Journal of Genetics

, 98:44 | Cite as

Rapid molecular assays for species and sex identification of swamp deer and other coexisting cervids in human-dominated landscapes of the Terai region and upper Gangetic plains, northern India: implications in understanding species distribution and population parameters

  • Shrutarshi Paul
  • Tista Ghosh
  • Bivash Pandav
  • Dhananjai Mohan
  • Bilal Habib
  • Parag Nigam
  • Samrat MondolEmail author


Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human-dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected reference samples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.


herbivore distribution non-protected areas species-specific assays molecular sexing swamp deer 



We thank the Forest Departments of Uttarakhand and Uttar Pradesh for providing necessary permits (Permission nos: 90/5, 978/6-32/56, 1127/23-2-12(G) and 2233/23-2-12 (G)) to conduct this research. We are thankful to the Forest Department officials, Suvankar Biswas, Supriya Bhatt, Imam, Ranju, Bhura, Annu and Ammi, for helping us with sampling. We thank the Forest Departments of Haryana and Rajasthan (Jaipur Zoo Authorities) and Dr. S. P. Goyal for providing reference samples. Mr. A. Madhanraj and Ms Garima provided critical technical help in the laboratory. Our sincere thanks to the Director, Dean and the Wildlife Forensics and Conservation Genetics Cell of the Wildlife Institute of India for their support. Shrutarshi Paul was awarded the Department of Science and Technology INSPIRE Research Fellowship (IF150680) and Samrat Mondol was supported by the Department of Science and Technology INSPIRE Faculty Award (IFA12-LSBM-47).


