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.
Highlights
Marcia Sittenthaler and Eva Maria Schöll contributed to this work.The use of non-invasive genetic methods in wildlife research and management has gained on importance due to continuous advances in molecular genetic techniques (Schwartz et al 2007; Beja-Pereira et al 2009; De Barba et al 2017; Andrews et al 2018; Carroll et al 2018)
Within the field of non-invasive genetic monitoring, faecal samples have been widely used as DNA from sloughed epithelial cells of the intestine wall of the defecating individual can be analysed (Kohn and Wayne 1997)
Hierarchical cluster analysis revealed a classification of otter samples into 5 diet categories: (1) samples containing amphibian bones, N = 79; (2) samples containing bird remains, N = 75; (3) samples consisting of fish remains only, N = 432; (4) samples containing mammalian and crayfish remains, N = 58; and (5) samples containing mainly crayfish, N = 70
Summary
Marcia Sittenthaler and Eva Maria Schöll contributed to this work.The use of non-invasive genetic methods in wildlife research and management has gained on importance due to continuous advances in molecular genetic techniques (Schwartz et al 2007; Beja-Pereira et al 2009; De Barba et al 2017; Andrews et al 2018; Carroll et al 2018). Marcia Sittenthaler and Eva Maria Schöll contributed to this work. For species of conservation concern and for elusive and nocturnal species, genetic non-invasive sampling facilitates their investigation without the need of disturbing, capturing and handling the animals (Waits and Paetkau 2005). Within the field of non-invasive genetic monitoring, faecal samples have been widely used as DNA from sloughed epithelial cells of the intestine wall of the defecating individual can be analysed (Kohn and Wayne 1997). Faeces are constantly produced by every animal in a population, and for many animal species, they are abundant in the field and relatively easy to detect.
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