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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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Samarasinghe DJ, Wikramanayake ED, Gopalaswamy AM, Jayewardene R, Kumara J, Fernando J, Gunawardene K, Alexander JS, Braczkowski A. Evidence for a critical leopard conservation stronghold from a large protected landscape on the island of Sri Lanka. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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3
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Paijmans JLA, Barlow A, Becker MS, Cahill JA, Fickel J, Förster DWG, Gries K, Hartmann S, Havmøller RW, Henneberger K, Kern C, Kitchener AC, Lorenzen ED, Mayer F, OBrien SJ, von Seth J, Sinding MHS, Spong G, Uphyrkina O, Wachter B, Westbury MV, Dalén L, Bhak J, Manica A, Hofreiter M. African and Asian leopards are highly differentiated at the genomic level. Curr Biol 2021; 31:1872-1882.e5. [PMID: 33848458 DOI: 10.1016/j.cub.2021.03.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Matthew S Becker
- Zambian Carnivore Programme, PO Box 80 Mfuwe, Eastern Province, Zambia
| | - James A Cahill
- Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA; Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, FL 32611
| | - Joerns Fickel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Daniel W G Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Katrin Gries
- Der Grüne Zoo Wuppertal, Hubertusallee 30, 42117 Wuppertal, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Rasmus Worsøe Havmøller
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark; Research and Collections, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen OE, Denmark
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Christian Kern
- Tierpark Berlin-Friedrichsfelde, Am Tierpark 125, 10319 Berlin, Germany
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK; Institute of Geography, School of Geosciences. Drummond Street, University of Edinburgh EH8 9XP, UK
| | - Eline D Lorenzen
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Invalidenstraße 43, 10115 Berlin, Germany
| | - Stephen J OBrien
- Laboratory of Genomics Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg, 197101, Russian Federation; Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, Florida 33004 USA
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Göran Spong
- Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 907 83 UMEA, SWEDEN
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, 159 Stoletiya Street, Vladivostok, 690022, Russia
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Michael V Westbury
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Clinomics, UNIST, Ulsan, 44919, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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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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Closely related species show species-specific environmental responses and different spatial conservation needs: Prionailurus cats in the Indian subcontinent. Sci Rep 2020; 10:18705. [PMID: 33127966 PMCID: PMC7599212 DOI: 10.1038/s41598-020-74684-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 10/05/2020] [Indexed: 11/09/2022] Open
Abstract
Phylogenetically closely related species are often assumed to have similar responses to environmental conditions, but species-specific responses have also been described. These two scenarios may have different conservation implications. We tested these two hypotheses for Prionailurus cats (P. rubiginosus, P. bengalensis, P. viverrinus) in the Indian subcontinent and show its implications on species current protected area coverage and climatic suitability trends through time. We fitted ecological niche models with current environmental conditions and calculated niche overlap. In addition, we developed a model for the Jungle Cat Felis chaus to compare species responses and niche overlap estimates within Prionailurus with those for a related sympatric small cat species. Then we estimated the proportion of current suitable environment covered by protected area and projected climatic models from past (last interglacial) to future (2070; RCP4.5 and RCP8.5) conditions to show implications on population management and conservation. The hypothesis of a similar response and niche overlap among closely related species is not supported. Protected area coverage was lowest for P. viverrinus (mean = 0.071, SD = 0.012) and highest for P. bengalensis (mean = 0.088, SD = 0.006). In addition, the proportion of the subcontinent with suitable climate varied through time and was species-specific. For P. bengalensis, climatic suitability shrunk since at least the mid-Holocene, a trend that can be intensified by human-induced climate warming. Concerning P. viverrinus, most predictions show stable future climatic suitability, but a few indicated potential loss. Climatic suitability for P. rubiginous was predicted to remain stable but the species exhibited a negative association with intensive agriculture. Similar responses to environmental change by phylogenetically closely related species should not be assumed and have implications on protected area coverage and natural trends of species climatic suitability over time. This should be taken into account during conservation and management actions.
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Hyun JY, Cho JH, Pandey P, Min MS, Kim KS, Lee H. Phylogenetic study of extirpated Korean leopard using mitochondrial DNA from an old skin specimen in South Korea. PeerJ 2020; 8:e8900. [PMID: 32435529 PMCID: PMC7227655 DOI: 10.7717/peerj.8900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
The leopard, Panthera pardus, is a threatened species in its range throughout the world. Although, historically, the Korean Peninsula had a high population density of leopards, they were extirpated from South Korea by 1970, leaving almost no genetic specimens. Traditionally, Korean leopards are classified as Panthera pardus orientalis; however, their classification is based only on locality and morphology. Therefore, there is a need for genetic studies to identify the phylogenetic status of Korean leopards at the subspecies level. Presently, no extant wild specimen is available from South Korea; therefore, we extracted genetic material from the old skin of a leopard captured in Jirisan, South Korea in the 1930s and conducted the first phylogenetic study of the South Korean leopard. A total of 726 bp of mitochondrial DNA, including segments of the NADH5 and control region, were amplified by PCR. A phylogenetic analysis of the fragment, along with sequences of nine leopard subspecies from GenBank revealed that the extinct South Korean leopard belonged to the Asian leopard group and in the same clade as the Amur leopard (Panthera pardus orientalis). Thus, the leopard that inhabited South Korea in the past was of the same subspecies as the Amur leopard population currently inhabiting the transboundary region of Russia, China, and North Korea. These results emphasize the importance of conserving the endangered wild Amur leopard population (estimated to be about 60–80 individuals) in Russia and China, for future restoration of leopards in the Korean Peninsula.
