Genotyping Faecal Samples of Bengal Tiger Panthera Tigris Tigris for Population Estimation: a Pilot Study

Overview

Journal BMC Genet

Publisher Biomed Central

Specialties Biotechnology
Molecular Biology

Date 2006 Oct 19

PMID 17044939

Citations 19

Authors

Jyotsna Bhagavatula

Lalji Singh

Affiliations

Soon will be listed here.

Abstract

Background: Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation.

Results: In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India.

Conclusion: Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

Citing Articles

Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.

Jeong D, Hyun J, Marchenkova T, Matiukhina D, Cho S, Lee J Sci Rep. 2024; 14(1):29985.

PMID: 39622961 PMC: 11611917. DOI: 10.1038/s41598-024-79970-3.

Simple Nested Allele-Specific approach with penultimate mismatch for precise species and sex identification of tiger and leopard.

Nittu G, Bhavana P, Shameer T, Ramakrishnan B, Archana R, Kaushal K Mol Biol Rep. 2021; 48(2):1667-1676.

PMID: 33479828 DOI: 10.1007/s11033-021-06139-w.

Heterologous microsatellite primers are informative for paca (Cuniculus paca), a large rodent with economic and ecological importance.

Roldan Gallardo F, DeMatteo K, Rinas M, Arguelles C BMC Res Notes. 2020; 13(1):470.

PMID: 33028373 PMC: 7542955. DOI: 10.1186/s13104-020-05312-x.

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal.

Karmacharya D, Manandhar P, Manandhar S, Sherchan A, Sharma A, Joshi J PLoS One. 2019; 14(8):e0221868.

PMID: 31465520 PMC: 6715213. DOI: 10.1371/journal.pone.0221868.

Physiological stress responses of tigers due to anthropogenic disturbance especially tourism in two central Indian tiger reserves.

Tyagi A, Kumar V, Kittur S, Reddy M, Naidenko S, Ganswindt A Conserv Physiol. 2019; 7(1):coz045.

PMID: 31321036 PMC: 6626984. DOI: 10.1093/conphys/coz045.

References

Walsh P, Metzger D, Higuchi R . Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991; 10(4):506-13. View

Frantz A, Pope L, CARPENTER P, Roper T, Wilson G, Delahay R . Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol Ecol. 2003; 12(6):1649-61. DOI: 10.1046/j.1365-294x.2003.01848.x. View

Kohn M, York E, Kamradt D, Haught G, Sauvajot R, Wayne R . Estimating population size by genotyping faeces. Proc Biol Sci. 1999; 266(1420):657-63. PMC: 1689828. DOI: 10.1098/rspb.1999.0686. View

Kumar S, Tamura K, Nei M . MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004; 5(2):150-63. DOI: 10.1093/bib/5.2.150. View

Reed J, Tollit D, Thompson P, Amos W . Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Mol Ecol. 1997; 6(3):225-34. DOI: 10.1046/j.1365-294x.1997.00175.x. View

Piggott M, Banks S, Stone N, Banffy C, Taylor A . Estimating population size of endangered brush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA. Mol Ecol. 2005; 15(1):81-91. DOI: 10.1111/j.1365-294X.2005.02783.x. View

OBrien S . Evolutionary conservation of ten microsatellite loci in four species of Felidae. J Hered. 1995; 86(4):319-22. DOI: 10.1093/oxfordjournals.jhered.a111594. View

Farrell L, Roman J, Sunquist M . Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol Ecol. 2000; 9(10):1583-90. DOI: 10.1046/j.1365-294x.2000.01037.x. View

Flagstad O, Roed K, Stacy J, Jakobsen K . Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Mol Ecol. 1999; 8(5):879-83. DOI: 10.1046/j.1365-294x.1999.00623.x. View

10.

Frantzen M, Silk J, Ferguson J, Wayne R, Kohn M . Empirical evaluation of preservation methods for faecal DNA. Mol Ecol. 1998; 7(10):1423-8. DOI: 10.1046/j.1365-294x.1998.00449.x. View

11.

Wasser S, Houston C, Koehler G, Cadd G, Fain S . Techniques for application of faecal DNA methods to field studies of Ursids. Mol Ecol. 1997; 6(11):1091-7. DOI: 10.1046/j.1365-294x.1997.00281.x. View

12.

Creel S, Spong G, Sands J, Rotella J, Zeigle J, Joe L . Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Mol Ecol. 2003; 12(7):2003-9. DOI: 10.1046/j.1365-294x.2003.01868.x. View

13.

Luo S, Kim J, Johnson W, van der Walt J, Martenson J, Yuhki N . Phylogeography and genetic ancestry of tigers (Panthera tigris). PLoS Biol. 2004; 2(12):e442. PMC: 534810. DOI: 10.1371/journal.pbio.0020442. View

14.

Sloane M, Sunnucks P, Alpers D, Beheregaray L, Taylor A . Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method. Mol Ecol. 2000; 9(9):1233-40. DOI: 10.1046/j.1365-294x.2000.00993.x. View

15.

Lukacs P, Burnham K . Review of capture-recapture methods applicable to noninvasive genetic sampling. Mol Ecol. 2005; 14(13):3909-19. DOI: 10.1111/j.1365-294X.2005.02717.x. View

16.

Waits L, Luikart G, Taberlet P . Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol. 2001; 10(1):249-56. DOI: 10.1046/j.1365-294x.2001.01185.x. View

17.

Prugh L, Ritland C, Arthur S, Krebs C . Monitoring coyote population dynamics by genotyping faeces. Mol Ecol. 2005; 14(5):1585-96. DOI: 10.1111/j.1365-294X.2005.02533.x. View

18.

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. Mol Ecol. 2002; 11(5):857-68. DOI: 10.1046/j.1365-294x.2002.01489.x. View

19.

Fernando P, Vidya T, Rajapakse C, Dangolla A, Melnick D . Reliable noninvasive genotyping: fantasy or reality?. J Hered. 2003; 94(2):115-23. DOI: 10.1093/jhered/esg022. View

20.

Wehausen J, Ramey 2nd R, Epps C . Experiments in DNA extraction and PCR amplification from bighorn sheep feces: the importance of DNA extraction method. J Hered. 2004; 95(6):503-9. DOI: 10.1093/jhered/esh068. View