Data from: Distinguishing the victim from the threat: SNP‐based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

The degree of introgressive hybridisation between the Scottish wildcat and
domestic cat has long been suspected to be advanced. Here we use a
35-SNP-marker test, designed to assess hybridisation between wildcat and
domestic cat populations in Scotland, to assess a database of 265
wild-living and captive cat samples, and test the assumptions of the test
using 3097 SNP markers generated independently in a subset of the data
using ddRAD. We discovered that despite increased genetic resolution
provided by these methods, wild-living cats in Scotland show a complete
genetic continuum or hybrid swarm structure when judged against reference
data. The historical population of wildcats, although hybridised, clearly
groups at one end of this continuum, as does the captive population of
wildcats. The interpretation of pelage scores against nuclear genetic data
continues to be problematic. This is probably because of a breakdown in
linkage disequilibrium between wildcat pelage genes as the two populations
have become increasingly mixed, meaning that pelage score or SNP score
alone are poor diagnostic predictors of hybrid status. Until better tools
become available, both should be used jointly, where possible, when making
management decisions about individual cats. We recommend that the
conservation community in Scotland must now define clearly what measures
are to be used to diagnose a wildcat in the wild in Scotland, if future
conservation action is to be effective.