Conservation Genetics Resources

, Volume 7, Issue 2, pp 353–361 | Cite as

Identifying species, sex and individual tigers and leopards in the Malenad-Mysore Tiger Landscape, Western Ghats, India

  • Samrat Mondol
  • N. Samba Kumar
  • Arjun Gopalaswamy
  • Kartik Sunagar
  • K. Ullas Karanth
  • Uma Ramakrishnan
Application Essays


Assessing the distribution, abundance and demographic ratios of endangered and elusive co-occurring carnivore species at a landscape level is important for their continued survival. Despite potential to determine distribution and dietary analyses, use of faecal samples has been relatively limited in the context of multiple sympatric species living at large landscapes. We developed and optimized a range of novel non-invasive molecular techniques for species, gender and individual identification of tiger (Panthera tigris) and leopard (Panthera pardus). We collected a large number of faecal samples as part of a pilot occupancy survey in the Malenad-Mysore Tiger Landscape, Western Ghats, India. We could genetically ascertain species and gender for 88 and 57 % of the field-collected samples respectively. Additionally, we also determined a panel of nine and eight polymorphic loci for tiger and leopard individual identification, resulting in 18 tigers and 39 leopards from varied quality field-collected samples. Our pilot study suggest such molecular approaches will help in future efforts to gather landscape level distribution, demographic and other ecological information on tigers and leopards across their distribution.


Species identification Molecular sexing Panthera tigris Panthera pardus Carnivore conservation 



We are thankful to the forest department of Karnataka for providing permits to carry out the research in this landscape. We also thank the CWS field teams, local forest officials and volunteers for their assistance. We thank V. Kolipakam, R. Samant, P. Yadav and other Ramakrishnan lab members for their help during this study. SM was supported by Department of Science and Technology INSPIRE Faculty Award. This research was funded by Department of Science and Technology, Government of India grant awarded to KUK and UR, National Centre for Biological Sciences, and Wildlife Conservation Society. Center for Wildlife Studies provided logistical and material supports for the fieldwork. UR was supported by the Ramanujan fellowship.


