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Sosale MS, Roelke-Parker M, Machange GA, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome of Meller's mongoose ( Rhynchogale melleri). Mitochondrial DNA B Resour 2024; 9:432-436. [PMID: 38586507 PMCID: PMC10993741 DOI: 10.1080/23802359.2024.2333567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.
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Affiliation(s)
- Medhini S. Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Melody Roelke-Parker
- Laboratory Animal Science Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
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2
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du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA, Hailer F. Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods. Mol Biol Evol 2023; 40:msad207. [PMID: 37713621 PMCID: PMC10630326 DOI: 10.1093/molbev/msad207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Centre for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | | | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, UK
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3
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Sosale MS, Songsasen N, İbiş O, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 2023; 866:147303. [PMID: 36854348 DOI: 10.1016/j.gene.2023.147303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
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Affiliation(s)
- Medhini S Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA
| | - Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Turkey
| | - Cody W Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
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4
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Coudrat CNZ, Chutipong W, Sukmak M, Sripiboon S, Klinsawat W. Taxonomic status of otter species in Nakai-Nam Theun National Park, Lao PDR, based on DNA evidence. Ecol Evol 2022; 12:e9601. [PMID: 36568871 PMCID: PMC9771668 DOI: 10.1002/ece3.9601] [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: 07/11/2022] [Revised: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Otter populations are threatened by habitat loss, pollution, conflicts with humans, and illegal wildlife trade to meet the demand for pets, for their fur, and for parts used in traditional medicines. Baseline information on the distribution, population genetic diversity, and connectivity is crucial to inform conservation management decisions; however, reliable data from otter populations in Southeast Asia remain scarce. In this study, we conducted baseline otter fecal DNA surveys based on mitochondrial DNA (mtDNA) to identify species, assess the occurrence, and map the spatial distribution of genetic diversity and evolutionary relationships of otter populations using 1700 bp Cytochrome B - Control Region and mitogenome from Nakai-Nam Theun National Park in the Annamite Mountains of Lao PDR. Of the total 56 samples identified to species, the majority (87.5%) was of the widely distributed Eurasian otter with three haplotypes (Lutra lutra; LLLA01-LLLA03), with a calculated haplotype diversity of 0.600 and a nucleotide diversity of 0.00141 based on mitogenome. The second species was the Asian small-clawed otter with only one haplotype detected (Aonyx cinereus; ACLA01). All Eurasian otter haplotypes were newly characterized and clustered within the strongly supported South-Southeast-North Asian clade of Lutra lutra. Compared with the European clade, the high mtDNA diversity of Lutra lutra in Nakai-Nam Theun National Park potentially reflects long-term demographic stability and lesser degree of population bottleneck during the last glacial maxima (LGM, ~21,000 years ago). The single haplotype detected in Asian small-clawed otters had not been detected in previous genetic studies. Our research is the first otter-specific noninvasive genetic study in Lao PDR and provides baseline insights into the otter population diversity in a regional priority site for biodiversity conservation.
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Affiliation(s)
| | - Wanlop Chutipong
- Conservation Ecology Program, Pilot Plant Development and Training InstituteKing Mongkut's University of Technology ThonburiBangkokThailand
| | - Manakorn Sukmak
- Department of Farm Resources and Production Medicine, Faculty of Veterinary MedicineKasetsart UniversityNakhon PathomThailand
| | - Supaphen Sripiboon
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary MedicineKasetsart UniversityNakhon PathomThailand
| | - Worata Klinsawat
- Conservation Ecology Program, School of Bioresources and TechnologyKing Mongkut's University of Technology ThonburiBangkokThailand
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5
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Sharma S, Chee‐Yoong W, Kannan A, Rama Rao S, Abdul‐Patah P, Ratnayeke S. Identification of three Asian otter species ( Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis. Ecol Evol 2022; 12:e9585. [PMCID: PMC9743061 DOI: 10.1002/ece3.9585] [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: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth‐coated otter, Asian small‐clawed otter, and hairy‐nosed otter have been reliably reported as residents. We designed a replicable and cost‐efficient PCR‐RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR‐RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D‐loop region and a 300‐bp fragment of the mt ND4 gene using primer sets TanaD, TanaD‐Mod, and OTR‐ND4, respectively. Amplification products were digested with restriction enzymes to generate species‐specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD‐Mod primer amplifying DNA from all 33 spraints. TanaD and OTR‐ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD‐Mod provided the expected species‐specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR‐ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR‐ND4 primer–enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD‐Mod (455 USD). We suggest the use of both OTR‐ND4 and TanaD‐Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR‐RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.
