Abstract
Noninvasive samples for genetic analyses have become essential to address ecological questions. Popular noninvasive samples such as faeces contain degraded DNA which may compromise genotyping success. Saliva is an excellent alternative DNA source but scarcity of suitable collection methods makes its use anecdotal in field ecological studies. We develop a noninvasive method of collection that combines baits and porous materials able to capture saliva. We report its potential in optimal conditions, using confined dogs and collecting saliva early after deposition. DNA concentration in saliva extracts was generally high (mean 14 ng μl-1). We correctly identified individuals in 78% of samples conservatively using ten microsatellite loci, and 90% of samples using only eight loci. Consensus genotypes closely matched reference genotypes obtained from hair DNA (99% of identification successes and 91% of failures). Mean genotyping effort needed for identification using ten loci was 2.2 replicates. Genotyping errors occurred at a very low frequency (allelic dropout: 2.3%; false alleles: 1.5%). Individual identification success increased with duration of substrate handling inside dog’s mouth and the volume of saliva collected. Low identification success was associated with baits rich in DNA-oxidant polyphenols and DNA concentrations <1 ng μl-1. The procedure performed at least as well as other noninvasive methods, and could advantageously allow detection of socially low-ranked individuals underrepresented in sources of DNA that are involved in marking behaviour (faeces or urine). Once adapted and refined, there is promise for this technique to allow potentially high rates of individual identification in ecological field studies requiring noninvasive sampling of wild vertebrates.
Highlights
The development of molecular techniques has increased the use of genetic analyses to test ecological hypotheses about the determinants of survival [1], habitat selection [2], dispersal [3], social organisation [4], demography [5], competition [6] or distribution [7]
Faecal DNA is likely to be degraded to some extent, especially if faeces are not collected soon after deposition, which produces a quick decrease in amplification success and an increase in genotyping error rates over time [11,12]
We assessed the amount of saliva in all substrates and performed genetic analyses on 134 pieces handled by 23 different dogs, for which we obtained hair samples
Summary
The development of molecular techniques has increased the use of genetic analyses to test ecological hypotheses about the determinants of survival [1], habitat selection [2], dispersal [3], social organisation [4], demography [5], competition [6] or distribution [7]. In mammals, faeces are the primary source of noninvasive DNA because they are easy to find, collect, handle and ship, and usually contain many epithelial cells [9,10]. The reduced quality of faecal DNA may pose problems for genotyping, especially when large molecular fragments are used [15], or the study population exhibits low genetic variability [16]. Obtaining DNA of high quality to establish the identity of individuals usually requires fresh faecal samples in the field and detection of many variable loci in the laboratory [17,18], conditions that greatly increase the cost of studies [10]
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