A simple and effective method for obtaining mammal DNA from faeces

Abstract

The use of faecal DNA, although a promising tool for the population monitoring of mammals, has not yet become a fully exploited and standard practice, mainly because low target DNA concentration, DNA degradation, and co‐purification of inhibitors demand extra laboratory procedures to improve success and reliability. Here we evaluate a simple method that enables sampling of DNA in the field through the collection of the intestinal cells present on the surface of a scat using a swab. The swab is immediately placed in a vial containing a lysis buffer that preserves the DNA for its later extraction. DNA extracts of three species of herbivores (goat, fallow deer and white‐tailed deer), two carnivores (Iberian lynx and domestic dog) and one omnivore species (brushtail possum) were characterised in terms of target and total DNA quantity, PCR inhibition and genotyping success. Direct comparison was carried out with duplicate samples preserved in 96% ethanol and extracted via a commonly used commercial DNA extraction kit for faecal material. Results from these comparisons show that swabbing the samples in situ not only simplifies field collection and sample handling in the laboratory, but generally optimises target DNA recovery, minimises co‐purification of PCR inhibitors and provides good quality DNA for the species tested, especially for herbivores. This method is also less time‐consuming and more cost‐effective, thus providing a more convenient and efficient alternative for non‐invasive genetic studies.

Extraction of DNA from captive‐sourced feces and molted feathers provides a novel method for conservation management of New Zealand kiwi (Apteryxspp.)

“…However, this appeared to be enough to reliably amplify genotypes. While target nuclear DNA concentration and genotype quality achieved here are lower than the values obtained in mammals (see Figure and (Ramón‐Laca et al., )), amplification failure and ADO rates are comparable, and false allele occurrence was lower than in other avian studies (Tables and S2) (Bayard de Volo, Reynolds, Douglas, & Antolin, ; Horváth et al., ; Johansson, McMahon, & Höglund, ; Miño & Lama, ; Pérez et al., ; Regnaut, Lucas, & Fumagalli, ; Rösner et al., ; Segelbacher & Steinbruck, ; Segelbacher & Storch, ).…”

“…Log 10 ‐transformed target DNA concentration (measured in ng/μl) and quality index results for kiwi feces and shed feather samples compared with six mammalian species from (Ramón‐Laca et al., ). QI scores range from 0 to 1, where 1 indicates complete agreement between all replicates…”

Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

“…The integrity of the pellet surface and epithelial cells on this surface are likely the critical factors in the recovery of DNA. In other species, swabbing or just collecting the outside surface has proved successful for genetic analyses (Wehausen et al 2004, Rutledge et al 2009, Ramón‐Laca et al 2015). Although we used whole or half pellets for DNA extraction, degradation of this outer layer was notable as pellet quality declined.…”

High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile

“…Significant improvements have been reported based on fecal DNA analysis for both extraction and quantification of nucleic acids as part of genotyping and species identification (Kanthaswamy, Premasuthan, Ng, Satkoski, & Goyal, ). Molecular analysis of feces is a noninvasive method with a high degree of integrity and quality when using specific commercial kits for these complex matrices (Deshpande, Villarreal, & Mills, ; Ramón‐Laca, Soriano, Gleeson, & Godoy, ; Tende, Hansson, Ottosson, & Bensch, ). The main challenge of this study was to obtain DNA of good quality from fecal samples collected in the Atacama Desert.…”