Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: A pilot study

BMC Genetics

Volumn 7, Issue , 2006, Pages

  Bhagavatula, Jyotsna ^a   Singh, Lalji ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B;

ARTICLE; CARNIVORE; DNA DETERMINATION; DNA EXTRACTION; ENDANGERED SPECIES; FEASIBILITY STUDY; FECES ANALYSIS; GENETIC VARIABILITY; GENOTYPE; INDIA; MICROSATELLITE MARKER; MITOCHONDRION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PILOT STUDY; POLYMERASE CHAIN REACTION; POPULATION RESEARCH; PROBABILITY; RELIABILITY; SIBLING; SPECIES IDENTIFICATION; TIGER;

ANIMALS; CYTOCHROMES B; DNA; DNA, MITOCHONDRIAL; FECES; FEMALE; GENOTYPE; INDIA; MALE; MICROSATELLITE REPEATS; PILOT PROJECTS; POLYMERASE CHAIN REACTION; POPULATION DENSITY; TIGERS;

ANIMALIA; PANTHERA TIGRIS TIGRIS;

EID: 33750981226     PISSN: 14712156     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-7-48     Document Type: Article

References (48)

1. Sunquist M, Karanth KU, Sunquist F: Ecology, behaviour and resilience of the tiger and its conservation needs. In Riding the tiger: Tiger conservation in human dominated landscapes Edited by: Seidensticker J, Christie S, Jackson P. Cambridge, Cambridge University Press; 1999:5-18.
2. Seidensticker J, Christie S, Jackson P: Riding the tiger: Tiger conservation in human dominated landscapes Cambridge, Cambridge University Press; 1999.
3. Karanth KU, Nichols JD, Seidensticker Dinerstein E, Smith JLD, McDougal C, Johnsingh AJT, Chundawat RS, Thapar V: Science deficiency in conservation practice: the monitoring of tiger populations in India. Animal Conservation 2003, 6:141-146.
4. Sharma S, Jhala Y, Sawarkar VB: Identification of individual tigers (Panthera tigris) from their pugmarks. Journal of Zoology 2005, 267:9-18.
5. Schaller GB: The deer and the tiger Chicago, Illinois, USA, University of Chicago Press; 1967.
6. Franklin N, Bastoni, Sriyanto, Siswomartono D, Manansang J, Tilson R: Last of the Indonesian tigers: a cause for optimism. In Riding the tiger: Tiger conservation in human dominated landscapes Edited by: Seidensticker J, Christie S, Jackson P. Cambridge, Cambridge University Press; 1999:130-165.
7. Karanth KU, Nichols JD: Estimation of tiger densities in India using photographic captures and recaptures. Ecology 1998, 79(8):2852-2862.
8. Karanth KU, Chundawat RS, Nichols JD, Kumar NS: Estimation of tiger densities in the tropical dry forests of Panna, Central India, using photographic capture-recapture sampling. Animal Conservation 2004, 7:285-290.
9. Kawanishi K, Sunquist ME: Conservation status of tigers in a primary rainforest of Peninsular Malaysia. Biological Conservation 2004, 120:329-344.
10. Piggott MP, Banks SC, Stone N, Banffy C, Taylor AC: Estimating population size of endangered bush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA. Molecular Ecology 2006, 15:81-91.
11. Prugh LR, Ritlands CE, Arthur SM, Krebs CJ: Monitoring coyote population dynamics by genotyping faeces. Molecular Ecology 2005, 14:1585-1596.
12. Eggert LS, Eggert JA, Woodruff DS: Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana. Molecular Ecology 2003, 12:1389-1402.
13. Wilson GJ, Frantz AC, Pope LC, Roper TJ, Burke TA, Cheeseman CL, Delahay RJ: Estimation of badger abundance using fecal DNA typing. Journal of Applied Ecology 2003, 40:658-666.
14. Creel S, Spong G, Sands JL, Rotella J, Zeigle J, Joe L, Murphy KM, Smith D: Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology 2003, 12(7):2003-2009.
15. Mowat G, Strobeck C: Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis. Journal of Wildlife Management 2000, 64(1):183-193.
16. Taberlet P, Luikart G: Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society 1999, 68:41-55.
17. Gagneux P, Boesch C, Woodruff DS: Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hairs. Molecular Ecology 1997, 6:862-868.
18. Wasser SK, Houston CS, Koehler GM, Cadd GG, Fain SR: Techniques for application of fecal DNA methods to field studies of Ursids. Molecular Ecology 1997, 6:1091-1098.
19. Waits LP, Luikart G, Taberlet P: Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 2001, 10:249-256.
20. Kohn MH, York EC, Kamradt DA, Haught G, Sauvajot RM, Wayne RK: Estimating population size by genotyping faeces. Proceedings of the Royal Society of London Series B 1999, 266:657-663.
21. Sloane MA, Sunnucks P, Alpers D, Beheregaray LB, Taylor AC: Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method. Molecular Ecology 2000, 9:1233-1240.
22. Frantz AC, Pope LC, Carpenter PJ, Roper TJ, Wilson GJ, Delahay RJ, Burke T: Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology 2003, 12:1649-1661.
