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Jaito W, Singchat W, Patta C, Thatukan C, Kumnan N, Chalermwong P, Budi T, Panthum T, Wongloet W, Wattanadilokchatkun P, Thong T, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins. Genomics Inform 2024; 22:12. [PMID: 39085978 PMCID: PMC11292921 DOI: 10.1186/s44342-024-00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Over hundreds of years, cats have been domesticated and selectively bred, resulting in numerous pedigreed breeds expedited by recent cat shows and breeding associations. Concerns have been raised about the limited breeding options and the genetic implications of inbreeding, indicating challenges in maintaining genetic diversity and accurate identification in purebred cats. In this study, genetic variability and structure were examined in 5 Thai domestic cat breeds using 15 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequencing. In total, 184 samples representing the Wichien Maat (WCM), Suphalak (SL), Khao-Manee (KM), Korat (KR), and Konja (KJ) breeds were analyzed. High genetic diversity (Ho and He > 0.5) was observed in all breeds, and mtDNA analysis revealed two primary haplogroups (A and B) that were shared among all domestic cat breeds in Thailand and globally. However, minor differences were observed between Thai domestic cat breeds based on clustering analyses, in which a distinct genetic structure was observed in the WCM breed. This suggests that allele fixation for distinctive morphological traits has occurred in Thai domestic cat breeds that emerged in isolated regions with shared racial origins. Analysis of relationships among individuals within the breed revealed high identification efficiency in Thai domestic cat breeds (P(ID)sibs < 10-4). Additionally, diverse and effective individual identification can be ensured by optimizing marker efficiency by using only nine loci. This comprehensive genetic characterization provides valuable insights into conservation strategies and breeding practices for Thai domestic cat breeds.
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Grants
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- Higher Education for Industry Consortium (Hi–FI)
- International SciKU Branding (ISB), Faculty of Science, Kasetsart University
- High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA)
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
| | - Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
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2
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Molinari-Jobin A, Zimmermann F, Borel S, Le Grand L, Iannino E, Anders O, Belotti E, Bufka L, Ćirović D, Drouet-Hoguet N, Engleder T, Figura M, Fuxjäger C, Gregorova E, Heurich M, Idelberger S, Kubala J, Kusak J, Melovski D, Middelhoff TL, Mináriková T, Molinari P, Mouzon-Moyne L, Moyne G, Mysłajek RW, Nowak S, Ozolins J, Ryser A, Sanaja B, Shkvyria M, Sin T, Sindičić M, Slijepčević V, Stauffer C, Tám B, Trajce A, Volfová J, Wölfl S, Zlatanova D, Vogt K. Rehabilitation and release of orphaned Eurasian lynx (Lynx lynx) in Europe: Implications for management and conservation. PLoS One 2024; 19:e0297789. [PMID: 38452124 PMCID: PMC10919842 DOI: 10.1371/journal.pone.0297789] [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: 09/17/2023] [Accepted: 01/13/2024] [Indexed: 03/09/2024] Open
Abstract
Rehabilitation of injured or immature individuals has become an increasingly used conservation and management tool. However, scientific evaluation of rehabilitations is rare, raising concern about post-release welfare as well as the cost-effectiveness of spending scarce financial resources. Over the past 20 years, events of juvenile Eurasian lynx presumably orphaned have been observed in many European lynx populations. To guide the management of orphaned lynx, we documented survival, rehabilitation and fate after the release and evaluated the potential relevance of lynx orphan rehabilitation for population management and conservation implications. Data on 320 orphaned lynx was collected from 1975 to 2022 from 13 countries and nine populations. The majority of orphaned lynx (55%) were taken to rehabilitation centres or other enclosures. A total of 66 orphans were released back to nature. The portion of rehabilitated lynx who survived at least one year after release was 0.66. Release location was the best predictor for their survival. Of the 66 released lynx, ten have reproduced at least once (8 females and 2 males). Conservation implications of rehabilitation programmes include managing genetic diversity in small, isolated populations and reintroducing species to historical habitats. The lynx is a perfect model species as most reintroduced populations in Central Europe show significantly lower observed heterozygosity than most of the autochthonous populations, indicating that reintroduction bottlenecks, isolation and post-release management have long-term consequences on the genetic composition of populations. The release of translocated orphans could be a valuable contribution to Eurasian lynx conservation in Europe. It is recommended to release orphans at the distribution edge or in the frame of reintroduction projects instead of a release in the core area of a population where it is not necessary from a demographic and genetic point of view. Rehabilitation programmes can have conservation implications that extend far beyond individual welfare benefits.
