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DNA Barcodes

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2299-1077
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Taxonomic rank of Indian tortoise: revisit with DNA barcoding perspective

Shantanu Kundu / Kulendra Chandra Das / Sankar Kumar Ghosh
Published Online: 2013-05-06 | DOI: https://doi.org/10.2478/dna-2013-0003

Abstract

Taxonomic rank of terrestrial tortoise inhabiting in India and adjacent countries has been an unresolved issue. Wild living species of Manouria and Indotestudo genera have been classified through conventional taxonomy, but not adequately discriminated by mitochondrial cytochrome b gene. Cytochrome oxidase (COI) marker has been quite successful to achieve the exact species level information. There needs of an accurate sequence based effort for the extant northeast (NE) Indian tortoises to identify them accurately and to provide locality information. To estimate the Kimura-2-Parameter (K2P) divergences and to construct the Neighbour- Joining (NJ) phylogeny, we generated six partial COI sequences derived from expert-identified tortoise specimens. Both BLASTn and Bold-IDs revealed the definitive identity of Manouria, whereas the congeners of Indotestudo remain inconclusive by only a two-fold interspecific divergence gap with the other named Indian tortoise species. The NJ phylogeny readily differentiated the three Indian tortoise genera with their respective conspecies but depicted a nonsynonomous group of Indotestudo congeners. This study shows that the molecular identification of Manouria emys phayrei, Indotestudo elongata and an allopatric population of Indotestudo forstenii in NE India corresponds correctly with existing morphological key support.

Keywords: Testudinidae; Northeast India; Morphology; Mitochondrial cytochrome oxidase (COI); Distribution

  • Turtle Taxonomic Working Group (2007) An annotated list of modern turtle taxa with comments on areas of taxonomic instability and recent change. Chelonian Res Monogr 4: 173- 199. Google Scholar

  • Ernst CH, Barbour RW (1989) Turtles of the World. Washington, DC: Smithsonian Institution Press. Google Scholar

  • IUCN (2011) IUCN Red List of Threatened Species. Version 2011.2. www.iucnredlist.org. Google Scholar

  • Gibbons JW, Scott DE, Ryan TJ (2000) The global decline of reptiles, deja vu amphibians. BioScience 50: 653-666. CrossrefGoogle Scholar

  • Van Dijk PP, Stuart BL, Rhodin AGJ (2000) Asian Turtle Trade – Proceedings of a Workshop on Conservation and Trade of Freshwater Turtles and Tortoises in Asia. Chelonian Research Foundation, Lunenburg. Google Scholar

  • Turtle Conservation Fund (2002) A global action plan for conservation of tortoises and freshwater turtles, Strategy and funding prospectus, Conservation International and Chelonian Research Foundation, Washington, DC, pp 30. Google Scholar

  • Das I (1991) Colour guide to the turtles and tortoises of the Indian Subcontinent, R and A Publishing Limited, Portishead, U. K. Google Scholar

  • Das I (1995) Turtles and tortoises of India, Oxford University Press, Bombay, India. Google Scholar

  • Das KC, Gupta A (2011) Site records of softshell turtles (Chelonia: Trionychidae) from Barak Valley, Assam, northeastern India. Journal of Threatened Taxa 3: 1722-1726. Google Scholar

  • UNEP-WCMC (2012) UNEP-WCMC Species Database: CITES-Listed Species. Google Scholar

  • Schlegel H, Muller S (1840) Over de Schildpadden van den Indischen Archipel., en beschrijving eener nieuwe soort van Sumatra, In: Verhandelingen over de natuurlijke geschiendenis der Nederlandsche Overzeesche Bezittingen, Zoologie, Schildpadden. Lieden, 3: 29-36. Google Scholar

  • Schaffer C, Morgan V (2002) Behavioral Observations of Captive Juvenile Manouria emys phayrei with Notes on Degrees of Intergradation with Manouria emys emys. Turtle and Tortoise Newsl 5: 2-6. Google Scholar

  • Williams EE (1952) A new fossil tortoise from Mona Island, West Indies, and a tentative arrangement of the tortoises of the world. Bull Am Mus Nat Hist 99:541-560. Google Scholar

  • Crumly CR (1982). A cladistic analysis of Geochelone using cranial osteology. J Herpetol 16: 215-234. CrossrefGoogle Scholar

  • Crumly CR (1984). A hypothesis for the relationship of land tortoise genera (family Testudinidae). Studia Geologica Salmanticensia, Studia Palaeochelonologica 1:115-124. Google Scholar

  • Pritchard PCH (2000) Indotestudo travancorica...Avalid species of tortoise? Reptile & Amphibian Hobbyist 5: 18-28. Google Scholar

  • Ives I (2006) Conservation of Sulawesi’s two endemic chelonians, Leucocephalon yuwonoi and Indotestudo forstenii; a preliminary investigation into in-situ and ex-situ conservation concerns. Thesis, Antioch University New England. Google Scholar

  • Ives I, Spinks PQ, Shaffer HB (2008) Morphological and genetic variation in the endangered Sulawesi tortoise Indotestudo forstenii: evidence of distinct lineages? Conserv Genet 9:709-713. Web of ScienceCrossrefGoogle Scholar

