On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat

While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T-1) was 3.3 generations (similar to 10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T-2). The model consistently predicts T-1 after T-2, estimated here to be 19.3 generations (similar to 60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.

Automated summary

This study demonstrates the presence of a population of Scottish wildcats genetically distinct from domestic cats, with high levels of gene-flow between the two populations. Most wild-living cats sampled showed evidence of introgression, and the model predicted significant recent hybridization after the captive breeding population was founded.