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Siziba VI, Scroeder MM, Wilson B, Sliwa A, Willows‐Munro S. A method for noninvasive individual genotyping of black-footed cat ( Felis nigripes). Ecol Evol 2024; 14:e11315. [PMID: 38660470 PMCID: PMC11040180 DOI: 10.1002/ece3.11315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.
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Affiliation(s)
- Vimbai I. Siziba
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | | | - Beryl Wilson
- McGregor MuseumKimberleyNorthern CapeSouth Africa
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Gajdárová B, Belotti E, Bufka L, Volfová J, Wölfl S, Mináriková T, Hollerbach L, Duľa M, Kleven O, Kutal M, Nowak C, Ozoliņš J, Tám B, Bryja J, Koubek P, Krojerová-Prokešová J. Long-term genetic monitoring of a reintroduced Eurasian lynx population does not indicate an ongoing loss of genetic diversity. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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3
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Ex situ versus in situ Eurasian lynx populations: implications for successful breeding and genetic rescue. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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4
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Barnes TM, Karlin M, vonHoldt BM, Adams JR, Waits LP, Hinton JW, Henderson J, Brzeski KE. Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas. BMC Ecol Evol 2022; 22:134. [PMID: 36376792 PMCID: PMC9664737 DOI: 10.1186/s12862-022-02084-9] [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: 05/18/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Hybridization can be a conservation concern if genomic introgression leads to the loss of an endangered species' unique genome, or when hybrid offspring are sterile or less fit than their parental species. Yet hybridization can also be an adaptive management tool if rare populations are inbred and have reduced genetic variation, and there is the opportunity to enhance genetic variation through hybridization. The red wolf (Canis rufus) is a critically endangered wolf endemic to the eastern United States, where all extant red wolves are descended from 14 founders which has led to elevated levels of inbreeding over time. Red wolves were considered extirpated from the wild by 1980, but before they disappeared, they interbred with encroaching coyotes creating a genetically admixed population of canids along coastal Texas and Louisiana. In 2018, a genetic study identified individuals on Galveston Island, Texas with significant amounts of red wolf ancestry. We collected 203 fecal samples from Galveston for a more in-depth analysis of this population to identify the amount of red wolf ancestry present and potential mechanisms that support retention of red wolf ancestry on the landscape. RESULTS We identified 24 individual coyotes from Galveston Island and 8 from mainland Texas with greater than 10% red wolf ancestry. Two of those individuals from mainland Texas had greater than 50% red wolf ancestry estimates. Additionally, this population had 5 private alleles that were absent in the North American reference canid populations used in this study, which included 107 southeastern coyotes, 19 captive red wolves, and 38 gray wolves, possibly representing lost red wolf genetic variation. We also identified several individuals on Galveston Island and the mainland of Texas that retained a unique red wolf mitochondrial haplotype present in the red wolf founding population. On Galveston Island, we identified a minimum of four family groups and found coyotes on the island to be highly related, but not genetically depauperate. We did not find clear associations between red wolf ancestry estimates and landscape features, such as open green space or developed areas. CONCLUSION Our results confirm the presence of substantial red wolf ancestry persisting on Galveston Island and adjacent mainland Texas. This population has the potential to benefit future red wolf conservation efforts through novel reproductive techniques and possibly through de-introgression strategies, with the goals of recovering extinct red wolf genetic variation and reducing inbreeding within the species.
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Affiliation(s)
- Tanner M Barnes
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Melissa Karlin
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, TX, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | | | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
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5
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De R, Nigam P, Williams AC, Goyal SP. Beyond consensus genotyping: a case study on the Asian elephant Elephas maximus. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Ausband DE. Genetic diversity and mate selection in a reintroduced population of gray wolves. Sci Rep 2022; 12:535. [PMID: 35017596 PMCID: PMC8752858 DOI: 10.1038/s41598-021-04449-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/16/2021] [Indexed: 11/12/2022] Open
Abstract
The genetic composition of an individual can markedly affect its survival, reproduction, and ultimately fitness. As some wildlife populations become smaller, conserving genetic diversity will be a conservation challenge. Many imperiled species are already supported through population augmentation efforts and we often do not know if or how genetic diversity is maintained in translocated species. As a case study for understanding the maintenance of genetic diversity in augmented populations, I wanted to know if genetic diversity (i.e., observed heterozygosity) remained high in a population of gray wolves in the Rocky Mountains of the U.S. > 20 years after reintroduction. Additionally, I wanted to know if a potential mechanism for such diversity was individuals with below average genetic diversity choosing mates with above average diversity. I also asked whether there was a preference for mating with unrelated individuals. Finally, I hypothesized that mated pairs with above average heterozygosity would have increased survival of young. Ultimately, I found that females with below average heterozygosity did not choose mates with above average heterozygosity and wolves chose mates randomly with respect to genetic relatedness. Pup survival was not higher for mated pairs with above average heterozygosity in my models. The dominant variables predicting pup survival were harvest rate during their first year of life and years pairs were mated. Ultimately, genetic diversity was relatively unchanged > 20 years after reintroduction. The mechanism for maintaining such diversity does not appear related to individuals preferentially choosing more genetically diverse mates. Inbreeding avoidance, however, appears to be at least one mechanism maintaining genetic diversity in this population.