  1. Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G (2009) Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Res 9:1279–1301CrossRefGoogle Scholar
  2. Bellemain E, Nawaz A, Valentini A, Swenson JE, Taberlet P (2007) Genetic tracking of the brown bear in northern Pakistan and implications for conservation. Biol Conserv 134:537–547CrossRefGoogle Scholar
  3. Bhagavatula J, Singh L (2006) Genotyping faecal samples of Bengal tiger (Panthera tigris tigris) for population estimation: a pilot study. BMC Genet 7:48CrossRefPubMedCentralPubMedGoogle Scholar
  4. Bidlack AL, Reed SE, Palsbøll PJ, Getz WM (2007) Characterization of a western North American carnivore community using PCR–RFLP of cytochrome b obtained from fecal samples. Conserv Genet 8:1511–1513CrossRefGoogle Scholar
  5. Busby GBJ, Gottelli D, Wacher T et al (2009) Genetic analysis of scat reveals leopard Panthera pardus and cheetah Acinonyx jubatus in southern Algeria. Oryx 43:412–415CrossRefGoogle Scholar
  6. Ceballos G, Erlich PR, Soberon J, Salazar I, Fay JP (2005) Global mammal conservation: What must we manage? Science 309:603–607CrossRefPubMedGoogle Scholar
  7. Cossíos D, Angers B (2006) Identification of Andean felid species using PCR-RFLP. Mastozool Neotrop 13:239–244Google Scholar
  8. Davison A, Birks JDS, Brookes RC, Braithwaite RC, Messenger JE (2002) On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats. J Zool 257:141–143CrossRefGoogle Scholar
  9. Excoffier L, Laval G, Schneider S (2005) ARLEQUIN ver 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedCentralGoogle Scholar
  10. Fernandes CA, Ginja C, Pereira I et al (2008) Species-specific mitochondrial DNA markers for identification of non-invasive samples from sympatric carnivores in the Iberian Peninsula. Conserv Genet 9:681–690CrossRefGoogle Scholar
  11. Foresman KR, Pearson DE (1998) Comparison of proposed survey techniques for detection of forest carnivores. J Wildl Manag 62:1217–1226CrossRefGoogle Scholar
  12. Goossens B, Bruford MW (2009) Non-invasive genetic analysis in conservation. In: Bertorelle G, Bruford MW, Hauffe HC, Rizzoli A, Vernesi C (eds) Population genetics for animal conservation. Cambridge University Press, United Kingdom, pp 167–201Google Scholar
  13. Haag T, Santos AS, Angelo CD et al (2009) Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies. Genetica 136:505–512CrossRefPubMedGoogle Scholar
  14. Hines JE, Nichols JD, Royle AJ et al (2010) Tigers on trails: occupancy modeling for luster sampling. Ecol Appl 20:1456–1466CrossRefPubMedGoogle Scholar
  15. Johnsingh AJT (1983) Large mammalian prey-predators in Bandipur. J Bombay Nat Hist Soc 80:1–57Google Scholar
  16. Karanth KU, Nichols JD (1998) Estimation of tiger densities in India using photographic captures and recaptures. Ecology 79:2852–2862CrossRefGoogle Scholar
  17. Karanth KU, Sunquist ME (1995) Prey selection by tiger leopard and dhole in tropical forests. J Anim Ecol 64:439–450CrossRefGoogle Scholar
  18. Karanth KU, Sunquist ME (2000) Behavioural correlates of predation by tiger (Panthera tigris) leopard (Panthera pardus) and dhole (Cuon alpinus) in Nagarahole, India. J Zool 250:255–265CrossRefGoogle Scholar
  19. Karanth KK, Nichols JD, Hines JE, Karanth KU, Christensen NL (2009) Patterns and determinants of mammal species occurrence in India. J Appl Ecol 46:1189–1200Google Scholar
  20. Karanth KU, Gopalaswamy A, Kumar NS et al (2011) Monitoring carnivore populations at the landscape scale: occupancy modelling of tigers from sign surveys. J Appl Ecol 48:1048–1056CrossRefGoogle Scholar
  21. Kim JH, Antunes A, Luo SJ et al (2006) Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. Gene 366:292–302CrossRefPubMedCentralPubMedGoogle Scholar
  22. Livia L, Francesca V, Antonella P, Fausto P, Bernardino R (2007) A PCR-RFLP method on faecal samples to distinguish Martes martes, Martes foina, Mustela putorius and Vulpes vulpes. Conserv Genet 8:757–759CrossRefGoogle Scholar
  23. McDougal C (1988) Leopard and tiger interactions at Royal Chitwan National Park, Nepal. J Bombay Nat Hist Soc 85:609–610Google Scholar
  24. Menotti-Raymond et al (1999) A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57:9–23CrossRefPubMedGoogle Scholar
  25. Miquelle DG, Stephens PA, Smirnov EN et al (2005) Tigers and wolves in the Russian Far East: competitive exclusion functional redundancy and conservation implications. In: Ray JC, Berger J, Redford KH, Steneck R (eds) Large carnivores and the conservation of biodiversity. Island Press, Washington, pp 179–207Google Scholar
  26. Mittermeier RA, Myers N, Thomsen JB, Da Fonesca GAB, Oliveri S (1998) Biodiversity hotspots and major tropical wilderness areas: approaches to setting conservation priorities. Conserv Biol 12:516–520CrossRefGoogle Scholar
  27. Mondol S, Karanth KU, Kumar NS et al (2009a) Evaluation of non-invasive genetic sampling methods for estimating tiger population size. Biol Conserv 142:2350–2360CrossRefGoogle Scholar
  28. Mondol S, Karanth KU, Ramakrishnan U (2009b) Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genet 5(8):e1000585CrossRefPubMedCentralPubMedGoogle Scholar
  29. Mondol S, Navya R, Athreya V et al (2009c) A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes. BMC Genet 10:79CrossRefPubMedCentralPubMedGoogle Scholar
  30. Mondol S, Thatte P, Yadav P, Ramakrishnan U (2012) A set of miniSTRs for population genetic analyses of tigers (Panthera tigris) with cross-species amplification for seven other Felidae. Conserv Genet Resour 4:63–66CrossRefGoogle Scholar
