Genetic structure and diversity of Naja oxiana (Eichwald, 1831) populations in Iran using cytochrome b mitochondrial marker

Document Type : (original research)

Authors

1 Department of Environment, Faculty of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran

2 Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran

Abstract

The phylogenetic relationships of the Caspian cobra (Naja oxiana), the easternmost species of the subgenus Naja, have remained contentious for long. The present study aims at investigating the genetic diversity and structure, as well as phylogenetic relationships of the Caspian cobra populations from northeastern Iran, Afghanistan and Turkmenistan. We sequenced 1107 base pairs of the mitochondrial gene cytochrome b for 54 samples to assess the genetic diversity, genetic structure and phylogenetic relationships of the Caspian cobra. Phylogenetic analyses were conducted under Bayesian and Maximum likelihood inferences using the best-fitting evolutionary model. Haplotype relationships were inferred using maximum parsimony. Reconstruction of the phylogenetic trees confirmed that the Caspian cobra is the sister taxon of Naja kaouthia. The estimated haplotype and nucleotide diversity were 0.42 and 0.00058, respectively, indicating low genetic variation among Caspian cobra populations. Our findings suggest that populations of the species have experienced a recent radiation and sudden range expansion from the northeast toward Golestan province. The results, based on a single mitochondrial marker, revealed no significant genetic differentiation between the populations and recommend that all populations of the Caspian cobra be considered as a significant evolutionary unit in future conservation plans.

