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Kunde MN, Barlow A, Klittich AM, Yakupova A, Patel RP, Fickel J, Förster DW. First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages. Ecol Evol 2023; 13:e9969. [PMID: 37082317 PMCID: PMC10111171 DOI: 10.1002/ece3.9969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.
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Affiliation(s)
- Miriam N. Kunde
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- School of EnvironmentGriffith UniversityNathan Campus, 170 Kessels Road, NathanBrisbaneQueensland4111Australia
| | - Axel Barlow
- School of Natural SciencesBangor UniversityBangorGwyneddLL57 2DGUK
| | - Achim M. Klittich
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Aliya Yakupova
- Computer Technologies LaboratoryITMO University197101Saint PetersburgRussia
| | - Riddhi P. Patel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
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2
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Bursell MG, Dikow RB, Figueiró HV, Dudchenko O, Flanagan JP, Aiden EL, Goossens B, Nathan SK, Johnson WE, Koepfli KP, Frandsen PB. Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories. iScience 2022; 25:105647. [PMID: 36590460 PMCID: PMC9801239 DOI: 10.1016/j.isci.2022.105647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.
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Affiliation(s)
- Madeline G. Bursell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Henrique V. Figueiró
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | | | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Center for Theoretical Biological Physics, Rice University, Houston, TX, USA,UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia,Departments of Computer Science and Computational and Applied Mathematics, Rice University,Houston, TX, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia,Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK,Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | | | - Warren E. Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA,The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA,Walter Reed Army Institute of Research, Silver Spring, MD, USA,Loyola University Maryland, Baltimore, MD, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA,Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA,Corresponding author
| | - Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA,Corresponding author
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3
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Juman MM, Woodman N, Miller-Murthy A, Olson LE, Sargis EJ. Taxonomic boundaries in Lesser Treeshrews (Scandentia, Tupaiidae: Tupaia minor ). J Mammal 2022. [DOI: 10.1093/jmammal/gyac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The Lesser Treeshrew, Tupaia minor Günther, 1876, is a small mammal from Southeast Asia with four currently recognized subspecies: T. m. minor from Borneo; T. m. malaccana from the Malay Peninsula; T. m. humeralis from Sumatra; and T. m. sincepis from Singkep Island and Lingga Island. A fifth subspecies, T. m. caedis, was previously synonymized with T. m. minor; it was thought to occur in northern Borneo and on the nearby islands of Banggi and Balambangan. These subspecies were originally differentiated based on pelage color, a plastic feature that has proven to be an unreliable indicator of taxonomic boundaries in treeshrews and other mammals. To explore infraspecific variation among T. minor populations across the Malay Peninsula, Borneo, Sumatra, and smaller islands, we conducted multivariate analyses of morphometric data collected from the hands and skulls of museum specimens. Principal component and discriminant function analyses reveal limited differentiation in manus and skull proportions among populations of T. minor from different islands. We find no morphometric support for the recognition of the four allopatric subspecies and no support for the recognition of T. m. caedis as a separate subspecies on Borneo.
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Affiliation(s)
- Maya M Juman
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
| | - Neal Woodman
- U.S. Geological Survey, Eastern Ecological Science Center , Laurel, Maryland 20708 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
| | - Ananth Miller-Murthy
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
| | - Link E Olson
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Department of Mammalogy, University of Alaska Museum, University of Alaska Fairbanks , Fairbanks, Alaska 99775 , USA
| | - Eric J Sargis
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
- Department of Anthropology, Yale University , New Haven, Connecticut 06520 , USA
- Yale Institute for Biospheric Studies , New Haven, Connecticut 06520 , USA
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4
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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5
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Skeletal Variation and Taxonomic Boundaries in the Pen-tailed Treeshrew (Scandentia: Ptilocercidae; Ptilocercus lowii Gray, 1848). J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Ng KKS, Kobayashi MJ, Fawcett JA, Hatakeyama M, Paape T, Ng CH, Ang CC, Tnah LH, Lee CT, Nishiyama T, Sese J, O'Brien MJ, Copetti D, Isa MNM, Ong RC, Putra M, Siregar IZ, Indrioko S, Kosugi Y, Izuno A, Isagi Y, Lee SL, Shimizu KK. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Commun Biol 2021; 4:1166. [PMID: 34620991 PMCID: PMC8497594 DOI: 10.1038/s42003-021-02682-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
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Affiliation(s)
- Kevin Kit Siong Ng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Masaki J Kobayashi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jeffrey A Fawcett
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Choon Cheng Ang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Tomoaki Nishiyama