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Affiliation(s)
- David E Ausband
- U.S. Geological Survey, Idaho Cooperative Fish and Wildlife Research Unit, University of Idaho, 875 Perimeter Drive, MS 1141, Moscow, ID, 83844, USA.
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7
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Ausband DE. Inherit the kingdom or storm the castle? Breeding strategies in a social carnivore. Ethology 2021. [DOI: 10.1111/eth.13250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David E. Ausband
- U.S. Geological Survey Idaho Cooperative Fish and Wildlife Research Unit University of Idaho Moscow Idaho USA
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8
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Long‐term monitoring using DNA sampling reveals the dire demographic status of the critically endangered Gobi bear. Ecosphere 2021. [DOI: 10.1002/ecs2.3696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Schoenecker KA, King SRB, Ekernas LS, Oyler‐McCance SJ. Using Fecal DNA and Closed‐Capture Models to Estimate Feral Horse Population Size. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Sarah R. B. King
- Natural Resource Ecology Laboratory Colorado State University Fort Collins CO 80523 USA
| | - L. Stefan Ekernas
- U.S. Geological Survey, Fort Collins Science Center Fort Collins CO 80526 USA
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Long-distance Eurasian lynx dispersal – a prospect for connecting native and reintroduced populations in Central Europe. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01363-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Population genetics of the African wolf (Canis lupaster) across its range: first evidence of hybridization with domestic dogs in Africa. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00059-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Ausband DE, Waits L. Does harvest affect genetic diversity in grey wolves? Mol Ecol 2020; 29:3187-3195. [PMID: 32657476 DOI: 10.1111/mec.15552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 01/01/2023]
Abstract
Harvest can affect vital rates such as reproduction and survival, but also genetic measures of individual and population health. Grey wolves (Canis lupus) live and breed in groups, and effective population size is a small fraction of total abundance. As a result, genetic diversity of wolves may be particularly sensitive to harvest. We evaluated how harvest affected genetic diversity and relatedness in wolves. We hypothesized that harvest would (a) reduce relatedness of individuals within groups in a subpopulation but increase relatedness of individuals between groups due to increased local immigration, (b) increase individual heterozygosity and average allelic richness across groups in subpopulations and (c) add new alleles to a subpopulation and decrease the number of private alleles in subpopulations due to an increase in breeding opportunities for unrelated individuals. We found harvest had no effect on observed heterozygosity of individuals or allelic richness at loci within subpopulations but was associated with a small, biologically insignificant effect on within-group relatedness values in grey wolves. Harvest was, however, positively associated with increased relatedness of individuals between groups and a net gain (+16) of alleles into groups in subpopulations monitored since harvest began, although the number of private alleles in subpopulations overall declined. Harvest likely created opportunities for wolves to immigrate into nearby groups and breed, thereby making groups in subpopulations more related over time. Harvest appears to affect genetic diversity in wolves at the group and population levels, but its effects are less apparent at the individual level given the population sizes we studied.
