues, but the relationship among 5-hmC, 5-methylcytosine (5-mC) and mtDNA content in HCC patients is still unknown. This study aimed to clarify the correlation among mtDNA content, 5-mC and 5-hmC by quantitative real-time PCR and liquid chromatography tandem mass spectrometry analysis. We demonstrated that 5-hmC correlated with tumour size [odds ratio (OR) 0.847, 95% confidence interval (CI) 0.746–0.962, P = 0.011], and HCC patients with a tumour size ≥5.0 cm showed a lower 5-hmC content and higher levels of fasting plasma aspartate aminotransferase, the ratio of alanine amiotransferase to aspartate aminotransferase, γ-glutamyltransferase, alpha-fetoprotein than those with a tumour size <5 cm (all P<0.05). We further revealed that the mtDNA content of HCC tumour tissues was 225.97(105.42, 430.54) [median (25th Percentile, 75th Percentile)] and was negatively correlated with 5-mC content (P = 0.035), but not 5-hmC content, in genomic DNA from HCC tumour tissues.
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Affiliation(s)
- Fan Shen
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Jia-Hui Qi
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Jing-Tao Huang
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xin Zhou
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Ying-Juan Liu
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Song-Mei Liu
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- * E-mail:
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41
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Keith Barker F, Oyler-McCance S, Tomback DF. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences. ACTA ACUST UNITED AC 2013; 26:384-8. [DOI: 10.3109/19401736.2013.840588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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42
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Harrigan RJ, Mazza ME, Sorenson MD. Computation vs. cloning: evaluation of two methods for haplotype determination. Mol Ecol Resour 2013; 8:1239-48. [PMID: 21586011 DOI: 10.1111/j.1755-0998.2008.02241.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nuclear sequence data, often from multiple loci, are increasingly being employed in analyses of population structure and history, yet there has been relatively little evaluation of methods for accurately and efficiently separating the alleles or haplotypes in heterozygous individuals. We compared the performance of a computational method of haplotype reconstruction and standard cloning methods using a highly variable intron (ornithine decarboxylase, intron 6) in three closely related species of dabbling ducks (genus Anas). Cloned sequences from 32 individuals were compared to results obtained from phase 2.1.1 . phase correctly identified haplotypes in 28 of 30 heterozygous individuals when the underlying model assumed no recombination. Haplotypes of the remaining two individuals were also inferred correctly except for unique polymorphisms, the phase of which was appropriately indicated as uncertain (phase probability = 0.5). For a larger set of 232 individuals, results were essentially identical regardless of the recombination model used and haplotypes for all 30 of the tested heterozygotes were correctly inferred, with the exception of uncertain phase for unique polymorphisms in one individual. In contrast, initial sequences of one clone per sample yielded accurate haplotype determination in only 26 of 30 individuals; polymerase chain reaction (PCR)/cloning errors resulting from misincorporation of individual nucleotides could be recognized and avoided by comparison to direct sequences, but errors due to PCR recombination resulted in incorrect haplotype reconstruction in four individuals. The accuracy of haplotypes reconstructed by phase, even when dealing with a relatively small number of samples and numerous variable sites, suggests broad utility of computational approaches for reducing the cost and improving the efficiency of data collection from nuclear sequence loci.
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Affiliation(s)
- Ryan J Harrigan
- Department of Biology, Boston University, 5 Cummington St., Boston, MA 02215, USA
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43
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Nyári ÁS, Joseph L. Comparative phylogeography of Australo-Papuan mangrove-restricted and mangrove-associated avifaunas. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700; Canberra; ACT; 2601; Australia
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44
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Mercer DM, Haig SM, Roby DD. Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0477-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Champagnon J, Crochet PA, Kreisinger J, Čížková D, Gauthier-Clerc M, Massez G, Söderquist P, Albrecht T, Guillemain M. Assessing the genetic impact of massive restocking on wild mallard. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00600.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - P-A. Crochet
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175 - CNRS; Montpellier Cedex 5; France
| | - J. Kreisinger
- Department of Zoology; Faculty of Science; Charles University in Prague; Praha 2; Czech Republic
| | - D. Čížková
- Department of Population Biology; Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno; Czech Republic
| | | | - G. Massez
- Les Marais du Vigueirat; Arles; France
| | | | | | - M. Guillemain
- Office National de la Chasse et de la Faune Sauvage; CNERA Avifaune Migratrice; Arles; France
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46
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Roffler GH, Adams LG, Talbot SL, Sage GK, Dale BW. Range overlap and individual movements during breeding season influence genetic relationships of caribou herds in south-central Alaska. J Mammal 2012. [DOI: 10.1644/11-mamm-a-275.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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47
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Liu Y, Keller I, Heckel G. Range-wide genetic population structure of common pochard (Aythya ferina): a potentially important vector of highly pathogenic avian influenza viruses. Ecol Evol 2012; 1:529-45. [PMID: 22393520 PMCID: PMC3287338 DOI: 10.1002/ece3.46] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 12/15/2022] Open
Abstract
An understanding of the distribution and spatial structure of the natural vectors of zoonothic pathogens is of interest for effective disease control and prevention. Here, we investigate the range-wide population genetic structure of common pochard (Aythya ferina), a long-distance migratory duck and potential vector of highly pathogenic avian influenza. We collected several hundred samples from breeding and wintering grounds across Eurasia including some H5N1-positive individuals and generated partial sequences of the mitochondrial control region and multilocus microsatellite genotypes. Genetic differentiation among breeding populations was significant for both marker types but higher for maternally inherited mtDNA than for biparentally inherited nuclear markers. There was only weak genetic divergence between ducks sampled in Europe and East Asia, and genetic differentiation between populations was not generally associated with geographical distance. No evidence of genetic substructure was detected for ducks sampled on the European wintering grounds. Our results suggest limited breeding-site fidelity, especially in females, but extensive population admixture on the wintering grounds. The specific role of pochards as natural vectors of zoonotic pathogens and in particular H5N1 remains to be clarified but our results point to wintering grounds as potential hotspots for disease transmission.
