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Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (Bethesda) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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2
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Muller JR, Selier SJ, Drouilly M, Broadfield J, Leighton GRM, Amar A, Naude VN. The hunter and the hunted: Using web‐sourced imagery to monitor leopard (
Panthera pardus pardus
) trophy hunting. Conservat Sci and Prac 2022. [DOI: 10.1111/csp2.12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jessica R. Muller
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
| | - Sarah‐Anne Jeanetta Selier
- South African National Biodiversity Institute (SANBI) Pretoria South Africa
- School of Life Sciences University of KwaZulu‐Natal Durban South Africa
| | - Marine Drouilly
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
- Panthera New York New York USA
| | | | - Gabriella R. M. Leighton
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
| | - Arjun Amar
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
- FitzPatrick Institute of African Ornithology University of Cape Town Cape Town South Africa
| | - Vincent N. Naude
- Department of Conservation Ecology and Entomology University of Stellenbosch Matieland South Africa
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Johannesburg South Africa
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3
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Bertola LD, Miller SM, Williams VL, Naude VN, Coals P, Dures SG, Henschel P, Chege M, Sogbohossou EA, Ndiaye A, Kiki M, Gaylard A, Ikanda DK, Becker MS, Lindsey P. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion ( Panthera leo). Evol Appl 2022; 15:22-39. [PMID: 35126646 PMCID: PMC8792481 DOI: 10.1111/eva.13318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.
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Affiliation(s)
- Laura D. Bertola
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- City College of New YorkNew YorkNew YorkUSA
| | - Susan M. Miller
- FitzPatrick Institute of African OrnithologyDSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Vivienne L. Williams
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Peter Coals
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Wildlife Conservation Research UnitUniversity of OxfordOxfordUK
| | | | | | - Monica Chege
- Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
- Kenya Wildlife ServiceNairobiKenya
| | | | | | - Martial Kiki
- Département de Génie de l’EnvironnementUniversité d’Abomey‐CalaviCotonouBenin
| | - Angela Gaylard
- Conservation Development & Assurance DepartmentAfrican Parks NetworkJohannesburgSouth Africa
| | | | | | - Peter Lindsey
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
- Wildlife Conservation NetworkSan FranciscoCaliforniaUSA
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4
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Wemer N, Naude VN, Merwe VC, Smit M, Lange G, Komdeur J. Successful predatory‐avoidance behaviour to lion auditory cues during soft‐release from captivity in cheetah. Ethology 2021. [DOI: 10.1111/eth.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nynke Wemer
- Behavioral Physiology and Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen the Netherlands
| | - Vincent N. Naude
- Institute for Communities and Wildlife in Africa University of Cape Town Rondebosch South Africa
| | - Vincent C. Merwe
- Institute for Communities and Wildlife in Africa University of Cape Town Rondebosch South Africa
- Endangered Wildlife Trust Johannesburg South Africa
| | - Marna Smit
- Ashia Cheetah Conservation Paarl South Africa
| | - Gerhard Lange
- Kuzuko Lodge Private Game Reserve Greater Addo Area South Africa
| | - Jan Komdeur
- Behavioral Physiology and Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen the Netherlands
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5
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John Power R, Rogan MS, Naude VN. Mountain refugia limit anthropogenic suppression in a re-established felid population: the case of the Magaliesberg leopard population in South Africa. African Zoology 2021. [DOI: 10.1080/15627020.2021.2011411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- R John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and Tourism, North West Provincial Government, Mmabatho, South Africa
| | - Matt S Rogan
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town, South Africa
- Centre for Statistics in Ecology, the Environment, and Conservation, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Vincent N Naude
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town, South Africa
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6
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Warmenhove C, Canning G, Davidson‐Phillips S, Merwe V, Burger A, Davidson‐Phillips P, Naude VN. Successful in situ supplementary feeding leads to the independence of orphaned cheetah cubs. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | | | - Vincent Merwe
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences University of Cape Town Cape Town South Africa
- Endangered Wildlife Trust Johannesburg South Africa
| | | | | | - Vincent N. Naude
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences University of Cape Town Cape Town South Africa
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7
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Williams VL, Coals PG, de Bruyn M, Naude VN, Dalton DL, Kotzé A. Monitoring compliance of CITES lion bone exports from South Africa. PLoS One 2021; 16:e0249306. [PMID: 33798210 PMCID: PMC8018656 DOI: 10.1371/journal.pone.0249306] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
From 2008 to 2018, South Africa permitted the export of captive-bred African lion (Panthera leo) skeletons to Southeast Asia under CITES Appendix II. Legal exports rose from approximately 50 individuals in 2008 to a maximum of 1,771 skeletons in 2016, and has led to ongoing concerns over possible laundering of non-lion, multiple-source and wild-sourced bones. South Africa is required under its obligations to CITES to employ mechanisms for monitoring and reporting trade, and to limit the potential for illegal trade and laundering of lion and other large felid bones. Monitoring tools for legal trade are critical to compliance with CITES. Here we evaluate the CITES-compliance procedure implemented by South Africa for export of lion bones and identify six essential general points for consideration in the implementation of animal export quota compliance protocols. We provide specific insight into the South African lion bone export monitoring system through: i) outlining the protocols followed; ii) assessing the utility of cranial morphology to identify species; iii) evaluating skeleton consignment weight as a monitoring tool; and iv) presenting molecular (DNA) species assignment and pairwise-comparative sample matching of individuals. We describe irregularities and illicit behaviour detected in the 2017 and 2018 lion bone quotas. Notably, we report that the compliance procedure successfully identified and prevented the attempted laundering of a tiger (P. tigris) skeleton in 2018. We emphasise the utility of mixed-method protocols for the monitoring of compliance in CITES Appendix II export quota systems.
