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Huang G, Qi D, Yang Z, Hou R, Shi W, Zhao F, Li Z, Yan L, Wei F. Gut microbiome as a key monitoring indicator for reintroductions of captive animals. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14173. [PMID: 37650395 DOI: 10.1111/cobi.14173] [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: 02/20/2023] [Revised: 07/04/2023] [Accepted: 07/15/2023] [Indexed: 09/01/2023]
Abstract
Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | | | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Wenyu Shi
- College of Biological Science, China Agricultural University, Beijing, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zitian Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
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2
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [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: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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Puckett EE, Davis IS, Harper DC, Wakamatsu K, Battu G, Belant JL, Beyer DE, Carpenter C, Crupi AP, Davidson M, DePerno CS, Forman N, Fowler NL, Garshelis DL, Gould N, Gunther K, Haroldson M, Ito S, Kocka D, Lackey C, Leahy R, Lee-Roney C, Lewis T, Lutto A, McGowan K, Olfenbuttel C, Orlando M, Platt A, Pollard MD, Ramaker M, Reich H, Sajecki JL, Sell SK, Strules J, Thompson S, van Manen F, Whitman C, Williamson R, Winslow F, Kaelin CB, Marks MS, Barsh GS. Genetic architecture and evolution of color variation in American black bears. Curr Biol 2023; 33:86-97.e10. [PMID: 36528024 PMCID: PMC10039708 DOI: 10.1016/j.cub.2022.11.042] [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: 09/14/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.
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Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA.
| | - Isis S Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Dawn C Harper
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerrold L Belant
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Dean E Beyer
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV 25801, USA
| | - Anthony P Crupi
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Maria Davidson
- The Louisiana Department of Wildlife and Fisheries, Baton Rouge, LA 70898, USA
| | - Christopher S DePerno
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Nicholas Forman
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, USA
| | - Nicholas L Fowler
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - David L Garshelis
- Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA; IUCN SSC Bear Specialist Group
| | - Nicholas Gould
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Kerry Gunther
- National Park Service, Yellowstone National Park, WY 82190-0168, USA
| | - Mark Haroldson
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - David Kocka
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Carl Lackey
- Nevada Department of Wildlife, Reno, NV 89512, USA
| | - Ryan Leahy
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Caitlin Lee-Roney
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Tania Lewis
- National Park Service, Glacier Bay National Park, Gustavus, AK 99826, USA
| | - Ashley Lutto
- U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, Soldotna, AK 99669, USA
| | - Kelly McGowan
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Mike Orlando
- Florida Fish and Wildlife Conservation Commission, Tallahassee, FL 32399, USA
| | - Alexander Platt
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew D Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Megan Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jaime L Sajecki
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Stephanie K Sell
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Jennifer Strules
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Seth Thompson
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Frank van Manen
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Craig Whitman
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Ryan Williamson
- National Park Service, Great Smoky Mountains National Park, Gatlinburg, TN 37738, USA
| | | | - Christopher B Kaelin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pathology and Laboratory Medicine and of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
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4
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Puckett EE, Davis IS. Spatial patterns of genetic diversity in eight bear (Ursidae) species. URSUS 2021. [DOI: 10.2192/ursus-d-20-00029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Isis S. Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
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5
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Light JE, Keane AS, Evans JW. Updating the Distribution of American Black Bears (Ursus americanus) in Texas Using Community Science, State Agencies, and Natural History Collections. WEST N AM NATURALIST 2021. [DOI: 10.3398/064.081.0308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jessica E. Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| | - Alaya S. Keane
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
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6
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Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Duncan SI, Robertson EP, Fletcher RJ, Austin JD. Urbanization and Population Genetic Structure of the Panama City crayfish (Procambarus econfinae). J Hered 2020; 111:204-215. [PMID: 31746328 DOI: 10.1093/jhered/esz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.