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Tokyo Tech RWBC-OIL, Meguro-ku, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Michael J O'Brien
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n., E-28933, Móstoles, Spain
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Mahardika Putra
- Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | | | - Sapto Indrioko
- Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia
| | - Yoshiko Kosugi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ayako Izuno
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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7
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Juman MM, Woodman N, Olson LE, Sargis EJ. Ecogeographic variation and taxonomic boundaries in Large Treeshrews (Scandentia, Tupaiidae: Tupaia tana Raffles, 1821) from Southeast Asia. J Mammal 2021. [DOI: 10.1093/jmammal/gyab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The Large Treeshrew, Tupaia tana Raffles, 1821, is a small mammal (~205 g) from Southeast Asia with a complicated taxonomic history. Currently, 15 subspecies are recognized from Borneo, Sumatra, and smaller islands, and many were originally differentiated based on minor pelage differences and small sample sizes. We explored intraspecific variation in T. tana using quantitative osteological data obtained from the hands and skulls of museum specimens. Multivariate analyses reveal extensive overlap among T. tana populations in morphospace, indicating that the majority of currently recognized subspecies are not morphometrically distinct. In contrast, the separation between Bornean and Sumatran populations of T. tana is sufficient to recognize them as different subspecies. Comparisons of Bornean specimens to those on small, offshore islands reveal that the latter average smaller body size. This pattern is inconsistent with Foster’s island rule, which predicts that island populations of small mammals (< 5 kg) will average larger body size relative to mainland forms. A similar lack of support for ecogeographic rules has been noted in T. glis (Diard, 1820), suggesting that these “rules” are poor predictors of geographic variation in treeshrews.
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Affiliation(s)
- Maya M Juman
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , USA
| | - Neal Woodman
- U.S. Geological Survey, Eastern Ecological Science Center , Laurel, MD , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Link E Olson
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Mammalogy, University of Alaska Museum, University of Alaska Fairbanks , Fairbanks, AK , USA
| | - Eric J Sargis
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, CT , USA
- Department of Anthropology, Yale University , New Haven, CT , USA
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8
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Mengüllüoğlu D, Ambarlı H, Barlow A, Paijmans JLA, Sayar AO, Emir H, Kandemir İ, Hofer H, Fickel J, Förster DW. Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx. Genes (Basel) 2021; 12:genes12081216. [PMID: 34440390 PMCID: PMC8392285 DOI: 10.3390/genes12081216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.
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Affiliation(s)
- Deniz Mengüllüoğlu
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Correspondence:
| | - Hüseyin Ambarlı
- Department of Wildlife Ecology and Management, Faculty of Forestry, Düzce University, Düzce 81620, Turkey;
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ali Onur Sayar
- Department of Game and Wildlife, Cankiri Karatekin University, Cankiri 18100, Turkey;
| | - Hasan Emir
- Wildlife Department of General Directorate of Nature Conservation and National Parks, Turkish Ministry of Agriculture and Forestry, Ankara 06000, Turkey;
| | - İrfan Kandemir
- Department of Biology, Ankara University, Ankara 06000, Turkey;
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
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9
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Gomez L, Shepherd CR. The illegal exploitation of the Javan Leopard (Panthera pardus melas) and Sunda Clouded Leopard (Neofelis diardi) in Indonesia. NATURE CONSERVATION 2021. [DOI: 10.3897/natureconservation.43.59399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Indonesia is home to the Javan Leopard (Panthera pardus melas) and the Sunda Clouded Leopard (Neofelis diardi), both of which are threatened by habitat loss, human-wildlife conflict issues and the illegal wildlife trade. Leopards and clouded leopards are threatened by the illegal wildlife trade across their range, however, very little is known of the illegal trade in these two species in Indonesia, or of the efforts made to tackle this crime. Both the Javan Leopard and Sunda Clouded Leopard are protected species in Indonesia and both species are listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), meaning commercial international trade is generally prohibited. To better understand the trade, and efforts to end this trade, we collected records of seizures and prosecutions relating to Javan Leopards and Sunda Clouded Leopards in Indonesia for the period 2011–2019. Despite both species being protected by law, this study reveals the prevalence of extensive poaching, illegal domestic trade and international trafficking of both species. A total of 41 seizure records were obtained from 2011 to 2019, which was estimated to amount to approximately 83 animals, which likely represents only a fraction of the total number of cases and therefore the risk may be substantially greater. Approximately half of the cases resulted in successful prosecution and of these, the highest sentence given was 2 years in jail and a fine of IDR50mil (~USD3300). The majority of the penalties handed down for these crimes were far below the maximum potential penalties and are unlikely to be effective deterrents.
