Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Abstract

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locusspecific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments' length, while error rates increase with amplicons' length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair-versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approaches.

Monitoring jaguar populationsPanthera oncawith non-invasive genetics: a pilot study in Brazilian ecosystems

“…However, non-invasive genetic sampling can be expensive, time consuming, and error prone, and thus it is necessary to assess the reliability of protocols for each species and biological setting Broquet et al, 2007;Valière et al, 2007).…”

Monitoring wild pig populations: a review of methods

“…Molecular techniques for individual genotyping have improved within the last two decades, providing an indirect way to count individual members of a population within an area (Broquet et al 2007). Microsatellite DNA analyses allow assessment of the species, sex, and individual, and these may be used to assess the population genetic structure and population connectivity according to geographical barriers and gene flow (Cowled et al 2008;Manel et al 2003;Poteaux et al 2009;Scandura et al 2008).…”

“…In contrast to tissue or blood sampling, such noninvasive samples can be collected without physical capture and visual contact, reducing some forms of potential sampling bias (Fickel and Hohmann 2006), leading to more precise estimates (Piggot and Taylor 2003;Poole et al 2001;Mitchell and Balogh 2007). However, the noninvasive genetic sampling methods are often associated with technical problems due to low DNA quality and quantity, leading to genotyping errors (Broquet et al 2007) and hence potentially biased estimates (Hoffman and Amos 2005). Several studies were conducted to optimize genotyping on such noninvasive samples and assure it maximum reliability.…”

Microsatellite repeat motif and amplicon length affect amplification success of degraded faecal DNA

“…Piggot et al 2004;Lampa et al 2008). Marker repeat motif and amplicon length have inconsistent effects on amplification success (Broquet et al 2007;Ishida et al 2012). It may be necessary to choose markers with the highest likelihood of amplification success.…”