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Affiliation(s)
- Sandeep Sharma
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany,Institute of Biology, Martin Luther University Halle‐WittenbergHalleGermany
| | - Woo Chee‐Yoong
- Department of Biological SciencesSunway UniversitySelangor Darul EhsanMalaysia,Malaysian Nature SocietyKuala LumpurMalaysia
| | - Adrian Kannan
- Department of Biological SciencesSunway UniversitySelangor Darul EhsanMalaysia
| | - Suganiya Rama Rao
- Department of Biological SciencesSunway UniversitySelangor Darul EhsanMalaysia
| | - Pazil Abdul‐Patah
- Department of Wildlife and National Parks (PERHILITAN), Peninsular MalaysiaKuala LumpurMalaysia
| | - Shyamala Ratnayeke
- Department of Biological SciencesSunway UniversitySelangor Darul EhsanMalaysia,Skidmore CollegeNew YorkSaratoga SpringsUSA
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6
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Gray A, Brito JC, Edwards CW, Figueiró HV, Koepfli KP. First complete mitochondrial genome of the Saharan striped polecat ( Ictonyx libycus). MITOCHONDRIAL DNA PART B 2022; 7:1957-1960. [DOI: 10.1080/23802359.2022.2141080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Autumn Gray
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - José C. Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Virginia, USA
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7
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de Ferran V, Figueiró HV, de Jesus Trindade F, Smith O, Sinding MHS, Trinca CS, Lazzari GZ, Veron G, Vianna JA, Barbanera F, Kliver S, Serdyukova N, Bulyonkova T, Ryder OA, Gilbert MTP, Koepfli KP, Eizirik E. Phylogenomics of the world's otters. Curr Biol 2022; 32:3650-3658.e4. [PMID: 35779528 DOI: 10.1016/j.cub.2022.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.
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Affiliation(s)
- Vera de Ferran
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Henrique Vieira Figueiró
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Fernanda de Jesus Trindade
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Oliver Smith
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Cristine S Trinca
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Gabriele Zenato Lazzari
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75231 Paris Cedex 5, France
| | - Juliana A Vianna
- Millennium Institute Center for Genome Regulation (CRG), Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuna Mackenna 4860, Santiago 782-0436, Chile
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Natalia Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Tatiana Bulyonkova
- A. P. Ershov Institute of Informatics Systems SB RAS, 6 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA; Department of Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA.
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil; Instituto Pró-Carnívoros, Av. Horácio Netto, 1030 - Parque Edmundo Zanoni, Atibaia, São Paulo 12945-010, Brazil.
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8
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Ji Y, Baker CCM, Popescu VD, Wang J, Wu C, Wang Z, Li Y, Wang L, Hua C, Yang Z, Yang C, Xu CCY, Diana A, Wen Q, Pierce NE, Yu DW. Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nat Commun 2022; 13:1555. [PMID: 35322033 PMCID: PMC8943135 DOI: 10.1038/s41467-022-28778-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas. Invertebrate-derived eDNA (iDNA) is an emerging tool for taxonomic and spatial biodiversity monitoring. Here, the authors use metabarcoding of leech-derived iDNA to estimate vertebrate occupancy over an entire protected area, the Ailaoshan Nature Reserve, China.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Christopher C M Baker
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA. .,US Army ERDC Cold Regions Research and Engineering Laboratory, 72 Lyme Road, Hanover, NH, 03755, USA.
| | - Viorel D Popescu
- Department of Biological Sciences and Sustainability Studies Theme, Ohio University, 107 Irvine Hall, Athens, OH, 45701, USA.,Center for Environmental Studies (CCMESI), University of Bucharest, 1 N. Balcescu Blvd., Bucharest, Romania
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Yuanheng Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China.,Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Lin Wang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Mengla, China
| | - Chaolang Hua
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Zhongxing Yang
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Charles C Y Xu
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montreal, PQ, H3A2K6, Canada
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Sibson Building, Canterbury, Kent, CT27FS, UK
| | - Qingzhong Wen
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK.
