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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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Bourke BP, Dusek RJ, Ergunay K, Linton YM, Drovetski SV. Viral pathogen detection in U.S. game-farm mallard ( Anas platyrhynchos) flags spillover risk to wild birds. Front Vet Sci 2024; 11:1396552. [PMID: 38860005 PMCID: PMC11163284 DOI: 10.3389/fvets.2024.1396552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
The threat posed by emerging infectious diseases is a major concern for global public health, animal health and food security, and the role of birds in transmission is increasingly under scrutiny. Each year, millions of mass-reared game-farm birds are released into the wild, presenting a unique and a poorly understood risk to wild and susceptible bird populations, and to human health. In particular, the shedding of enteric pathogens through excrement into bodies of water at shared migratory stop-over sites, and breeding and wintering grounds, could facilitate multi-species long-distance pathogen dispersal and infection of high numbers of naive endemic birds annually. The Mallard (Anas platyrhynchos) is the most abundant of all duck species, migratory across much of its range, and an important game species for pen-rearing and release. Major recent population declines along the US Atlantic coast has been attributed to game-farm and wild mallard interbreeding and the introduction maladaptive traits into wild populations. However, pathogen transmission and zoonosis among game-farms Mallard may also impact these populations, as well as wildlife and human health. Here, we screened 16 game-farm Mallard from Wisconsin, United States, for enteric viral pathogens using metatranscriptomic data. Four families of viral pathogens were identified - Picobirnaviridae (Genogroup I), Caliciviridae (Duck Nacovirus), Picornaviridae (Duck Aalivirus) and Sedoreoviridae (Duck Rotavirus G). To our knowledge, this is the first report of Aalivirus in the Americas, and the first report of Calicivirus outside domestic chicken and turkey flocks in the United States. Our findings highlight the risk of viral pathogen spillover from peri-domestically reared game birds to naive wild bird populations.
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Affiliation(s)
- Brian P. Bourke
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
| | - Robert J. Dusek
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Koray Ergunay
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
- Hacettepe University, Department of Medical Microbiology, Ankara, Türkiye
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
| | - Sergei V. Drovetski
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge, Laurel, MD, United States
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3
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Samake JN, Lavretsky P, Gunarathna I, Follis M, Brown JI, Ali S, Yared S, Carter TE. Population genomic analyses reveal population structure and major hubs of invasive Anopheles stephensi in the Horn of Africa. Mol Ecol 2023; 32:5695-5708. [PMID: 37795951 DOI: 10.1111/mec.17136] [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: 11/29/2022] [Revised: 08/15/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome-wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation-by-distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype-environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.
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Affiliation(s)
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | | | - Madison Follis
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Joshua I Brown
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Said Ali
- Ministry of Health Somaliland, Hargeisa, Somalia
| | - Solomon Yared
- Department of Biology, Jigjiga University, Jigjiga, Ethiopia
| | - Tamar E Carter
- Department of Biology, Baylor University, Waco, Texas, USA
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4
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Lavretsky P, Hernández F, Swale T, Mohl JE. Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos). G3 (BETHESDA, MD.) 2023; 13:jkad171. [PMID: 37523777 PMCID: PMC10542157 DOI: 10.1093/g3journal/jkad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023]
Abstract
The mallard (Anas platyrhynchos) is one of the most common, economically, and socially important birds around the world. Mallards were not only an important food source for early humans but eventually becoming intimately linked with people as they were domesticated over the last 2,000 years. To date, mallard genomes are largely reconstructed from samples of domestic or unknown genetic heritage. Here, we report the first high-quality genome assembly and annotation of a genetically vetted wild mallard from North America (NAwild_v1.0). The genome was assembled using a combination of shotgun libraries, proximity ligation Chicago, and Dovetail Hi-C libraries. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome-level scaffolds, and with a N50/L50 of 79.1 Mb/4 scaffolds. We used a combination of gene prediction and similarity approaches to annotate a total of 23,584 functional genes, of which 19,242 were associated to GO terms. The genome assembly and the set of annotated genes yielded a 95.4% completeness score when compared with the BUSCO aves_odb10 dataset. Next, we aligned 3 previously published mallard genomes to ours, and demonstrate how runs of homozygosity and nucleotide diversity are substantially higher and lower, respectively, to ours and how these artificially changed genomes resulted in profoundly different and biased demographic histories. Our wild mallard assembly not only provides a valuable resource to shed light onto genome evolution, speciation, and other adaptive processes, but also helping with identifying functional genes that have been significantly altered during the domestication process.
