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Sil M, Mahveen J, Roy A, Karanth KP, Aravind NA. Insight into the evolutionary history of Indoplanorbis exustus (Bulinidae: Gastropoda) at the scale of population and species. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac062] [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 history of a lineage is intertwined with the history of the landscape it inhabits. Here we showcase how the geo-tectonic and climatic evolution of South Asia and surrounding landmasses have shaped the biogeographical history of Indoplanorbis exustus, a tropical Asian, freshwater snail. We amplified partial COI gene fragments from all over India and combined this with a larger dataset from South and Southeast Asia to carry out phylogenetic reconstruction, species delimitation analysis and population genetic analyses. Two nuclear genes were also amplified from a few individuals per putative species to carry out divergence dating and ancestral area reconstruction analyses. The results suggest that I. exustus dispersed out of Africa into India during the Eocene. Furthermore, molecular data suggest I. exustus is a species complex consisting of multiple putative species. Primary diversification took place in the Northern Indian plains or in Northeast India. The speciation events appear to be primarily allopatric caused by a series of aridification events starting from the late Miocene to early Pleistocene. None of the species appears to have any underlying genetic structure suggestive of high vagility. All the species underwent population fluctuations during the Pleistocene, probably driven by the Quaternary climatic fluctuations.
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Affiliation(s)
- Maitreya Sil
- SMS Foundation Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment , Royal Enclave, Sriramapura, Jakkur PO, Bangalore 560064 , India
| | - Juveriya Mahveen
- SMS Foundation Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment , Royal Enclave, Sriramapura, Jakkur PO, Bangalore 560064 , India
- Department of Microbiology, St. Joseph’s College , Bangalore 560027 , India
| | - Abhishikta Roy
- SMS Foundation Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment , Royal Enclave, Sriramapura, Jakkur PO, Bangalore 560064 , India
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science , Bangalore 560012 , India
| | - N A Aravind
- SMS Foundation Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment , Royal Enclave, Sriramapura, Jakkur PO, Bangalore 560064 , India
- Yenepoya Research Centre, Yenepoya (deemed to be University) , University Road, Derlakatte, Mangalore 575018 , India
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Qi S, Ren JL, Wang Z, Yang HC, Jiang K. On the occurrence of Lygosoma siamense Siler, Heitz, Davis, Freitas, Aowphol, Termprayoon & Grismer, 2018 (Squamata, Scincidae) in China. HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e80151] [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
The genus Lygosoma Hardwicke & Gray, 1827 is a group of semi-fossorial supple skink from Southeast Asia, the members of which are still understudied in Indochina. Lysosoma quadrupes (Linnaeus, 1766) was once recorded from China based on historical literature; until recent its Indochina specimens were revised and placed into a newly described species, i.e., L. siamense Siler, Heitz, Davis, Freitas, Aowphol, Termprayoon & Grismer, 2018. However, Lygosoma quadrupes had long been unknown from China but the historical record had not been confirmed. Here we report a vouchered record for L. siamense from China for the first time based on four specimens collected in Sanya, Hainan, China. Furthermore, the taxonomic history of Lygosoma from China is also reviewed.
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Sidharthan C, Karanth KP. India's biogeographic history through the eyes of blindsnakes- filling the gaps in the global typhlopoid phylogeny. Mol Phylogenet Evol 2020; 157:107064. [PMID: 33387646 DOI: 10.1016/j.ympev.2020.107064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 12/05/2020] [Accepted: 12/24/2020] [Indexed: 11/25/2022]
Abstract
The Indian subcontinent's unique geological history is reflected in the diverse assemblage of its biota. The blindsnake superfamily Typhlopoidea, with its unique mix of ancient as well as younger lineages in Asia, provides an opportunity to understand the various biotic exchange scenarios proposed for the Indian landmass. In this study, we aim to understand the biogeographic origins of the four genera of typhlopoids found in India and to decipher their times and modes of arrival in the subcontinent. Five nuclear markers were sequenced for 12 samples collected from across India, encompassing all four genera under study. Published sequences of typhlopoid genera were compiled and combined with Indian sequences to generate a global dataset. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference methods. Divergence times were estimated using BEAST 1.8.2. Ancestral geographical ranges were estimated using DEC + J, implemented in BioGeoBEARS. Divergence time estimates suggest that Gerrhopilus is an ancient lineage, and the lineage leading to it was present on the Indian landmass since the last 100 million years. The other three genera are more recent dispersals into India, possibly trans-oceanic. Biogeographic reconstructions suggest an East Gondwanan origin for Typhlopoidea, an African origin for Grypotyphlops and an Asian origin for Indotyphlops and Argyrophis. It appears that India harbours a combination of ancient and more recently dispersed lineages of typhlopoids. The genus Gerrhopilus is of Gondwanan origin that likely dispersed out of India into Southeast Asia. The other genera are intrusive elements that dispersed into India from Africa (Grypotyphlops) and Asia (Indotyphlops and possibly Argyrophis) post break-up of Gondwana. Thus, our study provides further evidence on the ability of blindsnakes to undergo long distance trans-oceanic dispersal. Results also suggest an Asian origin for typhlopoids from Australasia, Philippines and Wallacea.