  31. Moruzzi TL, Fuller TK, DeGraaf RM, Brooks RT, Li W (2002) Assessing remotely triggered cameras for surveying carnivore distribution. Wildl Soc Bull 2:380–386Google Scholar
  32. Nagata J, Aramilev VV, Belozor A, Sugimoto T, McCullough DR (2005) Fecal genetic analysis using PCR-RFLP of cytochrome b to identify sympatric carnivores the tiger Panthera tigris and the leopard Panthera pardus in far eastern Russia. Conserv Genet 6:863–866CrossRefGoogle Scholar
  33. Odden M, Wegge P, Fredriksen T (2010) Do tigers displace leopards? If so why? Ecol Res 25:875–881CrossRefGoogle Scholar
  34. Palomares F, Rodriguez R, Laffitte R, Delibes M (1991) The status and distribution of the Iberian lynx Felis pardina (Temminck) in Coto Donana area, SW Spain. Biol Conserv 57:59–69CrossRefGoogle Scholar
  35. Palomares F, Godoy JA, Piriz A, O’Brien SJ, Johnson WE (2002) Fecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian Lynx. Mol Ecol 11:2171–2182CrossRefPubMedGoogle Scholar
  36. Pandey PK, Dhotre DP, Dharne MS et al (2007) Conservation and Evolutionary Genetics of Indian Leopard Panthera pardus fusca as studied by mitochondrial 12S rRNA gene sequence analysis. Curr Sci 92:1129–1133Google Scholar
  37. Patil N, Kumar NS, Gopalaswamy AM, Karanth KU (2011) Dispersing tiger makes a point. Oryx 45:472–475CrossRefGoogle Scholar
  38. Perez I, Geffen E, Mokady O (2006) Critically Endangered Arabian leopards Panthera pardus nimr in Israel: estimating population parameters using molecular scatology. Oryx 40:295–301CrossRefGoogle Scholar
  39. Pilgrim KL, Mckelvey KS, Riddle AE, Schwartz MK (2005) Felid sex-identification based on noninvasive genetic samples. Mol Ecol Notes 5:60–61CrossRefGoogle Scholar
  40. Prugh LR, Ritland CE (2005) Molecular testing of observer identification of carnivore feces in the field. Wildl Soc Bull 33:189–194CrossRefGoogle Scholar
  41. Ranganathan J, Chan KMA, Karanth KU, Smith JLD (2008) Where can tigers persist in the future? A landscape-scale density-based population model for the Indian subcontinent. Biol Conserv 141:67–77CrossRefGoogle Scholar
  42. Roques S, Adrados B, Chavez C et al (2010) Identification of neotropical felid faeces using RCP-PCR. Mol Ecol Res 11:171–175CrossRefGoogle Scholar
  43. Sanderson E, Forrest J, Loucks C et al (2006) Setting priorities for the conservation and recovery of wild tigers: 2005–2015. The Technical Assessment WCS WWF Smithsonian and NFWF-STF New York, Washington, DCGoogle Scholar
  44. Schipper J, Chanson JS, Chiozza F et al (2008) The status of the world’s land and marine mammals: diversity, threat and knowledge. Science 322:225–230CrossRefPubMedGoogle Scholar
  45. Seidensticker J (1976) On the ecological separation between tigers and leopards. Biotropica 8:225–234CrossRefGoogle Scholar
  46. Smallwood KS, Fitzhhugh EL (1995) A track count for estimating mountain lion Felis concolor californica population trend. Biol Conserv 71:251–259CrossRefGoogle Scholar
  47. Smith JLD (1993) The role of dispersal in structuring the Chitwan tiger population. Behaviour 124:165–195CrossRefGoogle Scholar
  48. Sugimoto T, Nagata J, Aramilev VV et al (2006) Species and sex identification from faecal samples of sympatric carnivores Amur leopard and Siberian tiger in the Russian Far East. Conserv Genet 7:799–802CrossRefGoogle Scholar
  49. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  50. Uphyrkina O, Johnson WE, Quigley H et al (2001) Phylogenetics, genome diversity and origin of modern leopard Panthera pardus. Mol Ecol 10:2617–2633CrossRefPubMedGoogle Scholar
  51. Valière N (2002) GIMLET: a computer program for analyzing genetic identification data. Mol Ecol Notes 2:377–379CrossRefGoogle Scholar
  52. Walston J, Robinson JG, Bennett EL et al (2010) Bringing the tiger back from the brink—the six percent solution. PLoS Biol 8:e1000485CrossRefPubMedCentralPubMedGoogle Scholar
  53. Wang S, Macdonald D (2009) Feeding habits and niche partitioning in a predator guild composed of tigers, leopards and dholes in a temperate ecosystem in central Bhutan. J Zool 277:275–283CrossRefGoogle Scholar
  54. Weber W, Rabinowitz A (1996) A global perspective on large carnivore conservation. Conserv Biol 10:1046–1054CrossRefGoogle Scholar
  55. Wegge P, Odden M, Pokharel CP, Storaas T (2009) Predator–prey relationships and responses of ungulates and their predators to the establishment of protected areas: a case study of tigers, leopards and their prey in Bardia National Park, Nepal. Biol Conserv 142:189–202CrossRefGoogle Scholar
  56. Wultsch C, Waits LP, Kelly MJ (2014) Noninvasive individual and species identification of jaguars (Panthera onca) pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize. Mol Ecol Res, Central America using cross-species microsatellites and faecal DNA. doi: 10.1111/1755-0998.12266 Google Scholar
  57. Zuercher GL, Gipson PS, Stewart GC (2003) Identification of carnivore feces by local peoples and molecular analyses. Wildl Soc Bull 31:961–970Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Samrat Mondol
    • 1
    • 2
    • 5
  • N. Samba Kumar
    • 3
  • Arjun Gopalaswamy
    • 3
  • Kartik Sunagar
    • 2
  • K. Ullas Karanth
    • 3
    • 4
  • Uma Ramakrishnan
    • 2
  1. 1.Centre for Cellular and Molecular PlatformsBangaloreIndia
  2. 2.National Centre for Biological SciencesTIFRBangaloreIndia
  3. 3.Center for Wildlife StudiesBangaloreIndia
  4. 4.Wildlife Conservation SocietyBronxUSA
  5. 5.INSPIRE Faculty, Wildlife Forensics and Conservation Genetics DepartmentWildlife Institute of IndiaDehradunIndia

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