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Affiliation(s)
- Jee Yun Hyun
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Tiger and Leopard Conservation Fund in Korea, Seoul, Republic of Korea
| | - Jang Hyuk Cho
- Tiger and Leopard Conservation Fund in Korea, Seoul, Republic of Korea
| | - Puneet Pandey
- Tiger and Leopard Conservation Fund in Korea, Seoul, Republic of Korea.,Amity Institute of Forestry and Wildlife, Amity University, Uttar Pradesh, India
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Tiger and Leopard Conservation Fund in Korea, Seoul, Republic of Korea
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Mengüllüoğlu D, Fickel J, Hofer H, Förster DW. Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species: Caucasian lynx as a case species. PLoS One 2019; 14:e0216549. [PMID: 31075125 PMCID: PMC6510455 DOI: 10.1371/journal.pone.0216549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/23/2019] [Indexed: 11/19/2022] Open
Abstract
The Caucasian lynx, Lynx lynx dinniki, has one of the southernmost distributions in the Eurasian lynx range, covering Anatolian Turkey, the Caucasus and Iran. Little is known about the biology and the genetic status of this subspecies. To collect baseline genetic, ecological and behavioural data and benefit future conservation of L. l. dinniki, we monitored 11 lynx territories (396 km2) in northwestern Anatolia. We assessed genetic diversity of this population by non-invasively collecting 171 faecal samples and trapped and sampled 12 lynx individuals using box traps. We observed high allelic variation at 11 nuclear microsatellite markers, and found no signs of inbreeding despite the potential isolation of this population. We obtained similar numbers of distinct genotypes from the two sampling sources. Our results indicated that first order female relatives occupy neighbouring territories (female philopatry) and that territorial male lynx were highly unrelated to each other and to female territorial lynx, suggesting long distance male dispersal. Particular male and female resident territorial lynx and their offspring (kittens and subadults) were more likely to be trapped than resident floaters or dispersing (unrelated) lynx. Conversely, we obtained more data for unrelated lynx and higher numbers of territorials using non-invasive sampling (faeces). When invasive and non-invasive samples were analysed separately, the spatial organisation of lynx (in terms of female philopatry and females and males occupying permanent ranges) affected measures of genetic diversity in such a way that estimates of genetic diversity were reduced if only invasive samples were considered. It appears that, at small spatial scales, invasive sampling using box traps may underestimate the genetic diversity in carnivores with permanent ranges and philopatry such as the Eurasian lynx. As non-invasive sampling can also provide additional data on diet and spatial organisation, we advocate the use of such samples for conservation genetic studies of vulnerable, endangered or data deficient territorial species.
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Affiliation(s)
- Deniz Mengüllüoğlu
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- * E-mail:
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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Stöck M, Fakharzadeh F, Kuhl H, Rozenblut-Kościsty B, Leinweber S, Patel R, Ebrahimi M, Voitel S, Schmidtler JF, Kami HG, Ogielska M, Förster DW. Shedding Light on a Secretive Tertiary urodelean Relict: Hynobiid salamanders ( Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental and Transcriptomic Data. Genes (Basel) 2019; 10:genes10040306. [PMID: 31003559 PMCID: PMC6523714 DOI: 10.3390/genes10040306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been described: Paradactylodon persicus from northwestern and P. gorganensis from northeastern Iran. Although P. gorganensis has been involved in studies on phylogeny and development, there is little data on the phylogeography, systematics, and development of the genus throughout the Hyrcanian Forests; genome-wide resources have been entirely missing. Given the huge genome size of hynobiids, making whole genome sequencing hardly affordable, we aimed to publish the first transcriptomic resources for Paradactylodon from an embryo and a larva (9.17 Gb RNA sequences; assembled to 78,918 unigenes). We also listed 32 genes involved in vertebrate sexual development and sex determination. Photographic documentation of the development from egg sacs across several embryonal and larval stages until metamorphosis enabled, for the first time, comparison of the ontogeny with that of other hynobiids and new histological and transcriptomic insights into early gonads and timing of their differentiation. Transcriptomes from central Elburz, next-generation sequencing (NGS) libraries of archival DNA of topotypic P. persicus, and GenBank-sequences of eastern P. gorganensis allowed phylogenetic analysis with three mitochondrial genomes, supplemented by PCR-amplified mtDNA-fragments from 17 museum specimens, documenting <2% uncorrected intraspecific genetic distance. Our data suggest that these rare salamanders belong to a single species P. persicus s.l. Humankind has a great responsibility to protect this species and the unique biodiversity of the Hyrcanian Forest ecosystems.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Fatemeh Fakharzadeh
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz 61357-43135, Iran.
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21,50-335 Wroclaw, Poland.
| | - Sophie Leinweber
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Rhiddi Patel
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
| | - Mehregan Ebrahimi
- Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran.
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia.
| | - Sebastian Voitel
- Independent Researcher, Spangenbergstraße 81, D-06295 Eisleben, Germany.
| | | | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan 49136-15759, Iran.
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21,50-335 Wroclaw, Poland.
| | - Daniel W Förster
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
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Paijmans JLA, Barlow A, Förster DW, Henneberger K, Meyer M, Nickel B, Nagel D, Worsøe Havmøller R, Baryshnikov GF, Joger U, Rosendahl W, Hofreiter M. Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations. BMC Evol Biol 2018; 18:156. [PMID: 30348080 PMCID: PMC6198532 DOI: 10.1186/s12862-018-1268-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1268-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo- and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Doris Nagel
- Institute for Paleontology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Rasmus Worsøe Havmøller
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Gennady F Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034, St. Petersburg, Russia
| | - Ulrich Joger
- State Natural History Museum, Pockelsstr. 10, 38106, Braunschweig, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn Museen and Curt-Engelhorn-Centre for Archaeometry, C4 8, 68159, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
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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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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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