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Macdonald DW, Bothwell HM, Kaszta Ż, Ash E, Bolongon G, Burnham D, Can ÖE, Campos‐Arceiz A, Channa P, Clements GR, Hearn AJ, Hedges L, Htun S, Kamler JF, Kawanishi K, Macdonald EA, Mohamad SW, Moore J, Naing H, Onuma M, Penjor U, Rasphone A, Mark Rayan D, Ross J, Singh P, Tan CKW, Wadey J, Yadav BP, Cushman SA. Multi‐scale habitat modelling identifies spatial conservation priorities for mainland clouded leopards (
Neofelis nebulosa
). DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12967] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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11
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Angelici FM, Ciucani MM, Angelini S, Annesi F, Caniglia R, Castiglia R, Fabbri E, Galaverni M, Palumbo D, Ravegnini G, Rossi L, Siracusa AM, Cilli E. The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population. Zoolog Sci 2019; 36:189-197. [PMID: 31251487 DOI: 10.2108/zs180180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/03/2019] [Indexed: 11/17/2022]
Abstract
Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.
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Affiliation(s)
| | - Marta M Ciucani
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Natural History Museum of Denmark, Copenhagen, Denmark
| | - Sabrina Angelini
- Dip.to Farmacia e Biotecnologia, Università di Bologna, Bologna, Italy
| | - Flavia Annesi
- Dip.to Biologia e Biotecnologie 'C. Darwin', Sapienza Università di Roma, Roma, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione BIO-CGE, ISPRA, Ozzano dell'Emilia, Bologna, Italy,
| | - Riccardo Castiglia
- Dip.to Biologia e Biotecnologie 'C. Darwin', Sapienza Università di Roma, Roma, Italy
| | - Elena Fabbri
- Area per la Genetica della Conservazione BIO-CGE, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | | | - Davide Palumbo
- Museo di Ecologia di Cesena, Piazza Pietro Zangheri, 6, 47521 Cesena (FC), Italy
| | - Gloria Ravegnini
- Dip.to Farmacia e Biotecnologia, Università di Bologna, Bologna, Italy
| | - Lorenzo Rossi
- Museo di Ecologia di Cesena, Piazza Pietro Zangheri, 6, 47521 Cesena (FC), Italy
| | - Agatino M Siracusa
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Sez. Biologia Animale "Marcello La Greca", Catania, Italy
| | - Elisabetta Cilli
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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Knott CD, Scott AM, O'Connell CA, Scott KS, Laman TG, Riyandi, Susanto TW. Possible Male Infanticide in Wild Orangutans and a Re-evaluation of Infanticide Risk. Sci Rep 2019; 9:7806. [PMID: 31127126 PMCID: PMC6534599 DOI: 10.1038/s41598-019-42856-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/08/2019] [Indexed: 11/08/2022] Open
Abstract
Infanticide as a male reproductive tactic is widespread across mammals, and is particularly prevalent in catarrhine primates. While it has never been observed in wild orangutans, infanticide by non-sire males has been predicted to occur due to their extremely long inter-birth intervals, semi-solitary social structure, and the presence of female counter-tactics to infanticide. Here, we report on the disappearance of a healthy four-month-old infant, along with a serious foot injury suffered by the primiparous mother. No other cases of infant mortality have been observed at this site in 30 years of study. Using photographic measurements of the injury, and information on the behavior and bite size of potential predators, we evaluate the possible causes of this injury. The context, including the behavior of the female and the presence of a new male at the time of the injury, lead us to conclude that the most likely cause of the infant loss and maternal injury was male infanticide. We suggest that in orangutans, and other species where nulliparous females are not preferred mates, these females may be less successful at using paternity confusion as an infanticide avoidance tactic, thus increasing the likelihood of infanticide of their first-born infants.
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Affiliation(s)
- Cheryl D Knott
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA.
