Developing a protocol for the use of non-invasive genetic sampling to monitor UK red fox abundance

Abstract

Developing a protocol for the use of non-invasive genetic sampling to monitor UK red fox abundance




Abstract
The red fox is an important UK predator and is widely managed, due to its impact on species of economic and conservation concern. However, UK fox populations are currently poorly monitored, and population size estimates are almost exclusively from index counts such as the national game bag census. Estimates of true abundance could improve the monitoring and management of UK foxes by reducing the levels of uncertainty in population estimates.
Non-invasive genetic sampling (NGS) has a lot of potential as a method for estimating the true abundance of foxes, and this study trialled hair collection and analysis techniques for use in NGS studies of UK foxes. Several trap designs, incorporating different baits and hair collection structures, were set up in Durham City woodland and trialled for their effectiveness in attracting foxes and collecting hair samples. The traps differed in their effectiveness at collecting hair, but neither food baits nor valerian oil were successful in attracting foxes to traps. Further research is needed to determine a reliable method for collecting hair samples.
The Chelex extraction method was tested for its reliability for extracting DNA from single-hair samples, and was found to be extremely reliable for this purpose. A range of microsatellite markers were then tested for use identifying individual red foxes from hair samples, and a useable set of primers was identified, and optimised. A sex-linked marker (SRY) was also tested and optimised, to provide additional information at from samples. The resulting protocol was also tested with domestic dog samples, and the results of the analysis were found to be genetically distinct, showing that mistakenly included samples from closely-related species could be identified.
The developed laboratory methods could be reliably used for individual recognition and sex identification from remotely-collected hair samples from red fox populations in the UK, and could form a basis for future capture-mark-recapture and population analysis of red fox samples, improving red fox monitoring in the UK.