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Vissia S, Fattebert J, van Langevelde F. Leopard density and interspecific spatiotemporal interactions in a hyena-dominated landscape. Ecol Evol 2022; 12:e9365. [PMID: 36225822 PMCID: PMC9534747 DOI: 10.1002/ece3.9365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/18/2022] [Accepted: 09/13/2022] [Indexed: 11/12/2022] Open
Abstract
Scavenging is widespread in the carnivore guild and can greatly impact food web structures and population dynamics by either facilitation or suppression of sympatric carnivores. Due to habitat loss and fragmentation, carnivores are increasingly forced into close sympatry, possibly resulting in more interactions such as kleptoparasitism and competition. In this paper, we investigate the potential for these interactions when carnivore densities are high. A camera trap survey was conducted in central Tuli, Botswana, to examine leopard Panthera pardus densities and spatiotemporal activity patterns of leopard and its most important competitors' brown hyena Parahyaena brunnea and spotted hyena Crocuta crocuta. Spatial capture-recapture models estimated leopard population density to be 12.7 ± 3.2 leopard/100 km2, which is one of the highest leopard densities in Africa. Time-to-event analyses showed both brown hyena and spotted hyena were observed more frequently before and after a leopard observation than expected by chance. The high spatiotemporal overlap of both hyena species with leopard is possibly explained by leopard providing scavenging opportunities for brown hyena and spotted hyena. Our results suggest that central Tuli is a high-density leopard area, despite possible intense kleptoparasitism and competition.
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Affiliation(s)
- Sander Vissia
- Wildlife Ecology and Conservation GroupWageningen UniversityWageningenThe Netherlands
| | - Julien Fattebert
- School of Life Sciences, Westville CampusUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Frank van Langevelde
- Wildlife Ecology and Conservation GroupWageningen UniversityWageningenThe Netherlands,School of Life Sciences, Westville CampusUniversity of KwaZulu‐NatalDurbanSouth Africa
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2
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Henson LH, Service C, Stronen AV, Moody J, Housty W, Reece D, vonHoldt B, Darimont CT. Genetic evidence to inform management of rare genetic variants and gene flow: Balancing the conservation of the rare “Spirit bear” allele and population genetic diversity across a complex landscape. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lauren H. Henson
- Department of Geography University of Victoria Victoria British Columbia Canada
- Raincoast Conservation Foundation Sidney British Columbia Canada
| | - Christina Service
- Kitasoo/Xai'xais Stewardship Authority Klemtu British Columbia Canada
| | - Astrid Vik Stronen
- Department of Biology University of Ljubljana Ljubljana Slovenia
- Department of Biotechnology and Life Sciences Insubria University Varese Italy
| | - Jason Moody
- Nuxalk Stewardship Office Bella Coola British Columbia Canada
| | - William Housty
- Heiltsuk Integrated Resource Management Department Bella Coola British Columbia Canada
| | - Donald Reece
- Gitga'at Oceans and Lands Department Hartley Bay British Columbia Canada
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey USA
| | - Chris T. Darimont
- Department of Geography University of Victoria Victoria British Columbia Canada
- Raincoast Conservation Foundation Sidney British Columbia Canada
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3
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GuibingaMickala A, Weber A, Ntie S, Gahlot P, Lehmann D, Mickala P, Abernethy K, Anthony N. Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lopé National Park, Gabon using a non-invasive genetic approach. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01458-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Puckett EE, Davis IS. Spatial patterns of genetic diversity in eight bear (Ursidae) species. URSUS 2021. [DOI: 10.2192/ursus-d-20-00029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Isis S. Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
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5
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Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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6
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Spatial proximity moderates genotype uncertainty in genetic tagging studies. Proc Natl Acad Sci U S A 2020; 117:17903-17912. [PMID: 32661176 DOI: 10.1073/pnas.2000247117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accelerating declines of an increasing number of animal populations worldwide necessitate methods to reliably and efficiently estimate demographic parameters such as population density and trajectory. Standard methods for estimating demographic parameters from noninvasive genetic samples are inefficient because lower-quality samples cannot be used, and they assume individuals are identified without error. We introduce the genotype spatial partial identity model (gSPIM), which integrates a genetic classification model with a spatial population model to combine both spatial and genetic information, thus reducing genotype uncertainty and increasing the precision of demographic parameter estimates. We apply this model to data from a study of fishers (Pekania pennanti) in which 37% of hair samples were originally discarded because of uncertainty in individual identity. The gSPIM density estimate using all collected samples was 25% more precise than the original density estimate, and the model identified and corrected three errors in the original individual identity assignments. A simulation study demonstrated that our model increased the accuracy and precision of density estimates 63 and 42%, respectively, using three replicated assignments (e.g., PCRs for microsatellites) per genetic sample. Further, the simulations showed that the gSPIM model parameters are identifiable with only one replicated assignment per sample and that accuracy and precision are relatively insensitive to the number of replicated assignments for high-quality samples. Current genotyping protocols devote the majority of resources to replicating and confirming high-quality samples, but when using the gSPIM, genotyping protocols could be more efficient by devoting more resources to low-quality samples.