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Affiliation(s)
- David E Ausband
- Idaho Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Idaho, Moscow, ID, USA
| | - Lisette Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
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13
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Bassing SB, Ausband DE, Mitchell MS, Schwartz MK, Nowak JJ, Hale GC, Waits LP. Immigration does not offset harvest mortality in groups of a cooperatively breeding carnivore. Anim Conserv 2020. [DOI: 10.1111/acv.12593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- S. B. Bassing
- Montana Cooperative Wildlife Research Unit Wildlife Biology Program University of Montana Missoula MT USA
| | - D. E. Ausband
- Idaho Department of Fish and Game Coeur d’Alene ID USA
| | - M. S. Mitchell
- U.S. Geological Survey Montana Cooperative Wildlife Research Unit Wildlife Biology Program University of Montana Missoula MT USA
| | - M. K. Schwartz
- U.S. Forest Service National Genomics Center for Wildlife and Fish Conservation Missoula MT USA
| | - J. J. Nowak
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula MT USA
| | - G. C. Hale
- Alberta Environment and Parks Blairmore AB Canada
| | - L. P. Waits
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID USA
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Soller JM, Ausband DE, Szykman Gunther M. The curse of observer experience: Error in noninvasive genetic sampling. PLoS One 2020; 15:e0229762. [PMID: 32168506 PMCID: PMC7069729 DOI: 10.1371/journal.pone.0229762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
Noninvasive genetic sampling (NGS) is commonly used to study elusive or rare species where direct observation or capture is difficult. Little attention has been paid to the potential effects of observer bias while collecting noninvasive genetic samples in the field, however. Over a period of 7 years, we examined whether different observers (n = 58) and observer experience influenced detection, amplification rates, and correct species identification of 4,836 gray wolf (Canis lupus) fecal samples collected in Idaho and Yellowstone National Park, USA and southwestern Alberta, Canada (2008-2014). We compared new observers (n = 33) to experienced observers (n = 25) and hypothesized experience level would increase the overall success of using NGS techniques in the wild. In contrast to our hypothesis, we found that new individuals were better than experienced observers at detecting and collecting wolf scats and correctly identifying wolf scats from other sympatric carnivores present in the study areas. While adequate training of new observers is crucial for the successful use of NGS techniques, attention should also be directed to experienced observers. Observer experience could be a curse because of their potential effects on NGS data quality arising from fatigue, boredom or other factors. The ultimate benefit of an observer to a project is a combination of factors (i.e., field savvy, local knowledge), but project investigators should be aware of the potential negative effects of experience on NGS sampling.
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Affiliation(s)
- Jillian M. Soller
- Department of Wildlife, Humboldt State University, Arcata, California, United States of America
- * E-mail:
| | - David E. Ausband
- University of Montana Cooperative Wildlife Research Unit, Missoula, Montana, United States of America
| | - Micaela Szykman Gunther
- Department of Wildlife, Humboldt State University, Arcata, California, United States of America
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15
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Tumendemberel O, Zedrosser A, Proctor MF, Reynolds HV, Adams JR, Sullivan JM, Jacobs SJ, Khorloojav T, Tserenbataa T, Batmunkh M, Swenson JE, Waits LP. Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia. PLoS One 2019; 14:e0220746. [PMID: 31408475 PMCID: PMC6692007 DOI: 10.1371/journal.pone.0220746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022] Open
Abstract
Knowledge of genetic diversity and population structure is critical for conservation and management planning at the population level within a species' range. Many brown bear populations in Central Asia are small and geographically isolated, yet their phylogeographic relationships, genetic diversity, and contemporary connectivity are poorly understood. To address this knowledge gap, we collected brown bear samples from the Gobi Desert (n = 2360), Altai, Sayan, Khentii, and Ikh Khyangan mountains of Mongolia (n = 79), and Deosai National Park in the Himalayan Mountain Range of Pakistan (n = 5) and generated 927 base pairs of mitochondrial DNA (mtDNA) sequence data and genotypes at 13 nuclear DNA microsatellite loci. We documented high levels of mtDNA and nDNA diversity in the brown bear populations of northern Mongolia (Altai, Sayan, Buteeliin nuruu and Khentii), but substantially lower diversity in brown bear populations in the Gobi Desert and Himalayas of Pakistan. We detected 3 brown bear mtDNA phylogeographic groups among bears of the region, with clade 3a1 in Sayan, Khentii, and Buteeliin nuruu mountains, clade 3b in Altai, Sayan, Buteeliin nuruu, Khentii, and Ikh Khyangan, and clade 6 in Gobi and Pakistan. Our results also clarified the phylogenetic relationships and divergence times with other brown bear mtDNA clades around the world. The nDNA genetic structure analyses revealed distinctiveness of Gobi bears and different population subdivisions compared to mtDNA results. For example, genetic distance for nDNA microsatellite loci between the bears in Gobi and Altai (FST = 0.147) was less than that of the Gobi and Pakistan (FST = 0.308) suggesting more recent male-mediated nuclear gene flow between Gobi and Altai than between Gobi and the Pakistan bears. Our results provide valuable information for conservation and management of bears in this understudied region of Central Asia and highlight the need for special protection and additional research on Gobi brown bears.
