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Tian H, Han W, Li L, Shi X, Han X, Wei Y, Cai Y, Han Z, Zhang Y, Xu Y, Li Q, Liu S. The complete mitochondrial genome and phylogenetic analysis of Rattus tanezumi (Niethammer, 1975), captured from North China. Mitochondrial DNA B Resour 2024; 9:1218-1222. [PMID: 39291128 PMCID: PMC11407395 DOI: 10.1080/23802359.2024.2404211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Rattus tanezumi (Niethammer, 1975) is one of the commensal rodent species in South China. With the development of transportation and climate change, R. tanezumi has gradually migrated north and become the dominant rat species for the past few years. In this study, we assembled a complete mitochondrial genome of R. tanezumi, captured from North China. The mitogenome contains 16,307 nucleotide pairs, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as one non-coding control region. Based on whole mitogenome phylogenetical analysis showed that R. tanezumi captured from North China had a close phylogenetic relationship with that from Japan and South Korea. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Asian commensal rodent.
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Affiliation(s)
- Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Weimin Han
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Luling Li
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xiaodong Shi
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xu Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yamei Wei
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yanan Cai
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Zhanying Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yanbo Zhang
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yonggang Xu
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Qi Li
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Shiyou Liu
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
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2
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Molbert N, Ghanavi HR, Johansson T, Mostadius M, Hansson MC. An evaluation of DNA extraction methods on historical and roadkill mammalian specimen. Sci Rep 2023; 13:13080. [PMID: 37567875 PMCID: PMC10421861 DOI: 10.1038/s41598-023-39465-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.
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Affiliation(s)
- Noëlie Molbert
- Centre for Environmental and Climate Science, Lund University, Ecology Building, 223 62, Lund, Sweden.
| | - Hamid Reza Ghanavi
- Department of Biology, Functional Zoology Unit, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Maria Mostadius
- The Biological Museum, Lund University, Arkivcentrum Syd, Porfyrvägen 20, 22478, Lund, Sweden
| | - Maria C Hansson
- Centre for Environmental and Climate Science, Lund University, Ecology Building, 223 62, Lund, Sweden
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Nasir MH, Bhassu S, Mispan MS, Bakar SA, Jing KJ, Omar H. Molecular Identification and Genetic Variation of Rattus Species From Oil Palm Plantations of Malaysia Based on Mitochondrial Cytochrome Oxidase Subunit I (COI) Gene Sequences. Zoolog Sci 2022; 39:554-561. [PMID: 36495490 DOI: 10.2108/zs210093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.
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Affiliation(s)
- Mohamad Harris Nasir
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sazaly Abu Bakar
- Tick Cell Biobank Asia Outpost, Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Khoo Jing Jing
- Tick Cell Biobank Asia Outpost, Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia, .,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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4
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Juman MM, Woodman N, Miller-Murthy A, Olson LE, Sargis EJ. Taxonomic boundaries in Lesser Treeshrews (Scandentia, Tupaiidae: Tupaia minor ). J Mammal 2022. [DOI: 10.1093/jmammal/gyac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The Lesser Treeshrew, Tupaia minor Günther, 1876, is a small mammal from Southeast Asia with four currently recognized subspecies: T. m. minor from Borneo; T. m. malaccana from the Malay Peninsula; T. m. humeralis from Sumatra; and T. m. sincepis from Singkep Island and Lingga Island. A fifth subspecies, T. m. caedis, was previously synonymized with T. m. minor; it was thought to occur in northern Borneo and on the nearby islands of Banggi and Balambangan. These subspecies were originally differentiated based on pelage color, a plastic feature that has proven to be an unreliable indicator of taxonomic boundaries in treeshrews and other mammals. To explore infraspecific variation among T. minor populations across the Malay Peninsula, Borneo, Sumatra, and smaller islands, we conducted multivariate analyses of morphometric data collected from the hands and skulls of museum specimens. Principal component and discriminant function analyses reveal limited differentiation in manus and skull proportions among populations of T. minor from different islands. We find no morphometric support for the recognition of the four allopatric subspecies and no support for the recognition of T. m. caedis as a separate subspecies on Borneo.