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7
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Barrueto M, Sawaya M, Clevenger A. Low wolverine (Gulo gulo) density in a national park complex of the Canadian Rocky Mountains. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2019-0165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Large carnivores are sensitive to human-caused extirpation due to large home ranges, low population densities, and low reproductive rates. Protected areas help maintain populations by acting as sources, but human-caused mortality, habitat displacement, and edge effects occurring at protected area boundaries may reduce that function. The national parks Banff, Yoho, and Kootenay in the Canadian Rocky Mountains are refugia for large carnivores, including wolverines (Gulo gulo (Linnaeus, 1758)). Despite growing conservation concern, empirical baseline population data for wolverines remain scarce throughout their range, including most of Canada. We hypothesized (i) that in these national parks, wolverine density matched values expected for high-quality habitat, and (ii) that edge effects decreased density towards park boundaries. We conducted systematic non-invasive genetic sampling surveys covering >7000 km2 (2011 and 2013). Using spatial capture–recapture models, we estimated mean (±SE) female (1.5 ± 0.3 and 1.4 ± 0.3 wolverine/1000 km2), male (1.8 ± 0.4 and 1.5 ± 0.3 wolverine/1000 km2), and combined (3.3 ± 0.5 and 3.0 ± 0.4 wolverine/1000 km2) densities for 2011 and 2013, respectively. These estimates were lower than predictions based on density extrapolation from nearby high-quality habitat, and density decreased towards park boundaries. To benefit the population, we recommend creating buffer zones around parks that protect female habitat and prohibit harvest.
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Affiliation(s)
- M. Barrueto
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - M.A. Sawaya
- Sinopah Wildlife Research Associates, 127 North Higgins, Suite 310, Missoula, MT 59802, USA
| | - A.P. Clevenger
- Western Transportation Institute, Montana State University, P.O. Box 174250, Bozeman, MT 59717-4250, USA
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8
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Affiliation(s)
- Michael J. Hooker
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Bobby T. Bond
- Georgia Department of Natural Resources, Wildlife Resources Division, Fort Valley, GA 31030, USA
| | - Michael J. Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
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9
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Cross TB, Schwartz MK, Naugle DE, Fedy BC, Row JR, Oyler‐McCance SJ. The genetic network of greater sage-grouse: Range-wide identification of keystone hubs of connectivity. Ecol Evol 2018; 8:5394-5412. [PMID: 29938061 PMCID: PMC6010832 DOI: 10.1002/ece3.4056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/02/2022] Open
Abstract
Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage-grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on spatially discrete leks that must remain connected by genetic exchange for population persistence. We genotyped 5,950 individuals from 1,200 greater sage-grouse leks distributed across the entire species' geographic range. We found a small-world network composed of 458 nodes connected by 14,481 edges. This network was composed of hubs-that is, nodes facilitating gene flow across the network-and spokes-that is, nodes where connectivity is served by hubs. It is within these hubs that the greatest genetic diversity was housed. Using indices of network centrality, we identified hub nodes of greatest conservation importance. We also identified keystone nodes with elevated centrality despite low local population size. Hub and keystone nodes were found across the entire species' contiguous range, although nodes with elevated importance to network-wide connectivity were found more central: especially in northeastern, central, and southwestern Wyoming and eastern Idaho. Nodes among which genes are most readily exchanged were mostly located in Montana and northern Wyoming, as well as Utah and eastern Nevada. The loss of hub or keystone nodes could lead to the disintegration of the network into smaller, isolated subnetworks. Protecting both hub nodes and keystone nodes will conserve genetic diversity and should maintain network connections to ensure a resilient and viable population over time. Our analysis shows that network models can be used to model gene flow, offering insights into its pattern and process, with application to prioritizing landscapes for conservation.