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Affiliation(s)
- Odbayar Tumendemberel
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Andreas Zedrosser
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | | | | | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack M. Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah J. Jacobs
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tumennasan Khorloojav
- Genetics Laboratory, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Tuya Tserenbataa
- Sunshine Village Complex, Bayanzurkh District, Ulaanbaatar, Mongolia
| | - Mijiddorj Batmunkh
- Mongolian-Chinese Joint Molecular Biology Laboratory, Ulaanbaatar, Mongolia
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
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17
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Detailed characterization of repeat motifs of nine canid microsatellite loci in African painted dogs (Lycaon pictus). MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00442-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Skrbinšek T, Luštrik R, Majić-Skrbinšek A, Potočnik H, Kljun F, Jelenčič M, Kos I, Trontelj P. From science to practice: genetic estimate of brown bear population size in Slovenia and how it influenced bear management. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1265-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bassing SB, Ausband DE, Mitchell MS, Lukacs P, Keever A, Hale G, Waits L. Stable pack abundance and distribution in a harvested wolf population. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sarah B. Bassing
- Montana Cooperative Wildlife Research UnitWildlife Biology ProgramUniversity of Montana205 Natural Sciences BuildingMissoulaMT59812USA
| | - David E. Ausband
- Idaho Department of Fish and Game2885 W Kathleen AvenueCoeur d'AleneID83815USA
| | - Michael S. Mitchell
- U.S. Geological SurveyMontana Cooperative Wildlife Research UnitWildlife Biology ProgramUniversity of Montana205 Natural Sciences BuildingMissoulaMT59812USA
| | - Paul Lukacs
- Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMT59812USA
| | - Allison Keever
- Montana Cooperative Wildlife Research UnitWildlife Biology ProgramUniversity of Montana205 Natural Sciences BuildingMissoulaMT59812USA
| | - Greg Hale
- Alberta Environment and Parks12501 20 AvenueBlairmoreABT7N 1A2Canada
| | - Lisette Waits
- Laboratory for EcologicalEvolutionary, and Conservation GeneticsDepartment of Fish and Wildlife SciencesUniversity of Idaho875 Perimeter Drive MS1136MoscowID83844USA
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20
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Murphy SM, Adams JR, Cox JJ, Waits LP. Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana. Conserv Lett 2018. [DOI: 10.1111/conl.12621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sean M. Murphy
- Large Carnivore Program Louisiana Department of Wildlife and Fisheries Lafayette Louisiana
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences University of Idaho Moscow Idaho
| | - John J. Cox
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences University of Idaho Moscow Idaho
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21
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Murphy SM, Augustine BC, Adams JR, Waits LP, Cox JJ. Integrating multiple genetic detection methods to estimate population density of social and territorial carnivores. Ecosphere 2018. [DOI: 10.1002/ecs2.2479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sean M. Murphy
- Louisiana Department of Wildlife and Fisheries; Large Carnivore Program; Lafayette Louisiana 70506 USA
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061 USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics; Department of Fish and Wildlife Sciences; University of Idaho; Moscow Idaho 83844 USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics; Department of Fish and Wildlife Sciences; University of Idaho; Moscow Idaho 83844 USA
| | - John J. Cox
- Department of Forestry and Natural Resources; University of Kentucky; Lexington Kentucky 40546 USA
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King SRB, Schoenecker KA, Fike JA, Oyler‐McCance SJ. Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for noninvasive sampling. Ecol Evol 2018; 8:4053-4064. [PMID: 29721279 PMCID: PMC5916305 DOI: 10.1002/ece3.3956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/30/2018] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA.
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Affiliation(s)
- Sarah R. B. King
- Natural Resource Ecology LaboratoryDepartment of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsCOUSA
| | | | - Jennifer A. Fike
- United States Geological SurveyFort Collins Science CenterFort CollinsCOUSA
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Davoli F, Cozzo M, Angeli F, Groff C, Randi E. Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. NATURE CONSERVATION 2018. [DOI: 10.3897/natureconservation.25.23776] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sexually Selected Infanticide (SSI) is thought of as a male reproductive strategy in social mammalian species, because females who lose cubs may quickly re-enter oestrus. SSI has rarely been documented in non-social mammals and, in brown bears, SSI has been studied mainly in an eco-ethological perspective. The authors examined the first genetically documented infanticide case which occurred in May 2015 in brown bears in Italy (Trentino, Central-Eastern Alps). The infanticide killed two cubs and their mother. Hair samples were collected from the corpses as well as saliva, through swabs on mother’s wounds, with the aim of identifying the genotype of the perpetrator. The samples were genotyped by PCR amplification of 15 autosomal microsatellite loci, following the protocol routinely used for individual bear identifications within the Interregional Action Plan for Brown Bear Conservation in the Central-Eastern Alps (PACOBACE). Reliable genotypes were obtained from the mother, cubs and putative perpetrator. The genotypes were matched with those populating the PACOBACE database and genealogies were reconstructed. Both mother and perpetrator genotypes were already present in the database. Kinship analyses confirmed mother-cubs relationships and identified the father of the cubs. In this study, for the first time, the authors used the open-source LRmix STUDIO software, designed to analyse human forensic genetic profiles, to solve a case in wildlife. Through LRmix STUDIO, those alleles that do not belong to the victims were isolated and, finally, the perpetrator was identified. This study presents a method that allows, through the application of different models, the genetic identification of the conspecific perpetrator with the highest probability. The identification of the infanticidal male is relevant for the better management and conservation of wild populations with small effective population size (Ne) and low population growth rate, especially in the case of recently established populations in human-dominated landscapes. This procedure will have predictably wide applications, supplying important data in the monitoring of small and isolated populations.