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Affiliation(s)
| | - Fridolin Zimmermann
- Stiftung KORA, Ittigen, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Stéphanie Borel
- Vetsuisse Faculty, Departement of Infectious diseases and Pathobiology, Institute for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | | | | | - Ole Anders
- Harz National Park, Wernigerode, Germany
| | - Elisa Belotti
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Nature Protection, Šumava National Park Administration, Kašperské Hory, Czech Republic
| | - Ludek Bufka
- Department of Nature Protection, Šumava National Park Administration, Kašperské Hory, Czech Republic
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Thomas Engleder
- Green Heart of Europe, Lynx Project Austria Northwest, Haslach an der Mühl, Austria
| | - Michał Figura
- Association for Nature "Wolf", Twardorzeczka, Poland
- Faculty of Biology, Department of Ecology, Institute of Functional Biology and Ecology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | | | | | - Marco Heurich
- Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
- Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | | | - Jakub Kubala
- Faculty of Forestry, Department of Applied Zoology and Wildlife Management, Technical University in Zvolen, Zvolen, Slovakia
- DIANA–Carpathian Wildlife Research, Banská Bystrica, Slovakia
| | - Josip Kusak
- Faculty of Veterinary Medicine, Department Veterinary Biology, University of Zagreb, Zagreb, Croatia
| | - Dime Melovski
- Macedonian Ecological Society, Skopje, North Macedonia
| | | | - Tereza Mináriková
- ALKA Wildlife, Dačice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | | | | | - Gilles Moyne
- Centre Athenas Wildlife Rescue Center, L’étoile, France
| | - Robert W. Mysłajek
- Association for Nature "Wolf", Twardorzeczka, Poland
- Faculty of Biology, Department of Ecology, Institute of Functional Biology and Ecology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabina Nowak
- Association for Nature "Wolf", Twardorzeczka, Poland
- Faculty of Biology, Department of Ecology, Institute of Functional Biology and Ecology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Janis Ozolins
- Latvian State Forest Research Institute ‘‘Silava”, Salaspils, Latvia
| | | | - Bardh Sanaja
- Environmentally Responsible Action ERA, Peja, Kosovo
| | | | - Teodora Sin
- Association for the Conservation of Biological Diversity, Focsani, Romania
| | - Magda Sindičić
- Faculty of Veterinary Medicine, Department for Game and Wildlife, University of Zagreb, Zagreb, Croatia
| | - Vedran Slijepčević
- Department of Wildlife Management and Nature Protection, Karlovac University of Applied Sciences, Karlovac, Croatia
| | | | - Branislav Tám
- Bojnice Zoological Garden, Bojnice, Slovakia
- Faculty of Agrobiology and Food Resources, Department of Small Animal Science, Slovak University of Agriculture, Nitra, Slovakia
| | - Aleksander Trajce
- Protection and Preservation of Natural Environment in Albania, Tirana, Albania
| | - Josefa Volfová
- Department of Nature Protection, Šumava National Park Administration, Kašperské Hory, Czech Republic
- Friends of the Earth Czech Republic—Carnivore Conservation Programme, Olomouc, Czech Republic
| | - Sybille Wölfl
- WildLink Institute, Association Lynx Bavaria, Waldmünchen, Germany
| | - Diana Zlatanova
- Faculty of Biology, Department of Zoology and Anthropology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
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3
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Barrientos R, Vickers W, Longcore T, Abelson ES, Dellinger J, Waetjen DP, Fandos G, Shilling FM. Nearby night lighting, rather than sky glow, is associated with habitat selection by a top predator in human-dominated landscapes. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220370. [PMID: 37899023 PMCID: PMC10613539 DOI: 10.1098/rstb.2022.0370] [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: 03/31/2023] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Artificial light at night (ALAN) is increasing in extent and intensity across the globe. It has been shown to interfere with animal sensory systems, orientation and distribution, with the potential to cause significant ecological impacts. We analysed the locations of 102 mountain lions (Puma concolor) in a light-polluted region in California. We modelled their distribution relative to environmental and human-disturbance variables, including upward radiance (nearby lights), zenith brightness (sky glow) and natural illumination from moonlight. We found that mountain lion probability of presence was highly related to upward radiance, that is, related to lights within approximately 500 m. Despite a general pattern of avoidance of locations with high upward radiance, there were large differences in degree of avoidance among individuals. The amount of light from artificial sky glow was not influential when included together with upward radiance in the models, and illumination from moonlight was not influential at all. Our results suggest that changes in visibility associated with lunar cycles and sky glow are less important for mountain lions in their selection of light landscapes than avoiding potential interactions with humans represented by the presence of nearby lights on the ground. This article is part of the theme issue 'Light pollution in complex ecological systems'.
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Affiliation(s)
- Rafael Barrientos
- Road Ecology Lab, Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Universidad Complutense de Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - Winston Vickers
- Wildlife Health Center, University of California, 1089 Veterinary Medicine Dr, Davis, CA 95616, USA
| | - Travis Longcore
- Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Eric S. Abelson
- Department of Integrative Biology, University of Texas Austin, Austin, TX 78705, USA
| | - Justin Dellinger
- Large Carnivore Section, Wyoming Game and Fish Department, 260 Buena Vista Dr., Lander, WY 82520, USA
| | - David P. Waetjen
- Road Ecology Center, Institute of Transportation Studies, University of California, Davis, CA 95616, USA
| | - Guillermo Fandos
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Universidad Complutense de Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - Fraser M. Shilling
- Road Ecology Center, Institute of Transportation Studies, University of California, Davis, CA 95616, USA
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4
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Gilbertson MLJ, Hart SN, VanderWaal K, Onorato D, Cunningham M, VandeWoude S, Craft ME. Seasonal changes in network connectivity and consequences for pathogen transmission in a solitary carnivore. Sci Rep 2023; 13:17802. [PMID: 37853051 PMCID: PMC10584909 DOI: 10.1038/s41598-023-44815-y] [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: 04/22/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
Seasonal variation in habitat use and animal behavior can alter host contact patterns with potential consequences for pathogen transmission dynamics. The endangered Florida panther (Puma concolor coryi) has experienced significant pathogen-induced mortality and continues to be at risk of future epidemics. Prior research has found increased panther movement in Florida's dry versus wet seasons, which may affect panther population connectivity and seasonally increase potential pathogen transmission. Our objective was to determine if Florida panthers are more spatially connected in dry seasons relative to wet seasons, and test if identified connectivity differences resulted in divergent predicted epidemic dynamics. We leveraged extensive panther telemetry data to construct seasonal panther home range overlap networks over an 11 year period. We tested for differences in network connectivity, and used observed network characteristics to simulate transmission of a broad range of pathogens through dry and wet season networks. We found that panthers were more spatially connected in dry seasons than wet seasons. Further, these differences resulted in a trend toward larger and longer pathogen outbreaks when epidemics were initiated in the dry season. Our results demonstrate that seasonal variation in behavioral patterns-even among largely solitary species-can have substantial impacts on epidemic dynamics.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA.
