Skip to main content

Genetic diversity and phylogenetic analysis of blackbuck (Antilope cervicapra) in southern India

Abstract

Blackbuck (Antilope cervicapra) is a threatened species endemic to the Indian subcontinent. Many populations of blackbuck are found in southern India. Populations of blackbuck are negatively affected in many places for various reasons, such as habitat destruction and poaching. Their range decreased sharply during the 20th century. There is very limited information available on the population dynamics of blackbuck in southern India. For the phylogenetic and genetic diversity analyses of blackbuck populations among different distribution ranges in southern India, we sequenced mt DNA of cytochrome b (Cyt b) for 120, cytochrome c oxidase subunit-1 (COI) for 137 and the control region (CR) for 137 fecal pellets from eleven different locations in southern India. We analyzed the genetic structure of three mitochondrial markers, the CR, Cyt b and the COI region, separately and in a combined dataset. The haplotype diversity and nucleotide diversity of CR were 0.969 and 0.047, respectively, and were higher than those of Cyt b and COI. A Bayesian phylogeny and an MJ network based on the CR and combined dataset (105 sequences) signified several distinct haplotype clusters within blackbuck, whereas no clusters were identified with the Cyt b and COI phylogenetic analyses. The analysis of molecular variance of the combined data set revealed 52.46% genetic variation within the population. Mismatch distribution analysis revealed that blackbuck populations underwent complex changes with analysis of the combined dataset in each population and analysis of each marker separately in the overall population. The results provide evidence that blackbuck in different geographic locations has a distinct population structure due to habitat fragmentation after the formation of the Western and Eastern Ghats.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Ranjitsinh MK (1989) The Indian blackbuck. Natraj Publishers, Dehradun

    Google Scholar 

  2. 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 44:31–42

    Google Scholar 

  3. Jarman PJ (1974) The social organisation of antelope in relation to their ecology. Behaviour 48(3–4):215–267

    Google Scholar 

  4. Meena R, Chourasia V (2017a) Forage availability and feeding preferences of blackbuck Antilope cervicapra (Linn) in Sorsan, Rajasthan, India. Int J Curr Adv Res 6(11):7370–7373

    Google Scholar 

  5. Rahmani AR (2001) India. In: Mallon DP, Kingswood SC (eds) Antelopes. Part 4: North Africa, the Middle East and Asia. International Union for Conservation of Nature and Natural Resources, Gland. Switzerland, pp 178–187

    Google Scholar 

  6. Menon RK (2000) The quintessential antelope—life of the Blackbuck. Nature watch, resonance. J Sci Edu 5:69–79

    Google Scholar 

  7. Madhusudan MD, Mishra C (2003) Why big, fierce animals are threatened: conserving large mammals in densely populated landscapes. In: Saberwal V, Rangarajan M (eds) Battles over nature: science and the politics of wildlife conservation. Permanent Black, New Delhi, India, pp 31–55

    Google Scholar 

  8. Davidson AD, Hamilton MJ, Boyer AG, Brown JH, Ceballos G (2009) Multiple ecological pathways to extinction in mammals. Proc Natl Acad Sci USA 106:10702–10705

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Jhala YV, Isvaran K (2016) In: Ahrestani S, Sankaran M (eds) The ecology of large herbivores in South and Southeast Asia, Ecological studies, Vol. 225. Springer, Berlin

    Google Scholar 

  10. Johnson JM (1975) The Blackbuck in point calimere sanctuary, Tamil Nadu. Population dynamics and observation on behaviour. Indian For 101(8):484–494

    Google Scholar 

  11. Singh P, Rahmani AR, Wangchuk S, Mishra C, Singh KD (2006) Report of the task force on grasslands and deserts. Planning Commission, Government of India, New Delhi