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Carpenter FM, Dziminski MA. Breaking down scats: degradation of DNA from greater bilby (Macrotis lagotis) faecal pellets. AUSTRALIAN MAMMALOGY 2017. [DOI: 10.1071/am16030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Isolating DNA from scats (faeces) of threatened species is a valuable, non-invasive method for identifying individuals. To establish whether genotyping of greater bilby (Macrotis lagotis) individuals from faecal pellets collected in the field can be useful for population monitoring, an understanding of the DNA degradation rates is necessary. To determine the relationship between time and degradation of bilby faecal DNA, and assess whether a two-step elution process during extraction results in better-quality DNA, faecal pellets were collected from captive individuals, maintained under seminatural conditions, then harvested at known periods. DNA was amplified from faecal pellets with a 99% success rate and error rates of less than 5% up to 14 days after deposition. The amplification rate decreases, and the rate of allelic dropout increases with time, but DNA can still be amplified at rates above 60% and error rates below 15% at 90–180 days. We found that a second elution step was unnecessary, with more DNA amplified over a longer period using the first eluate. Viable DNA exists on bilby faecal pellets for a long period after deposition, which is useful for obtaining genetic samples for population monitoring programs and studies on population genetics.
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25
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Stansbury CR, Ausband DE, Zager P, Mack CM, Waits LP. Identifying gray wolf packs and dispersers using noninvasive genetic samples. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21136] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carisa R. Stansbury
- University of Idaho; Department of Fish and Wildlife Sciences; P.O. Box 441136 Moscow ID 83844 USA
| | - David E. Ausband
- Montana Cooperative Wildlife Research Unit; University of Montana; 205 Natural Sciences Building Missoula MT 59812 USA
| | - Peter Zager
- Idaho Department of Fish and Game; 3316 16th St. Lewiston ID 83501 USA
| | - Curt M. Mack
- Nez Perce Tribe; Gray Wolf Recovery Project; P.O. Box 1922 McCall ID 83638 USA
| | - Lisette P. Waits
- University of Idaho; Department of Fish and Wildlife Sciences; P.O. Box 441136 Moscow ID 83844 USA
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26
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Harms V, Nowak C, Carl S, Muñoz-Fuentes V. Experimental evaluation of genetic predator identification from saliva traces on wildlife kills. J Mammal 2015. [DOI: 10.1093/jmammal/gyu014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Stansbury CR, Ausband DE, Zager P, Mack CM, Miller CR, Pennell MW, Waits LP. A long-term population monitoring approach for a wide-ranging carnivore: Noninvasive genetic sampling of gray wolf rendezvous sites in Idaho, USA. J Wildl Manage 2014. [DOI: 10.1002/jwmg.736] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Carisa R. Stansbury
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - David E. Ausband
- Montana Cooperative Wildlife Research Unit; Natural Sciences Room 205, University of Montana; Missoula MT 59812 USA
| | - Peter Zager
- Idaho Department of Fish and Game; 3316 16th Street Lewiston ID 83501 USA
| | - Curt M. Mack
- Wildlife Management Division; Nez Perce Tribe; 260 Phinney Drive Lapwai ID 83540 USA
| | - Craig R. Miller
- Department of Mathematics; University of Idaho; P.O. Box 441103 Moscow ID 83844 USA
- Department of Biological Sciences; University of Idaho; P.O. Box 441103 Moscow ID 83844 USA
| | - Matthew W. Pennell
- Department of Biological Sciences; University of Idaho; P.O. Box 441103 Moscow ID 83844 USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST); University of Idaho; PO Box 443051 Moscow ID 83844 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
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Tsaparis D, Karaiskou N, Mertzanis Y, Triantafyllidis A. Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region – Greece. J NAT HIST 2014. [DOI: 10.1080/00222933.2013.877992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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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Trinca CS, Jaeger CF, Eizirik E. Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12077] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Camila Fernandes Jaeger
- Laboratório de Biologia Genômica e Molecular; Faculdade de Biociências; Pontifícia Universidade Católica do Rio Grande do Sul; Avenida Ipiranga, 6681, prédio 12C, sala 134; Porto Alegre; RS; 90619-900; Brazil
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Sindičić M, Polanc P, Gomerčić T, Jelenčič M, Huber Đ, Trontelj P, Skrbinšek T. Genetic data confirm critical status of the reintroduced Dinaric population of Eurasian lynx. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0491-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Marucco F, Vucetich LM, Peterson RO, Adams JR, Vucetich JA. Evaluating the efficacy of non-invasive genetic methods and estimating wolf survival during a ten-year period. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0412-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kolodziej K, Theissinger K, Brün J, Schulz HK, Schulz R. Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives. EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0588-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Polanc P, Sindičić M, Jelenčič M, Gomerčić T, Kos I, Huber D. Genotyping success of historical Eurasian lynx (Lynx lynx L.) samples. Mol Ecol Resour 2011; 12:293-8. [PMID: 22040140 DOI: 10.1111/j.1755-0998.2011.03084.