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Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome

  • Malay Ashvinkumar Shukla
  • Bheem Dutt Joshi
  • Ved Prakash Kumar
  • Anil Kumar Mehta
  • Surendra Prakash GoyalEmail author
Original Article

Abstract

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.

Keywords

Mitochondrial DNA FINS DNA barcoding Sequence divergence Antelope Phylogenetics 

Notes

Acknowledgements

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 statement

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.

Supplementary material

11033_2019_5054_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 13 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Laboratory of Forensic Biology and Biotechnology, Institute of Forensic ScienceGujarat Forensic Sciences UniversityGandhinagarIndia
  2. 2.Wildlife Institute of IndiaDehradunIndia

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