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Affiliation(s)
| | - Ellen P Robertson
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Robert J Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
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8
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Lansink GMJ, Esparza-Salas R, Joensuu M, Koskela A, Bujnáková D, Kleven O, Flagstad Ø, Ollila T, Kojola I, Aspi J, Kvist L. Population genetics of the wolverine in Finland: the road to recovery? CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01264-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AbstractAfter decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes.
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9
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Lee DE, Fienieg E, Van Oosterhout C, Muller Z, Strauss M, Carter KD, Scheijen CPJ, Deacon F. Giraffe translocation population viability analysis. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Most populations of giraffes have declined in recent decades, leading to the recent IUCN decision to upgrade the species to Vulnerable status, and some subspecies to Endangered. Translocations have been used as a conservation tool to re-introduce giraffes to previously occupied areas or establish new populations, but guidelines for founding populations are lacking. To provide general guidelines for translocation projects regarding feasibility, we simulated various scenarios of translocated giraffe populations to identify viable age and sex distributions of founding populations using population viability analysis (PVA) implemented in Vortex software. We explored the parameter space for demography and the genetic load, examining how variation in founding numbers and sex ratios affected 100 yr probability of population extinction and genetic diversity. We found that even very small numbers of founders (N ≤ 10 females) can appear to be successful in the first decades due to transient positive population growth, but with moderate population growth rate and moderate genetic load, long-term population viability (probability of extinction <0.01) was only achieved with ≥30 females and ≥3 males released. To maintain >95% genetic diversity of the source population in an isolated population, 50 females and 5 males are recommended to compose the founding population. Sensitivity analyses revealed first-year survival and reproductive rate were the simulation parameters with the greatest proportional influence on probability of extinction and genetic diversity. These simulations highlight important considerations for translocation success and data gaps including true genetic load in wild giraffe populations.
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Affiliation(s)
- DE Lee
- Biology Department, Pennsylvania State University, Muller Laboratory, State College, PA 16801, USA
| | - E Fienieg
- European Association of Zoos and Aquaria, Plantage Kerklaan 40, 1018 CZ Amsterdam, The Netherlands
| | - C Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Z Muller
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - M Strauss
- Wild Nature Institute, 15 North Main Street #208, Concord, NH 03301, USA
| | - KD Carter
- Elephant Connection, Mwandi, Western Province, Zambia
| | - CPJ Scheijen
- Animal, Wildlife and Grassland Sciences, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - F Deacon
- Animal, Wildlife and Grassland Sciences, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
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10
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Meredith EP, Adkins JK, Rodzen JA. UrsaPlex: An STR multiplex for forensic identification of North American black bear (Ursus americanus). Forensic Sci Int Genet 2019; 44:102161. [PMID: 31677443 DOI: 10.1016/j.fsigen.2019.102161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
UrsaPlex is a forensic quality 5-dye multiplexed tetranucleotide STR and sex identification panel for individual genetic identification of North American black bears (Ursus americanus). The panel is validated for the identification of black bears involved in human-wildlife conflict events and poaching investigations. This is the first single multiplex panel composed solely of tetranucleotide STRs derived from black bear and bear-specific sex markers. UrsaPlex produces complete genetic profiles from as little as 78 pg of DNA template and has a probability of identity of 2.63 × 10-13. The panel has also been tested for utility in other ursids, and our results indicate with minor modifications, UrsaPlex should prove valuable in identification investigations involving these species as well.
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Affiliation(s)
- Erin P Meredith
- California Department of Fish and Wildlife - Wildlife Forensic Laboratory, 1415 North Market Blvd. Suite 3, Sacramento, CA, 95834, USA.