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Affiliation(s)
- Philip Lavretsky
- 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
| | - Thomas Swale
- Cantata Bio, 100 Enterprise Way Suite A101, Scotts Valley, CA 95066
| | - Jonathon E Mohl
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
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5
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Schell ER, McCracken KG, Scott GR, White J, Lavretsky P, Dawson NJ. Consistent changes in muscle metabolism underlie dive performance across multiple lineages of diving ducks. Proc Biol Sci 2023; 290:20231466. [PMID: 37752838 PMCID: PMC10523079 DOI: 10.1098/rspb.2023.1466] [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: 06/28/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Diving animals must sustain high activity with limited O2 stores to successfully capture prey. Studies suggest that increasing body O2 stores supports breath-hold diving, but less is known about metabolic specializations that underlie underwater locomotion. We measured maximal activities of 10 key enzymes in locomotory muscles (gastrocnemius and pectoralis) to identify biochemical changes associated with diving in pathways of oxidative and substrate-level phosphorylation and compared them across three groups of ducks-the longest diving sea ducks (eight spp.), the mid-tier diving pochards (three spp.) and the non-diving dabblers (five spp.). Relative to dabblers, both diving groups had increased activities of succinate dehydrogenase and cytochrome c oxidase, and sea ducks further showed increases in citrate synthase (CS) and hydroxyacyl-CoA dehydrogenase (HOAD). Both diving groups had relative decreases in capacity for anaerobic metabolism (lower ratio of lactate dehydrogenase to CS), with sea ducks also showing a greater capacity for oxidative phosphorylation and lipid oxidation (lower ratio of pyruvate kinase to CS, higher ratio of HOAD to hexokinase). These data suggest that the locomotory muscles of diving ducks are specialized for sustaining high rates of aerobic metabolism, emphasizing the importance of body O2 stores for dive performance in these species.
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Affiliation(s)
| | - Kevin G. McCracken
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, USA
- Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Jeff White
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas El Paso, El Paso, TX 79968, USA
| | - Neal J. Dawson
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
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6
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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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7
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Roberts AJ, Hostetler JA, Stiller JC, Devers PK, Link WA. Population dynamics and harvest management of eastern mallards. J Wildl Manage 2023. [DOI: 10.1002/jwmg.22405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Affiliation(s)
- Anthony J. Roberts
- U.S. Fish and Wildlife Service Division of Migratory Bird Management Laurel MD 20708 USA
| | - Jeffrey A. Hostetler
- U.S. Fish and Wildlife Service Division of Migratory Bird Management Laurel MD 20708 USA
| | - Joshua C. Stiller
- New York State Department of Environmental Conservation, Albany NY 12233 USA
| | - Patrick K. Devers
- U.S. Fish and Wildlife Service Division of Migratory Bird Management Laurel MD 20708 USA
| | - William A. Link
- U.S. Geological Survey Eastern Ecological Science Center Laurel MD 20708 USA
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8
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Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa). Genomics 2023; 115:110591. [PMID: 36849018 DOI: 10.1016/j.ygeno.2023.110591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (FIS and FROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.
