Abstract
High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success.
Highlights
fijos más los efectos aleatorios (Feces) are a very useful source of information to study free–ranging animals
The performance of the two field sampling methods was evaluated by polymerase chain reaction (PCR) amplification success using
Sampling fragments of feces followed by DNA extraction using the Qiagen kit (EM1) yielded the highest rate of PCR success (80 %, table 3), but the same field sampling method had the lowest rate of PCR success (10 %) when DNA was extracted with beads (EM2)
Summary
Feces are a very useful source of information to study free–ranging animals. They can be used to study many aspects of their ecology such as dietary habits, scent marks, parasite loads, hormonal levels, hunting ranges and distribution, and importantly, yield DNA. Fecal DNA offers a special insight into rare or endangered species and is noninvasive, so it has become increasingly used for ecological studies. Feces are a sub–optimal source of DNA for molecular analyses as they are not widely suitable for genomic studies, with few reports of success (Perry et al, 2010)
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