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
| | - Amy M Scott
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA
| | - Caitlin A O'Connell
- Department of Biological Sciences, Human and Evolutionary Biology, 3616 Trousdale Parkway, University of Southern California, Los Angeles, CA, 90089, USA
| | - Katherine S Scott
- Department of Social Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Timothy G Laman
- Department of Ornithology, Harvard Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Riyandi
- Department of Biology, Jl. Dr. Hadari Nawawi, University of Tanjungpura, Pontianak, 7812, Indonesia
| | - Tri Wahyu Susanto
- Department of Biology, National University, Indonesia, Jakarta, 1250, Indonesia
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PAPAKOSTA MA, KITIKIDOU K, BAKALOUDIS DE, VLACHOS CG, CHATZINIKOS E, ALEXANDROU O, SAKOULIS A. Geographical variation in morphometry, craniometry, and diet of amammalian species (Stone marten, Martes foina) using data mining. TURK J ZOOL 2018. [DOI: 10.3906/zoo-1611-29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Veera Singham G, Othman AS, Lee CY. Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia. PLoS One 2017; 12:e0186690. [PMID: 29186140 PMCID: PMC5706666 DOI: 10.1371/journal.pone.0186690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 10/05/2017] [Indexed: 11/19/2022] Open
Abstract
Dispersal of soil-dwelling organisms via the repeatedly exposed Sunda shelf through much of the Pleistocene in Southeast Asia has not been studied extensively, especially for invertebrates. Here we investigated the phylogeography of an endemic termite species, Macrotermes gilvus (Hagen), to elucidate the spatiotemporal dynamics of dispersal routes of terrestrial fauna in Pleistocene Southeast Asia. We sampled 213 termite colonies from 66 localities throughout the region. Independently inherited microsatellites and mtDNA markers were used to infer the phylogeographic framework of M. gilvus. Discrete phylogeographic analysis and molecular dating based on fossil calibration were used to infer the dynamics of M. gilvus dispersal in time and space across Southeast Asia. We found that the termite dispersal events were consistently dated within the Pleistocene time frame. The dispersal pattern was multidirectional, radiating eastwards and southwards out of Indochina, which was identified as the origin for dispersal events. We found no direct dispersal events between Sumatra and Borneo despite the presence of a terrestrial connection between them during the Pleistocene. Instead, central Java served as an important link allowing termite colonies to be established in Borneo and Sumatra. Our findings support the hypothesis of a north-south dispersal corridor in Southeast Asia and suggest the presence of alternative dispersal routes across Sundaland during the Pleistocene. For the first time, we also propose that a west-east dispersal through over-water rafting likely occurred across the Pleistocene South China Sea. We found at least two independent entry routes for terrestrial species to infiltrate Sumatra and Borneo at different times.
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Affiliation(s)
- G. Veera Singham
- Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
- Population Genetics Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Population Genetics Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Chow-Yang Lee
- Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
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Anyone with a Long-Face? Craniofacial Evolutionary Allometry (CREA) in a Family of Short-Faced Mammals, the Felidae. Evol Biol 2017. [DOI: 10.1007/s11692-017-9421-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Threatened but understudied: supporting conservation by understanding the genetic structure of the flat-headed cat. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0990-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Klegarth A, Sanders S, Gloss A, Lane‐deGraaf K, Jones‐Engel L, Fuentes A, Hollocher H. Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of
Macaca fascicularis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:658-670. [DOI: 10.1002/ajpa.23235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/21/2017] [Accepted: 04/10/2017] [Indexed: 11/05/2022]
Affiliation(s)
- A.R. Klegarth
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of AnthropologyUniversity of WashingtonSeattle Washington
| | - S.A. Sanders
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- National Center for Genome Analysis SupportPervasive Technology Institute, Indiana UniversityBloomington Indiana
| | - A.D. Gloss
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucson Arizona
| | - K.E. Lane‐deGraaf
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of BiologyFontbonne UniversitySt. Louis Missouri
| | - L. Jones‐Engel
- Department of AnthropologyUniversity of WashingtonSeattle Washington
- National Primate Research CenterUniversity of WashingtonSeattle Washington
| | - A. Fuentes
- Department of AnthropologyUniversity of Notre DameNotre Dame Indiana
| | - H. Hollocher
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
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Martins RF, Fickel J, Le M, van Nguyen T, Nguyen HM, Timmins R, Gan HM, Rovie-Ryan JJ, Lenz D, Förster DW, Wilting A. Phylogeography of red muntjacs reveals three distinct mitochondrial lineages. BMC Evol Biol 2017; 17:34. [PMID: 28122497 PMCID: PMC5267393 DOI: 10.1186/s12862-017-0888-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/17/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia. RESULTS We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. CONCLUSIONS Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.