| | - Jillian K Adkins
- California Department of Fish and Wildlife - Wildlife Forensic Laboratory, 1415 North Market Blvd. Suite 3, Sacramento, CA, 95834, USA
| | - Jeff A Rodzen
- California Department of Fish and Wildlife - Genetic Research Laboratory, 1415 North Market Blvd. Suite 9, Sacramento, CA, 95834, USA
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11
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Burkhart JJ, Puckett EE, Beringer CJ, Sholy CN, Semlitsch RD, Eggert LS. Post-Pleistocene differentiation in a Central Interior Highlands endemic salamander. Ecol Evol 2019; 9:11171-11184. [PMID: 31641463 PMCID: PMC6802018 DOI: 10.1002/ece3.5619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 11/07/2022] Open
Abstract
AIM For many endemic species with limited dispersal capacities, the relationship between landscape changes and species distributions is still unclear. We characterized the population structure of the endemic ringed salamander (Ambystoma annulatum) across its distribution in the Central Interior Highlands (CIH) of North America, an area of high species endemism, to infer the ecological and evolutionary history of the species. METHODS We sampled 498 individuals across the species distribution and characterized the population genetic structure using nuclear microsatellite and mitochondrial DNA (mtDNA) markers. RESULTS Ambystoma annulatum exist in two strongly supported nuclear genetic clusters across the CIH that correspond to a northern cluster that includes the Missouri Ozark populations and a southern cluster that includes the Arkansas and Oklahoma Ozarks and the Ouachita Mountains. Our demographic models estimated that these populations diverged approximately 2,700 years ago. Pairwise estimates of genetic differentiation at microsatellite and mtDNA markers indicated limited contemporary gene flow and suggest that genetic differentiation was primarily influenced by changes in the post-Pleistocene landscape of the CIH. MAIN CONCLUSIONS Both the geologic history and post-European settlement history of the CIH have influenced the population genetic structure of A. annulatum. The low mtDNA diversity suggests a retraction into and expansion out of refugial areas in the south-central Ozarks, during temperature fluctuations of the Pleistocene and Holocene epochs. Similarly, the estimated divergence time for the two nuclear clusters corresponds to changes in the post-Pleistocene landscape. More recently, decreased A. annulatum gene flow may be a result of increased habitat fragmentation and alteration post-European settlement.
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Affiliation(s)
| | - Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTNUSA
| | | | | | | | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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12
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Murphy SM, Hast JT, Augustine BC, Weisrock DW, Clark JD, Kocka DM, Ryan CW, Sajecki JL, Cox JJ. Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA. URSUS 2019. [DOI: 10.2192/ursu-d-18-00011.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - John T. Hast
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - Ben C. Augustine
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - David W. Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Joseph D. Clark
- United States Geological Survey, Northern Rocky Mountain Science Center, Southern Appalachian Research Branch, University of Tennessee, Knoxville, TN 37996, USA
| | - David M. Kocka
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - Christopher W. Ryan
- West Virginia Division of Natural Resources, South Charleston, WV 25303, USA
| | - Jaime L. Sajecki
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - John J. Cox
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
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13
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Modeling Heterogeneity in the Genetic Architecture of Ethnically Diverse Groups Using Random Effect Interaction Models. Genetics 2019; 211:1395-1407. [PMID: 30796011 PMCID: PMC6456318 DOI: 10.1534/genetics.119.301909] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
In humans, most genome-wide association studies have been conducted using data from Caucasians and many of the reported findings have not replicated in other populations. This lack of replication may be due to statistical issues (small sample sizes or confounding) or perhaps more fundamentally to differences in the genetic architecture of traits between ethnically diverse subpopulations. What aspects of the genetic architecture of traits vary between subpopulations and how can this be quantified? We consider studying effect heterogeneity using Bayesian random effect interaction models. The proposed methodology can be applied using shrinkage and variable selection methods, and produces useful information about effect heterogeneity in the form of whole-genome summaries (e.g., the proportions of variance of a complex trait explained by a set of SNPs and the average correlation of effects) as well as SNP-specific attributes. Using simulations, we show that the proposed methodology yields (nearly) unbiased estimates when the sample size is not too small relative to the number of SNPs used. Subsequently, we used the methodology for the analyses of four complex human traits (standing height, high-density lipoprotein, low-density lipoprotein, and serum urate levels) in European-Americans (EAs) and African-Americans (AAs). The estimated correlations of effects between the two subpopulations were well below unity for all the traits, ranging from 0.73 to 0.50. The extent of effect heterogeneity varied between traits and SNP sets. Height showed less differences in SNP effects between AAs and EAs whereas HDL, a trait highly influenced by lifestyle, exhibited a greater extent of effect heterogeneity. For all the traits, we observed substantial variability in effect heterogeneity across SNPs, suggesting that effect heterogeneity varies between regions of the genome.