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Affiliation(s)
- Todd B. Cross
- USDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationMissoulaMontana
- College of Forestry and ConservationUniversity of MontanaMissoulaMontana
| | - Michael K. Schwartz
- USDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationMissoulaMontana
| | - David E. Naugle
- College of Forestry and ConservationUniversity of MontanaMissoulaMontana
| | - Brad C. Fedy
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
| | - Jeffrey R. Row
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
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10
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Green DS, Matthews SM, Swiers RC, Callas RL, Scott Yaeger J, Farber SL, Schwartz MK, Powell RA. Dynamic occupancy modelling reveals a hierarchy of competition among fishers, grey foxes and ringtails. J Anim Ecol 2018; 87:813-824. [DOI: 10.1111/1365-2656.12791] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 11/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Green
- Institute for Natural Resources Oregon State University Corvallis OR USA
| | - Sean M. Matthews
- Institute for Natural Resources Oregon State University Corvallis OR USA
| | - Robert C. Swiers
- Department of Applied Ecology North Carolina State University Raleigh NC USA
| | | | | | | | | | - Roger A. Powell
- Department of Applied Ecology North Carolina State University Raleigh NC USA
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11
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Nakamura M, Godinho R, Rio-Maior H, Roque S, Kaliontzopoulou A, Bernardo J, Castro D, Lopes S, Petrucci-Fonseca F, Álvares F. Evaluating the predictive power of field variables for species and individual molecular identification on wolf noninvasive samples. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1112-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Slauson KM, Zielinski WJ, Schwartz MK. Ski areas affect Pacific marten movement, habitat use, and density. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Keith M. Slauson
- U.S. Department of Agriculture; Forest Service; Pacific Southwest Research Station; 1700 Bayview Avenue Arcata CA 95521 USA
| | - William J. Zielinski
- U.S. Department of Agriculture; Forest Service; Pacific Southwest Research Station; 1700 Bayview Avenue Arcata CA 95521 USA
| | - Michael K. Schwartz
- U.S. Department of Agriculture; Forest Service; Rocky Mountain Research Station; 800 E. Beckwith Avenue Missoula MT 59801 USA
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13
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Brazeal JL, Weist T, Sacks BN. Noninvasive genetic spatial capture-recapture for estimating deer population abundance. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21236] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jennifer L. Brazeal
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Terri Weist
- California Department of Fish and Wildlife; North Central Region; 1701 Nimbus Road Rancho Cordova CA 95670 USA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; Department of Population Health and Reproduction; University of California, Davis; One Shields Avenue/Old Davis Road Davis CA 95616 USA
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14
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Sun CC, Fuller AK, Hare MP, Hurst JE. Evaluating population expansion of black bears using spatial capture-recapture. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21248] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Catherine C. Sun
- New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Angela K. Fuller
- U.S. Geological Survey; New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Matthew P. Hare
- Department of Natural Resources; Cornell University; Ithaca NY 14853 USA
| | - Jeremy E. Hurst
- New York State Department of Environmental Conservation; Albany NY 12233 USA
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15
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Rothstein AP, McLaughlin R, Acevedo-Gutiérrez A, Schwarz D. wisepair: a computer program for individual matching in genetic tracking studies. Mol Ecol Resour 2016; 17:267-277. [PMID: 27488501 DOI: 10.1111/1755-0998.12590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/23/2016] [Accepted: 07/11/2016] [Indexed: 11/29/2022]
Abstract
Individual-based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A 'permanent' genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python-based computer-modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without-reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.