  1. Costa E. B. V., de Oliveira M. L., Peres P. H. D. F, Grotta-Neto F., Vogliotti A., Piovezan U. et al. 2016 Low accuracy of identifying neotropical deer species by scat morphology. Stud. Neotrop. Fauna E 52, 37–42.CrossRefGoogle Scholar
  2. Duarte J. M. B., Talarico Â. C., Vogliotti A., Garcia J. E., Oliveira M. L., Maldonado J. E. et al. 2016 Scat detection dogs, DNA and species distribution modelling reveal a diminutive geographical range for the vulnerable small red brocket deer Mazama bororo. Oryx 51, 656–664.CrossRefGoogle Scholar
  3. Duckworth J. W., Kumar N. S., Pokheral C. P., Baral H. S. and Timmins R. J. 2015 Rucervus duvaucelii. The IUCN Red List of Threatened Species v31.Google Scholar
  4. Geist V. 1998 Deer of the world, their evolution, behaviour, and ecology. Stackpole Books, Pennsylvania, US.Google Scholar
  5. Gonzalez S., Maldonado J. E., Ortega R. J., Talarico A. C., Batista L. B., Garcia J. E. et al. 2009 Identification of the endangered small red brocket deer (Mazama bororo) using noninvasive genetic techniques (Mammalia; Cervidae). Mol. Ecol. Res. 9, 754–758.CrossRefGoogle Scholar
  6. Gupta S. K., Kumar A. and Hussain S. A. 2012 Extraction of PCR-amplifiable DNA from a variety of biological samples with uniform success rate. Conserv. Genet. Resour. 5, 215–217.CrossRefGoogle Scholar
  7. Gupta S. K., Kumar A. and Hussain S. A. 2014 Novel primers for sequencing of the complete mitochondrial cytochrome b gene of ungulates using non-invasive and degraded biological samples. Conserv. Genet. Resour. 6, 499–501.CrossRefGoogle Scholar
  8. Harihar A. 2011 Understanding the response of wild ungulate prey to livestock-mediated competition in western Terai Arc Landscape, India, implications for developing management strategies to restore corridors. A report to Rufford Small Grant for Nature Conservation (available at
  9. Johnsingh A. J. T., Ramesh K., Qureshi Q., David A. and Goyal S. 2004 Conservation status of tiger and associated species in the Terai Arc Landscape, pp. 110. Dehradun, India.Google Scholar
  10. Karanth K. K., Nichols J. D., Karanth K. U., Hines J. E. and Christensen N. L. Jr. 2010 The shrinking ark, patterns of large mammal extinctions in India. Proc. R. Soc. B. Biol. Sci. 277, 1971–1979.CrossRefGoogle Scholar
  11. Kumar A., Bargali H. S., David A. and Edgaonkar A. 2017 Patterns of crop raiding by wild ungulates and elephants in Ramnagar Forest Division, Uttarakhand. Hum-Wildl. Interact. 11, 41–49.Google Scholar
  12. Mukherjee N., Mondol S., Andheria A. and Ramkrishnan U. 2007 Rapid multiplex PCR based species identification of wild tigers using non-invasive samples. Conserv. Genet. 8, 1465–1470.CrossRefGoogle Scholar
  13. Oliveira M. L. and Duarte J. 2013 Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from faecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae). Genet. Mol. Res. 12, 44–52.CrossRefGoogle Scholar
  14. Pajares G. E., Álvarez I. S., Fernández I. V., Pérez-Pardal L. U., Goyache F. É. and Royo L. J. 2007 A sexing protocol for wild ruminants based on PCR amplification of amelogenin genes AMELX and AMELY. Arch. Animal Breed. 50, 442–446.CrossRefGoogle Scholar
  15. Palomares F., Godoy J. A., Piriz A. and Johnson W. E. 2002 Faecal genetic analysis to determine the presence and distribution of elusive carnivores, design and feasibility for the Iberian lynx. Mol. Ecol. 11, 2171–2182.CrossRefGoogle Scholar
  16. Paul S., Pandav B., Mohan D., Habib B., Nigam P. and Mondol S. 2018 Current distribution and status of swamp deer (Rucervus duvaucelii duvaucelii) along upper Gangetic plains in north India. Oryx 52, 646–653.CrossRefGoogle Scholar
  17. Pelizzon C., da Silva Carvalho C., Caballero S., Junior P. M. G. and Sanches A. 2016 Sex identification of the extant mega mammal, the lowland tapir, Tapirus terrestris (Tapiridae, Mammalia), by means of molecular markers, new outlook for non-invasive samples. Conserv. Genet. Res. 9, 17–19.CrossRefGoogle Scholar
  18. Qureshi Q., Sawarkar V. B., Rahmani A. R. and Mathur P. K. 2004 Swamp deer or barasingha (Cervus duvauceli Cuvier, 1823) In Ungulates of India (ed. K. Sankar and S. P. Goyal) Envis Bulletin, Wildlife and Protected Areas, 7(1), Wildlife Institute of India, Dehradun, India, pp. 181–192.Google Scholar
  19. Rawat G. S. and Adhikari B. S. 2015 Ecology and management of grassland habitats in India. ENVIS Bulletin, Wildlife & Protected Area, 17.Google Scholar
  20. Ripple W. J., Newsome T. M., Wolf C., Dirzo R., Everatt K. T., Galetti M. et al. 2015 Collapse of the world’s largest herbivores. Sci. Adv. 1, 1400103.CrossRefGoogle Scholar
  21. Sharma L. K., Charoo S. A. and Sathyakumar S. 2015 Species identification and molecular sexing from feces of Kashmir stag (Cervus elaphus hanglu). Conserv. Genet. Res. 7, 677–680.CrossRefGoogle Scholar
  22. Takahashi M., Masuda R., Uno H., Yokayama M., Suzuki Yoshida M. C. and Ohtaishi N. 1998 Sexing of carcass remains of the sika deer (Cervus nippon) using PCR amplification of SRY gene. J. Vet. Med. Sci. 60, 713–716.CrossRefGoogle Scholar
  23. Tamura K., Stecher G., Peterson D., Filipski A. and Kumar S. 2013 MEGA6, molecular evolutionary genetics analysis version 60. Mol. Biol. Evol. 30, 2725–2729.CrossRefGoogle Scholar
  24. Yamauchi K., Hamasaki S., Miyazaki K., Kikusui T., Takeuchi Y. and Mori Y. 2000 Sex determination based on faecal DNA analysis of the amelogenin gene in sika deer (Cervus nippon). J. Vet. Med. Sci. 62, 669–671.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.Wildlife Institute of IndiaDehradunIndia
  2. 2.Uttarakhand Forest DepartmentDehradunIndia

Personalised recommendations