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Affiliation(s)
- Chinta Sidharthan
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India.
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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Freitas ES, Miller AH, Reynolds RG, Siler CD. A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar. Mol Phylogenet Evol 2020; 146:106754. [PMID: 32028030 DOI: 10.1016/j.ympev.2020.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphological data, we examine lineage diversification in a cryptic radiation of Riopa skinks in Myanmar. Four species of Riopa skinks are currently recognized from Myanmar based on morphological traits, but the boundaries between three of these species, R. anguina, R. lineolata, and R. popae, are not well-defined. We find high levels of genetic diversity within these three species. Our analyses suggest that they may comprise as many as 12 independently evolving lineages, highlighting the extent to which species diversity in the region is underestimated. However, quantitative trait data suggest that these lineages have not differentiated morphologically, possibly indicating that this cryptic radiation represents non-adaptive evolution, although additional data is needed to corroborate this.
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Affiliation(s)
- Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Aryeh H Miller
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - R Graham Reynolds
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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Freitas ES, Datta-Roy A, Karanth P, Grismer LL, Siler CD. Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.
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Affiliation(s)
- Elyse S Freitas
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Aniruddha Datta-Roy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, California, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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Joshi J, Edgecombe GD. Evolutionary biogeography of the centipede genus Ethmostigmus from Peninsular India: testing an ancient vicariance hypothesis for Old World tropical diversity. BMC Evol Biol 2019; 19:41. [PMID: 30709332 PMCID: PMC6359765 DOI: 10.1186/s12862-019-1367-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/18/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Understanding the relative influence of vicariance and dispersal in shaping Old World tropical biodiversity remains a challenge. We aimed to infer the roles of these alternative biogeographic processes using a species time-tree for the centipede genus Ethmostigmus from the Old World tropics. Additionally, we explored fine-scale biogeographic patterns for an endemic radiation of Ethmostigmus from the peninsular Indian Plate (PIP), an area with complex geological and climatic history. RESULTS Divergence time estimates suggest that Ethmostigmus began diversifying in the Late Cretaceous, 99 (± 25) million years ago (Ma), its early biogeographic history shaped by vicariance. Members of Ethmostigmus in PIP form a monophyletic group that underwent endemic radiation in the Late Cretaceous, 72 (± 25) Ma. In contrast, a new species of Ethmostigmus from north-east India formed a clade with African/Australian species. Fine-scale biogeographic analyses in PIP predict that Indian Ethmostigmus had an ancestor in southern-central parts of the Western Ghats. This was followed by four independent dispersal events from the southern-central Western Ghats to the Eastern Ghats, and between different parts of the Western Ghats in the Cenozoic. CONCLUSIONS Our results are consistent with Gondwanan break-up driving the early evolutionary history of the genus Ethmostigmus. Multiple dispersal events coinciding with geo-climatic events throughout the Cenozoic shaped diversification in PIP. Ethmostigmus species in PIP are restricted to wet forests and have retained that niche throughout their diversification.