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Affiliation(s)
- Renata F. Martins
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
- Potsdam University, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 22-24, 14476 Potsdam-Golm, Germany
| | - Minh Le
- Faculty of Environmental Science, Hanoi University of Science, Vietnam National University, 334 Nguyen Trai Road, Hanoi, Vietnam
- Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam
| | - Thanh van Nguyen
- Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam
| | - Ha M. Nguyen
- Centre for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong Street, Hanoi, Vietnam
- Present address: U.S. Agency for International Development, Governance for Inclusive Growth Program, Chemonics International Inc, 115 Tran Hung Dao Street, Hanoi, Vietnam
| | | | - Han Ming Gan
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
| | - Jeffrine J. Rovie-Ryan
- Department of Wildlife and National Parks (DWNP) Peninsular Malaysia, National Wildlife Forensic Laboratory (NWFL), 56100 Kuala Lumpur, Malaysia
| | - Dorina Lenz
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
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Patel RP, Förster DW, Kitchener AC, Rayan MD, Mohamed SW, Werner L, Lenz D, Pfestorf H, Kramer-Schadt S, Radchuk V, Fickel J, Wilting A. Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160350. [PMID: 27853549 PMCID: PMC5098974 DOI: 10.1098/rsos.160350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.
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Affiliation(s)
- Riddhi P. Patel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
- Freie Universität Berlin, Kaiserswerther Strasse 16–18, 14195 Berlin, Germany
| | - Daniel W. Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Mark D. Rayan
- WWF Malaysia, 1 Jalan PJS 5/28A, Petaling Jaya Commercial Centre (PJCC), 46150 Petaling Jaya, Selangor, Malaysia
| | - Shariff W. Mohamed
- WWF Malaysia, 1 Jalan PJS 5/28A, Petaling Jaya Commercial Centre (PJCC), 46150 Petaling Jaya, Selangor, Malaysia
| | - Laura Werner
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Hans Pfestorf
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Stephanie Kramer-Schadt
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Viktoriia Radchuk
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
| | - Andreas Wilting
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
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20
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Cooper DM, Dugmore AJ, Gittings BM, Scharf AK, Wilting A, Kitchener AC. Predicted Pleistocene–Holocene range shifts of the tiger (
Panthera tigris
). DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12484] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- David M. Cooper
- Institute of Geography The University of Edinburgh Drummond Street EH8 9XP Edinburgh United Kingdom
| | - Andrew J. Dugmore
- Institute of Geography The University of Edinburgh Drummond Street EH8 9XP Edinburgh United Kingdom
| | - Bruce M. Gittings
- Institute of Geography The University of Edinburgh Drummond Street EH8 9XP Edinburgh United Kingdom
| | - Anne K. Scharf
- Leibniz Institute for Zoo and Wildlife Research Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Andrew C. Kitchener
- Institute of Geography The University of Edinburgh Drummond Street EH8 9XP Edinburgh United Kingdom
- Department of Natural Sciences National Museums of Scotland Chambers Street EH1 1JF Edinburgh United Kingdom
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21
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Oshida T, Yasuda M, Sasaki M. Preliminary Study on Phylogeography ofCallosciurus prevostiiin Southeast Asia: Mitochondrial DNA Evidence Supports Riverine Barrier Hypothesis. MAMMAL STUDY 2016. [DOI: 10.3106/041.041.0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Wilting A, Patel R, Pfestorf H, Kern C, Sultan K, Ario A, Peñaloza F, Kramer-Schadt S, Radchuk V, Foerster DW, Fickel J. Evolutionary history and conservation significance of the Javan leopard Panthera pardus melas. J Zool (1987) 2016. [DOI: 10.1111/jzo.12348] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- A. Wilting
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - R. Patel
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - H. Pfestorf
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute for Biochemistry and Biology; Plant Ecology and Nature Conservation; Potsdam University; Potsdam Germany
| | - C. Kern
- Tierpark Berlin; Berlin Germany
| | - K. Sultan
- Taman Safari Indonesia; Bogor West Java Indonesia
| | - A. Ario
- Conservation International Indonesia; Jakarta Selatan Indonesia
| | - F. Peñaloza
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | | | - V. Radchuk
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - D. W. Foerster
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - J. Fickel
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute for Biochemistry and Biology; Potsdam University; Potsdam Germany