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Historical samples, like tanned hides and trophy skulls, can be extremely important for genetic studies of endangered or elusive species. Selection of a sampling protocol that is likely to provide sufficient amount and quality of DNA with a minimum damage to the original specimen is often critical for a success of the study. We investigated microsatellite genotyping success of DNA isolated from three different types of Eurasian lynx historical samples. We analysed a total of 20 microsatellite loci in 106 historical samples from the endangered Dinaric lynx population, established from re-introduction of three pairs of lynx in 1973 from Slovakian Carpathians. Of the three tested sample types, turbinal bone and septum from the nasal cavity of the trophy skulls had the lowest percentage of samples successfully genotyped for all 20 microsatellite loci. Footpad samples, collected using a cork drill, exhibited better results in polymerase chain reaction amplification and genotyping than samples of footpad epidermis cut with a scalpel. We report simple and efficient sampling protocols, which could be widely applied for future studies utilizing historical samples.
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Affiliation(s)
- Primož Polanc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia.
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Microsatellite diversity and structure of Carpathian brown bears (Ursus arctos): consequences of human caused fragmentation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0271-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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36
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Dellinger JA, Mcvey JM, Cobb DT, Moorman CE. Diameter thresholds for distinguishing between red wolf and other canid scat. WILDLIFE SOC B 2011. [DOI: 10.1002/wsb.60] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Adams JR, Vucetich LM, Hedrick PW, Peterson RO, Vucetich JA. Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population. Proc Biol Sci 2011; 278:3336-44. [PMID: 21450731 DOI: 10.1098/rspb.2011.0261] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant's fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves' prey declined). These conditions probably explain why the immigration event did not obviously improve the population's demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.
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Affiliation(s)
- Jennifer R Adams
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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Pérez T, Vázquez JF, Quirós F, Domínguez A. Improving non-invasive genotyping in capercaillie (Tetrao urogallus): redesigning sexing and microsatellite primers to increase efficiency on faeces samples. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9385-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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39
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SKRBINŠEK TOMAŽ, JELENČIČ MAJA, WAITS LISETTE, KOS IVAN, TRONTELJ PETER. Highly efficient multiplex PCR of noninvasive DNA does not require pre‐amplification. Mol Ecol Resour 2010; 10:495-501. [DOI: 10.1111/j.1755-0998.2009.02780.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- TOMAŽ SKRBINŠEK
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - MAJA JELENČIČ
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - LISETTE WAITS
- Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, ID 83844‐1136, USA
| | - IVAN KOS
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - PETER TRONTELJ
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
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40
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An efficient noninvasive method for discriminating among faeces of sympatric North American canids. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9215-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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De Barba M, Waits LP, Genovesi P, Randi E, Chirichella R, Cetto E. Comparing opportunistic and systematic sampling methods for non-invasive genetic monitoring of a small translocated brown bear population. J Appl Ecol 2010. [DOI: 10.1111/j.1365-2664.2009.01752.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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DE Barba M, Waits LP. Multiplex pre-amplification for noninvasive genetic sampling: is the extra effort worth it? Mol Ecol Resour 2009; 10:659-65. [PMID: 21565070 DOI: 10.1111/j.1755-0998.2009.02818.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Microsatellite genotyping of hair and faeces using standard polymerase chain reaction (PCR) resulted in low success rates and high error rates in a 2003-2004 pilot study using noninvasive genetic sampling for the brown bear (Ursus arctos) in the Italian Alps. Thus, we evaluated the performance of multiplex pre-amplification for improving microsatellite genotyping results. Brown bear faecal DNA extracts of varying quality (n = 33) and hair DNA extracts of poor (n = 32) and good (n = 34) quality were used to compare standard PCR and pre-amplification. In contrast to previous studies, there was no significant difference between methods for individual locus amplification success, genotyping error and genotyping success rates for scat and hair samples. The use of pre-amplification requires an additional investment of time and resources, and our results raise questions about the universal value of pre-amplification approaches. We suggest that researchers carefully evaluate the performance of pre-amplification compared to standard PCR using field-collected samples from the study area of interest before engaging in large-scale noninvasive genetic analyses.