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Barbanti A, Martin C, Blumenthal JM, Boyle J, Broderick AC, Collyer L, Ebanks-Petrie G, Godley BJ, Mustin W, Ordóñez V, Pascual M, Carreras C. How many came home? Evaluating ex situ conservation of green turtles in the Cayman Islands. Mol Ecol 2019; 28:1637-1651. [PMID: 30636347 DOI: 10.1111/mec.15017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 01/15/2023]
Abstract
Ex situ management is an important conservation tool that allows the preservation of biological diversity outside natural habitats while supporting survival in the wild. Captive breeding followed by re-introduction is a possible approach for endangered species conservation and preservation of genetic variability. The Cayman Turtle Centre Ltd was established in 1968 to market green turtle (Chelonia mydas) meat and other products and replenish wild populations, thought to be locally extirpated, through captive breeding. We evaluated the effects of this re-introduction programmme using molecular markers (13 microsatellites, 800-bp D-loop and simple tandem repeat mitochondrial DNA sequences) from captive breeders (N = 257) and wild nesting females (N = 57) (sampling period: 2013-2015). We divided the captive breeders into three groups: founders (from the original stock), and then two subdivisions of F1 individuals corresponding to two different management strategies, cohort 1995 ("C1995") and multicohort F1 ("MCF1"). Loss of genetic variability and increased relatedness was observed in the captive stock over time. We found no significant differences in diversity among captive and wild groups, and similar or higher levels of haplotype variability when compared to other natural populations. Using parentage and sibship assignment, we determined that 90% of the wild individuals were related to the captive stock. Our results suggest a strong impact of the re-introduction programmme on the present recovery of the wild green turtle population nesting in the Cayman Islands. Moreover, genetic relatedness analyses of captive populations are necessary to improve future management actions to maintain genetic diversity in the long term and avoid inbreeding depression.
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Affiliation(s)
- Anna Barbanti
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - Clara Martin
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | | | - Jack Boyle
- Department of Environment, Grand Cayman, Cayman Islands
| | | | - Lucy Collyer
- Department of Environment, Grand Cayman, Cayman Islands
| | | | - Brendan J Godley
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Víctor Ordóñez
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
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15
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Evans MJ, Rittenhouse TAG, Hawley JE, Rego PW, Eggert LS. Spatial genetic patterns indicate mechanism and consequences of large carnivore cohabitation within development. Ecol Evol 2018; 8:4815-4829. [PMID: 29876060 PMCID: PMC5980631 DOI: 10.1002/ece3.4033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 02/19/2018] [Accepted: 02/26/2018] [Indexed: 12/26/2022] Open
Abstract
Patterns of human development are shifting from concentrated housing toward sprawled housing intermixed with natural land cover, and wildlife species increasingly persist in close proximity to housing, roads, and other anthropogenic features. These associations can alter population dynamics and evolutionary trajectories. Large carnivores increasingly occupy urban peripheries, yet the ecological consequences for populations established entirely within urban and exurban landscapes are largely unknown. We applied a spatial and landscape genetics approach, using noninvasively collected genetic data, to identify differences in black bear spatial genetic patterns across a rural‐to‐urban gradient and quantify how development affects spatial genetic processes. We quantified differences in black bear dispersal, spatial genetic structure, and migration between differing levels of development within a population primarily occupying areas with >6 houses/km2 in western Connecticut. Increased development disrupted spatial genetic structure, and we found an association between increased housing densities and longer dispersal. We also found evidence that roads limited gene flow among bears in more rural areas, yet had no effect among bears in more developed ones. These results suggest dispersal behavior is condition‐dependent and indicate the potential for landscapes intermixing development and natural land cover to facilitate shifts toward increased dispersal. These changes can affect patterns of range expansion and the phenotypic and genetic composition of surrounding populations. We found evidence that subpopulations occupying more developed landscapes may be sustained by male‐biased immigration, creating potentially detrimental demographic shifts.
