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

Lobo, Diana and Godinho, Raquel and Álvares, Francisco and López-Bao, José Vicente and Rodríguez, Alejandro (2015). A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research. PloS one. 10:10, 1-21
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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 mu l(-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 mu l(-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.

Authors/Creators:Lobo, Diana and Godinho, Raquel and Álvares, Francisco and López-Bao, José Vicente and Rodríguez, Alejandro
Title:A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research
Series/Journal:PloS one (1932-6203)
Year of publishing :2015
Volume:10
Number:10
Page range:1-21
Number of Pages:21
Publisher:Public Library of Science
ISSN:1932-6203
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
Keywords:noninvasive samples, genetic analyses, saliva
URN:NBN:urn:nbn:se:slu:epsilon-e-3350
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3350
Additional ID:
Type of IDID
Web of Science (WoS)000363309200008
DOI10.1371/journal.pone.0139765
ID Code:13161
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Ecology
(S) > Dept. of Ecology
Deposited By: SLUpub Connector
Deposited On:04 Apr 2016 08:37
Metadata Last Modified:04 Apr 2016 08:37

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