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Molecular systematics of the small-toothed palm civet (Arctogalidia trivirgata) reveals a strong divergence of Bornean populations. Mamm Biol 2015. [DOI: 10.1016/j.mambio.2015.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Mohamad SW, Rayan DM, Christopher WCT, Hamirul M, Mohamed A, Lau CF, Siwan ES. The first description of population density and habitat use of the mainland clouded leopard Neofelis nebulosa within a logged-primary forest in South East Asia. POPUL ECOL 2015. [DOI: 10.1007/s10144-015-0494-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Wilting A, Courtiol A, Christiansen P, Niedballa J, Scharf AK, Orlando L, Balkenhol N, Hofer H, Kramer-Schadt S, Fickel J, Kitchener AC. Planning tiger recovery: Understanding intraspecific variation for effective conservation. SCIENCE ADVANCES 2015; 1:e1400175. [PMID: 26601191 PMCID: PMC4640610 DOI: 10.1126/sciadv.1400175] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/05/2015] [Indexed: 05/21/2023]
Abstract
Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.
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Affiliation(s)
- Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Alexandre Courtiol
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | | | - Jürgen Niedballa
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Anne K. Scharf
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Ludovic Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Niko Balkenhol
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
- Institute for Biochemistry and Biology, Potsdam University, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
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26
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McCarthy JL, Wibisono HT, McCarthy KP, Fuller TK, Andayani N. Assessing the distribution and habitat use of four felid species in Bukit Barisan Selatan National Park, Sumatra, Indonesia. Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2014.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Is the clouded leopard Neofelis nebulosa extinct in Taiwan, and could it be reintroduced? An assessment of prey and habitat. ORYX 2014. [DOI: 10.1017/s003060531300063x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AbstractDuring 1997–2012 we conducted a nationwide camera-trapping survey and assessed the availability of prey and habitat for the clouded leopard Neofelis nebulosa in Taiwan. We surveyed 1,249 camera-trap sites over 113,636 camera-trap days, from the seashore to an altitude of 3,796 m and covering various types of vegetation. No clouded leopards were photographed during 128,394 camera-trap days, including at 209 sites in other studies, confirming the presumed extinction of clouded leopards in Taiwan. Assessment of the prey base revealed altitudinal distribution patterns of prey species and prey biomass. Areas at lower altitudes and with less human encroachment and hunting supported a higher prey biomass and more of the typical prey species of clouded leopards. Habitat analysis revealed 8,523 km2 of suitable habitat but this was reduced to 6,734 km2 when adjacent areas of human encroachment were subtracted. In the absence of hunting and large mammalian carnivores the major prey of clouded leopards in Taiwan, such as Formosan macaques Macaca cyclopis, Reeves's muntjacs Muntiacus reevesi, Formosan serow Capricornis swinhoei and sambar Rusa unicolor, could become over-abundant. Thus, it is important to address the cascading effect of the disappearance of top-down predator control. Our assessment indicated that, with proper regulation of hunting, habitat restoration and corridor improvement, it may be possible to reintroduce the clouded leopard.
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Zarowiecki M, Linton YM, Post RJ, Bangs MJ, Htun PT, Hlaing T, Seng CM, Baimai V, Ding TH, Sochantha T, Walton C. Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo-Oriental Region. Mol Ecol 2014; 23:2573-89. [PMID: 24750501 DOI: 10.1111/mec.12761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus s.l. sampled from 18 populations across its pan-Asian species range, using sequences from mitochondrial cytochrome c oxidase subunit 1 (CO1), the internal transcribed spacer 2 (ITS2) and the mannose phosphate isomerase (Mpi) gene. A hypothesis of ecological speciation for A. sundaicus involving divergent adaptation to brackish and freshwater larval habitats was also previously proposed, based on a deficiency of heterozygotes for Mpi allozyme alleles in sympatry. This hypothesis was not supported by Mpi sequence data, which exhibited no fixed differences between brackish and freshwater larval habitats. Mpi and CO1 supported the presence of up to eight genetically distinct population groupings. Counter to the hypothesis of three allopatric species, divergence was often no greater between Borneo, Sumatra/Java and the Southeast Asian mainland than it was between genetic groupings within these landmasses. An isolation-with-migration (IM) model indicates recurrent gene flow between the current major landmasses. Such gene flow would have been possible during glacial periods when the current landmasses merged, presenting opportunities for dispersal along expanding and contracting coastlines. Consequently, Pleistocene climatic variation has proved a homogenizing, rather than diversifying, force for A. sundaicus diversity.