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Affiliation(s)
- Michael J Evans
- Wildlife and Fisheries Conservation Center Department of Natural Resources and the Environment University of Connecticut Storrs CT USA
| | - Tracy A G Rittenhouse
- Wildlife and Fisheries Conservation Center Department of Natural Resources and the Environment University of Connecticut Storrs CT USA
| | - Jason E Hawley
- Wildlife Division Connecticut Department of Energy and Environmental Protection Sessions Woods WMA Burlington CT USA
| | - Paul W Rego
- Wildlife Division Connecticut Department of Energy and Environmental Protection Sessions Woods WMA Burlington CT USA
| | - Lori S Eggert
- Division of Biological Sciences University of Missouri Columbia MO USA
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16
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Genetic diversity, effective population size, and structure among black bear populations in the Lower Mississippi Alluvial Valley, USA. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1075-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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17
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Kristensen TV, Puckett EE, Landguth EL, Belant JL, Hast JT, Carpenter C, Sajecki JL, Beringer J, Means M, Cox JJ, Eggert LS, White D, Smith KG. Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history. Heredity (Edinb) 2018; 120:329-341. [PMID: 29234157 PMCID: PMC5842220 DOI: 10.1038/s41437-017-0019-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 09/29/2017] [Indexed: 11/08/2022] Open
Abstract
Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago-in the Interior Highlands and Southern Appalachian Mountains, United States. We used spatially explicit, individual-based genetic simulations to model gene flow under scenarios with varying levels of population density, genetic diversity, and female philopatry. Using measures of genetic distance and spatial autocorrelation, we compared metrics between sexes, between population types (historic and recent), and among simulated scenarios which varied in density, genetic diversity, and sex-biased philopatry. In empirical populations, females in recent populations exhibited stronger patterns of isolation-by-distance (IBD) than females and males in historic populations. In simulated populations, low-density populations had a stronger indication of IBD than medium- to high-density populations; however, this effect varied in empirical populations. Condition-dependent dispersal strategies may permit species to cope with novel conditions and rapidly expand populations. Pattern-process modeling can provide qualitative and quantitative means to explore variable dispersal patterns, and could be employed in other species, particularly to anticipate range shifts in response to changing climate and habitat conditions.
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Affiliation(s)
- Thea V Kristensen
- Department of Biological Sciences, Science and Engineering, University of Arkansas, Fayetteville, AR, USA.
- Biology Department, Amherst College, P.O. Box 5000, Amherst, MA, 01002, USA.
