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Fan R, Tang K, Dou L, Fu C, Faiz AUH, Wang X, Wang Y, Chen S, Liu S. Molecular phylogeny and taxonomy of the genus Nectogale (Mammalia: Eulipotyphla: Soricidae). Ecol Evol 2022; 12:e9404. [PMID: 36311392 PMCID: PMC9596327 DOI: 10.1002/ece3.9404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
The elegant water shrew, Nectogale elegans, is one of the small mammal species most adapted to a semi-aquatic lifestyle. The taxonomy of the genus Nectogale has received little attention due to difficulties in specimen collection. In this study, we sequenced one mitochondrial and eight nuclear genes to infer the phylogenetic relationship of Nectogale. Phylogenetic analyses revealed two large clades within Nectogale. One clade represented N. elegans, and the other was regarded as N. sikhimensis. The split between N. elegans and N. sikhimensis dated back to the early Pleistocene (2.15 million years ago [Ma]), which might be relevant to the Qinghai-Tibet Plateau (QTP) uplift. The morphological comparison showed several distinguishing characters within Nectogale: the shape of the mastoids, the first lower unicuspid (a1), and the second upper molar (M2). Overall, the molecular and the morphological evidences supported that the genus Nectogale consists of two valid species: N. elegans and N. sikhimensis.
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Affiliation(s)
- Ronghui Fan
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Liang Dou
- Museum of Natural History/School of Life Sciences, Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan ProvinceSichuan UniversityChengduChina
| | - Changkun Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Abu ul Hassan Faiz
- Department of ZoologyWomen University of Azad Jammu and KashmirBaghPakistan
| | | | | | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
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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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Kamalakannan M, Sivaperuman C, Kundu S, Gokulakrishnan G, Venkatraman C, Chandra K. Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India. Sci Rep 2021; 11:9416. [PMID: 33941819 PMCID: PMC8093265 DOI: 10.1038/s41598-021-88859-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/16/2021] [Indexed: 02/02/2023] Open
Abstract
We discovered a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is of medium size (head and body lengths) and has a distinct external morphology (darker grey dense fur with a thick, darker tail) and craniodental characters (braincase is rounded and elevated with weak lambdoidal ridges) in comparison to other close congeners. This is the first discovery of a shrew from this volcanic island and increases the total number of Crocidura species catalogued in the Indian checklist of mammals to 12. The newly discovered species shows substantial genetic distances (12.02% to 16.61%) to other Crocidura species known from the Indian mainland, the Andaman and Nicobar Archipelago, Myanmar, and from Sumatra. Both Maximum-Likelihood and Bayesian phylogenetic inferences, based on mitochondrial (cytochrome b) gene sequences showed distinct clustering of all included soricid species and exhibit congruence with the previous evolutionary hypothesis on this mammalian group. The present phylogenetic analyses also furnished the evolutionary placement of the newly discovered species within the genus Crocidura.
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Affiliation(s)
| | | | - Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India.
| | | | | | - Kailash Chandra
- Mammal and Osteology Section, Zoological Survey of India, Kolkata, 700053, India
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India
- Andaman and Nicobar Regional Centre, Zoological Survey of India, Port Blair, 744102, India
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Oshida T, Than W, Oo T, Swe KYY, Saito H, Motokawa M, Kimura J, Nguyen ST, Bui HT, Dang PH. Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar. ACTA ZOOL ACAD SCI H 2021. [DOI: 10.17109/azh.67.1.87.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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Mori A, Obara Y, Kawada SI, Vogel P. Chromosomal Relationships between Two Species of Water Shrew,Chimarrogale platycephalusandNeomys fodiens. MAMMAL STUDY 2016. [DOI: 10.3106/041.041.0104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China. Heredity (Edinb) 2015; 116:23-32. [PMID: 26286667 DOI: 10.1038/hdy.2015.62] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/30/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022] Open
Abstract
The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.
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Chen S, Sun Z, He K, Jiang X, Liu Y, Koju NP, Zhang X, Tu F, Fan Z, Liu S, Yue B. Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 2015; 84:245-53. [PMID: 25617490 DOI: 10.1016/j.ympev.2014.12.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.
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Affiliation(s)
- Shunde Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China; College of Life Sciences, Sichuan Normal University, Chengdu 610066, China; Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhiyu Sun
- Sichuan Academy of Forestry, Chengdu 610081, China
| | - Kai He
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuelong Jiang
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu 610081, China
| | - Narayan Prasad Koju
- Mammal Ecology and Evolution Research Group, State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Feiyun Tu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Zhenxing Fan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu 610081, China.
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu 610064, China.
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Agarwal I, Bauer AM, Jackman TR, Karanth KP. Insights into Himalayan biogeography from geckos: A molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae). Mol Phylogenet Evol 2014; 80:145-55. [DOI: 10.1016/j.ympev.2014.07.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/08/2014] [Accepted: 07/24/2014] [Indexed: 11/15/2022]
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An annotated checklist of the insectivores (Mammalia, Lipotyphla) of Vietnam. RUSSIAN JOURNAL OF THERIOLOGY 2013. [DOI: 10.15298/rusjtheriol.12.2.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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