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - S Niamh Hart
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - Dave Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, 34114, USA
| | - Mark Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
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5
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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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6
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Ash E, Cushman S, Kaszta Ż, Landguth E, Redford T, Macdonald DW. Female-biased introductions produce higher predicted population size and genetic diversity in simulations of a small, isolated tiger (Panthera tigris) population. Sci Rep 2023; 13:11199. [PMID: 37433862 DOI: 10.1038/s41598-023-36849-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/11/2023] [Indexed: 07/13/2023] Open
Abstract
Isolation of wildlife populations represents a key conservation challenge in the twenty-first century. This may necessitate consideration of translocations to ensure population viability. We investigated the potential population and genetic trajectory of a small, isolated tiger (Panthera tigris) population in Thailand's Dong Phayayen-Khao Yai forest complex across a range of scenarios. Using an individual-based, spatially-explicit population modelling approach, we simulate population and genetic trajectories and evaluate the relative impact of translocations from a related population. Population and genetic trajectories in our study were most sensitive to sex and number of individuals translocated and translocation frequency. Translocation of females produced consistently higher population, allelic richness, and heterozygosity compared to equal numbers of males. Despite population increases, declines in allelic richness and heterozygosity across simulations were stark, with simulations predicting a mean decline of allelic richness and heterozygosity of 46.5% and 53.5% without intervention, respectively. Translocations of four females every generation or every other generation were required to prevent substantial heterozygosity declines. While translocations could increase population size, they may fail to prevent long-term loss of genetic diversity in small populations unless applied frequently. This reinforces the importance of incorporating realistic processes of genetic inheritance and gene flow in modelling small populations.
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Affiliation(s)
- Eric Ash
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK.
| | - Samuel Cushman
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
| | - Żaneta Kaszta
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
- Department of Biological Sciences, Northern Arizona University, 617 S Beaver, Flagstaff, AZ, 86011, USA
| | - Erin Landguth
- School of Public and Community Health Sciences, Center for Population Health Research, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Tim Redford
- Freeland Foundation, Lumpini Ville Phahon-Sutthisan, 23/90 7th Floor, Bldg. B, Sutthisan Winitchai Rd., Samsen Nai, Phaya Thai, Bangkok, 10400, Thailand
| | - David W Macdonald
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
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7
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Conservation genomics reveals low connectivity among populations of threatened roseate terns (Sterna dougallii) in the Atlantic Basin. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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8
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Petersen C, Krahn A, Leippe M. The nematode Caenorhabditis elegans and diverse potential invertebrate vectors predominantly interact opportunistically. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1069056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Some small animals migrate with the help of other, more mobile animals (phoresy) to leave short-lived and resource-poor habitats. The nematode Caenorhabditis elegans lives in ephemeral habitats such as compost, but has also been found associated with various potential invertebrate vectors. Little research has been done to determine if C. elegans is directly attracted to these invertebrates. To determine whether C. elegans is attracted to compounds and volatile odorants of invertebrates, we conducted chemotaxis experiments with the isopods Porcellio scaber, Oniscus asellus, and Armadillidium sp. and with Lithobius sp. myriapods, Drosophila melanogaster fruit flies, and Arion sp. slugs as representatives of natural vectors. Because phoresy is an important escape strategy in nature, especially for dauer larvae of C. elegans, we examined the attraction of the natural C. elegans isolate MY2079 in addition to the laboratory-adapted strain N2 at the dauer and L4 stage. We found that DMSO washing solution of Lithobius sp. and the odor of live D. melanogaster attracted C. elegans N2 L4 larvae. Surprisingly, the natural isolate MY2079 was not attracted to any invertebrate during either the dauer or L4 life stages and both C. elegans strains were repelled by various compounds from O. asellus, P. scaber, Armadillidium sp., Lithobius sp., and Arion sp. feces. We hypothesize that this is due to defense chemicals released by the invertebrates. Although compounds from Lithobius sp. and D. melanogaster odorants were mildly attractive, the lack of attraction to most invertebrates suggests a predominantly opportunistic association between C. elegans and invertebrate vectors.
