Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome
Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004–0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225–0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.
KeywordsMitochondrial DNA FINS DNA barcoding Sequence divergence Antelope Phylogenetics
The authors are thankful to the Director, Dean and Research Coordinator, Wildlife Institute of India (WII), Dehradun, for their strong support. The authors would like to thank Nodal Officer of Wildlife Forensic Cell for providing laboratory facilities during Ph.D. research work. Authors extend their sincere thanks to Director General and Dean Gujarat Forensic Sciences University (GFSU); and Director, Institute of Forensic Science, GFSU for their kind support during Ph.D. work. We also acknowledge University Grant Commission, New Delhi for providing fellowship in the form of JRF/SRF to MS. Contribution of Forest Department across India is acknowledged for extending valuable support in establishing a repository of reference samples at the Institute.
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest. The authors have no funding or financial support for wet-lab analysis.
Ethical approval was not required for this study because most of the samples were procured from a reference repository of WII and non-invasively collected from field sampling in India.
- 1.Schipper J, Chanson JS, Chiozza F, Cox NA, Hoffmann M, Katariya V, Lamoreux J, Rodrigues AS, Stuart SN, Temple HJ, Baillie J, Young BE (2008) The status of the world’s land and marine mammals: diversity, threat, and knowledge. Science 322:225. https://doi.org/10.1126/science.1165115 CrossRefGoogle Scholar
- 2.Chauhan N (1999) Evaluation of crop damage in the eco-development project area to suggest mitigating measures. FREEP-GHNP research project, Wildlife Institute of India, DehradunGoogle Scholar
- 3.Mallon D, Kingswood SC (2001) Antelopes: global survey and regional action plans. IUCN. http://www.iucn.org. Accessed 15 June 2017
- 4.Mallon DP (2008) Antilope cervicapra. The IUCN red list of threatened species 2008. IUCN, Gland. http://dx.doi.org/10.2305/IUCN.UK.2008.RLTS.T1681A6448761.en%0ADisclaimer. Accessed 15 June 2017
- 7.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. Mol Mar Biol Biotechnol 3:294-9Google Scholar
- 15.Kumar A, Ghazanfar M, Ghazi U, Singh B, Hussain SA (2017) Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples. Mitochondrial DNA Part B Resour. https://doi.org/10.1080/23802359.2016.1247672 Google Scholar
- 16.Bartlett SE, Davidson WS (1992) FINS (Forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. Biotechniques 12:408–411Google Scholar
- 17.Chapela MJ, Sotelo CG, Calo-Mata P, Pérez-Martín RI, Rehbein H, Hold GL, Quinteiro J, Rey‐Méndez M, Rosa C, Santos AT (2002) Identification of cephalopod species (Ommastrephidae and Loliginidae) in seafood products by forensically informative nucleotide sequencing (FINS). J Food Sci 67(5):1672–1676. https://doi.org/10.1111/j.1365-2621.2002.tb08703.x CrossRefGoogle Scholar
- 19.Thakur M, Javed R, Kumar VP, Shukla M, Singh N, Maheshwari A, Mohan N, Wu DD, Zhang YP (2017) DNA forensics in combating food frauds: a study from China in identifying canned meat labelled as deer origin. Curr Sci 112(12):2449–2452. https://doi.org/10.18520/cs/v112/i12/2449-2452 CrossRefGoogle Scholar
- 22.Kumar VP, Shukla M, Rajpoot A, Thakur M, Nigam P, Kumar D, Mehta AK, Goyal SP (2018) DNA barcoding as a tool for robust identification of cervids of India and its utility in wildlife forensics. Mitochondrial DNA Part B Resour 3(1):250–255. https://doi.org/10.1080/23802359.2018.1438858 CrossRefGoogle Scholar
- 24.Meena R, Saran RP (2018) Distribution, ecology and conservation status of blackbuck (Antilope cervicapra): an update. Int J Biol Res 3(1):79–86Google Scholar
- 25.Palumbi S, Martin A, Romano S, McMillan OW, Stice L, Grabowski G (1991) The simple fool’s guide to PCR version 2. Honolulu Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, HonoluluGoogle Scholar
- 26.Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, vol. 41, Article-ID: 691774, pp. 95–98Google Scholar
- 28.Nylander JAA (2004) Mr Modeltest v2. Program Distributed by the Author Evolutionary Biology Centre. Uppsala University, UppsalaGoogle Scholar
- 33.Ahmad K, Kumar VP, Joshi BD, Raza M, Nigam P, Khan AA, Goyal SP (2016) Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications. BMC Res Notes 9(1):477. https://doi.org/10.1186/s13104-016-2271-4 CrossRefGoogle Scholar
- 35.Kumar A, Ghazi MGU, Hussain SA, Bhatt D, Gupta SK (2017) Mitochondrial and nuclear DNA based genetic assessment indicated distinct variation and low genetic exchange among the three subspecies of swamp deer (Rucervus duvaucelii). Evol Biol 44(1):31–42. https://doi.org/10.1007/s11692-016-9387-2 CrossRefGoogle Scholar