Characterization of 12S rRNA Gene for Species Identification of Common Indian Wild and Domestic Birds

Authors

  • Amit Oad School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, Jabalpur-482001, M.P., India
  • Awadh B Shrivastav School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, Jabalpur-482001, M.P., India
  • Kajal Jadav School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, Jabalpur-482001, M.P., India
  • Nidhi Rajput School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, Jabalpur-482001, M.P., India
  • Amol Rokde School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, Jabalpur-482001, M.P., India
  • Kumar Govil Department of Animal Nutrition, College of Veterinary Science and Animal Husbandry, Rewa- 486001, NDVSU, M.P., India

DOI:

https://doi.org/10.48165/ijvsbt.20.2.08

Keywords:

Birds, FINS, Forensic, Phylogeny, Wildlife

Abstract

Poaching is a major threat to birds, mammals, plants and reptiles. The Indian peafowl (Pavo cristatus), a ‘gallinaceous bird’, is the national bird of India and belongs to Schedule I of the Indian Wildlife (Protection) Act, 1972. The bird is often killed for its tail feathers and meat. For the effective implementation of law and order, firm evidences are required against the poachers. Additionally, phylogenetic analysis is required to study the biodiversity of avian fauna for better understanding of genetic evolution. Hence, in the present study, characterization of 12S rRNA gene was performed for genomic analysis and phylogentic relationship of Indian peafowl with other free-ranging and domestic birds. A total of 54 Forensically Informative Nucleotide Sequences (FINS) were identified in the present study for identification of species of the panel birds. The phylogenetic analysis was inferred using the Neighbor-joining tree in which different wild bird species were found to be restricted to different clades. Data obtained in the present study using partial fragment of 12S rRNA gene for tissue and faecal samples might be a useful and convenient tool for species identification and can be readily applied to other bird assemblages, making them particularly relevant to a broad range of further avian research.

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References

Arif, I. A., Khan, H,A., Bahkali, A. H., Ali, A., Homaidan, A., Farhan, A. H. A., Sadoon, M. A. and Shobrak, M. (2011). DNA marker technology for wildlife conservation. Saudi Journal of Biological Sciences, 18, 219-225.

Clayton, T. M., Guest, J. L., Urquhart, A. J. and Gill, P. D. (2004). A genetic basis for anomalous band patterns encountered during DNA STR profiling. Journal of Forensic Sciences, 49(6), 1207-1214.

Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. and Francis, C. M. (2004). Identification of birds through DNA barcodes. PLOS Biology, 2(10), 312-316.

Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-79.

Ghosh, A., Basu, S., Jabin, G., Khatri, H., Singh, S. K., Maheswaran, G., Chandra, K and Thakur, M. (2019). Wildlife forensics in voiding false offences: A case study to deal with unidentified cooked meat. Forensic Science International, 1, 100011.

Jadav, K. K., Rajput, N., Shrivastav, A. B., Mandal, S and Shrivastav, G. (2014). Application of 12S rRNA gene sequence for identification of Indian wild pig (Sus scrofa cristatus). Journal of meat science and technology, 12, 35-39.

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.

Kocher, T. D., Thomas, W. K., Meyer, A., Edverds, S. V., Paabo, S., Villablanca, F. C and Wilson, A. (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA, 86, 6196-6200.

Kumar, V. P., Rajpoot, A., Shukla, M., Kumar, D. and Goyal, S. P. (2016). Illegal trade of Indian pangolin (Manis crassicaudata): Genetic study from scales based on mitochondrial genes. Egyptian Journal of Forensic Sciences, 6(4), 524-533.

Lijtmaer, D. A., Kerr, K. C. R., Stoeckle, M. Y. and Tubaro, P. L. (2012). DNA Barcoding birds: from field collection to data. In: DNA Barcodes. Methods in Molecular Biology (Methods and Protocols), Kress, W.J. and Erickson, D.L., vol. 858, Humana Press, Totowa, NJ, pp. 127-152.

Livezey, B. C and Zusi, R. L. (2007). Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society, 149 (1), 1-95.

Prakash, S., Patole, M. S., Ghumatkar, S. V., Nandode, S. K., Shinde, B. M and Yogesh, S. S .(2000). Mitochondrial 12S rRNA sequence analysis in wildlife forensics. Current Science, 78, 1239-1246.

Pereira, S. L. (2000). Mitochondrial genome organization and vertebrate phylogenetics. Genetics and Molecular Biology, 23, 745-752.

Rajput. N., Shrivastav, A. B., Parmar, S. N. S., Joseph, E., Ranjan, R. and Singh, S. (2013). Characterization of 12S-rRNA gene for meat identification of common wild and domestic small herbivores as an aid to wildlife forensic. Veterinary World, 6(5), 254-259.

Rudnick, A., Katzner, E., Bragin, A and Andrew, J. (2007). Species identification of birds through genetic analysis of naturally shed Feathers. Journal of Molecular Evolution, 7(5), 757-762.

Saitou, N and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Journal of Molecular Evolution, 4, 406-425.

Sambrook, J., Frisch, E. F and Maniatis, T. (1989). Molecular cloning: a molecular approach laboratory manual. New York: Harbour Laboratory Press.

Tamura, K., Stecher, G., Peterson, D., Filipski, A and Kumar, S. (2013). MEGA 6: Molecular evolutionary genetics analysis Version 6.0. Journal of Molecular Evolution, 30, 2725-2729.

Thakur, M. (2014). Role of DNA forensics in curbing illegal wildlife trade. WWF newsletter (Panda) Illegal Wildlife Trade in India (Special issue), pp. 11-12.

Thakur, M,, Singh, S. K., Shukla, M., Mohan, N., Goyal, S. P and Sathyakumar, S. (2013). Identification of Galliformes through Forensically informative Nucleotide Sequencing (FINS) and its Implication in Wildlife Forensics. Journal of Forensic Research, 4, 195.

Thompson, D., Higgins, D. G., Gibson, T. J and Clustal, W. (1994). 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.

Tobe, S. S and Linacre, A. M. T. (2008). A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures. Forensic Science International: Genetics, 2(4), 249–256.

Verma, S. K and Singh, L. (2003). Novel universal primers establish identity of an enormous number of animal species for forensic application. Molecular Ecology Notes, 3(1), 28-31.

Published

2024-03-10

How to Cite

Oad, A., Shrivastav, A.B., Jadav, K., Rajput, N., Rokde, A., & Govil, .K. (2024). Characterization of 12S rRNA Gene for Species Identification of Common Indian Wild and Domestic Birds. Indian Journal of Veterinary Sciences and Biotechnology, 20(2), 37–43. https://doi.org/10.48165/ijvsbt.20.2.08