Factors influencing genotyping success and genotyping error rate of Eurasian otter ( Lutra lutra ) faeces collected in t
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ORIGINAL ARTICLE
Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe Marcia Sittenthaler 1,2 & Eva Maria Schöll 1 & Christoph Leeb 2 Rosemarie Parz-Gollner 1 & Klaus Hackländer 1
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Elisabeth Haring 2,3
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Received: 6 April 2020 / Revised: 24 August 2020 / Accepted: 18 November 2020 # The Author(s) 2020
Abstract The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature. Keywords Allelic dropout . Lutra lutra . Microsatellites . Non-invasive genetic monitoring . Otter spraint . Scat
Introduction Marcia Sittenthaler and Eva Maria Schöll contributed equally to this work. * Marcia Sittenthaler [email protected]; [email protected] 1
Institute of Wildlife Biology and Game Management, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria
2
Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
3
Department of Evolutionary Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
The use of non-invasive genetic methods in wildlife research and management has gained on importance due to continuous advanc
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