Abstract
The red panda (Ailurus fulgens) is an endangered species distributed in the Himalaya and Hengduan Mountains and extremely difficult to monitor because it is elusive, wary and nocturnal. However, recent advances in noninvasive genetics are allowing conservationists to indirectly estimate population size of this animal. Here, we present a pilot study of individual identification of wild red pandas using DNA extracted from faeces. A chain of optimal steps in noninvasive studies were used to maximize genotyping success and minimize error rate across sampling, selection of microsatellite loci, DNA extraction and amplification and data checking. As a result, 18 individual red pandas were identified successfully from 33 faecal samples collected in the field using nine red panda-specific microsatellite loci with a low probability of identity of 1.249 × 10−3 for full siblings. Multiple methods of tracking genotyping error showed that the faecal genetic profiles possessed very few genotyping errors, with an overall error rate of 1.12 × 10−5. Our findings demonstrate the feasibility and reliability of using faeces as an effective source of DNA for estimating and monitoring wild red panda populations.
This is a preview of subscription content, log in via an institution to check access.
References
Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G (2009) Advancing ecological understanding through technological transformations in noninvasive genetics. Mol Ecol Resour 9:1279–1301
Choudhury A (2001) An overview of the status and conservation of the red panda in India, with reference to its global status. Oryx 35:250–259
Creel S, Spong G, Sand JL, Rotella J, Zeigle J, Joe L, Murphy KM, Smith D (2003) Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Mol Ecol 12:2003–2009
Gagneux P, Boesch C, Woodruff DS (1997) Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Mol Ecol 6:861–868
Li M, Wei FW, Goossens B, Feng ZJ, Tamate HB, Bruford MW, Funk SM (2005) Mitochondrial phylogeography and subspecific variation in the red panda (Ailurus fulgens): implications for conservation. Mol Phylogenet Evol 36:78–89
Liang X, Zhang ZH, Zhang L, Zhang WP, Shen FJ, Yang Z, Hou R, He W, Wei K, Yue BS (2007) Isolation and characterization of 16 tetranucleotide microsatellite loci in the red panda (Ailurus fulgens). Mol Ecol Notes 7:1012–1014
Liu ZJ, Zhang BW, Wei FW, Li M (2005) Isolation and characterization of microsatellite loci for the red panda, Ailurus fulgens. Mol Ecol Notes 5:27–29
Miller CR, Joyce P, Waits LP (2002) Assessing allelic drop-out and genotype reliability using maximum likelihood. Genetics 160:357–366
Murphy MA, Waits LP, Kendall KC, Wasser SK, Higbee JA, Bogden R (2002) An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Conserv Genet 3:435–440
Roberts MS, Gittleman JL (1984) Ailurus fulgens. Mammal Species 222:1–8
Rousset F (2008) GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual (2nd edition). Cold Spring Harbour Press, Cold Spring Harbour
Su B, Fu YX, Wang YX, Jin L, Chakraborty R (2001) Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations. Mol Biol Evol 18:1070–1076
Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, Waits LP, Bouvet J (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res 24:3189–3194
Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends Ecol Evol 14:323–327
Valière N (2002) GIMLET: a computer program for analyzing genetic individual identification data. Mol Ecol Notes 2:377–379
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Wei FW, Feng ZJ, Wang ZW, Hu JC (1999) Current distribution, status and conservation of wild red pandas (Ailurus fulgens) in China. Biol Conserv 89:285–291
Zhan XJ, Li M, Zhang ZJ, Goossens B, Chen YP, Wang HJ, Bruford MW, Wei FW (2006) Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr Biol 16:451–452
Zhan XJ, Zheng XD, Bruford MW, Wei FW, Tao Y (2010) A new method for quantifying genotyping errors for noninvasive genetic studies. Conserv Genet 11:1567–1571
Zhang BW, Li M, Ma LC, Wei FW (2006) A widely applicable protocol for DNA isolation from faecal samples. Biochem Genet 44:503–512
Acknowledgments
This research was supported by the National Natural Science Foundation of China (30770399), Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-Z-4) and the Royal Society. We thank two anonymous referees for helpful comments on this manuscript.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by P. C. Alves
Rights and permissions
About this article
Cite this article
Guo, Y., Hu, Y., Qi, D. et al. Genotyping faeces of red pandas (Ailurus fulgens): implications for population estimation. Eur J Wildl Res 57, 1231–1235 (2011). https://doi.org/10.1007/s10344-011-0556-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10344-011-0556-4