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Affiliation(s)
- M DE Barba
- Department of Fish & Wildlife Resources, University of Idaho, PO Box 441136, Moscow, ID 83844-1136, USA
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43
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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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Oliveira R, Castro D, Godinho R, Luikart G, Alves PC. Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9947-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Soto-Calderón ID, Ntie S, Mickala P, Maisels F, Wickings EJ, Anthony NM. Effects of storage type and time on DNA amplification success in tropical ungulate faeces. Mol Ecol Resour 2009; 9:471-9. [PMID: 21564676 DOI: 10.1111/j.1755-0998.2008.02462.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study compares the effect of three storage media (silica, RNAlater®, ethanol) and time to extraction (1 week, 1 month and 3 months) on mitochondrial and nuclear marker amplification success in faecal DNA extracts from a sympatric community of small to medium-sized Central African forest ungulates (genera Cephalophus, Tragelaphus, Hyemoschus). The effect of storage type and time on nuclear DNA concentrations, genotyping errors and percentage recovery of consensus genotypes was also examined. Regardless of storage method, mitochondrial and nuclear amplification success was high in DNA extracted within the first week after collection. Over longer storage periods, RNAlater yielded better amplification success rates in the mitochondrial assay. However, samples stored on silica showed (i) highest nuclear DNA concentrations, (ii) best microsatellite genotyping success, (iii) lowest genotyping errors, and (iv) greatest percentage recovery of the consensus genotype. The quantity of nuclear DNA was generally a good predictor of microsatellite performance with 83% amplification success or greater achieved with sample DNA concentrations of ≥ 50 pg/µL. If faecal DNA samples are to be used for nuclear microsatellite analyses, we recommend silica as the best storage method. However, for maximum mitochondrial amplification success, RNAlater appears to be the best storage medium. In contrast, ethanol appeared inferior to the other two methods examined here and should not be used to store tropical ungulate faeces. Regardless of storage method, samples should be extracted as soon as possible after collection to ensure optimal recovery of DNA.
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Affiliation(s)
- Iván D Soto-Calderón
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
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46
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Smith S, McRae P, Hughes J. Faecal DNA analysis enables genetic monitoring of the species recovery program for an arid-dwelling marsupial. AUST J ZOOL 2009. [DOI: 10.1071/zo09035] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The greater bilby, Macrotis lagotis, is a species of conservation significance in the arid and semiarid zones of Australia. A species recovery program has been underway since the mid-1990s but the incorporation of molecular genetic data within the program has been difficult due to the problems of obtaining regular, population-wide samples of this trap-shy and sparsely distributed species. In this study, we demonstrate that faecal pellets collected from around burrows in the dry, arid habitat of western Queensland provide a viable source for DNA extraction and analysis. Faecal DNA was used to generate population-level estimates of microsatellite and mtDNA diversity for comparison with previous estimates for the natural population derived from tissue samples. Data were used to assess both the reliability of faecal-derived genotypes and the extent of any diversity loss since the previous study. Microsatellite diversity recorded from eight polymorphic markers for the natural population (A = 4.31 ± 0.30, HE = 0.76 ± 0.03) was comparable with the previous study, indicating little change in genetic diversity for the natural population in the 10-year interim. Faecal genotypes generated for the recently reintroduced population matched the known number of founders as well as a known genotype, providing support for the reliability of the faecal DNA approach. The captive and reintroduced populations had significantly lower diversity levels than the natural population (A = 3.59 ± 0.28, HE = 0.68 ± 0.03; A = 3.57 ± 0.20, HE = 0.65 ± 0.03 respectively). Mitochondrial control region analysis, incorporating nested clade phylogeographic analysis (NCPA), agrees with earlier findings that populations of bilbies across the arid zone in Australia have only recently become fragmented, but the case for Queensland bilbies being strongly differentiated from other regions is diminished. Implications from this study include the need to further supplement the captive and reintroduced populations with additional out-bred individuals and that faecal DNA can be used effectively for ongoing monitoring and management of this species.