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Affiliation(s)
- Vivienne L. Williams
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Zoology, Wildlife Conservation Research Unit, Recanati-Kaplan Centre, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Peter G. Coals
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Zoology, Wildlife Conservation Research Unit, Recanati-Kaplan Centre, University of Oxford, Oxford, United Kingdom
| | - Marli de Bruyn
- South African National Biodiversity Institute, Pretoria, South Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town, South Africa
| | - Desiré L. Dalton
- South African National Biodiversity Institute, Pretoria, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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8
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Naude VN, Balme GA, Rogan MS, Needham MD, Whittington‐Jones G, Dickerson T, Mabaso X, Nattrass N, Bishop JM, Hunter L, O'Riain MJ. Longitudinal assessment of illegal leopard skin use in ceremonial regalia and acceptance of
faux
alternatives among followers of the Shembe Church, South Africa. Conservat Sci and Prac 2020. [DOI: 10.1111/csp2.289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Vincent N. Naude
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
- Panthera New York USA
| | | | - Matt S. Rogan
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
- Panthera New York USA
| | - Mark D. Needham
- Department of Forest Ecosystems and Society Oregon State University Corvallis Oregon USA
| | | | | | - Xolani Mabaso
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
| | - Nicoli Nattrass
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
| | - Luke Hunter
- Wildlife Conservation Society New York New York USA
| | - M. Justin O'Riain
- Institute for Communities and Wildlife in Africa (iCWild) University of Cape Town Cape Town South Africa
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9
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Naude VN, Balme GA, O'Riain J, Hunter LT, Fattebert J, Dickerson T, Bishop JM. Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards. Ecol Evol 2020; 10:3605-3619. [PMID: 32313621 PMCID: PMC7160178 DOI: 10.1002/ece3.6089] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 11/07/2022] Open
Abstract
Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home-ranges) could disrupt natal dispersal mechanisms, with long-term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male-biased natal dispersal. Using a combination of spatial (home-range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin-clustering in males of this historically exploited population is comparable to that of females in a well-protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.
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Affiliation(s)
- Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
- PantheraNew YorkNYUSA
| | | | - Justin O'Riain
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Luke T.B. Hunter
- Wildlife Conservation SocietyBronxNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julien Fattebert
- PantheraNew YorkNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
- Wyoming Cooperative Fish and Wildlife Research UnitDepartment of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
| | | | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
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10
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Naude VN, Becker FS, Mayberry JL, Vieira WF, Toit JT. Logging roads as surrogates for elephant trails: Facilitating social signaling by small forest ungulates despite increasing risks. Conservat Sci and Prac 2019. [DOI: 10.1111/csp2.43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Vincent N. Naude
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological SciencesUniversity of Cape Town Cape Town South Africa
| | - François S. Becker
- Gobabeb Research and Training CentreNamib Naukluft Park Walvis Bay Namibia
| | - Jillian L. Mayberry
- Institute of Biological and Environmental SciencesUniversity of Aberdeen Aberdeen UK
| | - Wilson F. Vieira
- Centre for Research in AnthropologyUniversity of Lisbon Lisbon Portugal
| | - Johan T. Toit
- Department of Wildland ResourcesUtah State University Logan Utah
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