Abstract
Noninvasive sampling, for example, of droppings or feathers, is a promising approach for molecular genetic studies on endangered and elusive animal species. Yet, such specimens are known for containing only minute amounts of DNA, resulting in lower typing success rates relative to analyses on fresh tissues such as muscle or blood. Furthermore, artefactual signals as well as contamination are more likely to occur when DNA is limited. To increase the reliability of DNA typing from noninvasive samples, optimized DNA extraction and polymerase chain reaction protocols were developed, taking advantage of developments in the forensic field aiming at successful molecular genetic analysis of DNA templates being low in quality and quantity. In the framework of an extensive monitoring project on population dynamics of capercaillie and black grouse in the Tyrolean Alps, feces samples and molted feathers from both species were collected. On a subset comprising about 200 specimens of either species, eight polymorphic short tandem repeat (STR) markers were analyzed to test these improved protocols. Besides optimizing DNA yields, both lowered sample consumption and reduced hands‐on time were achieved, and the rates of informative profiles amounted to 90.7% for capercaillie and 92.4% for black grouse. Similarly, high success rates had not been achieved in earlier studies and demonstrate the benefit of the improved methodology, which should be easily adaptable for use on animal species other than those studied here. The STR genotypes were not only powerful enough to discriminate among unrelated birds but also appeared fit for telling apart closely related animals, as indicated by Pi and Pisib values. The software package allelematch aided analysis of genotypes featuring possible dropout and drop‐in effects. Finally, a comparison between molecular genetic and morphology‐based species‐of‐origin determination revealed a high degree of concordance.
Highlights
Count-based population size estimates have been considered inappropriate for assessment of long-term population trends (Cayford & Walker, 1991; Jacob, Debrunner, Gugerli, Schmid, & Bollmann, 2010)
Such clusters help to control for genotyping error, as they may be considered a mimic of genotype alignments obtained by a multiple tubes approach
This study describes an optimized DNA extraction method for the molecular genetic analysis of noninvasive samples including feces and feathers
Summary
Conservation and population genetic studies are indispensable sources of information in decision-making processes regarding environmental management and the protection of endangered species. A downside of routine genotyping approaches is that they typically require a direct sampling approach involving capture of the animals and invasive collection of DNA sources such as blood or muscle. This may cause unacceptably high levels of disturbance (Regnaut, 2004). Systematic sampling of capercaillie and black grouse feces and feathers covered the entire area of interest, and lek site information was not forwarded to the field surveyors. Fieldwork took place between March and May 2012, and study sites were visited twice within a period of 10–14 days During this sampling period, both black grouse and capercaillie aggregated around lek sites for mating, which aided representative sampling of the local populations (Höglund & Alatalo, 1995). Fresh feathers and feces were collected from all reference birds and stored at −20°C
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