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Muller-Girard M, Fowles G, Duchamp J, Kouneski S, Mollohan C, Smyser TJ, Turner GG, Westrich B, Doyle JM. A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population. BMC Ecol Evol 2022; 22:137. [PMID: 36418951 PMCID: PMC9686018 DOI: 10.1186/s12862-022-02083-w] [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: 01/26/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. RESULTS We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. CONCLUSIONS Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
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Affiliation(s)
- Megan Muller-Girard
- grid.265122.00000 0001 0719 7561Department of Environmental Science and Studies, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | - Gretchen Fowles
- Endangered and Nongame Species Program, New Jersey DEP Fish and Wildlife, 1255 County Rd 629, Lebanon, NJ 08833 USA
| | - Joseph Duchamp
- grid.257427.10000000088740847Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, PA 15705-1081 USA
| | - Samantha Kouneski
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | | | - Timothy J. Smyser
- grid.413759.d0000 0001 0725 8379USDA-APHIS-WS National Wildlife Research Center, Fort Collins, CO USA
| | - Gregory G. Turner
- Pennsylvania Game Commission, 2001 Elmerton Avenue, Harrisburg, PA 17110 USA
| | - Bradford Westrich
- grid.448453.a0000 0004 1130 5264Indiana Department of Natural Resources, 5596 East State Road 46, Bloomington, IN 47401 USA
| | - Jacqueline M. Doyle
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
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10
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Gilbertson MLJ, Ketz AC, Hunsaker M, Jarosinski D, Ellarson W, Walsh DP, Storm DJ, Turner WC. Agricultural land use shapes dispersal in white-tailed deer (Odocoileus virginianus). MOVEMENT ECOLOGY 2022; 10:43. [PMID: 36289549 PMCID: PMC9608933 DOI: 10.1186/s40462-022-00342-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Dispersal is a fundamental process to animal population dynamics and gene flow. In white-tailed deer (WTD; Odocoileus virginianus), dispersal also presents an increasingly relevant risk for the spread of infectious diseases. Across their wide range, WTD dispersal is believed to be driven by a suite of landscape and host behavioral factors, but these can vary by region, season, and sex. Our objectives were to (1) identify dispersal events in Wisconsin WTD and determine drivers of dispersal rates and distances, and (2) determine how landscape features (e.g., rivers, roads) structure deer dispersal paths. METHODS We developed an algorithmic approach to detect dispersal events from GPS collar data for 590 juvenile, yearling, and adult WTD. We used statistical models to identify host and landscape drivers of dispersal rates and distances, including the role of agricultural land use, the traversability of the landscape, and potential interactions between deer. We then performed a step selection analysis to determine how landscape features such as agricultural land use, elevation, rivers, and roads affected deer dispersal paths. RESULTS Dispersal predominantly occurred in juvenile males, of which 64.2% dispersed, with dispersal events uncommon in other sex and age classes. Juvenile male dispersal probability was positively associated with the proportion of the natal range that was classified as agricultural land use, but only during the spring. Dispersal distances were typically short (median 5.77 km, range: 1.3-68.3 km), especially in the fall. Further, dispersal distances were positively associated with agricultural land use in potential dispersal paths but negatively associated with the number of proximate deer in the natal range. Lastly, we found that, during dispersal, juvenile males typically avoided agricultural land use but selected for areas near rivers and streams. CONCLUSION Land use-particularly agricultural-was a key driver of dispersal rates, distances, and paths in Wisconsin WTD. In addition, our results support the importance of deer social environments in shaping dispersal behavior. Our findings reinforce knowledge of dispersal ecology in WTD and how landscape factors-including major rivers, roads, and land-use patterns-structure host gene flow and potential pathogen transmission.
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Affiliation(s)
- Marie L J Gilbertson
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Dr, 53706, Madison, WI, USA.
| | - Alison C Ketz
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Dr, 53706, Madison, WI, USA
| | - Matthew Hunsaker
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Dr, 53706, Madison, WI, USA
| | - Dana Jarosinski
- Wisconsin Department of Natural Resources, 1500 N Johns St, 53533, Dodgeville, WI, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green St, 30602, Athens, GA, USA
| | - Wesley Ellarson
- Wisconsin Department of Natural Resources, 1500 N Johns St, 53533, Dodgeville, WI, USA
| | - Daniel P Walsh
- U.S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, 32 Campus Drive NS 205, 59812, Missoula, MT, USA
| | - Daniel J Storm
- Wisconsin Department of Natural Resources, 1300 West Clairemont Ave, 54701, Eau Claire, WI, USA
| | - Wendy C Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Dr, 53706, Madison, WI, USA
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11
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Assessing the success of the first cheetah reintroduction in Malawi. ORYX 2022. [DOI: 10.1017/s0030605321000788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
In an effort to restore parts of their historical geographical range, and in recognition of their ability to restore ecosystem functioning and of the financial benefits they can provide through ecotourism, large carnivores have been reintroduced in many protected areas from which they were previously extirpated. Similar to dispersing animals, translocated individuals often undertake long-distance exploratory movements before establishing home ranges. Post-release monitoring of reintroduced carnivores is common, but the mechanisms of population establishment are rarely examined, limiting our understanding of reintroduction success. We monitored survival and post-release movements of seven cheetahs Acinonyx jubatus reintroduced to Liwonde National Park, Malawi, to evaluate early population establishment. Exploratory phases post-release lasted 29–174 days. Duration of pre-release holding periods in the boma had no significant effect on daily distance moved. Males travelled significantly farther and established home ranges later than females. All cheetahs showed release site fidelity and all females birthed their first litter within 4 months of release. Within 2 years of reintroduction, the newly established population consisted of 14 cheetahs, with demographic attributes similar to those recorded in the source populations. Based on individual settlement, survival and reproduction rates, we deemed this reintroduction successful in re-establishing a breeding population of cheetahs in Liwonde. Our findings suggest the drivers of settlement and population establishment for reintroduced cheetahs are complex, highlighting the importance of assessing and reporting post-release monitoring data.