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Affiliation(s)
- Andrew P Rothstein
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Ryan McLaughlin
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | | | - Dietmar Schwarz
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
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16
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Tumendemberel O, Proctor M, Reynolds H, Boulanger J, Luvsamjamba A, Tserenbataa T, Batmunkh M, Craighead D, Yanjin N, Paetkau D. Gobi bear abundance and inter-oases movements, Gobi Desert, Mongolia. URSUS 2015. [DOI: 10.2192/ursus-d-15-00001.1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Odbayar Tumendemberel
- Institute of General and Experimental Biology, Mongolian Academy of Sciences, Jukov Avenue, Ulaanbaatar 51, Mongolia
| | - Michael Proctor
- Birchdale Ecological, P.O. Box 606, Kaslo, BC V0G 1M0, Canada
| | - Harry Reynolds
- Gobi Bear Fund, Gobi Bear Project, P.O. Box 80843, Fairbanks, AK 99708, USA
| | - John Boulanger
- Integrated Ecological Research, 924 Innes, Nelson, BC V1L 5T2, Canada
| | - Amgalan Luvsamjamba
- Institute of General and Experimental Biology, Mongolian Academy of Sciences, Jukov Avenue, Ulaanbaatar 51, Mongolia
| | - Tuya Tserenbataa
- United Nations Development Program, 202 ESC Center, 2B Building, Zaluuchuud Avenue, 6 Khoroo, Sukbaatar District, Ulaanbaatar, Mongolia
| | | | - Derek Craighead
- Craighead Beringia South, P.O. Box 147, Kelly, WY 83011, USA
| | | | - David Paetkau
- Wildlife Genetics International, 200-182 Baker Street, P.O. Box 274, Nelson BC V1L 5P9, Canada
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17
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Assessing temporal genetic variation in a cougar population: influence of harvest and neighboring populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0790-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Smith O, Wang J. When can noninvasive samples provide sufficient information in conservation genetics studies? Mol Ecol Resour 2014; 14:1011-23. [PMID: 24620908 DOI: 10.1111/1755-0998.12250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
Noninvasive sampling, of faeces and hair for example, has enabled many genetic studies of wildlife populations. However, two prevailing problems common to these studies are small sample sizes and high genotyping errors. The first problem stems from the difficulty in collecting noninvasive samples, particularly from populations of rare or elusive species, and the second is caused by the low quantity and quality of DNA extracted from a noninvasive sample. A common question is therefore whether noninvasive sampling provides sufficient information for the analyses commonly conducted in conservation genetics studies. Here, we conducted a simulation study to investigate the effect of small sample sizes and genotyping errors on the precision and accuracy of the most commonly estimated genetic parameters. Our results indicate that small sample sizes cause little bias in measures of expected heterozygosity, pairwise FST and population structure, but a large downward bias in estimates of allelic diversity. Allelic dropouts and false alleles had a much smaller effect than missing data, which effectively reduces sample size further. Overall, reasonable estimates of genetic variation and population subdivision are obtainable from noninvasive samples as long as error rates are kept below a frequency of 0.2. Similarly, unbiased estimates of population clustering can be made with genotyping error rates below 0.5 when the populations are highly differentiated. These results provide a useful guide for researchers faced with studying the conservation genetics of small, endangered populations from noninvasive samples.
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Affiliation(s)
- O Smith
- Division of Biology, Imperial College London, Silwood Park, Ascot, Berks, London, SL5 7PY, UK; Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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19
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Lampa S, Henle K, Klenke R, Hoehn M, Gruber B. How to overcome genotyping errors in non-invasive genetic mark-recapture population size estimation-A review of available methods illustrated by a case study. J Wildl Manage 2013. [DOI: 10.1002/jwmg.604] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Simone Lampa
- UFZ-Helmholtz Centre for Environmental Research; Department of Conservation Biology; Permoserstrasse 15 04318 Leipzig Germany
- Institute of Ecology; Friedrich Schiller University Jena; Dornburger Strasse 159 07743 Jena Germany
| | - Klaus Henle
- UFZ-Helmholtz Centre for Environmental Research; Department of Conservation Biology; Permoserstrasse 15 04318 Leipzig Germany
| | - Reinhard Klenke
- UFZ-Helmholtz Centre for Environmental Research; Department of Conservation Biology; Permoserstrasse 15 04318 Leipzig Germany
| | - Marion Hoehn
- UFZ-Helmholtz Centre for Environmental Research; Department of Conservation Biology; Permoserstrasse 15 04318 Leipzig Germany
| | - Bernd Gruber
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures; University of Canberra; ACT 2601 Canberra Australia
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20
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McCall BS, Mitchell MS, Schwartz MK, Hayden J, Cushman SA, Zager P, Kasworm WF. Combined use of mark-recapture and genetic analyses reveals response of a black bear population to changes in food productivity. J Wildl Manage 2013. [DOI: 10.1002/jwmg.617] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Barbara S. McCall
- Montana Cooperative Wildlife Research Unit; University of Montana; Natural Sciences Building Room 205 Missoula MT 59812 USA
| | - Michael S. Mitchell
- U.S. Geological Survey; Montana Cooperative Wildlife Research Unit; University of Montana; Natural Sciences Building Room 205 Missoula MT 59812 USA
| | - Michael K. Schwartz
- U.S. Forest Service Rocky Mountain Research Station; 800 East Beckwith Missoula MT 59801 USA
| | - Jim Hayden
- Idaho Department of Fish and Game; 2885 Kathleen Avenue Coeur d'Alene ID 83815 USA
| | - Samuel A. Cushman
- U.S. Forest Service Rocky Mountain Research Station; 2500 S. Pine Knoll Drive Flagstaff AZ 86001 USA
| | - Pete Zager
- Idaho Department of Fish and Game; 3316 16th Street Lewiston ID 83501 USA
| | - Wayne F. Kasworm
- US Fish and Wildlife Service; 475 Fish Hatchery Road Libby MT 59923 USA
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Zielinski WJ, Schlexer FV, George TL, Pilgrim KL, Schwartz MK. Estimating Abundance and Survival in the Endangered Point Arena Mountain Beaver Using Noninvasive Genetic Methods. NORTHWEST SCIENCE 2013. [DOI: 10.3955/046.087.0205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sharma S, Dutta T, Maldonado JE, Wood TC, Panwar HS, Seidensticker J. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India. Ecol Evol 2012; 3:48-60. [PMID: 23403813 PMCID: PMC3568842 DOI: 10.1002/ece3.432] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/21/2012] [Accepted: 10/29/2012] [Indexed: 01/28/2023] Open
Abstract
We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.