23. Lucchini V, Fabbri E, Marucco F, Ricci S, Boitani L, Randi E: Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology 2002, 11:857-868.
24. Mills LS, Citta JJ, Lair KP, Schwartz MK, Tallmon DA: Estimating animal abundance using noninvasive DNA sampling: promise and pitfalls. Ecological Applications 2000, 10:283-294.
25. Walsh PS, Metzger DA, Higuchi R: Chelex-100 as a medium for the simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991, 10:506-513.
26. Reed JZ, Tollit DJ, Thompson P, Amos W: Molecular Scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Molecular Ecology 1997, 6:225-234.
27. Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: A Laboratory Manual 2nd edition. Cold Spring Harbour Laboratory, Cold Spring Harbour Press; 1989.
28. Fernando P, Vidya TNC, Rajapakse C, Dangolla A, Melnick DJ: Reliable noninvasive genotyping: Fantasy or Reality? Journal of Heredity 2003, 94(2):115-123.
29. Farrell LE, Roman J, Sunquist ME: Dietary separation of sympatric carnivores identified by molecular analysis of scats. Molecular Ecology 2000, 9:1583-1590.
30. Pilgrim KL, Mckelvey KS, Riddle AE, Schwartz MK: Felid sex-identification based on noninvasive genetic samples. Molecular Ecology Notes 2005, 5:60-61.
31. Wehausen JD, Ramey RR, Epps CW: Experiments in DNA extraction and PCR amplification from bighorn sheep faeces: the importance of DNA extraction method. Journal of Heredity 2004, 95(6):503-509.
32. Reddy HS, Srinivasulu C, Rao KT: Prey selection by the Indian tiger (Panthera tigris tigris) in Nagarjunasagar Srisailam Tiger Reserve, India. Mammalian Biology, Zeitscrift fur Saugetier kunde 2004, 69(6):384-391.
33. Bagchi S, Goyal SP, Sankar K: Prey abundance and prey selection by tigers in a semi-arid dry deciduous forest in Western India. Journal of Zoology 2003, 260:285-290.
34. Biswas S, Sankar K: Prey abundance and food habit of tigers (Panthera tigris tigris) in Pench National Park, Madhya Pradesh, India. Journal of Zoology London 2002, 256:411-420.
35. Davison A, Birks JDS, Brookes RC, Braithwaithe TC, Messenger JE: On the origin of faeces: morphological versus molecular methods for surveying rare carnivores from their scats. Journal of Zoology London 2002, 257:141-143.
36. Frantzen MAJ, Silk JB, Ferguson JWH, Wayne RK, Kohn MH: Emperical evaluation of preservation methods for faecal DNA. Molecular Ecology 1998, 7:1423-1428.
37. Goossens B, Chikhi L, Utami SS, de Ruiter J, Bruford MW: A multisample, multi-extract approach for microsatellite analysis of faecal samples in an arboreal ape. Conservation Genetics 2000, 1:157-162.
38. Flagstad Ø, Røed K, Stacy JE, Jakobsen KS: Reliable noninvasive genotyping based an excremental PCR of nuclear DNA purified with a magnetic bead protocol. Molecular Ecology 1999, 8:879-883.
39. Lukacs PM, Burnham KP: Review of capture-recapture methods applicable to noninvasive genetic sampling. Molecular Ecology 2005, 14:3909-3919.
40. Kumar S, Tamura K, Nei M: MEGA 3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 2004, 5:150-163.
41. Baruah A, Naik V, Hendre PS, Rajkumar R, Rajendrakumar P, Aggarwal RK: Isolation and characterization of nine microsatellite markers from Coffea arabica L, showing wide cross-species amplifications. Molecular Ecology Notes 2003, 3:647-650.
42. Singh A, Shailaja K, Gaur A, Singh L: Development and characterization of novel microsatellite markers in the Asiatic Lion (Panthera leo persica). Molecular Ecology Notes 2002, 2:542-54.
43. Williamson JE, Heubinger RM, Sommer JA, Louis EE, Barber RC: Development and cross-species amplification of 18 microsatellite markers in the Sumatran tiger (Panthera tigris sumatroe). Molecular Ecology Notes 2002, 2:110-112.
44. Menotti-Raymond MA, O'Brien SJ: Evolutionary Conservation of ten microsatellite markers in Felidae. Journal of Heredity 1995, 86(4):319-321.
45. Luo S-J, Kim J-H, Johnson WE, vanderValt J, Martenson J, Yukhi N, Miquelle DG, Uprykhina O, Goodrich JM, Quigley HB, Tilson P, Brady G, Martelli P, Subramaniam V, McDougal C, Hean S, Huang S-H, Pan W, Karanth UK, Sunquist M, Smith JLD, O'Brien SJ: Phylogeography and genetic ancestry of tigers (Panthera tigris). PLoS Biology 2004, 2(12):e442.
46. Ayres KL, Overall ADJ: API-CALC: A program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Molecular Ecology Notes 2004, 4:315-318.
47. Valière N: GIMLET, a computer program for analyzing genetic identification data. Molecular Ecology Notes 2002, 2:377-379.
48. Verma SK, Singh L: Novel universal primers establish identity of enormous number of animal species for forensic application. Molecular Ecology Notes 2003, 3:28-31.