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.

Highlights

  • There are significant limitations to the routine use of faecal DNA

  • Since all the above limitations are intrinsic to the sample, finding more efficient methods of collection, preservation and DNA extraction that are viable in the field and laboratory should widen the use of faecal DNA for population monitoring and genetic studies, and eventually facilitate its use in the expanding field of genomics (Perry et al 2010)

  • Since epithelial cells are supposed to accumulate in the outer layer of the scat, several sampling strategies have targeted the enrichment of these cells by peeling off, scraping or washing the outer layer of the scat before DNA extraction

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Summary

Introduction

There are significant limitations to the routine use of faecal DNA These include scarcity and degradation of the DNA and the co-purification of PCR inhibitors. These factors dramatically reduce the genotyping success of faecal samples and impose the need for pilot optimisation analyses and multiple genotyping replicates, which overall increase the cost of such studies (Fernando et al 2003). These limitations have historically made faecal DNA either impracticable or unaffordable. Results are compared against the most common, more laborious and costly method of preserving the sample in 96% ethanol, collecting the outer layer, and extracting it with the QIAamp DNA Stool Mini Kit (Qiagen)

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