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12
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Lioy FG, Franculli D, Calandri S, Francescangeli D, Pecorella S, Gaudiano L, Filacorda S, Valvo ML, Nielsen CK, Anile S. Show me your tail, if you have one! Is inbreeding depression occurring in wildcats (Felis silvestris silvestris) from Italy? MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00627-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Development of a 95 SNP panel to individually genotype mountain lions (Puma concolor) for microfluidic and other genotyping platforms. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01255-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe mountain lion (Puma concolor) is one of the few remaining large predators in California, USA with density estimation from fecal genotypes becoming an essential component of conservation and management. In highly urbanized southern California, mountain lions are fragmented into small, inbred populations making proper marker selection critical for individual identification. We developed a panel of single nucleotide polymorphism (SNP) markers that can be used for consistent, routine mountain lion monitoring by different laboratories. We used a subset of existing Illumina HiSeq data for 104 individuals from throughout California to design a single, highly heterozygous multiplex of 95 SNPs for the Fluidigm platform. This panel confidently differentiates individual mountain lions, identifies sex, and discriminates mountain lions from bobcats. The panel performed well on fecal DNA extracts and based on design, had sufficient resolution to differentiate individual genotypes in even the population with lowest genetic diversity in southern California.
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14
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Gustafson KD, Gagne RB, Buchalski MR, Vickers TW, Riley SP, Sikich JA, Rudd JL, Dellinger JA, LaCava ME, Ernest HB. Multi‐population puma connectivity could restore genomic diversity to at‐risk coastal populations in California. Evol Appl 2021; 15:286-299. [PMID: 35233248 PMCID: PMC8867711 DOI: 10.1111/eva.13341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/25/2021] [Indexed: 12/01/2022] Open
Abstract
Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double‐digest restriction‐site associated DNA (ddRAD) sequencing to analyze 16,285 genome‐wide single‐nucleotide polymorphisms (SNPs) from 401 pumas sampled broadly across the state. Our analyses indicated support for 4–10 geographically nested, broad‐ to fine‐scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer‐scale genetic clusters, some of which exhibited fixed alleles and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at risk populations are typically nested within a broader‐scale group of interconnected populations that collectively retain high genetic diversity and heterogenous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state‐ and genome‐wide results are critically important for science‐based conservation and management practices. Our nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.
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Affiliation(s)
- Kyle D. Gustafson
- Arkansas State University Department of Biological Sciences Jonesboro 72401
| | - Roderick B. Gagne
- University of Pennsylvania School of Veterinary Medicine Department of Pathobiology Kennett Square Wildlife Futures Program PA USA
| | | | - T. Winston Vickers
- University of California ‐ Davis School of Veterinary Medicine Karen C. Drayer Wildlife Health Center Davis 95616
| | - Seth P.D. Riley
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jeff A. Sikich
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jaime L. Rudd
- California Department of Fish and Wildlife Rancho Cordova 95670
| | | | - Melanie E.F. LaCava
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
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15
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Cao L, Mulder HA, Liu H, Nielsen HM, S Rensen AC. Competitive gene flow does not necessarily maximize the genetic gain of genomic breeding programs in the presence of genotype-by-environment interaction. J Dairy Sci 2021; 104:8122-8134. [PMID: 33934864 DOI: 10.3168/jds.2020-19823] [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: 10/23/2020] [Accepted: 03/15/2021] [Indexed: 11/19/2022]
Abstract
National and international across-population selection is often recommended and fairly common in the current breeding practice of dairy cattle, with the primary aims to increase genetic gain and genetic variability. The aim of this study was to test the hypothesis that the strategy of truncation selection of sires across populations [i.e., competitive gene flow strategy (CGF)] may not necessarily maximize genetic gain in the long term in the presence of genotype-by-environment interaction (G×E). Two alternative strategies used to be compared with CGF were forced gene flow (FGF) strategies, with 10 or 50% of domestic dams forced to be mated with foreign sires (FGF10%, FGF50%). Two equal-size populations (Ndams = 1,000) that were selected for the same breeding goal trait (h2 = 0.3) under G×E correlation (rg) of either 0.9 or 0.8 were simulated to test these 3 different strategies. Each population first experienced either 5 or 20 differentiation generations (Gd), then 15 migration generations. Discrete generations were simulated for simplicity. Each population performed a within-population conventional breeding program during differentiation generations and the 3 across-population sire selection strategies based on joint genomic prediction during migration generations. The 4 Gd_rg combinations defined 4 different levels of differentiation degree between the 2 populations at the start of migration. The true rate of inbreeding over the last 10 migration generations in each scenario was constrained at 0.01 to provide a fair basis for comparison of genetic gain across scenarios. Results showed that CGF maximized the genetic gain after 15 migration generations in 5_0.9 combination only, the case of the lowest differentiation degree, with a superiority of 0.4% (0.04 genetic SD units) over the suboptimal strategy. While in 5_0.8, 20_0.9, and 20_0.8 combinations, 2 FGF strategies had a superiority in genetic gain of 2.3 to 12.5% (0.21-1.07 genetic SD units) over CGF after 15 migration generations, especially FGF50%. The superiority of FGF strategies over CGF was that they alleviated inbreeding, introduced new genetic variance in the early migration period, and improved accuracy in the entire migration period. Therefore, we concluded that CGF does not necessarily maximize the genetic gain of across-population genomic breeding programs given moderate G×E. The across-population selection strategy remains to be optimized to maximize genetic gain.
