Faeces as a source of DNA for molecular studies in a threatened population of great bustards

• Main Authors: Y Idaghdour, D Broderick, & A Korrida
• Other Authors: The Pennsylvania State University CiteSeerX Archives
• Format: Text
• Language: English
• Published: 2003
• Subjects: Otis; Avian Studies
• Online Access: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1040.5887; http://centrostudinatura.it/public2/documenti/196-30249.pdf

Abstract With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in faeces to noninvasively sample endangered species for genetic studies. A highly vulnerable population of approximately 100 great bustards (Otis tarda) exists in Morocco necessitating the use of non-invasive protocols to study their genetic structure. Here we report a reliable silica-based method to extract DNA from great bustard faeces. We found that successful extraction and amplification correlated strongly with faeces freshness and composition. We could not extract amplifiable DNA from 30% of our samples as they were dry or contained insect material. However 100% of our fresh faecal samples containing no obvious insect material worked, allowing us to assess the levels of genetic variation among 25 individuals using a 542 bp control region sequence. We were able to extract DNA from four out of five other avian species, demonstrating that faeces represents a suitable source of DNA for population genetics studies in a broad range of species. Faeces, egg membranes and feathers have all been utilized as non-invasive sources of DNA in avian studies (e.g. Taberlet 1991; Nuechterlein and Buitron 2000; Segelbacher and Steinbrück 2001). Extracting amplifiable DNA from faeces is perhaps the most challenging due to (i) trace amounts of available DNA, (ii) the potential cocktail of exogenous and endogenous nucleases and PCR inhibitors We collected 34 great bustard faecal samples in 90% ethanol and stored them within five days of collection at −20 • C. To provide a comparison, we collected fresh faeces from another bustard (Chlamydotis undulata) and four other species (Phasianus colchicus, Turdus merula, Pica pica and Geronticus eremita). We monitored DNA contamination with negative extraction controls and monitored the presence of PCR inhibitors by mixing a known concentration of houbara bustard gDNA to the faecal extracts. Initial extraction trials using a standard phenol/ chloroform method