1,417
Views
1
CrossRef citations to date
0
Altmetric
Mitogenome Announcement

DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & show all
Pages 2525-2530 | Received 05 May 2020, Accepted 30 May 2020, Published online: 19 Jun 2020

References

  • Ali JR, Aitchison JC. 2008. Gondwana to Asia: plate tectonics, paleogeography and the biological connectivity of the Indian subcontinent from the Middle Jurassic through latest Eocene (166-35 Ma). Eart Sci Rev. 88(3–4):145–166.
  • Alirol E, Sharma SK, Bawaskar HS, Kuch U, Chappuis F. 2010. Snake bite in South Asia: a review. PLoS Negl Trop Dis. 4(1):e603.
  • Ashraf MR, Nadeem A, Smith EN, Javed M, Smart U, Yaqub T, Hashmi AS. 2019. Molecular phylogenetics of Black Cobra (Naja naja) in Pakistan. Electron J Biotechn. 42:23–29.
  • Barlow A, Pook CE, Harrison RA, Wüster W. 2009. Coevolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution. Proc Biol Sci. 276(1666):2443–2449.
  • Burbrink FT, Lawson R. 2007. How and when did old world ratsnakes disperse into the new world? Mol Phylogenet Evol. 43(1):173–189.
  • Chambers EA, Hebert PD. 2016. Assessing DNA barcodes for species identifcation in North American reptiles and amphibians in natural history collections. PLoS One. 11(4):e0154363.
  • Clement M, Snell Q, Walker P, Posada D, Crandall K. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9(10):1657–1659.
  • Daltry JC, Wüster W, Thorpe RS. 1996. Diet and snake venom evolution. Nature. 379(6565):537–540.
  • Dandona R, Kumar GA, Kharyal A, George S, Akbar M, Dandona L. 2018. Mortality due to snakebite and other venomous animals in the Indian state of Bihar: findings from a representative mortality study. PLoS One. 13(6):e0198900.
  • Deka A, Reza MA, Hoque KMF, Deka K, Saha S, Doley R. 2019. Comparative analysis of Naja kaouthia venom from North-East India and Bangladesh and its cross reactivity with Indian polyvalent antivenoms. Toxicon. 164:31–43.
  • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
  • Dutta S, Chanda A, Kalita B, Islam T, Patra A, Mukherjee AK. 2017. Proteomic analysis to unravel the complex venom proteome of eastern India Naja naja: correlation of venom composition with its biochemical and pharmacological properties. J Proteomics. 156:29–39.
  • Ezard T, Fujisawa T, Barraclough TG. 2009. Splits: SPecies’ LImits by Threshold Statistics. R Package Version 1.0-14/r31. http://R-Forge.R-project.org/projects/splits/
  • Figueroa A, McKelvy AD, Grismer LL, Bell CD, Lailvaux SP. 2016. A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus. PLoS One. 11(9):e0161070.
  • Fujisawa T, Barraclough TG. 2013. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol. 62(5):707–724.
  • Gutiérrez JM, Theakston RDG, Warrell DA. 2006. Confronting the neglected problem of snake bite envenoming: the need for a global partnership. PLoS Med. 3(6):e150.
  • Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci. 270(1512):313–321.
  • IUCN. 2020. The IUCN Red List of Threatened Species. Version 2020.1. [Accessed 1 May 2020]. https://www.iucnredlist.org
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549.
  • Kundu S, Lalremsanga HT, Tyagi K, Biakzuala L, Kumar V, Chandra K. 2020. Mitochondrial DNA discriminates distinct population of two deadly snakes (Reptilia: Elapidae) in Northeast India. Mitochondrial DNA Part B. 5(2):1530–1534.
  • Laopichienpong N, Muangmai N, Supikamolseni A, Twilprawat P, Chanhome L, Suntrarachun S, Peyachoknagul S, Srikulnath K. 2016. Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand. Gene. 594(2):238–247.
  • Laskar BA, Kumar V, Kundu S, Tyagi K, Chandra K. 2018. Taxonomic quest: validating two mahseer fishes (Actinopterygii: Cyprinidae) through molecular and morphological data from biodiversity hotspots in India. Hydrobiologia. 815(1):113–124.
  • Laxme SRR, Khochare S, de Souza HF, Ahuja B, Suranse V, Martin G, Whitaker R, Sunagar K. 2019. Beyond the ‘big four’: venom profiling of the medically important yet neglected Indian snakes reveals disturbing antivenom deficiencies. PLoS Negl Trop Dis. 13(12):e0007899.
  • Leigh JW, Bryant D. 2015. POPART: full-feature software for haplotype network construction. Methods Ecol Evol. 6(9):1110–1116.
  • Letunic I, Bork P. 2007. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 23(1):127–128.
  • Lin H-C, Li S-H, Fong J, Lin S-M. 2008. Ventral coloration differentiation and mitochondrial sequences of the Chinese cobra (Naja atra) in Taiwan. Conserv Genet. 9(5):1089–1097.
  • Lin L-H, Hua L, Qu Y-F, Gao J-F, Ji X. 2014. The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences. PLoS One. 9(9):e106944.
  • Lin L-H, Zhao Q, Ji X. 2008. Conservation genetics of the Chinese cobra (Naja atra) investigated with mitochondrial DNA sequences. Zool Sci. 25(9):888–893.
  • Mohapatra B, Warrell DA, Suraweera W, Bhatia P, Dhingra N, Jotkar RM, Rodriguez PS, Mishra K, Whitaker R, Jha P. 2011. Snakebite mortality in India: a nationally representative mortality survey. PLoS Negl Trop Dis. 5(4):e1018.