| | - Emily E Puckett
- Division of Biological Sciences, Tucker Hall, University of Missouri, Columbia, MO, USA
- Department of Biological Sciences and the Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, 10504, USA
| | - Erin L Landguth
- Computational Ecology Laboratory, School of Public and Community Health Sciences, University of Montana, Missoula, MT, USA
| | - Jerrold L Belant
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - John T Hast
- Department of Forestry, University of Kentucky, Lexington, KY, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV, USA
| | - Jaime L Sajecki
- Virginia Department of Game and Inland Fisheries, Forest, VA, USA
| | - Jeff Beringer
- Missouri Department of Conservation, Resource Science Center, Columbia, MO, USA
| | - Myron Means
- Arkansas Game and Fish Commission, Fort Smith, AR, USA
| | - John J Cox
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - Lori S Eggert
- Division of Biological Sciences, Tucker Hall, University of Missouri, Columbia, MO, USA
| | - Don White
- University of Arkansas Agricultural Experiment Station, Arkansas Forest Resources Center, University of Arkansas-Monticello, Monticello, AR, USA
| | - Kimberly G Smith
- Department of Biological Sciences, Science and Engineering, University of Arkansas, Fayetteville, AR, USA
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Malaney JL, Lackey CW, Beckmann JP, Matocq MD. Natural rewilding of the Great Basin: Genetic consequences of recolonization by black bears (Ursus americanus
). DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jason L. Malaney
- Department of Natural Resources and Environmental Science; University of Nevada; Reno NV USA
- Program in Ecology, Evolution, and Conservation Biology; University of Nevada Reno; Reno NV USA
| | - Carl W. Lackey
- Game Division; Nevada Department of Wildlife; Reno NV USA
| | - Jon P. Beckmann
- Wildlife Conservation Society; North America Program; Bozeman MT USA
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science; University of Nevada; Reno NV USA
- Program in Ecology, Evolution, and Conservation Biology; University of Nevada Reno; Reno NV USA
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19
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McLennan EA, Gooley RM, Wise P, Belov K, Hogg CJ, Grueber CE. Pedigree reconstruction using molecular data reveals an early warning sign of gene diversity loss in an island population of Tasmanian devils (Sarcophilus harrisii). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1017-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin). PLoS One 2017; 12:e0181898. [PMID: 28792964 PMCID: PMC5549917 DOI: 10.1371/journal.pone.0181898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States’ Constitution—which initiated the prohibition of alcoholic drinks—and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin’s coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.
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Murphy SM, Augustine BC, Ulrey WA, Guthrie JM, Scheick BK, McCown JW, Cox JJ. Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population. PLoS One 2017; 12:e0181849. [PMID: 28738077 PMCID: PMC5524351 DOI: 10.1371/journal.pone.0181849] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/07/2017] [Indexed: 11/19/2022] Open
Abstract
Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the degree of contemporary habitat fragmentation and investigate the consequences of habitat fragmentation on population density and genetics of the HGS. Remaining natural habitats sustaining the HGS were significantly more fragmented and patchier than those supporting Florida’s largest black bear subpopulation. Genetic diversity was low (AR = 3.57; HE = 0.49) and effective population size was small (NE = 25 bears), both of which remained unchanged over a period spanning one bear generation despite evidence of some immigration. Subpopulation density (0.054 bear/km2) was among the lowest reported for black bears, was significantly female-biased, and corresponded to a subpopulation size of 98 bears in available habitat. Conserving remaining natural habitats in the area occupied by the small, genetically depauperate HGS, possibly through conservation easements and government land acquisition, is likely the most important immediate step to ensuring continued persistence of bears in this area. Our study also provides evidence that preferentially placing detectors (e.g., hair traps or cameras) primarily in quality habitat across fragmented landscapes poses a challenge to estimating density-habitat covariate relationships using spatial capture-recapture models. Because habitat fragmentation and loss are likely to increase in severity globally, further investigation of the influence of habitat fragmentation and detector placement on estimation of this relationship is warranted.
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Affiliation(s)
- Sean M. Murphy
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Wade A. Ulrey
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Joseph M. Guthrie
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Brian K. Scheick
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
| | - J. Walter McCown
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, Florida, United States of America
| | - John J. Cox
- Department of Forestry, University of Kentucky, Lexington, Kentucky, United States of America
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22
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Stepien CA, Karsiotis SI, Sullivan TJ, Klymus KE. Population genetic structure and comparative diversity of smallmouth bass Micropterus dolomieu: congruent patterns from two genomes. JOURNAL OF FISH BIOLOGY 2017; 90:2125-2147. [PMID: 28321848 DOI: 10.1111/jfb.13296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Genetic diversity and divergence patterns of smallmouth bass Micropterus dolomieu spawning groups are analysed across its northern native range with mtDNA cytochrome b gene sequences and eight unlinked nuclear DNA microsatellite loci. Results reveal high levels of genetic variability and significant differences in allelic representation among populations (mtDNA: mean ± s.e., HD = 0·50 ± 0·06, mean ± s.e., θST = 0·41 ± 0·02 and microsatellites: mean ± s.e. HO = 0·46 ± 0·03, mean ± s.e. θST = 0·25 ± 0·01). The distributions of 28 variant mtDNA haplotypes, which differ by an average of 3·94 nucleotides (range = 1-8), denote divergent representation among geographic areas. Microsatellite data support nine primary population groups, whose high self-assignment probabilities likewise display marked divergence. Genetic patterns demonstrate: (1) high genetic diversity in both genomes, (2) significant divergence among populations, probably resulting from natal site homing and low lifetime migration, (3) support for three post-glacial refugia that variously contributed to the current northern populations, which remain evident today despite waterway connectivity and (4) a weak yet significant genetic isolation by geographic distance pattern, indicating that other processes affect the differences among populations, such as territoriality and site fidelity.