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Affiliation(s)
- Magdalena Zarowiecki
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Veron G, Willsch M, Dacosta V, Patou ML, Seymour A, Bonillo C, Couloux A, Wong ST, Jennings AP, Fickel J, Wilting A. The distribution of the Malay civetViverra tangalunga(Carnivora: Viverridae) across Southeast Asia: natural or human-mediated dispersal? Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geraldine Veron
- Unité Origine; Structure et Evolution de la Biodiversité; UMR CNRS MNHN 7205; Département Systématique et Evolution; Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier 75231 Paris Cedex 05 France
| | - Maraike Willsch
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Victor Dacosta
- Unité Origine; Structure et Evolution de la Biodiversité; UMR CNRS MNHN 7205; Département Systématique et Evolution; Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier 75231 Paris Cedex 05 France
| | - Marie-Lilith Patou
- Unité Origine; Structure et Evolution de la Biodiversité; UMR CNRS MNHN 7205; Département Systématique et Evolution; Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier 75231 Paris Cedex 05 France
| | - Adrian Seymour
- Operation Wallacea; Old Bolingbroke; Lincolnshire PE23 4EX UK
| | - Celine Bonillo
- Service de Systématique Moléculaire; UMS 2700; Département Systématique et Evolution; Muséum National d'Histoire Naturelle; CP 26, 57 rue Cuvier 75231 Paris Cedex 05 France
| | - Arnaud Couloux
- Genoscope; Centre National de Séquençage; 2 rue Gaston Crémieux, CP5706 91057 Evry Cedex France
| | - Siew Te Wong
- Bornean Sun Bear Conservation Center; PPM 219, Elopura 90000 Sandakan Sabah Malaysia
| | - Andrew P. Jennings
- Unité Origine; Structure et Evolution de la Biodiversité; UMR CNRS MNHN 7205; Département Systématique et Evolution; Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier 75231 Paris Cedex 05 France
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research; Alfred-Kowalke-Str. 17 10315 Berlin Germany
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Ohtani M, Kondo T, Tani N, Ueno S, Lee LS, Ng KKS, Muhammad N, Finkeldey R, Na'iem M, Indrioko S, Kamiya K, Harada K, Diway B, Khoo E, Kawamura K, Tsumura Y. Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South-East Asia. Mol Ecol 2013; 22:2264-79. [PMID: 23432376 DOI: 10.1111/mec.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/26/2012] [Accepted: 01/05/2013] [Indexed: 11/29/2022]
Abstract
Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28-0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
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Affiliation(s)
- Masato Ohtani
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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Wilting A, Fickel J. Phylogenetic relationship of two threatened endemic viverrids from the
S
unda
I
slands,
H
ose's civet and
S
ulawesi civet. J Zool (1987) 2012. [DOI: 10.1111/j.1469-7998.2012.00939.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. Wilting
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - J. Fickel
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
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Density of the Vulnerable Sunda clouded leopard Neofelis diardi in two commercial forest reserves in Sabah, Malaysian Borneo. ORYX 2012. [DOI: 10.1017/s0030605311001694] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractRecently the Sunda clouded leopard Neofelis diardi was recognized as a separate species distinct from the clouded leopard Neofelis nebulosa of mainland Asia. Both species are categorized as Vulnerable on the IUCN Red List. Little is known about the newly identified species and, in particular, information from forests outside protected areas is scarce. Here we present one of the first density estimates calculated with spatial capture–recapture models using camera-trap data. In two commercial forest reserves in Sabah (both certified for their sustainable management practices) the density of the Sunda clouded leopard was estimated to be c. 1 per 100 km2 (0.84±SE 0.42 and 1.04±SE 0.58). The presence of the Sunda clouded leopard in such forests is encouraging for its conservation but additional studies from other areas, including protected forests, are needed to compare and evaluate these densities.
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