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9
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Oboudi R, Malekian M, Khosravi R, Fadakar D, Adibi MA. Genetic structure and ecological niche segregation of Indian gray mongoose ( Urva edwardsii) in Iran. Ecol Evol 2021; 11:14813-14827. [PMID: 34765143 PMCID: PMC8571580 DOI: 10.1002/ece3.8168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 01/01/2023] Open
Abstract
Combining genetic data with ecological niche models is an effective approach for exploring climatic and nonclimatic environmental variables affecting spatial patterns of intraspecific genetic variation. Here, we adopted this combined approach to evaluate genetic structure and ecological niche of the Indian gray mongoose (Urva edwardsii) in Iran, as the most western part of the species range. Using mtDNA, we confirmed the presence of two highly differentiated clades. Then, we incorporated ensemble of small models (ESMs) using climatic and nonclimatic variables with genetic data to assess whether genetic differentiation among clades was coupled with their ecological niche. Climate niche divergence was also examined based on a principal component analysis on climatic factors only. The relative habitat suitability values predicted by the ESMs for both clades revealed their niche separation. Between-clade climate only niche comparison revealed that climate space occupied by clades is similar to some extent, but the niches that they utilize differ between the distribution ranges of clades. We found that in the absence of evidence for recent genetic exchanges, distribution models suggest the species occurs in different niches and that there are apparent areas of disconnection across the species range. The estimated divergence time between the two Iranian clades (4.9 Mya) coincides with the uplifting of the Zagros Mountains during the Early Pliocene. The Zagros mountain-building event seems to have prevented the distribution of U. edwardsii populations between the western and eastern parts of the mountains as a result of vicariance events. Our findings indicated that the two U. edwardsii genetic clades in Iran can be considered as two conservation units and can be utilized to develop habitat-specific and climate change-integrated management strategies.
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Affiliation(s)
- Razie Oboudi
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
| | - Mansoureh Malekian
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
| | - Rasoul Khosravi
- Department of Natural ResourcesSchool of AgricultureShiraz UniversityShirazIran
| | - Davoud Fadakar
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
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10
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Genetic and viability assessment of a reintroduced Eurasian otter Lutra lutra population on the River Ticino, Italy. ORYX 2021. [DOI: 10.1017/s0030605321000107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
On the River Ticino in northern Italy, a small number of captive Eurasian otters Lutra lutra, belonging to the European breeding programme for self-sustaining captive populations, were reintroduced in 1997, after the species had been declared locally extinct in the 1980s. We surveyed for otter signs in 2008, 2010, 2016–2017 and 2018, confirming the presence of what is probably a small population. To assess the abundance and viability of the population, we genotyped fresh spraints collected during the last two surveys, using 11 microsatellite markers, and modelled the population trend using Vortex. A minimum of six individuals were identified from 25 faecal samples. The analysis of mitochondrial DNA determined that the reintroduced otters share a transversion that is characteristic of the Asiatic subspecies Lutra lutra barang, confirming the contribution of the Asiatic subspecies to the genetic pool of the captive-bred founder population. Population size was consistent with the release of three pairs of otters and all models implied that the number of founders was too small to ensure the long-term survival of the population. Stochastic factors are therefore likely to threaten the success of this reintroduction.
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11
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Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, Mohd Salleh F. Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:502-504. [PMID: 33628904 PMCID: PMC7889269 DOI: 10.1080/23802359.2021.1872433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru, Malaysia
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12
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Dias CAR, Santos Júnior JE, Pinto CM, Santos FR, Perini FA. Mitogenomics of
Didelphis
(Mammalia; Didelphimorphia; Didelphidae) and insights into character evolution in the genus. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cayo Augusto Rocha Dias
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - José Eustáquio Santos Júnior
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Christian Miguel Pinto
- Departamento de Biologia Facultad de Ciencias Escuela Politécnica Nacional Quito Ecuador
| | - Fabrício Rodrigues Santos
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Fernando Araújo Perini
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
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13
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Taxonomic Revision and Evolutionary Phylogeography of Dusky Langur ( Trachypithecus obscurus) in Peninsular Malaysia. Zool Stud 2020; 59:e64. [PMID: 34140981 DOI: 10.6620/zs.2020.59-64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/04/2020] [Indexed: 11/18/2022]
Abstract
Dusky langur, Trachypithecus obscurus, inhabits tropical rainforests in Peninsular Malaysia, Thailand, and Myanmar. Morphologically, five subspecies are distributed in Peninsular Malaysia, but few studies have used genetic data to verify the classification. It is difficult to differentiate subspecies based on morphological characteristics, so this study used molecular data to differentiate subspecies of T. obscurus. The issue was addressed by analyzing 723 and 649 base pairs of the mitochondrial D-loop region and COI, respectively. DNA amplifications were performed using species-specific primer toward 35 individuals representing different populations. Phylogenetic analyses showed that two main clades representing populations in southern and northern Peninsular Malaysia. The results demonstrate that subspecies of T. obscurus in Peninsular Malaysia does not support classification based on the morphology that recognizes five subspecies. Previous study based on morphology that classified the subspecies on Perhentian Island, Terengganu, as T. obscurus styx is not recognized in this study. This subspecies happened to merge with the population in northern Peninsular Malaysia. Trachypithecus o. styx probably inhabited the southern peninsula and, due to the terminal Pleistocene sea level rise, spread to the east coast but could not spread farther because the subspecies was situated on offshore islands during the period. This assumption was supported by the molecular clock, which showed that subspecies on Perhentian Island spread after the Perlis population (T. obscurus flavicauda).
