Genetic diversity and population structure of Barilius barna (Hamilton, 1822) in the sub-Himalayan Dooars region of West Bengal, India through Mitochondrial Cytochrome Oxidase I Sequence analyses

Ajoy Paul, Tanmay Mukhopadhyay, Soumen Bhattacharjee


The genetic diversity and the population structure of Barilius barna (Hamilton, 1822) wild population from the Teesta River were assessed through mtDNA cytochrome oxidase I (COI) sequence analyses. The haplotype and nucleotide diversity analyses revealed low level of genetic diversity in the B. barna wild populations, especially in the lower reaches of Teesta (Bholarhat). The genetic differentiation and gene flow between the two study sites were 0.08434 and 2.71, respectively. Tajima’s D, Fu and Li’s D and Fu and Li’s F analyses were used to assess population differentiation in the two study sites. Haplotype networking and phylogenetic analyses clearly distinguished the two populations from each other, as well as from other populations from other parts of the country. Nature and implications of the genetic and haplotype diversities among the populations are discussed. Phylogenetic analyses also indicated that the Gajoldoba population is genetically closer to north Indian river populations, than that to Bholarhat population.


Teesta, COI, Haplotype, Phylogeny.

Full Text:



Avise J.C. (1994). Molecular markers, natural history and evolution. Chapman and Hall. New York. 511 p.

Bandelt H.J., Forster P., Rohl A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16: 37-48.

Billington N. (2003). Mitochondrial DNA. In: E.M. Hallerman (Ed.) Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, MD. pp: 59-100.

Boonkusol D., Tongbai W. (2016). Genetic variation of striped snakehead fish (Channa striata) in river basin of central Thailand inferred from mtDNA COI gene sequence analysis. Journal of Biological Sciences, 16: 37-43.

Du X., Chen Z., Deng Y., Wang Q. (2009). Comparative analysis of genetic diversity and population structure of Sipunculus nudus as revealed by mitochondrial COI sequences. Biochemical Genetics, 47: 884-891.

Excoffier L., Smouse P.E. (1994). Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics, 136: 343-359.

Felsenstein J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17: 368-376.

Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3: 294-299.

Fu Y.X., Li W.H. (1993). Statistical tests of neutrality of mutations. Genetics, 133: 693-709.

Galtier N., Nabholz B., Glemin M.S., Hurst G.D.D. (2009). Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology, 18: 4541-4550.

Govindaraju D.R. (1989). Variation in gene flow level among predominantly self-pollinated plants. Journal of Evolutionary Biology, 2: 173-181.

Guindon S., Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52: 696-704.

Hall T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium, Series 41: 95-98.

Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294: 2310-2314.

Kimura M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111-120.

Librado P., Rozas J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.

Low V.N., Adler P.H., Takaoka H., Yacob Z., Lim P.E., Tan T.K., Lim Y.A.L., Chen C.D., Rashid Y.N., Azirun M.S. (2014). Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the Black fly Simulium tani Takaoka and Davies along an elevational gradient in Malaysia. PLOS One, 9: e100152.

Molur S., Walker S. (1998). Conservation Assessment and Management Plan for freshwater fishes of India. Zoo Outreach Organization, Conservation Breeding Specialist Group. Coimbatore, India. 5 p.

Paul A., Mukhopadhyay T., Bhattacharjee S. (2018). Genetic characterization of Barilius barna (Hamilton, 1822) in the Teesta river of sub-Himalayan West Bengal, India, through RAPD and ISSR fingerprinting. Proceedings of the Zoological Society, 7: 203-212.

Posada D. (2008). jModel Test: phylogenetic model averaging. Molecular Biology and Evolution, 25: 1253-1256.

Prim R.C. (1957). Shortest connection networks and some generalizations. Bell System Technical Journal, 36: 1389-1401.

Rambaut A., Drummond A.J. (2003). Tracer: MCMC trace analysis tool, 2nd. University of Oxford, Oxford, UK. Available from: http: // Retrieved 10/13/2017.

Rohlf F.J. (1973). Algorithm 76. Hierarchical clustering using the minimum spanning tree. The Computer Journal, 16: 93-95.

Ronquist F., Huelsenbeck J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574.

Rozen S., Skaletsky H. (2000). Bioinformatics methods and protocols. In: S. Krawetz, S. Misener (Eds.). Methods in Molecular Biology. Humana Press, Totowa, NJ. 365 p.

Shaw G.E., Shebbeare E.O. (1937). The fishes of North Bengal. Journal of the Royal Asiatic Society of Bengal Science, 3: 1-137.

Tajima F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123: 585-95.

Talwar P.K., Jhingran A.G. (1991). Inland fishes of India and adjacent countries. Oxford and IBH Company Private Limited. New Delhi, India. 344 p.

Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30: 2725-2729.

Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins G.G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25: 4876-4882.

Thompson J.D., Higgins D.G., 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, 22: 4673-4680.

Wake D.B. (1991). Homoplasy: the result of natural selection, or evidence of design limitations? American Naturalist, 138 (3): 543-567.

Wake D.B., Wake M.H., Specht C.D. (2011). Homoplasy: from detecting pattern to determining process and mechanism of evolution. Science, 331: 1032–1035.

Ward R.D., Zemlak T.S., Innes B.H., Last P.R., Hebert P.D.N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B, 360: 1847-1857.

Wright S. (1978). Evolution and the genetics of populations, variability within and among natural populations. University of Chicago Press, Chicago, USA. 465 p.


  • There are currently no refbacks.