Keywords

Main Subjects

References

  1. Avise, J.C., 2000. Phylogeography: the history and formation of species. Harvard university press. 285 p.
  2. Burbrink, F.T., 2002. Phylogeographic analysis of the cornsnake (Elaphe guttata) complex as inferred from maximum likelihood and Bayesian analyses. Molecular phylogenetics and evolution. Vol. 53, No. 2, pp: 465-476.
  3. Burbrink, F.T.; Lawson, R. and Slowinski, J.B., 2000. Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution. Vol. 54, pp: 2107-2118.
  4. Bolfíková, B.C.; Eliásová, K.; Loudová, M.; Krytufek, B.; Lymberakis, P.; Sándor, A.D. and Hulva, P., 2017. Glacial allopatry vs. postglacial parapatry and peripatry: the case of hedgehogs. Peer J. Vol. 5, pp: e3163.
  5. Darriba, D.; Taboada, G.L.; Doallo, R. and Posada, D., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods. Vol. 9, pp: 772.
  6. Darvish, J. and Rastegar-Pouyani, E., 2012. Biodiversity conservation of reptiles and mammals in the Khorasan Provinces, northeast of Iran. Progress in Biological Sciences. Vol. 2, pp: 95-10.
  7. Excoffier, L., 2004. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Molecular Ecology. Vol. 13, pp: 853-864.
  8. Excoffier, L.; Laval, G. and Schneider, S., 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatic. Vol.1, pp: 47-50.
  9. Frankham, R., 2005. Genetics and extinction. Biological journal of Conservation. Vol. 126, pp: 131-140.
  10. Fraser, D.J. and Bernatchez, L., 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology. Vol. 10, pp: 274-2752.
  11. Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. Vol. 147, pp: 915-925.
  12. Gold, B.S.; Dart, R.C. and Barish, R.A., 2002. Bites of venomous snakes. The New England Journal of Medicine. Vol. 347, pp: 347-335.
  13. Hall, T.A., 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. Vol. 41, pp: 95-98.
  14. Hung, C.; Drovetski, S.V. and Zink, R.M., 2012. Multilocus coalescence analyses support a mtDNA-based phylogeographic history for a widespread palearctic passerine bird, Sitta europaea. Evolution. Vol. 66, pp:
    2850 -2864.
  15. IUCN. 2019. The IUCN Red List of Threatened Species. Version 2019-2 (Accessed 08 August 2019) http://www. iucnredlist.org.
  16. Kapli, P.; Botoni, D.; Ilgaz, Ç.; Kumlutaş, Y.; Avcı, A.; Rastegar-Pouyani, N.; Fathinia, B.; Lymberakis, P.; Ahmadzadeh, F. and Poulakakis, N., 2013. Molecular phylogeny and historical biogeography of the Anatolian lizard Apathya (Squamata, Lacertidae). Molecular Phylogenetics and Evolution. Vol. 66, pp: 992-1001.
  17. Klemmer, K., 1968. Classification and distribution of European, North African, and north and west Asiatic venomous snakes. Venom. Anim. Their Venoms. Vol. 1, pp: 309-325.
  18. Latifi, M., 1991. The Snakes of Iran., English edition. Society for the study of Amphibians and Reptiles, Oxford, Ohio. viii 159 pp., 24 text-figs; 25 col. pls; 3 tables. (Translated from the Iranian edition by Sajadian, S., volume editors, Leviton, A. and Zug, G.,).
  19. Leigh, J.W. and Bryant, D., 2015. POPART: full-feature software for haplotype network Construction. Methods in Ecology and Evolution. Vol. 6, pp: 1110-1116.
  20. Li, H.L.; Fong, E.S. and Lin, S., 2008. Ventral coloration differentiation and mitochondrial sequences of the Chinese Cobra (Naja atra) in Taiwan. Conservation Genetic. Vol. 9, pp: 1089-1097.
  21. Librado, P. and Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. Vol. 25, pp: 1451-1452.
  22. Lin, A.L.; Zhao, Q.; Ji, X.; Lin, L.; Zhao, Q. and Ji, X., 2008. Conservation Genetics of the Chinese Cobra (Naja atra) Investigated with Mitochondrial DNA Sequences Conservation Genetics of the Chinese Cobra (Naja atra). Investigated with Mitochondrial DNA Sequences. Zoological Science. Vol. 25, pp: 888-893.
  23.  Lin, L.; Qu, Y.; Li, H.; Zhou, K. and Ji, X., 2012. Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as homogenous show population divergence. Vol 7, pp: e36334.
  24. Lin, L.; Hua, L.; Qu, Y.; Gao, J. and 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. Vol. 9, pp: e106944.
  25. Meister, B.; Hofer, U.; Ursenbacher, S. and Baur, B., 2010. Spatial genetic analysis of the grass snake, Natrix natrix(Squamata: Colubridae), in an intensively used agricultural landscape. Biological journal of linnean society. Vol. 101, pp: 51-58.
  26. Mohammadabadi, M.R., 2017. Role of clostridium perfringens in pathogenicity of some domestic animals. Journal of Advances in Agriculture. Vol. 7, pp: 1117-1121.
  27. Moritz, C., 1994.  Defining ‘evolutionarily significant units’ for conservation. Trends ecology evolution. Vol. 9, pp: 373-375.
  28. Nazarizadeh, M.; Kaboli, M., Rezaie, H.R.; Harisini, J.I. and Pasquet, E., 2016.  Phylogenetic relationships of Eurasian Nuthatches (Sitta europaea Linnaeus, 1758) from the Alborz and Zagros Mountains, Iran. Zoology in the Middle East. Vol. 62, pp: 217-226.
  29. O’Shea, M., 2008. Venomous snakes of the world. New Holland Publishers.
  30. Pook, C.E.; Joger, U.; Stümpel, N. and Wüster, W., 2009. When continents collide: phylogeny, historical biogeography and systematics of the medically important viper genus Echis (Squamata: Serpentes: Viperidae). Molecular Phylogenetics and Evolution. Vol. 53, pp: 792-807.
  31. Queiroz, A.; Lawson, R., and Lemos-Espinal, J., 2002. Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough? MolecularPhylogenetics and Evolution. Vol. 22, No. 2, pp: 315-329.
  32. Rambaut, A.; Drummond, A.J.; Xie, D.; Baele, G. and Suchard, M.A., 2018. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology. Vol. 67, pp: 901-904.
  33. Ronquist, F. and Huelsenbeck, J.P., 2003.  MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. Vol. 19, pp: 1572-1574.
  34. Rogers, A.R. and Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular biology and evolution. Vol 9, No. 3, pp: 552-569.
  35. Ryder, O.A., 1986.  Species conservation and systematics: the dilemma of subspecies. Trends Ecology Evolution. Vol. 1, pp: 9-10.
  36. Sambrook, J.; Fritsch, E.F. and Maniatis, T., 1989. Molecular cloning: a laboratory manual. Cold Spring Harbour: ColdSpring Harbour Press.
  37. Slatkin, M. and Hudson, R.R., 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. Vol. 129, pp: 555-562.
  38. Slowinski, J.B. and Wüster, W., 2000. A new cobra (Elapidae: Naja) from Myanmar (Burma). Herpetologica. pp: 257-270.
  39. Smith, J.M. and Haigh, J., 1974. The hitch-hiking effect of a favourable gene. Genetics Research. Vol. 23, No. 1, pp: 23-35. 
  40. Stamatakis, A.; Ludwig, T. and Meier, H., 2005. RAxML III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. Vol. 21, pp: 456- 463.
  41. Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. Vol.123, pp: 585-595.
  42. Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M., and Kumar, S., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution. Vol. 28, pp: 2731-2739.
  43. Thompson, J.D.; Higgins, D.G. and Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research. Vol. 22, No. 22, pp: 4673-4680.
  44. Valenta, J., 2009. Venomous Snakes: Envenoming, Therapy. Nova Science Publishers.
  45. Wallach, V.; Wuester, W. and Broadley, D.G., 2009. In praise of subgenera: taxonomic status of cobras of the genus Naja Laurenti (Serpentes: Elapidae). Zoo taxa. Vol. 2236, pp: 26-36.
  46. Wüster, W., 1990. Population evolution of the Asiatic cobra (Naja naja) species complex. Univ. Aberdeen 500.
  47. Wüster, W. and Broadley, D.G., 2003. A new species of spitting cobra from north-eastern Africa (Serpentes: Elapidae: Naja). Journal of Zoology, London. Vol. 259, pp: 345-359.
  48. Wüster, W.; Crookes, S.; Ineich, I.; Mané, Y.; Pook, C.E.; Trape, J.F. and Broadley, D.G., 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). MolecularPhylogenetics and Evolution. Vol. 45, pp: 437- 453.
  49. Wüster, W. and Thorpe, R.S., 1988. Population affinities of the asiatic cobra (Naja naja) species complex in south-east Asia: reliability and random resampling. Biological Journal of Linnean Society. Vol. 36, pp: 391-409.
  50. Xia, X. and Lemey, P., 2009. The phylogenetic handbook: a practical approach to DNA and protein phylogeny.
  51. Young, A.G., 2000. Genetics, demography and viability of fragmented populations. Cambridge University Press.
  52. Zhao, E.; Wang, S. and Commission, E.S.S., 1998. China red data book of endangered animals: Amphibia and reptilia. Amphibia & reptilia/chief compiler Zhao Ermi. Science Press.
Journal of Animal Environment
Volume 13, Issue 1
May 2021
Pages 197-206

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