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9
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Population structure and hybridisation in a population of Hawaiian feral chickens. Heredity (Edinb) 2023; 130:154-162. [PMID: 36725960 PMCID: PMC9981564 DOI: 10.1038/s41437-022-00589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
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Schummer ML, Simpson J, Shirkey B, Kucia SR, Lavretsky P, Tozer DC. Population genetics and geographic origins of mallards harvested in northwestern Ohio. PLoS One 2023; 18:e0282874. [PMID: 36920978 PMCID: PMC10016643 DOI: 10.1371/journal.pone.0282874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/25/2023] [Indexed: 03/16/2023] Open
Abstract
The genetic composition of mallards in eastern North America has been changed by release of domestically-raised, game-farm mallards to supplement wild populations for hunting. We sampled 296 hatch-year mallards harvested in northwestern Ohio, October-December 2019. The aim was to determine their genetic ancestry and geographic origin to understand the geographic extent of game-farm mallard introgression into wild populations in more westward regions of North America. We used molecular analysis to detect that 35% of samples were pure wild mallard, 12% were early generation hybrids between wild and game-farm mallards (i.e., F1-F3), and the remaining 53% of samples were assigned as part of a hybrid swarm. Percentage of individuals in our study with some form of hybridization with game-farm mallard (65%) was greater than previously detected farther south in the mid-continent (~4%), but less than the Atlantic coast of North America (~ 92%). Stable isotope analysis using δ2Hf suggested that pure wild mallards originated from areas farther north and west than hybrid mallards. More specifically, 17% of all Ohio samples had δ2Hf consistent with more western origins in the prairies, parkland, or boreal regions of the mid-continent of North America, with 55%, 35%, and 10% of these being genetically wild, hybrid swarm, and F3, respectively. We conclude that continued game-farm introgression into wild mallards is not isolated to the eastern population of mallards in North America, and may be increasing and more widespread than previously detected. Mallards in our study had greater incidence of game-farm hybridization than other locales in the mid-continent but less than eastern North American regions suggesting further need to understand game-farm mallard genetic variation and movement across the continent.
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Affiliation(s)
- Michael L. Schummer
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
- * E-mail:
| | - John Simpson
- Winous Point Marsh Conservancy, Port Clinton, Ohio, United States of America
| | - Brendan Shirkey
- Winous Point Marsh Conservancy, Port Clinton, Ohio, United States of America
| | - Samuel R. Kucia
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Douglas C. Tozer
- Long Point Waterfowl and Wetlands Research Program, Birds Canada, Port Rowan, Ontario, Canada
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11
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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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Campagna L, Toews DP. The genomics of adaptation in birds. Curr Biol 2022; 32:R1173-R1186. [DOI: 10.1016/j.cub.2022.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Lin R, Li J, Yang Y, Yang Y, Chen J, Zhao F, Xiao T. Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province. Animals (Basel) 2022; 12:ani12172302. [PMID: 36078022 PMCID: PMC9454422 DOI: 10.3390/ani12172302] [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: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary The aim of this study was to conduct a genome-wide comparative analysis of four indigenous Chinese duck breeds (Jinding, Liancheng white, Putian black, and Shanma ducks) from Fujian Province, to understand their genetic diversity and population structure. Population parameters showed that the four indigenous breeds were separated groups. Five genomic regions are presented as hotspots of autozygosity among these indigenous duck breeds, with candidate genes involved in muscle growth, pigmentation, and neuroregulation. Genomic information may play a vital role in the improvement of conservation strategies. Abstract The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.
