A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research

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.

Spatial assessment of wolf-dog hybridization in a single breeding period

“…In fact, the allelic dropout and false allele rates observed in our work were only comparable with studies using invasive sampling ( e.g. tissue or blood 17 31 ) or to a recent study using non-invasively collected saliva 32 . A higher number of loci with lower error rates increases the accuracy of results, and thereby helps to overcome the main limitation associated with using low quality DNA to simultaneously detect both parental species and hybrids.…”

Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods

“…Saliva is also a great source of DNA that can be collected non-invasively by using e.g. baits and porous material (Vargas et al 2009, Lobo et al 2015. Additionally, DNA samples can be obtained from mineral lick (Schoenecker et al 2015), rests of prey (Harms et al 2015, Wheat et al 2016 or damaged crop (Saito et al 2008).…”

The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise

“…Recently, new techniques to enrich for host DNA from feces has greatly improved sequence output and quality, and these types of improvements can facilitate future work from these samples (Perry et al 2010;Hart et al 2015;Mathay et al 2015). Similarly, further development and validation of methods for collecting and sequencing nucleic acids from samples that require direct contact but are relatively easy to obtain, such as saliva, could also be beneficial (Lobo et al 2015). Increasingly, clever uses of archival museum or fossilized specimens have generated usable DNA providing a window into host-pathogen interactions on timescales of hundreds to thousands of years (Avila-Arcos et al 2013;Weyrich et al 2017).…”