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Affiliation(s)
- C A Stepien
- Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, University of Toledo, Toledo, OH, 43606, U.S.A
- NOAA Pacific Marine Environmental Laboratory (PMEL), 7600 Sand Point Way NE, Seattle, WA, 98115, U.S.A
| | - S I Karsiotis
- Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, University of Toledo, Toledo, OH, 43606, U.S.A
| | - T J Sullivan
- Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, University of Toledo, Toledo, OH, 43606, U.S.A
| | - K E Klymus
- Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, University of Toledo, Toledo, OH, 43606, U.S.A
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23
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Duquette JF, Belant JL, Wilton CM, Fowler N, Waller BW, Beyer DE, Svoboda NJ, Simek SL, Beringer J. Black bear (Ursus americanus) functional resource selection relative to intraspecific competition and human risk. CAN J ZOOL 2017. [DOI: 10.1139/cjz-2016-0031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The spatial scales at which animals make behavioral trade-offs is assumed to relate to the scales at which factors most limiting resources and increasing mortality risk occur. We used global positioning system collar locations of 29 reproductive-age female black bears (Ursus americanus Pallas, 1780) in three states to assess resource selection relative to bear population-specific density, an index of vegetation productivity, riparian corridors, or two road classes of and within home ranges during spring–summer of 2009–2013. Female resource selection was best explained by functional responses to vegetation productivity across nearly all populations and spatial scales, which appeared to be influenced by variation in bear density (i.e., intraspecific competition). Behavioral trade-offs were greatest at the landscape scale, but except for vegetation productivity, were consistent for populations across spatial scales. Females across populations selected locations nearer to tertiary roads, but females in Michigan and Mississippi selected main roads and avoided riparian corridors, whereas females in Missouri did the opposite, suggesting population-level trade-offs between resource (e.g., food) acquisition and mortality risks (e.g., vehicle collisions). Our study emphasizes that female bear population-level resource selection can be influenced by multiple spatially dependent factors, and that scale-dependent functional behavior should be identified for management of bears across their range.
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Affiliation(s)
- Jared F. Duquette
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jerrold L. Belant
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Clay M. Wilton
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nicholas Fowler
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Brittany W. Waller
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Dean E. Beyer
- Michigan Department of Natural Resources, Wildlife Division, Marquette, MI 49855, USA
| | - Nathan J. Svoboda
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Stephanie L. Simek
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jeff Beringer
- Missouri Department of Conservation, Columbia, MO 65201, USA
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Sollmann R, Gardner B, Belant JL, Wilton CM, Beringer J. Habitat associations in a recolonizing, low‐density black bear population. Ecosphere 2016. [DOI: 10.1002/ecs2.1406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Rahel Sollmann
- Department of Wildlife, Fish and Conservation Biology University of California Davis 1088 Academic Surge, One Shields Avenue Davis California 95616 USA
| | - Beth Gardner
- School of Environmental and Forest Sciences University of Washington Seattle Washington 98195 USA
| | - Jerrold L. Belant
- Carnivore Ecology Laboratory Forest and Wildlife Research Center Mississippi State University Box 9690 Mississippi State Mississippi 39762 USA
| | - Clay M. Wilton
- Carnivore Ecology Laboratory Forest and Wildlife Research Center Mississippi State University Box 9690 Mississippi State Mississippi 39762 USA
| | - Jeff Beringer
- Missouri Department of Conservation 3500 E Gans Road Columbia Missouri 65202 USA
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25