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14
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Jahari PNS, Mohd Azman S, Munian K, M Fauzi NF, Shamsir MS, Richter SR, Mohd Salleh F. The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3262-3264. [PMID: 33458132 PMCID: PMC7781998 DOI: 10.1080/23802359.2020.1812449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy’s rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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15
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Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. J Hum Evol 2020; 146:102852. [DOI: 10.1016/j.jhevol.2020.102852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/17/2022]
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16
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Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, Gilbert MTP, Mohd Salleh F. Molecular identification and phylogenetic analysis of a Callosciurus notatus complete mitogenome from Peninsular Malaysia. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3004-3006. [PMID: 33458034 PMCID: PMC7782351 DOI: 10.1080/23802359.2020.1797583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis against other available datasets showed that the mitogenome matched with 99.49% similarity to a previously published C. notatus mitogenome from Peninsular Malaysia. However, it also diverged by nearly 8% (92.24% match) from a second previously published mitogenome for the same species, sampled in East Kalimantan, Indonesia. This suggests a difference in landscape features between both localities might affect its genetic connectivity.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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17
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Jahari PNS, Abdul Malik NF, Shamsir MS, Gilbert MP, Mohd Salleh F. The first complete mitochondrial genome data of Hippocampus kuda originating from Malaysia. Data Brief 2020; 31:105721. [PMID: 32490085 PMCID: PMC7260291 DOI: 10.1016/j.dib.2020.105721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022] Open
Abstract
The spotted seahorse, Hippocampus kuda population is exponentially decreasing globally due to habitat loss contributed by massive coastal urbanization as well as its large exploitation for Chinese herbal medicine. Genomic data would be highly useful to improve biomonitoring of seahorse populations in Malaysia via the usage of non-invasive approaches such as water environmental DNA. Here we report the first complete mitogenome of two H. kuda individuals originating from Malaysia, generated using BGISEQ-500RS sequencer. The lengths of both mitogenomes are 16,529bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall base composition was 32.46% for A, 29.40% for T, 14.73% for G and 23.41% for C with AT rich features (61.86%). The gene organization of Malaysian H. kuda were similar to that of most teleost species. A phylogenetic analysis of the genome against mtDNA data from other Hippocampus species showed that Malaysian H. kuda samples clustered with H. capensis, H. reidi and H. kuda. Notably however, analysis of the data using BLASTn revealed they had 99.18% similarity to H. capensis, and only 97.66% to H. kuda and H. reidi, which are all part of the unresolved H. kuda complex. The mitogenomes are deposited in Genbank under the accession number MT221436 (HK1) and MT221436 (HK2).
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Affiliation(s)
- Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Nur Fatihah Abdul Malik
- Johor Biotechnology & Biodiversity Corporation (J-Biotech), Level 2, Bio-XCell Malaysia, No. 2, Jalan Bioteknologi 1, SiLC Industrial Park, 79200 Iskandar Puteri, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5a, 1353, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
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18
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Ge D, Feijó A, Abramov AV, Wen Z, Liu Z, Cheng J, Xia L, Lu L, Yang Q. Molecular phylogeny and morphological diversity of the Niviventer fulvescens species complex with emphasis on species from China. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species, N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer, N. fulvescens, N. huang, N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia; Joint Russian–Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhengjia Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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19
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Margaryan A, Sinding MHS, Liu S, Vieira FG, Chan YL, Nathan SKSS, Moodley Y, Bruford MW, Gilbert MTP. Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
The Javan rhinoceros (Rhinoceros sondaicus) is one of five extant rhinoceros species and among the rarest large mammals on Earth. Once widespread across Southeast Asia, it is now on the verge of extinction, with only one wild population remaining (estimated at ~60 individuals) on the island of Java, Indonesia. To assess the past genetic diversity of the female lineage of R. sondaicus, we generated mitochondrial genome data from eight museum specimens dating back to the 19th century, before the range of the Javan rhinoceros was dramatically reduced, for comparison against mitochondrial DNA (mtDNA) sequences of current R. sondaicus and other rhinoceros species. We succeeded in reconstructing five full and three partial ancient mitogenomes from the eight samples. We used BEAST to assess the phylogenetic relationship of the five extant rhinoceros species and the historical samples. The results show that the oldest and most diverse mtDNA lineages of R. sondaicus are found in historical samples, indicating a significant reduction of mtDNA diversity in modern Javan rhinos. We anticipate that the newly sequenced data will represent a useful resource for improving our understanding of evolutionary history of this species, should future studies be able to increase the available dataset. We hope this information may help in conservation efforts for this species.