    Google Scholar 

  12. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA

    Google Scholar 

  13. Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237

    Google Scholar 

  14. Gissi C, Iannelli F, Pesole G (2008) Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101:301–320

    CAS  PubMed  Google Scholar 

  15. Reyes A, Nevo E, Saccone C (2003) DNA sequence variation in the mitochondrial control region of subterranean mole rats, Spalax ehrenbergi superspecies, in Israel. Mol Biol Evol 20:622–632

    CAS  PubMed  Google Scholar 

  16. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 24:167–172

    Google Scholar 

  17. Hsieh HM, Chiang HL, Tsai LC, Lai SY, Huang NE, Linacre A, Lee JCI (2001) Cytochrome b gene for species identification of the conservation animals. Forensic Sci Int 122:7–18

    CAS  PubMed  Google Scholar 

  18. Wan QH, Wu H, Fujihara T, Fang SG (2004) Which genetic marker for which conservation genetics issue? Electrophoresis 25:2165–2176

    CAS  PubMed  Google Scholar 

  19. Kvie KS, Hogner S, Aarvik L, Lifjeld JT, Johnsen A (2013) Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata). Ecol Evol 3:126–144

    PubMed Central  Google Scholar 

  20. Puillandre N, Lambert A, Brouillet S, Achaz G (2012) ABGD, automatic barcode gap discovery for primary species delimitation. Mol Ecol 21:1864–1877

    CAS  PubMed  Google Scholar 

  21. Kholodova MV, Milner-Gulland EJ, Easton AJ, Amgalan L, Arylov Iu A, Bekenov A, Grachev Iu A, Lushchekina AA, Ryder O (2006) Mitochondrial DNA variation and population structure of the critically endangered saiga antelope Saiga tatarica. Oryx 40:103–107

    Google Scholar 

  22. Faria PJ, Kavembe GD, Jung’a JO, Kimwele CN, Estes LD, Reillo PR, Mwangi AG, Bruford MW (2011) The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation. Conserv Genet 12:745–751

    Google Scholar 

  23. Kumar A, Ghazi MGU, Hussain SA, Bhatt D, Gupta SK (2017) Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples. Mitochondrial DNA Part B 2:64–66

    PubMed  PubMed Central  Google Scholar 

  24. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  25. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  27. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    PubMed  Google Scholar 

  28. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGX: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 28:2731–2739

    Google Scholar 

  30. Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    PubMed  PubMed Central  Google Scholar 

  31. Bandelt HJ, Forster P, Ro¨hl A (1999) Median–joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    CAS  PubMed  Google Scholar 

  32. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–2100

    CAS  PubMed  Google Scholar 

  35. Dantas GPM, Meyer D, Godinho R, Ferrand N, Stenghel J (2012) Morgante1Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast. Genet Mol Biol 35(4):874–885

    Google Scholar 

  36. Hasegawa M, Iida Y, Yano T, Takaiwa F, Iwabuchi M (1985) Phyogenetic relationships amongeukaryotic kingdoms inferred by ribosmal RNA sequences. J Mol Evol 22(1):32–38

    CAS  PubMed  Google Scholar 

  37. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526

    CAS  PubMed  Google Scholar 

  38. Alpers DL, Van Vuuren BJ, Arctander P, Robinson TJ (2004) Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation. Mol Ecol 13:1771–1784

    CAS  PubMed  Google Scholar 

  39. Kvie KS, Heggenes J, Knut HR (2016) Merging and comparing three mitochondrial markers forphylogenetic studies of Eurasian reindeer (Rangifer tarandus). Ecol Evol 6:4347–4358

    PubMed  PubMed Central  Google Scholar 

  40. Zhao Y, Zhang J, Zhao E, Zhang X, Liu X, Zhang N (2011) Mitochondrial DNA diversity and origins of domestic goats in southwest China (excluding Tibet). Small Rumin Res 95:40–47

    Google Scholar 

  41. Røed KH, Bjørnstad G, Flagstad Ø, Haanes H, Hufthammer AK, Jordhøy P et al (2014) Ancient DNA reveals prehistoric habitat fragmentation and recent domestic introgression into native wild reindeer. Conserv Genet 15:1137–1149