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Wilton CM, Beringer J, Puckett EE, Eggert LS, Belant JL. Spatiotemporal factors affecting detection of black bears during noninvasive capture–recapture surveys. J Mammal 2015. [DOI: 10.1093/jmammal/gyv176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Accounting for low and heterogeneous detection probabilities in large mammal capture–recapture sampling designs is a persistent challenge. Our objective was to improve understanding of ecological and biological factors driving detection using multiple data sources from an American black bear ( Ursus americanus ) DNA hair trap study in south-central Missouri. We used Global Positioning System telemetry and remote camera data to examine how a bear’s distance to traps, probability of space use, sex-specific behavior, and temporal sampling frame affect detection probability and number of hair samples collected at hair traps. Regression analysis suggested that bear distance to nearest hair trap was the best predictor of detection probability and indicated that detection probability at encounter was 0.15 and declined to < 0.05 at nearest distances > 330 m from hair traps. From remote camera data, number of hair samples increased with number of visits, but the proportion of hair samples from known visits declined 39% from early June to early August. Bears appeared attracted to lured hair traps from close distances and we recommend a hair trap density of 1 trap/2.6 km 2 with spatial coverage that encompasses potentially large male home ranges. We recommend sampling during the late spring and early summer molting period to increase hair deposition rates.
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26
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Simek SL, Belant JL, Fan Z, Young BW, Leopold BD, Fleming J, Waller B. Source populations and roads affect American black bear recolonization. EUR J WILDLIFE RES 2015. [DOI: 10.1007/s10344-015-0933-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Puckett EE, Etter PD, Johnson EA, Eggert LS. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture. Mol Biol Evol 2015; 32:2338-50. [DOI: 10.1093/molbev/msv114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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28
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Murphy SM, Cox JJ, Clark JD, Augustine BC, Hast JT, Gibbs D, Strunk M, Dobey S. Rapid growth and genetic diversity retention in an isolated reintroduced black bear population in the central appalachians. J Wildl Manage 2015. [DOI: 10.1002/jwmg.886] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - John J. Cox
- Department of Forestry; University of Kentucky; 102 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - Joseph D. Clark
- United States Geological Survey; Southern Appalachian Research Branch; University of Tennessee; 274 Ellington Plant Sciences Building, Knoxville TN 37996 USA
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; 318 Cheatham Hall, Blacksburg VA 24061 USA
| | - John T. Hast
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building, Lexington KY 40546 USA
| | - Dan Gibbs
- Tennessee Wildlife Resources Agency; 3030 Wildlife Way, Morristown TN 37814 USA
| | - Michael Strunk
- Kentucky Department of Fish & Wildlife Resources; 11990 N Highway 27, Parkers Lake KY 42634 USA
| | - Steven Dobey
- Kentucky Department of Fish & Wildlife Resources; #1 Sportsman's Lane, Frankfort KY 40601 USA
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29
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Wilton CM, Puckett EE, Beringer J, Gardner B, Eggert LS, Belant JL. Trap array configuration influences estimates and precision of black bear density and abundance. PLoS One 2014; 9:e111257. [PMID: 25350557 PMCID: PMC4211732 DOI: 10.1371/journal.pone.0111257] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/29/2014] [Indexed: 11/20/2022] Open
Abstract
Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193-406) bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information needed to inform parameters with high precision.
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Affiliation(s)
- Clay M. Wilton
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS, United States of America
| | - Emily E. Puckett
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States of America
| | - Jeff Beringer
- Missouri Department of Conservation, Columbia, MO, United States of America
| | - Beth Gardner
- North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC, United States of America
| | - Lori S. Eggert
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States of America
| | - Jerrold L. Belant
- Carnivore Ecology Laboratory, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS, United States of America
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