Conservation Genetics

, Volume 1, Issue 2, pp 157-162

First online:

A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape

  • Benoît GoossensAffiliated withBiodiversity and Ecological Processes Group, School of Biosciences, Cardiff University Email author 
  • , Lounès ChikhiAffiliated withInstitute of Zoology, The Zoological Society of London
  • , Sri S. UtamiAffiliated withEthologie and Socio-Oecologie, University of UtrechtFakultas Biologi, Universitas Nasional
  • , Jan de RuiterAffiliated withDepartment of Anthropology, University of Durham
  • , Michael W. BrufordAffiliated withBiodiversity and Ecological Processes Group, School of Biosciences, Cardiff University

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We investigated the effect of the number of faecal samples, ofextracts per sample and of PCRs per extract on the reliability ofgenotypes for a microsatellite locus in free-living orang-utans.For each individual 36 PCRs were performed using DNA extractionsfrom up to four faecal samples. We found a very largeinter-individual variation in positive PCRs (P+) (36/36 for oneindividual and 0/36 for another). As many as 30% of the cases ledto erroneous genotypes when only one P+ was obtained. It ispreferable to use at least 4 P+ per extract to reduce thisproportion to less than 1%. With 3 P+ results, erroneousgenotypes were still observed in 26% of the cases together. Theseresults indicate that it is necessary to do a minimum of 4 PCRsper extract. In order to have a chance to observe 4 P+, threeextracts should be ideally analysed for each sample. We alsorecommend that when possible two or more samples should becollected in the field to increase the chance of having extractscontaining DNA and to provide independent replicates. While werecognise the difficulty of working with faecal samples, weadvocate the use of faecal material for genetic studies ofcertain wild animal populations where the advantages of avoidingdisturbance, stress and injury are deemed of critical importance.

conservation genetics faeces microsatellites non-invasive methods Pongo pygmaeus abelii