  • Stoeckle M (2003) Taxonomy, DNA, and the bar code of life. BioScience 53: 2-3. Google Scholar

  • Bury RB (1979) Population ecology of freshwater turtle. Turtle’s prospectives and research. John Wiley & Sons. New york, 571- 602. Google Scholar

  • Pritchard PCH (1979) Encyclopedia of Turtles. T.F.H. Publications, Neptune, N.J., 895. Google Scholar

  • Moll EO (1984) India’s freshwater turtles in India their status, conservation and management. Hamadryad 9: 49-55. Google Scholar

  • Ratnasingham S, Hebert PDN (2007) BOLD : The Barcode of Life Data System . Mol Ecol Notes 7: 355–364. PubMedWeb of ScienceCrossrefGoogle Scholar

  • Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci 270: S96–S99. Google Scholar

  • Hebert PDN, Stoeckle MY, Zemlak TS, Frances CM (2004) Identification of birds through DNA barcodes. PLoS Biol, 2: 1657-1663. Google Scholar

  • Vargas SM, Araujo FC, Santos FR (2009) DNA barcoding of brazilian sea turtles (testudines). Genet Mol Biol 32: 608-612. Web of SciencePubMedCrossrefGoogle Scholar

  • Naro-Maciel E, Reid B, Fitzsimmons NN, Le M, Desalle R, Amato G (2010) DNA barcodes for globally threatened marine turtles: a novel registry approach to documenting biodiversity. Mol Ecol Resour 10: 252-263. Web of ScienceCrossrefGoogle Scholar

  • Reid BN, Le M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, Desalle R, Naro-Maciel E (2011) Comparing and combining distance-based and characterbased approaches for barcoding turtles. Mol Ecol Resour 11: 956-967. Web of SciencePubMedCrossrefGoogle Scholar

  • DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B 360: 1905-1916. Google Scholar

  • Kelly RP, Sarkar IN, Eernisse DJ, Desalle R (2007) DNA barcoding using chitons (genus Mopalia). Mol Ecol Notes 7: 177-83. Web of ScienceCrossrefGoogle Scholar

  • Sambrook J, Russell DW (2001) Molecular cloning - a laboratory manual, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor). Google Scholar

  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B 360: 1847-1857. Google Scholar

  • Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2: 23. Google Scholar

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120. PubMedCrossrefGoogle Scholar

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739. Web of ScienceCrossrefGoogle Scholar

  • Iverson JB, Spinks PQ, Shaffer HB, McCord WP, Das I (2001) Phylogenetic relationships among the Asian tortoises of the genus Indotestudo (Reptilia: Testudines: Testudinidae). Hamadryad 26: 272 - 275. Google Scholar

  • Blyth E (1853) Notices and descriptions of various reptiles, new or little-known. J. Asiat. Soc. Bengal 22: 639-655. Google Scholar

  • Boulenger GA (1907) A new tortoise from Travancore. J Bombay Nat Hist Soc 17: 560-564. Google Scholar

  • Hoogmoed MS, Crumly CR (1984) Land tortoise types in the Rijksmuseum van Natuurlijke Histoire with comments on nomenclature and systematics (Reptilia: Testudines: Testudinidae). Proc Zool Soc Lond 58: 241-259. Google Scholar

  • Hausmann A, Haszprunar G, Hebert PD (2011) DNA barcoding the geometrid fauna of Bavaria (Lepidoptera): successes, surprises, and questions. PLoS ONE 6: 223-24. Web of ScienceGoogle Scholar

  • Park DS, Foottit R, Maw E, Hebert PD (2011) Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera). PLoS ONE 6: e18749. Web of ScienceCrossrefGoogle Scholar

  • Laskar BA, Bhattacharjee MJ, Dhar B, Mahadani P, Kundu S, et al. (2013) The Species Dilemma of Northeast Indian Mahseer (Actinopterygii: Cyprinidae): DNA Barcoding in Clarifying the Riddle. PLoS ONE 8: e53704. CrossrefWeb of ScienceGoogle Scholar

  • Bhattacharjee MJ, Laskar BA, Dhar B, Ghosh SK (2012) Identification and Re-Evaluation of Freshwater Catfishes through DNA Barcoding. PLoS ONE 7: e49950. Web of ScienceCrossrefGoogle Scholar

  • Bickham JW (1981) Two-hundred-million-year-old chromosomes: deceleration in the rate of karyotypic evolution in turtles. Science 212: 1291-1293. PubMedCrossrefGoogle Scholar

  • Avise JC, Bowen BW, Lamb T, Meylan AB, Bermingham E (1992) Mitochondrial DNA evolution at a turtle’s pace: evidence for low genetic variability and reduced microevolutionary rate in Testudines. Mol Biol Evol 9: 457- 473.Google Scholar

About the article


Received: 2012-10-10

Accepted: 2013-02-03

Published Online: 2013-05-06


Citation Information: DNA Barcodes, ISSN (Online) 2299-1077, DOI: https://doi.org/10.2478/dna-2013-0003.

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