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Affiliation(s)
- L Cao
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark.
| | - H A Mulder
- Animal Breeding and Genomics Group, Wageningen University and Research, 6700 AH Wageningen, the Netherlands
| | - H Liu
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - H M Nielsen
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - A C S Rensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark; Danish Pig Research Centre, SEGES, Axeltorv 3, 1609 Copenhagen V, Denmark
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16
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Dellinger JA, Gustafson KD, Gammons DJ, Ernest HB, Torres SG. Minimum habitat thresholds required for conserving mountain lion genetic diversity. Ecol Evol 2020; 10:10687-10696. [PMID: 33072289 PMCID: PMC7548186 DOI: 10.1002/ece3.6723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
Jointly considering the ecology (e.g., habitat use) and genetics (e.g., population genetic structure and diversity) of a species can increase understanding of current conservation status and inform future management practices. Previous analyses indicate that mountain lion (Puma concolor) populations in California are genetically structured and exhibit extreme variation in population genetic diversity. Although human development may have fragmented gene flow, we hypothesized the quantity and quality of remaining habitat available would affect the genetic viability of each population. Our results indicate that area of suitable habitat, determined via a resource selection function derived using 843,500 location fixes from 263 radio‐collared mountain lions, is strongly and positively associated with population genetic diversity and viability metrics, particularly with effective population size. Our results suggested that contiguous habitat of ≥10,000 km2 may be sufficient to alleviate the negative effects of genetic drift and inbreeding, allowing mountain lion populations to maintain suitable effective population sizes. Areas occupied by five of the nine geographic–genetic mountain lion populations in California fell below this habitat threshold, and two (Santa Monica Area and Santa Ana) of those five populations lack connectivity to nearby populations. Enhancing ecological conditions by protection of greater areas of suitable habitat and facilitating positive evolutionary processes by increasing connectivity (e.g., road‐crossing structures) might promote persistence of small or isolated populations. The conservation status of suitable habitat also appeared to influence genetic diversity of populations. Thus, our results demonstrate that both the area and status (i.e., protected or unprotected) of suitable habitat influence the genetic viability of mountain lion populations.
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Affiliation(s)
| | - Kyle D Gustafson
- Department of Biological Sciences Arkansas State University Jonesboro Arkansas USA.,Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Daniel J Gammons
- California Department of Fish and Wildlife Sacramento California USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Steven G Torres
- California Department of Fish and Wildlife Sacramento California USA
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Gooley RM, Tamazian G, Castañeda‐Rico S, Murphy KR, Dobrynin P, Ferrie GM, Haefele H, Maldonado JE, Wildt DE, Pukazhenthi BS, Edwards CW, Koepfli K. Comparison of genomic diversity and structure of sable antelope ( Hippotragus niger) in zoos, conservation centers, and private ranches in North America. Evol Appl 2020; 13:2143-2154. [PMID: 32908610 PMCID: PMC7463370 DOI: 10.1111/eva.12976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022] Open
Abstract
As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, Hippotragus niger, have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal-to-no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single-nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic-based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ.
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Affiliation(s)
- Rebecca M. Gooley
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome BioinformaticsSaint Petersburg State UniversitySt. PetersburgRussian Federation
| | - Susette Castañeda‐Rico
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Katherine R. Murphy
- Laboratories of Analytical BiologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
| | - Pavel Dobrynin
- Computer Technologies LaboratoryITMO UniversitySt. PetersburgRussian Federation
| | - Gina M. Ferrie
- Animals, Science and EnvironmentDisney’s Animal KingdomLake Buena VistaFLUSA
| | | | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - David E. Wildt
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Cody W. Edwards
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Department of BiologyGeorge Mason UniversityFairfaxVAUSA
| | - Klaus‐Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
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18
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Valladares-Gómez A, Celis-Diez JL, Sepúlveda-Rodríguez C, Inostroza-Michael O, Hernández CE, Palma RE. Genetic Diversity, Population Structure, and Migration Scenarios of the Marsupial "Monito del Monte" in South-Central Chile. J Hered 2020; 110:651-661. [PMID: 31420661 DOI: 10.1093/jhered/esz049] [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: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023] Open
Abstract
In this study, we quantified the 3 pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring, and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte," in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient, and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least 2 consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the 2 genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred 1) from the Southern cluster to the Northern cluster and 2) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
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Affiliation(s)
- Alejandro Valladares-Gómez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Casilla 4-D, Quillota, Chile
| | - Constanza Sepúlveda-Rodríguez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Oscar Inostroza-Michael
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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19
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Zeller KA, Wattles DW, Conlee L, Destefano S. Response of female black bears to a high‐density road network and identification of long‐term road mitigation sites. Anim Conserv 2020. [DOI: 10.1111/acv.12621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. A. Zeller
- Massachusetts Cooperative Fish and Wildlife Research Unit University of Massachusetts Amherst MA USA
| | - D. W. Wattles
- Massachusetts Division of Fisheries and Wildlife Westborough MA USA
| | - L. Conlee
- Missouri Department of Conservation Jefferson MO USA
| | - S. Destefano
- Massachusetts Cooperative Fish and Wildlife Research Unit University of Massachusetts Amherst MA USA
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20
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LaCava MEF, Gagne RB, Stowell SML, Gustafson KD, Buerkle CA, Knox L, Ernest HB. Pronghorn population genomics show connectivity in the core of their range. J Mammal 2020; 101:1061-1071. [PMID: 33100929 DOI: 10.1093/jmammal/gyaa054] [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: 10/25/2019] [Accepted: 04/21/2020] [Indexed: 01/17/2023] Open
Abstract
Preserving connectivity in the core of a species' range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that pronghorn populations declined significantly in the early 1900s, have only partially recovered, and are experiencing modern threats from landscape modification, conserving connectivity among populations is important for their long-term persistence in North America. To assess the genetic structure and diversity of pronghorn in the core of their range, we genotyped 4,949 genome-wide single-nucleotide polymorphisms and 11 microsatellites from 398 individuals throughout the state of Wyoming. We found no evidence of genetic subdivision and minimal evidence of isolation by distance despite a range that spans hundreds of kilometers, multiple mountain ranges, and three interstate highways. In addition, a rare variant analysis using putatively recent mutations found no genetic division between pronghorn on either side of a major highway corridor. Although we found no evidence that barriers to daily and seasonal movements of pronghorn impede gene flow, we suggest periodic monitoring of genetic structure and diversity as a part of management strategies to identify changes in connectivity.