  • Nagy ZT, Sonet G, Glaw F, Vences M. 2012. First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One. 7(3):e34506.
  • Nylander J. 2004. Mr.Modeltest v2, program distributed by the author. Uppsala (Sweden): Evolutionary Biology Centre, Uppsala University.
  • Panagides N, Jackson TN, Ikonomopoulou MP, Arbuckle K, Pretzler R, Yang DC, Ali SA, Koludarov I, Dobson J, Sanker B, et al. 2017. How the cobra got its flesh-eating venom: cytotoxicity as a defensive innovation and its co-evolution with hooding, aposematic marking, and spitting. Toxins. 9(3):103.
  • Paradis E, Claude J, Strimmer K. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 20(2):289–290.
  • Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol. 21(8):1864–1877.
  • Pyron RA, Burbrink FT, Wiens JJ. 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol. 13:93.
  • Rahman R, Faiz MA, Selim S, Rahman B, Basher A, Jones A, d’Este C, Hossain M, Islam Z, Ahmed H, et al. 2010. Annual incidence of snake bite in rural Bangladesh. PLoS Negl Trop Dis. 4(10):e860.
  • Ratnarathorn N, Harnyuttanakorn P, Chanhome L, Evans SE, Day JJ. 2019. Geographical differentiation and cryptic diversity in the monocled cobra, Naja kaouthia (Elapidae), from Thailand. Zool Scr. 48(6):711–726.
  • Raxworthy CJ, Forstner MRJ, Nussbaum RA. 2002. Chameleon radiation by oceanic dispersal. Nature. 415(6873):784–787.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19(12):1572–1574.
  • Rozas J, Ferrer-Mata A, Sanchez-DelBarrio J, Guirao-Rico S, Librado P, Ramos-Onsins S, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34(12):3299–3302.
  • Sharma SK, Kuch U, Höde P, Bruhse L, Pandey DP, Ghimire A, Chappuis F, Alirol E. 2016. Use of molecular diagnostic tools for the identification of species responsible for snakebite in Nepal: a pilot study. PLoS Negl Trop Dis. 10(4):e0004620.
  • Slowinski JB, Keogh JS. 2000. Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences. Mol Phylogenet Evol. 15(1):157–164.
  • Slowinski JB, Lawson R. 2002. Snake phylogeny: evidence from nuclear and mitochondrial genes. Mol Phylogenet Evol. 24(2):194–202.
  • Smith CF, McGlaughlin ME, Mackessy SP. 2018. DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms. BioTechniques. 65(6):339–345.
  • Smith MA. 1943. Fauna of British India, Ceylon and Burma. In: Reptilia and amphibia. Vol. 3: Serpentes. London (UK): Tailor and Francis Ltd.
  • Stamatakis A, 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25(24):4876–4882.
  • Thorpe RS, Pook CE, Malhotra A. 2007. Phylogeography of the Russell’s viper (Daboia russelii) complex in relation to variation in the colour pattern and symptoms of envenoming. Herpetol J. 17:209–218.
  • Tordoff AW, Bezuijen MR, Duckworth JW, Fellowes JR, Koenig K, Pollard EHB, Royo AG. 2011. Ecosystem profile: Indo-Burma biodiversity hotspot, 2011 Update. Critical Ecosystem Partnership Fund. Washington, DC. p. 381.
  • Tyagi K, Kumar V, Kundu S, Pakrashi A, Prasad P, Caleb JTD, Chandra K. 2019. Identification of Indian Spiders through DNA barcoding: cryptic species and species complex. Sci Rep. 9(1):14033.
  • Tyagi K, Kumar V, Singha D, Chandra K, Laskar BA, Kundu S, Chakraborty R, Chatterjee S. 2017. DNA barcoding studies on thrips in India: cryptic species and species complexes. Sci Rep. 7(1):4898.
  • Wallach V, Williams KL, Boundy J. 2014. Snakes of the world: a catalogue of living and extinct species. Boca Raton (FL): CRC Press.
  • Whitaker R, Captain A. 2004. Snakes of India- the field guide. Chennai (India): Draco Books.
  • WHO. 2019. Snakebite envenoming: a strategy for prevention and control. Geneva (Switzerland): World Health Organization. Licence: CC BY-NC-SA 3.0 IGO.
  • Williams DJ, Faiz MA, Abela-Ridder B, Ainsworth S, Bulfone TC, Nickerson AD, Habib AG, Junghanss T, Fan HW, Turner M, et al. 2019. Strategy for a globally coordinated response to a priority neglected tropical disease: snakebite envenoming. PLoS Negl Trop Dis. 13(2):e0007059.
  • Wüster W. 1996. Taxonomic changes and toxinology: systematic revisions of the Asiatic cobras (Naja naja species complex). Toxicon. 34(4):399–406.
  • Wüster W. 1998. The Cobras of the genus Naja in India. Hamadryad. 23:15–32.
  • Wüster W, Crookes S, Ineich I, Mané Y, Pook CE, Trape J-F, Broadley DG. 2007. The phylogeny of cobras inferred from mitochondrial DNA sequences: evolution of venom spitting and the phylogeography of the African spitting cobras (Serpentes: Elapidae: Naja nigricollis complex). Mol Phylogenet Evol. 45(2):437–453.
  • Wüster W, Thorpe RS. 1989. Population affinities of the Asiatic cobra (Naja naja) species complex in south-east Asia: reliability and random resampling. Biol J Linn Soc. 36(4):391–409.
  • Wüster W, Thorpe RS, Cox MJ, Jintakune P, Nabhitabhata J. 1995. Population systematics of the snake genus Naja (Reptilia: Serpentes: Elapidae) in Indochina: multivariate morphometrics and comparative mitochondrial DNA sequencing (cytochrome oxidase I). J Evolution Biol. 8(4):493–510.
  • Zhang J, Kapli P, Pavlidis P, Stamatakis AA. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 29(22):2869–2876.