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

Abstract

The degree of introgressive hybridization 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 hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild‐living and captive cat samples, and test the assumptions of the test using 3,097 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 hybridized, 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 equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is 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.

Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland

“…summer coat without spots, long pointed ears, large antlers) could reduce the threat to red deer from sika introgression. A similar strategy is currently in use to preserve both the genetics and phenotypes of Scottish wildcats, where individuals with both high phenotypic and genetic scores are preferentially protected and used in a captive breeding program (Senn et al 2018). Given the presence of so many advanced backcrosses in this system, any management considered should account for this introgression.…”

“…Thus, if a situation requires the use of fewer markers (e.g. to lower the cost of genotyping individuals, or because of the need for rapid testing (Senn et al 2018)), it would be best to focus on diagnostic or ancestry informative markers, with the caveat that more markers will always lead to improved detection of hybrid individuals (McFarlane & Pemberton 2019). For example, Galaverni et al (2017) compared 48, 96, and 192 AIMs taken from a set of approximately 25,000 markers that had been thinned for linkage disequilibrium (LD).…”

Range-wide patterns of human-mediated hybridisation in European wildcats

“…1). Samples from Scotland were originally provided as examples of clear morphological hybrids based on pelage, thus reflecting the hybrid swarm that occurs there today (Senn et al 2018). Therefore, the Scottish samples may be biased more towards hybrids that are closer to domestic cats than wildcats.…”

Genetic tools in the management of invasive mammals: recent trends and future perspectives

“…Hybridisation among species which are naturally separated is undoubtedly increasing due to anthropogenic impacts, including species' invasions (McFarlane & Pemberton ). Extensive introgression from invading populations can put already endangered native populations at risk (Senn et al ). Identifying hybrids based on phenotypic characteristics is problematic due to intermediate phenotypes and observer biases (McDevitt et al ).…”

“…In a well‐studied hybrid zone between sika deer and red deer in Kintyre, Scotland, an increased panel of 45000 SNPs reclassified 26% of individuals as hybrids that had originally been assigned to one of the parental species from a previous study based on 22 microsatellites (McFarlane et al ). In attempting to preserve Scottish wildcats from extensive introgression with domestic/feral cats, only wildcat individuals with both high genetic scores (using a SNP panel) and high phenotype scores of wildcat ‘purity’ are selected for the captive breeding and reintroduction programmes (Senn et al ).…”