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Affiliation(s)
- Melanie E F LaCava
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Roderick B Gagne
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Sierra M Love Stowell
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Kyle D Gustafson
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Biology and Environmental Health, Missouri Southern State University, Joplin, MO, USA
| | - C Alex Buerkle
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Lee Knox
- Wyoming Game and Fish Department, Laramie, WY, USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
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21
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Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O'Brien SJ, O'Connell B, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villela PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun 2019; 10:4769. [PMID: 31628318 PMCID: PMC6800433 DOI: 10.1038/s41467-019-12741-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 11/09/2022] Open
Abstract
Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Ashley Byrne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Luiz Lehmann Coutinho
- Laboratório de Biotecnologia Animal, Departamento de Zootecnia, ESALQ, Universidade de São Paulo, Caixa Postal 09, Piracicaba, SP, 13418-900, Brazil
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden
| | - Henrique V Figueiró
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20002, USA.,Walter Reed Biosystematics Unit, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA
| | - Heather J Milne
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41 Sredniy Prospekt, Saint Petersburg, 199004, Russia
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Road, Naples, FL, 34114, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Jeff A Sikich
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY, 82190, USA
| | | | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Eduardo Eizirik
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Christopher C Wilmers
- Environmental Studies Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA. .,Howard Hughes Medical Institute, 400 Jones Bridge Road, Chevy Chase, MD, 20815, USA.
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22
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Hasselgren M, Angerbjörn A, Eide NE, Erlandsson R, Flagstad Ø, Landa A, Wallén J, Norén K. Genetic rescue in an inbred Arctic fox ( Vulpes lagopus) population. Proc Biol Sci 2019; 285:rspb.2017.2814. [PMID: 29593110 DOI: 10.1098/rspb.2017.2814] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox (Vulpes lagopus), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient (f), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness.
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Affiliation(s)
- Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nina E Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Rasmus Erlandsson
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | | | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Johan Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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23
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Benson JF, Mahoney PJ, Vickers TW, Sikich JA, Beier P, Riley SPD, Ernest HB, Boyce WM. Extinction vortex dynamics of top predators isolated by urbanization. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01868. [PMID: 30892753 DOI: 10.1002/eap.1868] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 05/18/2023]
Abstract
Extinction risk is elevated in small, isolated populations due to demographic and genetic interactions. Therefore, it is critical to model these processes realistically in population viability analyses (PVA) to inform local management and contribute to a greater understanding of mechanisms within the extinction vortex. We conducted PVA's for two small mountain lion populations isolated by urbanization in southern California to predict population growth, extinction probability, and loss of genetic diversity with empirical data. Specifically, we (1) provide the first PVA for isolated mountain lions in the Santa Ana Mountains (SAM) that considers both demographic and genetic risk factors and (2) test the hypothesis that variation in abundance and mortality between the SAM and Santa Monica Mountains (SMM) result in differences in population growth, loss of heterozygosity, and extinction probability. Our models predicted 16-21% probability of local extinction in the SAM due purely to demographic processes over 50 yr with current low levels or no immigration. Our models also predicted that genetic diversity will further erode in the SAM such that concern regarding inbreeding depression is warranted unless gene flow is increased, and that if inbreeding depression occurs, rapid local extinction will be highly likely. Dynamics of the two populations were broadly similar, but they also exhibited differences driven by larger population size and higher mortality in the SAM. Density-independent scenarios predicted a rapidly increasing population in the SMM, whereas growth potential did not differ from a stable trend in the SAM. Demographic extinction probability and loss of heterozygosity were greater in the SMM for density-dependent scenarios without immigration. However, higher levels of immigration had stronger, positive influences on both demographic viability and retention of genetic diversity in the SMM driven by lower abundance and higher adult survival. Our results elucidate demographic and genetic threats to small populations within the extinction vortex, and how these vary relative to demographic structure. Importantly, simulating seemingly attainable increases in connectivity was sufficient to greatly reduce extinction probability. Our work highlights that conservation of large carnivores is achievable within urbanized landscapes, but requires land protection, connectivity, and strategies to promote coexistence with humans.