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Affiliation(s)
- Maya M Juman
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
| | - Neal Woodman
- U.S. Geological Survey, Eastern Ecological Science Center , Laurel, Maryland 20708 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
| | - Ananth Miller-Murthy
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
| | - Link E Olson
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Department of Mammalogy, University of Alaska Museum, University of Alaska Fairbanks , Fairbanks, Alaska 99775 , USA
| | - Eric J Sargis
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
- Department of Anthropology, Yale University , New Haven, Connecticut 06520 , USA
- Yale Institute for Biospheric Studies , New Haven, Connecticut 06520 , USA
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Forcina G, Camacho-Sanchez M, Cornellas A, Leonard JA. Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The garden dormouse Eliomys quercinus is a poorly known Western Palearctic species experiencing a global decline. Even though the availability of genetic information is key to assess the driversunderlying demographic changes in wild populations and plan adequate management, data on E. quercinus are still scant. In this study, we reconstructed the complete mitogenomes of four E. quercinus individuals from southern Spain using in–solution enriched libraries, and found evidence of limited genetic variability. We then compared their cytochrome b sequences to those of conspecifics from other countries and supported the divergent but genetically depauperate position of this evolutionarily significant unit (ESU). The information produced will assist future conservation studies on this little–studied rodent.
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Affiliation(s)
- G. Forcina
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - M. Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - A. Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - J. A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
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Liu S, Li F, Zhou J, Lv J, Tan Z, Zhang Y, Ge X. The phylogeny of the Anderson's White‐bellied Rat (
Niviventer andersoni
) based on complete mitochondrial genomes. Ecol Evol 2022; 12:e8663. [PMID: 35261750 PMCID: PMC8890005 DOI: 10.1002/ece3.8663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Shu‐Jing Liu
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
| | - Fu‐Li Li
- Institute of Preventive MedicineSchool of Public HealthDali UniversityDaliChina
| | - Ji‐Hua Zhou
- Yunnan Provincial Key Laboratory for Zoonosis Control and PreventionYunnan Institute of Endemic Diseases Control and PreventionDaliChina
| | - Ji‐Zhou Lv
- Institute of Animal QuarantineChinese Academy of Inspection and QuarantineBeijingChina
| | - Zhong‐Yang Tan
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
| | - Yun‐Zhi Zhang
- Institute of Preventive MedicineSchool of Public HealthDali UniversityDaliChina
| | - Xing‐Yi Ge
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
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Skeletal Variation and Taxonomic Boundaries in the Pen-tailed Treeshrew (Scandentia: Ptilocercidae; Ptilocercus lowii Gray, 1848). J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Juman MM, Woodman N, Olson LE, Sargis EJ. Ecogeographic variation and taxonomic boundaries in Large Treeshrews (Scandentia, Tupaiidae: Tupaia tana Raffles, 1821) from Southeast Asia. J Mammal 2021. [DOI: 10.1093/jmammal/gyab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The Large Treeshrew, Tupaia tana Raffles, 1821, is a small mammal (~205 g) from Southeast Asia with a complicated taxonomic history. Currently, 15 subspecies are recognized from Borneo, Sumatra, and smaller islands, and many were originally differentiated based on minor pelage differences and small sample sizes. We explored intraspecific variation in T. tana using quantitative osteological data obtained from the hands and skulls of museum specimens. Multivariate analyses reveal extensive overlap among T. tana populations in morphospace, indicating that the majority of currently recognized subspecies are not morphometrically distinct. In contrast, the separation between Bornean and Sumatran populations of T. tana is sufficient to recognize them as different subspecies. Comparisons of Bornean specimens to those on small, offshore islands reveal that the latter average smaller body size. This pattern is inconsistent with Foster’s island rule, which predicts that island populations of small mammals (< 5 kg) will average larger body size relative to mainland forms. A similar lack of support for ecogeographic rules has been noted in T. glis (Diard, 1820), suggesting that these “rules” are poor predictors of geographic variation in treeshrews.
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Affiliation(s)
- Maya M Juman
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , USA
| | - Neal Woodman
- U.S. Geological Survey, Eastern Ecological Science Center , Laurel, MD , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Link E Olson
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Mammalogy, University of Alaska Museum, University of Alaska Fairbanks , Fairbanks, AK , USA
| | - Eric J Sargis
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, CT , USA
- Department of Anthropology, Yale University , New Haven, CT , USA
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Hinckley A, Camacho-Sanchez M, Ruedi M, Hawkins MTR, Mullon M, Cornellas A, Tuh Yit Yuh F, Leonard JA. Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Abstract
The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.
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Affiliation(s)
- Arlo Hinckley
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA) Centro Las Torres, Alcalá del Río, Spain
| | | | - Melissa T R Hawkins
- National Museum of Natural History, Department of Vertebrate Zoology, Smithsonian Institution, USA
| | | | - Anna Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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