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47
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Hájková P, Zemanová B, Roche K, Hájek B. An evaluation of field and noninvasive genetic methods for estimating Eurasian otter population size. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9745-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kays RW, Gompper ME, Ray JC. Landscape ecology of eastern coyotes based on large-scale estimates of abundance. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2008; 18:1014-1027. [PMID: 18536259 DOI: 10.1890/07-0298.1] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Since their range expansion into eastern North America in the mid-1900s, coyotes (Canis latrans) have become the region's top predator. Although widespread across the region, coyote adaptation to eastern forests and use of the broader landscape are not well understood. We studied the distribution and abundance of coyotes by collecting coyote feces from 54 sites across a diversity of landscapes in and around the Adirondacks of northern New York. We then genotyped feces with microsatellites and found a close correlation between the number of detected individuals and the total number of scats at a site. We created habitat models predicting coyote abundance using multi-scale vegetation and landscape data and ranked them with an information-theoretic model selection approach. These models allow us to reject the hypothesis that eastern forests are unsuitable habitat for coyotes as their abundance was positively correlated with forest cover and negatively correlated with measures of rural non-forest landscapes. However, measures of vegetation structure turned out to be better predictors of coyote abundance than generalized "forest vs. open" classification. The best supported models included those measures indicative of disturbed forest, especially more open canopies found in logged forests, and included natural edge habitats along water courses. These forest types are more productive than mature forests and presumably host more prey for coyotes. A second model with only variables that could be mapped across the region highlighted the lower density of coyotes in areas with high human settlement, as well as positive relationships with variables such as snowfall and lakes that may relate to increased numbers and vulnerability of deer. The resulting map predicts coyote density to be highest along the southwestern edge of the Adirondack State Park, including Tug Hill, and lowest in the mature forests and more rural areas of the central and eastern Adirondacks. Together, these results support the need for a nuanced view of how eastern coyotes use forested habitats.
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Affiliation(s)
- Roland W Kays
- New York State Museum, CEC 3140, Albany, New York 12230, USA.
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49
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Piggott MP, Wilson R, Banks SC, Marks CA, Gigliotti F, Taylor AC. Evaluating exotic predator control programs using non-invasive genetic tagging. WILDLIFE RESEARCH 2008. [DOI: 10.1071/wr08040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Carnivorous predators are difficult to detect using conventional survey methods, especially at low levels of abundance. The introduced red fox (Vulpes vulpes) in Australia is monitored to determine the effectiveness of control programs, but assessing population parameters such as abundance and recruitment is difficult. We carried out a feasibility study to determine the effectiveness of using faecal DNA analysis methods to identify individual foxes and to assess abundance before and after lethal control. Fox faeces were collected in two sampling periods over four separate transects, and genotyped at five microsatellite loci. Two transects were subject to lethal control between collection periods. DNA was extracted from 170 fox faeces and, in total, 54 unique genotypes were identified. Fifteen biopsy genotypes from 30 foxes killed during lethal control were detected among the faecal genotypes. Overall, a similar number of genotypes were detected in both sampling periods. The number of individuals sampled in both periods was low (n = 6) and new individuals (n = 24) were detected in the second collection period. We were also able to detect animals that avoided lethal control, and movement of individuals between transects. The ability to identify individual foxes using these DNA techniques highlighted the shortcomings of the sample design, in particular the spatial scale and distances between transects. This study shows that non-invasive DNA sampling can provide valuable insight into pre and post fox abundance in relation to lethal control, individual behaviour and movement, as well as sample design. The information gained from this study will contribute to the design of future studies and, ultimately, control strategies.
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50
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Adams JR, Lucash C, Schutte L, Waits LP. Locating hybrid individuals in the red wolf (Canis rufus) experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping. Mol Ecol 2007; 16:1823-34. [PMID: 17444895 DOI: 10.1111/j.1365-294x.2007.03270.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization with coyotes (Canis latrans) continues to threaten the recovery of endangered red wolves (Canis rufus) in North Carolina and requires the development of new strategies to detect and remove coyotes and hybrids. Here, we combine a spatially targeted faecal collection strategy with a previously published reference genotype data filtering method and a genetic test for coyote ancestry to screen portions of the red wolf experimental population area for the presence of nonred wolf canids. We also test the accuracy of our maximum-likelihood assignment test for identifying hybrid individuals using eight microsatellite loci instead of the original 18 loci and compare its performance to the Bayesian approach implemented in newhybrids. We obtained faecal DNA genotypes for 89 samples, 73 of which were matched to 23 known individuals. The performance of two sampling strategies - comprehensive sweep and opportunistic spot-check was evaluated. The opportunistic spot-check sampling strategy required less effort than the comprehensive sweep sampling strategy but identified fewer individuals. Six hybrids or coyotes were detected and five of these individuals were subsequently captured and removed from the population. The accuracy and power of the genetic test for coyote ancestry is decreased when using eight loci; however, nonred wolf canids are identified with high frequency. This combination of molecular and traditional field-based approaches has great potential for addressing the challenge of hybridization in other species and ecosystems.
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Affiliation(s)
- Jennifer R Adams
- Department of Fish and Wildlife, University of Idaho, College of Natural Resources, Moscow, Idaho 83844-1136, USA.
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