    Google Scholar 

  42. Zhang F, Jiang Z (2006) Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata): implications for conservation. Mol Phylogenet Evol 41:313–321

    CAS  PubMed  Google Scholar 

  43. Shukla MA, Joshi BD, Kumar VP, Mehta AK, Goyal SP (2019) Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome. Mol Biol Rep 46:6187–6195

    CAS  PubMed  Google Scholar 

  44. Birungi J, Arctander P (2000) Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob). Mol Ecol 9:1997–2008

    CAS  PubMed  Google Scholar 

  45. Christopher N, Balakrishaan SL, Minfort AG, Lalji S, Michael DS (2003) Phyogeography and conservation genetics of Eld’s deer (Cervus eldi). Mol Ecol 12:1–10

    Google Scholar 

  46. Gupta SK, Kumar A, Angom S, Singh B, Ghazi MGU, Tuboi C, Syed Ainul Hussain SA (2018) Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent. Sci Rep 8:16308

    PubMed  PubMed Central  Google Scholar 

  47. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569

    CAS  PubMed  Google Scholar 

  48. Rogers AR (1995) Genetic evidence for a Pleistocene population expansion. Evolution 49:608–615

    PubMed  Google Scholar 

  49. Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13:853–864

    CAS  PubMed  Google Scholar 

  50. Pichler FB (2002) Genetic assessment of population boundaries and gene exchange in Hector’s dolphin, DOC science internal series, Vol. 44. University of California, Berkeley, CA

    Google Scholar 

  51. Doak DF, Morris W (1999) Detecting population-level consequences of ongoing environmental change without long-term monitoring. Ecology (Washington, DC) 80(5):1537–1551

    Google Scholar 

  52. Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC (2004) Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303:223–226

    CAS  PubMed  Google Scholar 

  53. Morin PA, Moore JJ, Chakraorty R, Jin L, Goodall J, Woodru VDS (1994) Kin selection, social structure, geneXow, and the evolution of chimpanzees. Science 265:1193–1201

    CAS  PubMed  Google Scholar 

  54. “Western Ghats”. UNESCO. http://whc.unesco.org/en/list/1342/multiple=1&unique_number=1921. Retrieved 3 Jan 2013

  55. Simonsen BT, Siegismund HR, Arctander P (1998) Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation. Mol Ecol 7:225–237

    CAS  PubMed  Google Scholar 

  56. Ferris SD, Sage RD, Huang CM, Nielsen JT, Ritter U, Wilson AC (1983a) Flow of mitochondrial DNA across a species boundary. Proc Natl Acad Sci USA 80:2290–2294

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S et al (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA 100:171–176

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank our Director, the Zoological Survey of India, Kolkata, Ministry of Environment, Forest and Climate Change (MoEF&CC) for providing financial support and necessary facilities. We sincerely acknowledge our Officer-in-Charge Dr. K. A. Subramanian, Southern Regional Centre, Zoological Survey of India, Chennai for their support and encouragement. We thank the PCCF, (Wildlife) and APCCF of Tamil Nadu, Chennai Zoo, Telangana, Karnataka and Andhra Pradesh for permission to collect samples.

Funding

Financial support was provided by our Director, the Zoological Survey of India, Kolkata, Ministry of Environment, Forest and Climate Change (MoEF&CC).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ranjana Bhaskar.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Bhaskar, R., Kanaparthi, P. & Sakthivel, R. Genetic diversity and phylogenetic analysis of blackbuck (Antilope cervicapra) in southern India. Mol Biol Rep 48, 1255–1268 (2021). https://doi.org/10.1007/s11033-021-06180-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-021-06180-9

Keywords

  • Mitochondrial DNA
  • COI
  • CR
  • Cyt b
  • Phylogenetic
  • Antilope cervicapra