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Affiliation(s)
- Sandeep Sharma
- Smithsonian Conservation Biology Institute, National Zoological Park Washington, District of Columbia, 20013-7012 ; Environmental Science & Policy Department, George Mason University Fairfax, Virginia, 22030-4444
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Zielinski WJ, Schlexer FV, Parks SA, Pilgrim KL, Schwartz MK. Small geographic range but not panmictic: how forests structure the endangered Point Arena mountain beaver (Aplodontia rufa nigra). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0387-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Drewry JM, Van Manen FT, Ruth DM. Density and genetic structure of black bears in coastal South Carolina. J Wildl Manage 2012. [DOI: 10.1002/jwmg.443] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Uno R, Kondo M, Yuasa T, Yamauchi K, Tsuruga H, Tamate HB, Yoneda M. Assessment of genotyping accuracy in a non-invasive DNA-based population survey of Asiatic black bears (Ursus thibetanus): lessons from a large-scale pilot study in Iwate prefecture, northern Japan. POPUL ECOL 2012. [DOI: 10.1007/s10144-012-0328-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Chang Z, Liu Z, Yang J, Li M, Vigilant L. Noninvasive genetic assessment of the population trend and sex ratio of the Shennongjia population of Sichuan snub-nosed monkeys (Rhinopithecus roxellana). ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4872-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mowry RA, Gompper ME, Beringer J, Eggert LS. River otter population size estimation using noninvasive latrine surveys. J Wildl Manage 2011. [DOI: 10.1002/jwmg.193] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Sawaya MA, Ruth TK, Creel S, Rotella JJ, Stetz JB, Quigley HB, Kalinowski ST. Evaluation of noninvasive genetic sampling methods for cougars in Yellowstone National Park. J Wildl Manage 2011. [DOI: 10.1002/jwmg.92] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael A. Sawaya
- Department of Ecology, Montana State University, Bozeman, MT 59717, USA and Wildlife Conservation Society, 301 N Wilson Avenue, Bozeman, MT, USA
| | - Toni K. Ruth
- Hornocker Wildlife Institute/Wildlife Conservation Society, 301 N Wilson Avenue, Bozeman, MT 59715, USA
| | - Scott Creel
- Department of Ecology, Montana State University, Bozeman, MT 59717, USA
| | - Jay J. Rotella
- Department of Ecology, Montana State University, Bozeman, MT 59717, USA
| | - Jeffrey. B. Stetz
- Montana Cooperative Wildlife Research Unit, Glacier Field Station, Glacier National Park, West Glacier, MT 59936, USA
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Proctor M, McLellan B, Boulanger J, Apps C, Stenhouse G, Paetkau D, Mowat G. Ecological investigations of grizzly bears in Canada using DNA from hair, 1995–2005: a review of methods and progress. URSUS 2010. [DOI: 10.2192/1537-6176-21.2.169] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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BEJA‐PEREIRA ALBANO, OLIVEIRA RITA, ALVES PAULOC, SCHWARTZ MICHAELK, LUIKART GORDON. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 2009; 9:1279-301. [DOI: 10.1111/j.1755-0998.2009.02699.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ALBANO BEJA‐PEREIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
| | - RITA OLIVEIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - PAULO C. ALVES
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - MICHAEL K. SCHWARTZ
- USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - GORDON LUIKART
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Garshelis DL, Hao W, Dajun W, Xiaojian Z, Sheng L, McShea WJ. Do Revised Giant Panda Population Estimates Aid in Their Conservation. URSUS 2008. [DOI: 10.2192/07per011.1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Schwartz MK, McKelvey KS. Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9622-1] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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