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Kundu S, Kamalakannan M, Kim AR, Hegde VD, Banerjee D, Jung WK, Kim YM, Kim HW. Morphology and Mitochondrial Lineage Investigations Corroborate the Systematic Status and Pliocene Colonization of Suncus niger (Mammalia: Eulipotyphla) in the Western Ghats Biodiversity Hotspot of India. Genes (Basel) 2023; 14:1493. [PMID: 37510398 PMCID: PMC10379166 DOI: 10.3390/genes14071493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Manokaran Kamalakannan
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
| | - Ah Ran Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Vishwanath D Hegde
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Dhriti Banerjee
- Mammal and Osteology Section, Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
| | - Won-Kyo Jung
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Kundu S, Kamalakannan M, Mukherjee T, Banerjee D, Kim HW. Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication. Genes (Basel) 2023; 14:genes14030765. [PMID: 36981035 PMCID: PMC10048616 DOI: 10.3390/genes14030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Dhriti Banerjee
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
- Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians. Sci Rep 2022; 12:877. [PMID: 35042947 PMCID: PMC8766473 DOI: 10.1038/s41598-022-04907-7] [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: 09/06/2021] [Accepted: 12/29/2021] [Indexed: 11/09/2022] Open
Abstract
The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.
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Voyta LL, Abramov AV, Lavrenchenko LA, Nicolas V, Petrova EA, Kryuchkova LY. Dental polymorphisms in Crocidura (Soricomorpha: Soricidae) and evolutionary diversification of crocidurine shrew dentition. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab103] [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]
Abstract
Abstract
The upper dentition of Crocidura exhibits polymorphic characters that were revealed for the first time in this study via high-resolution X-ray computed microtomography. Our analyses of 11 Crocidura species and selected Diplomesodon, Suncus and Sylvisorex species from different geographical regions and size groups revealed the most complex character states of upper dentition in the Ethiopian endemic species Crocidura yaldeni. A three-dimensionally based geometric morphometric analysis revealed the dependence of variation in skull muzzle shape on alterations in general upper dentition, such as a reduction in the number of antemolars. Principal components analysis revealed highly significant shape alterations and morphological trajectories in C. yaldeni (and more moderate ones in Suncus murinus) toward the Sorex-like morphotype in the outgroup, and less significant shape alterations in Crocidura obscurior, Crocidura phanluongi and Crocidura sapaensis with double-rooted third antemolar. Cladistic analysis based on a new data matrix for 20 species and 46 characters allowed us to determine the directions of the morphological trajectories: the apomorphic state of the most complex antemolars of C. yaldeni is associated with deviating skull muzzle shape changes, which we determined to be attributable to neomorphosis, and the less significant alterations in the shape of other Crocidura with complex antemolars are attributable to regional adaptation.
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Affiliation(s)
- Leonid L Voyta
- Laboratory of Theriology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Alexei V Abramov
- Laboratory of Theriology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Leonid A Lavrenchenko
- Laboratory of Mammalian Microevolution, A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, Paris, France
| | - Ekaterina A Petrova
- Laboratory of Theriology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Lyudmila Yu Kryuchkova
- Research Centre for X-ray Diffraction Studies, Saint Petersburg State University, Saint Petersburg, Russia
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Kundu S, Kamalakannan M, Tyagi K, Kumar V. Complete mitochondrial genome of critically endangered Crocidura nicobarica (Soricidae: Eulipotyphla) from the Great Nicobar Island, India. Mitochondrial DNA B Resour 2021; 6:3418-3422. [PMID: 34869866 PMCID: PMC8638613 DOI: 10.1080/23802359.2021.1999188] [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: 07/12/2021] [Accepted: 10/23/2021] [Indexed: 11/30/2022] Open
Abstract
The mitogenome (17,388 bp) of the Nicobar shrew, Crocidura nicobarica was determined in the present study. The mitogenome comprises 13 PCGs (11,427 bp), 22 tRNAs (1507 bp), two rRNAs (2538 bp), and a major non-coding control region (1932 bp). The Maximum Likelihood phylogeny clearly discriminates all the studied Crocidura species with high bootstrap support by concatenated PCGs. The studied species, C. nicobarica shows a close relationship with Crocidura orientalis, distributed in Java, Indonesia. The lineage diversification and zoogeographic patterns are congruent in the present analyses and encouraged further sampling and more molecular data to elucidate their in-depth evolutionary relationship.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | | | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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