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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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15
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Kulikova IV, Shedko SV, Zhuravlev YN, Lavretsky P, Peters JL. Z‐chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot‐billed Duck (Anatidae). ZOOL SCR 2022. [DOI: 10.1111/zsc.12540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irina V. Kulikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Sergei V. Shedko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Yury N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia
| | - Philip Lavretsky
- Department of Biological Sciences University of Texas El Paso Texas USA
| | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton Ohio USA
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16
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Brown JI, Harrigan RJ, Lavretsky P. Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex. Mol Ecol 2022; 31:2578-2593. [PMID: 35263000 DOI: 10.1111/mec.16423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Ryan J Harrigan
- Center for Tropical Research, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA, 90095, U.S.A
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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17
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Campana MG, Hawkins MTR, Caballero S. Editorial: Assessing Biodiversity in the Phylogenomic Era. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.803188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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19
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Devers PK, Emmet RL, Boomer GS, Zimmerman GS, Royle JA. Evaluation of a two-season banding program to estimate and model migratory bird survival. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02425. [PMID: 34296480 DOI: 10.1002/eap.2425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/22/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
The management of North American waterfowl is predicated on long-term, continental-scale banding implemented prior to the hunting season (i.e., July-September) and subsequent reporting of bands recovered by hunters. However, single-season banding and encounter operations have a number of characteristics that limit their application to estimating demographic rates and evaluating hypothesized limiting factors throughout the annual cycle. We designed and implemented a two-season banding program for American Black Ducks (Anas rubripes), Mallards (A. platyrhynchos), and hybrids in eastern North America to evaluate potential application to annual life cycle conservation and sport harvest management. We assessed model fit and compared estimates of annual survival among data types (i.e., pre-hunting season only [July-September], post-hunting season only [January-March], and two-season [pre- and post-hunting season]) to evaluate model assumptions and potential application to population modeling and management. There was generally high agreement between estimates of annual survival derived using two-season and pre-season only data for all age and sex cohorts. Estimates of annual survival derived from post-season banding data only were consistently higher for adult females and juveniles of both sexes. We found patterns of seasonal survival varied by species, age, and to a lesser extent, sex. Hunter recovered birds exhibited similar spatial distributions regardless of banding season suggesting banded samples were from the same population. In contrast, goodness-of-fit tests suggest this assumption was statistically violated in some regions and years. We conclude that estimates of seasonal and annual survival for Black Ducks and Mallards based on the two-season banding program are valid and accurate based on model fit statistics, similarity in survival estimates across data and models, and similarities in the distribution of recoveries. The two-season program provides greater precision and insight into the survival process and will improve the ability of researchers and managers to test competing hypotheses regarding population regulation resulting in more effective management.
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Affiliation(s)
- Patrick K Devers
- Division of Migratory Bird Management, U.S. Fish and Wildlife Service, 11510 American Holly Drive, Laurel, Maryland, 20708, USA
| | - Robert L Emmet
- College of the Environment, University of Washington, Seattle, Washington, 98195, USA
| | - G Scott Boomer
- Division of Migratory Bird Management, U.S. Fish and Wildlife Service, 11510 American Holly Drive, Laurel, Maryland, 20708, USA
| | - Guthrie S Zimmerman
- Division of Migratory Bird Management, U.S. Fish and Wildlife Service, 3020 State University Drive East, Modoc Hall, Suite 2007, Sacramento, California, 95819, USA
| | - J Andrew Royle
- U.S. Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, Maryland, 20708, USA
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20
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Hernández F, Brown JI, Kaminski M, Harvey MG, Lavretsky P. Genomic Evidence for Rare Hybridization and Large Demographic Changes in the Evolutionary Histories of Four North American Dove Species. Animals (Basel) 2021; 11:ani11092677. [PMID: 34573643 PMCID: PMC8468798 DOI: 10.3390/ani11092677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022] Open
Abstract
Introductions and invasions provide opportunities for interaction and hybridization between colonists and closely related native species. We investigate this phenomenon using the mitochondrial DNA COI and 81,416 base-pairs of overlapping nuclear variation to examine the evolutionary histories and signatures of hybridization among introduced feral Rock Pigeon and Eurasian Collared-Dove and native White-winged and Mourning doves in southwestern North America. First, we report all four species to be highly divergent across loci (overall pair-wise species ΦST range = 0.17-0.70) and provide little evidence for gene flow at evolutionary timescales. Despite this, evidence from multiple population genetics analyses supports the presence of six putative contemporary late-stage hybrids among the 182 sampled individuals. These putative hybrids contain various ancestry combinations, but all involve the most populous species, the Mourning Dove. Next, we use a novel method to reconstruct demographic changes through time using partial genome sequence data. We identify recent, species-specific fluctuations in population size that are likely associated with changing environments since the Miocene and suggest that these fluctuations have influenced the genetic diversity of each dove species in ways that may impact their future persistence. Finally, we discuss the importance of using multiple marker types when attempting to infer complex evolutionary histories and propose important considerations when analyzing populations that were recently established or of domestic origins.