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Affiliation(s)
- Yang Liu
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of BernBaltzerstrasse 6, 3012, Bern, Switzerland
- Swiss Institute of BioinformaticsGenopode, 1015 Lausanne, Switzerland
| | - Irene Keller
- Department of Aquatic Ecology and Department of Fish Ecology and EvolutionEawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of BernBaltzerstrasse 6, 3012, Bern, Switzerland
- Swiss Institute of BioinformaticsGenopode, 1015 Lausanne, Switzerland
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Wilson RE, Peters JL, McCracken KG. Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies. Evolution 2012; 67:170-84. [PMID: 23289570 DOI: 10.1111/j.1558-5646.2012.01740.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species' range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America. Cinnamon teal showed strong divergence in body size (PC1; P(ST) = 0.56) and exhibited significant frequency differences in a single nonsynonymous α-hemoglobin amino acid polymorphism (Asn/Ser-α9; F(ST) = 0.60) between environmental extremes, despite considerable admixture of mtDNA and intron loci (F(ST) = 0.004-0.168). Inferences of strong population segregation were further supported by the observation of few mismatched individuals in either environmental extreme. Coalescent analyses indicated that the highlands were most likely colonized from lowland regions but following divergence, gene flow has been asymmetric from the highlands into the lowlands. Multiple selection pressures associated with high-altitude habitats, including cold and hypoxia, have likely shaped morphological and genetic divergence within South American cinnamon teal populations.
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Affiliation(s)
- Robert E Wilson
- Institute of Arctic Biology, Department of Biology and Wildlife, and University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
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Liu Y, Keller I, Heckel G. Breeding site fidelity and winter admixture in a long-distance migrant, the tufted duck (Aythya fuligula). Heredity (Edinb) 2012; 109:108-16. [PMID: 22549516 PMCID: PMC3400747 DOI: 10.1038/hdy.2012.19] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 02/03/2012] [Accepted: 02/23/2012] [Indexed: 01/18/2023] Open
Abstract
Long-distance migrants are, by definition, highly mobile but it is poorly understood if this leads to high rates of gene flow and an essentially panmictic global population structure. Genetic divergence in migratory species could be promoted, for example, by fidelity to distinct migratory pathways. In this study, we investigate the population genetic structure of tufted duck (Aythya fuligula), a long-distance migrant with a largely continuous breeding distribution across Eurasia. Distinct, longitudinally oriented flyways have been postulated based on geographically disjunct wintering areas and are supported by evidence from ringing data. We generated sequences of the mitochondrial control region and multi-locus microsatellite genotypes for several hundreds of samples from the European and Asian breeding and wintering grounds including some individuals infected with highly pathogenic avian influenza virus H5N1. Significant differentiation between breeding sites was observed for both marker types, but F(ST) values were approximately 10 times higher for maternally inherited mitochondrial DNA than for biparentally transmitted nuclear markers. The genetic differentiation between the postulated European and Asian flyways was similar to that observed within continents and, in general, genetic divergence was not associated with geographic distance. Neither marker type showed evidence of genetic substructure among aggregations on the European wintering grounds. Our results suggest some breeding site fidelity, especially in females, but extensive population admixture on the wintering grounds. Several scenarios may explain the observed lack of genetic divergence between Europe and Asia including non-equilibrium conditions following a recent range expansion or contemporary gene flow across the postulated migratory divides.
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Affiliation(s)
- Y Liu
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - I Keller
- Eawag, Department of Fish Ecology and Evolution, Kastanienbaum, Switzerland
| | - G Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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50
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PETERS JEFFREYL, McCRACKEN KEVING, PRUETT CHRISTINL, ROHWER SIEVERT, DROVETSKI SERGEIV, ZHURAVLEV YURIYN, KULIKOVA IRINA, GIBSON DANIELD, WINKER KEVIN. A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato). Mol Ecol 2012; 21:4563-77. [DOI: 10.1111/j.1365-294x.2012.05711.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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