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Affiliation(s)
- John F Benson
- School of Natural Resources, University of Nebraska, Lincoln, Nebraska, 68583, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
| | - Peter J Mahoney
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - T Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
| | - Jeff A Sikich
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Paul Beier
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Seth P D Riley
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Holly B Ernest
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, 82071, USA
| | - Walter M Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
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24
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Grueber CE, Fox S, McLennan EA, Gooley RM, Pemberton D, Hogg CJ, Belov K. Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild. Evol Appl 2019; 12:280-291. [PMID: 30697339 PMCID: PMC6346650 DOI: 10.1111/eva.12715] [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: 02/27/2018] [Revised: 08/15/2018] [Accepted: 09/04/2018] [Indexed: 12/18/2022] Open
Abstract
For bottlenecked populations of threatened species, supplementation often leads to improved population metrics (genetic rescue), provided that guidelines can be followed to avoid negative outcomes. In cases where no "ideal" source populations exist, or there are other complicating factors such as prevailing disease, the benefit of supplementation becomes uncertain. Bringing multiple data and analysis types together to plan genetic management activities can help. Here, we consider three populations of Tasmanian devil, Sarcophilus harrisii, as candidates for genetic rescue. Since 1996, devil populations have been severely impacted by devil facial tumour disease (DFTD), causing significant population decline and fragmentation. Like many threatened species, the key threatening process for devils cannot currently be fully mitigated, so species management requires a multifaceted approach. We examined diversity of 31 putatively neutral and 11 MHC-linked microsatellite loci of three remnant wild devil populations (one sampled at two time-points), alongside computational diversity projections, parameterized by field data from DFTD-present and DFTD-absent sites. Results showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade. Stochastic simulations projected further diversity losses. For a given population size, the effects of DFTD on population demography (including earlier age at death and increased female productivity) did not impact diversity retention, which was largely driven by final population size. Population sizes ≥500 (depending on the number of founders) were necessary for maintaining diversity in otherwise unmanaged populations, even if DFTD is present. Models indicated that smaller populations could maintain diversity with ongoing immigration. Taken together, our results illustrate how multiple analysis types can be combined to address complex population genetic challenges.
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Affiliation(s)
- Catherine E. Grueber
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- San Diego Zoo GlobalSan DiegoCalifornia
| | - Samantha Fox
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
- Toledo ZooToledoOhio
| | - Elspeth A. McLennan
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Rebecca M. Gooley
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - David Pemberton
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
| | - Carolyn J. Hogg
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Zoo and Aquarium Association AustralasiaMosmanNew South WalesAustralia
| | - Katherine Belov
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
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25
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Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1125-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Evidence of Recent Fine-Scale Population Structuring in South American Puma concolor. DIVERSITY 2017. [DOI: 10.3390/d9040044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Multi-level, multi-scale resource selection functions and resistance surfaces for conservation planning: Pumas as a case study. PLoS One 2017; 12:e0179570. [PMID: 28609466 PMCID: PMC5469479 DOI: 10.1371/journal.pone.0179570] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/31/2017] [Indexed: 11/19/2022] Open
Abstract
The importance of examining multiple hierarchical levels when modeling resource use for wildlife has been acknowledged for decades. Multi-level resource selection functions have recently been promoted as a method to synthesize resource use across nested organizational levels into a single predictive surface. Analyzing multiple scales of selection within each hierarchical level further strengthens multi-level resource selection functions. We extend this multi-level, multi-scale framework to modeling resistance for wildlife by combining multi-scale resistance surfaces from two data types, genetic and movement. Resistance estimation has typically been conducted with one of these data types, or compared between the two. However, we contend it is not an either/or issue and that resistance may be better-modeled using a combination of resistance surfaces that represent processes at different hierarchical levels. Resistance surfaces estimated from genetic data characterize temporally broad-scale dispersal and successful breeding over generations, whereas resistance surfaces estimated from movement data represent fine-scale travel and contextualized movement decisions. We used telemetry and genetic data from a long-term study on pumas (Puma concolor) in a highly developed landscape in southern California to develop a multi-level, multi-scale resource selection function and a multi-level, multi-scale resistance surface. We used these multi-level, multi-scale surfaces to identify resource use patches and resistant kernel corridors. Across levels, we found puma avoided urban, agricultural areas, and roads and preferred riparian areas and more rugged terrain. For other landscape features, selection differed among levels, as did the scales of selection for each feature. With these results, we developed a conservation plan for one of the most isolated puma populations in the U.S. Our approach captured a wide spectrum of ecological relationships for a population, resulted in effective conservation planning, and can be readily applied to other wildlife species.
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28
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Gustafson KD, Vickers TW, Boyce WM, Ernest HB. A single migrant enhances the genetic diversity of an inbred puma population. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170115. [PMID: 28573020 PMCID: PMC5451821 DOI: 10.1098/rsos.170115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/25/2017] [Indexed: 05/11/2023]
Abstract
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier. Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
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Affiliation(s)
- Kyle D. Gustafson
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
| | - T. Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Walter M. Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
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