Abstract
We evaluated the feasibility of using faeces as a non-invasively collected DNA source for the genetic study of an endangered bird population (capercaillie; Tetrao urogallus). We used a multitube approach, and for our panel of 11 microsatellites genotyping reliability was estimated at 98% with five repetitions. Experiments showed that free DNases in faecal material were the major cause of DNA degradation. Our results demonstrate that using avian faeces as a source of DNA, reliable microsatellite genotyping can be obtained with a reasonable number of PCR replicates.
This is a preview of subscription content, log in via an institution to check access.
References
Broquet T, Petit E (2004). Quantifying genotyping errors in noninvasive population genetics. Mol. Ecol. 13: 3601–3608
Caizergues A, Dubois S, Loiseau A, Mondor G, Rasplus JY (2001). Isolation and characterization of microsatellite loci in black grouse (Tetrao tetrix). Mol. Ecol. Notes 1: 36–38
Fridolfsson AK, Ellegren H (1999). A simple and universal method for molecular sexing of non-ratite birds. J. Avian Biol., 30: 116–121
Goudet J (1995). FSTAT (vers. 1.2): a computer program to calculate F-statistics. J. Hered. 86: 485–486
Höss M, Jagura P, Zastawny TH, Dizdaroglu M, Pääbo S (1996). DNA damages and DNA sequences retrival from ancient tissues. Nucleic Acids Res. 24: 1304–1307
Maudet C, Luikart G, Dubray D, Von Hardenberg A, Taberlet P (2004). Low genotyping error rates in wild ungulate faeces sampled in winter. Mol. Ecol. Notes 4: 772–775
Monteiro L, Bonnemaison D, Vekris A, Petry KG, Bonnet Jo, Vidal R, Cabrita Jo, Megraud FA (1997). Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J. Clin. Microbiol. 35: 995–998
Ruiz TR, Andrews S, Smith GB (2000). Identification and characterisation of nuclease activity in anaerobic environmental samples. Can. J. Microbiol. 46: 736–740
Segelbacher G, Paxton RJ, Steinbrück G, Trontelj P, Storch I (2000). Characterization of microsatellites in capercaillie Tetrao urogallus (Aves). Mol. Ecol. 9: 1934–1935
Segelbacher G, Steinbrück G (2001). Bird faeces for sex identification and microsatellite analysis. Vogelwarte 41: 139–142
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 analysing genetic individual identification data. Mol. Ecol. Notes 2: 377–379
Valière N, Berthier P, Mouchiroud D, Pontier D (2002). Gemini: software for testing the effects of genotyping errors and multitubes approach for individual identification. Mol. Ecol. Notes 2: 83–86
Acknowledgements
We are indebt to T. Broquet, R. Hammond, P. Taberlet and N. Valière for helpful discussions and valuable comments on the manuscript. We also thank C. Decoster, I. Py, M. Rosset (Bern Zoological Garden) and C. Salamin.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Regnaut, S., Lucas, F.S. & Fumagalli, L. DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations. Conserv Genet 7, 449–453 (2006). https://doi.org/10.1007/s10592-005-9023-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-005-9023-7