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21
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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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22
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Grant AH, Ayala-Marin YM, Mohl JE, Robles-Escajeda E, Rodriguez G, Dutil J, Kirken RA. The Genomic Landscape of a Restricted ALL Cohort from Patients Residing on the U.S./Mexico Border. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18147345. [PMID: 34299796 PMCID: PMC8307122 DOI: 10.3390/ijerph18147345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/12/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has identified unique biomarkers yielding new strategies in precision medicine for the treatment of Acute lymphoblastic leukemia (ALL). Hispanics show marked health disparities in ALL, often absent in clinical trials or cancer research. Thus, it is unknown whether Hispanics would benefit equally from curated data currently guiding precision oncology. Using whole-exome sequencing, nine ALL patients were screened for mutations within genes known to possess diagnostic, prognostic and therapeutic value. Genes mutated in Hispanic ALL patients from the borderland were mined for potentially pathogenic variants within clinically relevant genes. KRAS G12A was detected in this unique cohort and its frequency in Hispanics from the TARGET-ALL Phase II database was three-fold greater than that of non-Hispanics. STAT5B N642H was also detected with low frequency in Hispanic and non-Hispanic individuals within TARGET. Its detection within this small cohort may reflect a common event in this demographic. Such variants occurring in the MAPK and JAK/STAT pathways may be contributing to Hispanic health disparities in ALL. Notable variants in ROS1, WT1, and NOTCH2 were observed in the ALL borderland cohort, with NOTCH2 C19W occurring most frequently. Further investigations on the pathogenicity of these variants are needed to assess their relevance in ALL.
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Affiliation(s)
- Alice Hernandez Grant
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Yoshira Marie Ayala-Marin
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Jonathon Edward Mohl
- Department of Mathematical Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Elisa Robles-Escajeda
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Georgialina Rodriguez
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Julie Dutil
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00716, USA;
| | - Robert Arthur Kirken
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
- Correspondence: ; Tel.: +1-(915)-747-5536
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23
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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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24
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Lavretsky P, Wilson RE, Talbot SL, Sonsthagen SA. Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini). Mol Phylogenet Evol 2021; 161:107164. [PMID: 33798675 DOI: 10.1016/j.ympev.2021.107164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022]
Abstract
Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79668, USA; US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA.
| | - Robert E Wilson
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Sandra L Talbot
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Sarah A Sonsthagen
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
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25
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Meehan TD, Kaminski RM, Lebaron GS, Michel NL, Bateman BL, Wilsey CB. Half‐Century Winter Duck Abundance and Temperature Trends in the Mississippi and Atlantic Flyways. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Richard M. Kaminski
- James C. Kennedy Waterfowl and Wetlands Conservation Center, Belle W. Baruch Institute of Coastal Ecology and Forest Science Clemson University P.O. Box 596 Georgetown SC 29442 USA
| | | | - Nicole L. Michel
- National Audubon Society 225 Varick Street New York NY 10014 USA
| | | | - Chad B. Wilsey
- National Audubon Society 225 Varick Street New York NY 10014 USA
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26
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Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zool Res 2021; 42:43-50. [PMID: 33269825 PMCID: PMC7840458 DOI: 10.24272/j.issn.2095-8137.2020.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.
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Affiliation(s)
- Xing Guo
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xin-Xin He
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hong Chen
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhi-Cheng Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui-Fang Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Jiang-Xian Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA. E-mail:
| | - Run-Shen Jiang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China. E-mail:
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27
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Guo X, Wang ZC, Wang S, Li HF, Suwannapoom C, Wang JX, Zhang C, Shao Y, Wang MS, Jiang RS. Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks. Anim Genet 2020; 51:866-875. [PMID: 33020910 DOI: 10.1111/age.13002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6 M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticated ducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.
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Affiliation(s)
- X Guo
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Z-C Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - S Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - H-F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, 58 cangjie Rode, Yangzhou, Jiangsu, 225125, China
| | - C Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, 19 Moo 2 Tambon Maeka, Amphur Muang, Phayao, 56000, Thailand
| | - J-X Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - C Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Y Shao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - M-S Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA
| | - R-S Jiang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
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