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Affiliation(s)
- Jahnavi Joshi
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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New Supple Skink, GenusLygosoma(Reptilia: Squamata: Scincidae), from Indochina and Redescription ofLygosoma quadrupes(). J HERPETOL 2018. [DOI: 10.1670/16-064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Laskar BA, Kumar V, Kundu S, Darshan A, Tyagi K, Chandra K. DNA barcoding of fishes from River Diphlu within Kaziranga National Park in northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:126-134. [PMID: 29669453 DOI: 10.1080/24701394.2018.1463373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
DNA barcoding technique has been gaining importance in biodiversity research for its easy and rapid ability of delineating organisms' partial DNA sequences into molecular operational taxonomic units (MOTUs), and identification based on referral sequences from expert identified species. We generated mtCOI barcode sequences from morphologically identified fishes from River Diphlu in northeast India. A portion of this river falls within an important rhinoceros and tiger conservation site, the Kaziranga National Park. Partial mtCOI sequences for 103 fish specimens belonging to six orders, 19 families, 37 genera and 47 a priori identified species, were delineated into 48 MOTUs based on reciprocal monophyly criteria in maximum likelihood and Bayesian tree, and 49 groups by automatic barcode gap discovery (ABGD). Morphological and molecular basis of species identification was congruent for around 80% straightforward cases. We contributed barcodes for eight species which either had no barcodes in databases or are having ambiguous barcodes. We detected four 'near threatened' and two data deficient species as per the IUCN Red List status, besides a few 'least concerned' species. We also observed a wide scope of barcoding studies on fishes from northeast India to cover the endemic species and to resolve the prevailing taxonomic problems.
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Affiliation(s)
- Boni Amin Laskar
- a Freshwater Biology Regional Centre, Zoological Survey of India , Hyderabad , India
| | - Vikas Kumar
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Shantanu Kundu
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Achom Darshan
- c Center with Potential for Excellence in Biodiversity, Rajiv Gandhi University , Doimukh , India
| | - Kaomud Tyagi
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Kailash Chandra
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
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Kundu S, Kumar V, Laskar BA, Tyagi K, Chandra K. Morphology and genetic variation in the endangered tortoise Manouria emys: distinct lineages or plastron anomalies? Mitochondrial DNA B Resour 2018; 3:166-170. [PMID: 33474106 PMCID: PMC7800038 DOI: 10.1080/23802359.2018.1437795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Shantanu Kundu
- 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
| | - Boni Amin Laskar
- Freshwater Biology Regional Centre, Zoological Survey of India, Hyderabad, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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Rajpoot A, Bahuguna A, Kumar VP, Kumar D. The preliminary molecular study of four skink species in Rajaji Tiger Reserve (RTR), Uttarakhand, using 12S rRNA mitochondrial locus. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:495-499. [PMID: 33490460 PMCID: PMC7800989 DOI: 10.1080/23802359.2017.1357435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Skinks are present under the Scincidae family, widely distributed species in Indian subcontinent. Uttarakhand is one of the hotspot where number of identified and unidentified skink species reported. Herein, we first time provided the 12S rRNA genetic reference database of four skink species, i.e. Eutropis macularia, Eutropis carinata, Asymblepharus himalayanus and Lygosoma punctata, in Rajaji Tiger Reserve (RTR), Uttarakhand (India). The identified four species belong to three different genera, where Eutropis carinata and Asymblepharus himalayanus listed Least Concern and Vulnerable in IUCN, respectively. Here, we collected tissue samples of four different skink species from Rajaji Tiger Reserve during field survey. After successful laboratory procedure, we compared obtained sequences with publically available genetic database and we observed four sequences matched with respective species. Furthermore, the evolutionary sequence divergence result revealed that the Eutropis carinata and Eutropis macularia are close to each other with 0.11 genetic distance. The present study indicates that the exact number and population distribution of skink species are unidentified; therefore, herein we suggest the proper screening of Uttarakhand population around should be investigated, further genetic study in combination with a good sampling strategy to investigate species biology and status for conservation program.
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Affiliation(s)
| | | | - Ved Prakash Kumar
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Dehradun, India
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Heitz BB, Diesmos AC, Freitas ES, Ellsworth ED, Grismer LL, Aowphol A, Brown RM, Siler CD. A New Supple Skink, GenusLygosoma(Reptilia: Squamata: Scincidae), from the Western Philippines. HERPETOLOGICA 2016. [DOI: 10.1655/herpetologica-d-16-00023.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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