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Affiliation(s)
- Ashot Margaryan
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Shanlin Liu
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE, Sweden
| | | | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Norway
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20
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Jewgenow K, Azevedo A, Albrecht M, Kirschbaum C, Dehnhard M. Hair cortisol analyses in different mammal species: choosing the wrong assay may lead to erroneous results. CONSERVATION PHYSIOLOGY 2020; 8:coaa009. [PMID: 32153782 PMCID: PMC7055589 DOI: 10.1093/conphys/coaa009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/05/2019] [Accepted: 01/22/2020] [Indexed: 05/25/2023]
Abstract
Wild animals are faced with a broad range of environmental stressors and research is needed to better understand their effect on populations. Hormone analysis based on enzyme immunoassays (EIAs) can provide valuable information on adrenocortical activity (stress), and assessment of cortisol in hair may allow the quantification of cortisol production. To validate hair hormone analysis, we compared two EIAs based on antibodies against cortisol-3-CMO-BSA and cortisol-21-HS-BSA for hair glucocorticoid (hGC) measurements in Egyptian mongoose, Iberian lynx, Alpine marmot, Asiatic black bear, spotted hyena and cheetah, with results obtained by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) measurements. Both EIAs were also characterized by HPLC immunograms. Our results revealed that the cortisol-21-HS EIA measured 2.3- to 12-fold higher hGC concentrations than the cortisol-3-CMO assay. In dependence of the species, high-performance liquid chromatography (HPLC) immunograms showed that up to 70% of immunoreactivities determined by the cortisol-21-HS constituted of unknown unpolar compounds leading to an overestimation of hGC. The cortisol-3-CMO EIA expressed a better specificity, with 32.1-67.4% of immunoreactivity represented by cortisol and cortisone. The LC-MS/MS analyses (gold standard) revealed that the cortisol-3-CMO EIA also resulted in an (up to 3-fold) overestimation of hGC, but EIA results were correlated with LC-MS/MS in the mongoose, the lynx, the spotted hyena and the marmot. No correlation was obtained for Asiatic black bears. As a result of our study, we strongly recommend to test any cortisol EIA for its specificity towards extracted hair components. In all analyzed species, except the Asiatic black bear, cortisone and cortisol were simultaneously present in hair extracts; consequently, an appropriate EIA should cross-react to these two glucocorticoid hormones and express negligible affinity towards substances with less polarity than corticosterone. Choosing the wrong EIA for hGC analyses may lead to overestimations of hGC or-in the worst case-to results that do not mirror real adrenocortical activity.
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Affiliation(s)
- Katarina Jewgenow
- Department Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str.17, D-10315 Berlin, Germany
| | - Alexandre Azevedo
- Department Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str.17, D-10315 Berlin, Germany
- Instituto de Ciências Biomédicas Abel Salazar, R. Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Mareen Albrecht
- Department Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str.17, D-10315 Berlin, Germany
| | - Clemens Kirschbaum
- Faculty of Psychology, Department of Biopsychology, Technical University of Dresden, Helmholtzstraße 10, D-01069 Dresden, Germany Germany
| | - Martin Dehnhard
- Department Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str.17, D-10315 Berlin, Germany
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21
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Mitra S, Kunteepuram V, Koepfli KP, Mehra N, Tabasum W, Sreenivas A, Gaur A. Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications. PeerJ 2019; 7:e8033. [PMID: 31788354 PMCID: PMC6882423 DOI: 10.7717/peerj.8033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 10/14/2019] [Indexed: 12/03/2022] Open
Abstract
The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
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Affiliation(s)
- Siuli Mitra
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Vaishnavi Kunteepuram
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, D.C., USA
| | - Neha Mehra
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Wajeeda Tabasum
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Ara Sreenivas
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Ajay Gaur
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
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22
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Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, Wilting A. An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. Gigascience 2019; 8:giz029. [PMID: 30997489 PMCID: PMC6461710 DOI: 10.1093/gigascience/giz029] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
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Affiliation(s)
- Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex Crampton-Platt
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Lisa A Hörig
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Charles C Y Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
- Redpath Museum and Department of Biology, McGill University 859 Sherbooke Street West, Montreal, PQ, Canada H3A 2K6
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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23
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Mohd Salleh F, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP. An expanded mammal mitogenome dataset from Southeast Asia. Gigascience 2018; 6:1-8. [PMID: 28873965 PMCID: PMC5737531 DOI: 10.1093/gigascience/gix053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/02/2017] [Indexed: 11/24/2022] Open
Abstract
Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds
approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic
diversity is still poorly characterized. The growing interest in using environmental DNA
to assess and monitor SE Asian species, in particular threatened mammals—has created the
urgent need to expand the available reference database of mitochondrial barcode and
complete mitogenome sequences. We have partially addressed this need by generating 72 new
mitogenome sequences reconstructed from DNA isolated from a range of historical and modern
tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data,
we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9
and ×55.2 for modern samples and historical samples, respectively. This dataset represents
52 species, of which 30 species had no previous mitogenome data available. The mitogenomes
were geotagged to their sampling location, where known, to display a detailed geographical
distribution of the species. Our new database of 52 taxa will strongly enhance the utility
of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases
the likelihoods that identification of metabarcoding sequencing reads can be assigned to
reference sequences. This magnifies the confidence in species detections and thus allows
more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity.
The extensive collections of historical samples from SE Asia in western and SE Asian
museums should serve as additional valuable material to further enrich this reference
database.
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Affiliation(s)
- Faezah Mohd Salleh
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Jazmín Ramos-Madrigal
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Fernando Peñaloza
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,Undergraduate Program on Genomic Sciences, Universidad Nacional Autonoma de Mexico, 62210 Cuernavaca, Mexico
| | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, GuangDong, China
| | - S Sinding Mikkel-Holger
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - P Patel Riddhi
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,Freie Universität Berlin, Kaiserswerther Str. 16-18, 14195 Berlin, Germany
| | - Renata Martins
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Dorina Lenz
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str 24-25, 14476 Potsdam, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Mohammad Shahfiz Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia
| | - K Lim Burton
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
| | - J Rossiter Stephen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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24
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Kunteepuram V, Sreenivas A, Tabasum W, Challagandla AK, Gaur A. The complete mitochondrial genome of Asian palm civet ( Paradoxurus hermaphroditus) with phylogenetic consideration. Mitochondrial DNA B Resour 2018; 3:294-295. [PMID: 33474149 PMCID: PMC7800665 DOI: 10.1080/23802359.2018.1443853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Asian palm civet (Paradoxurus hermaphroditus) is one of the smallest palm civet which is least studied. Here, we report the first complete mitochondrial (mt) genome of Asian palm civet (P. hermaphroditus). The circular mt genome with a length of 16,706 bp contained 1 control region, 2 rRNAs, 13 protein-coding genes, and 22 tRNAs. Overall base composition of the complete mt DNA was 33.7% A, 30.5% T, 22.9% C, and 12.9% G. All the genes in mt genome of Asian palm civet (P. hermaphroditus) were distributed on the H-strand, except ND6 and eight tRNA genes encoded on the L-strand. Maximum likelihood (ML) and Bayesian inference (BI) methods were used to infer the phylogenetic relationship of P. hermaphroditus. The phylogenetic analysis shows that all species from the family Viverridae cluster together, in which P. hermaphroditus exhibits the closest relationship with P. larvata.
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Affiliation(s)
- Vaishnavi Kunteepuram
- Laboratory for the Conservation of Endangered Species, CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Ara Sreenivas
- Laboratory for the Conservation of Endangered Species, CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Wajeeda Tabasum
- Laboratory for the Conservation of Endangered Species, CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Anil K. Challagandla
- Laboratory for the Conservation of Endangered Species, CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Ajay Gaur
- Laboratory for the Conservation of Endangered Species, CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
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