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. We develop 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 6,546 loci,
we show that a population of wildcats genetically distant from domestic
cats is still present in Scotland. These individuals are found almost
exclusively within the captive breeding program. 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 (T1) was 3.3 generations (~10 years) before
present. Though the model had limited power to detect signals of ancient
admixture, we find evidence that significant recent hybridisation may have
occurred subsequent to the founding of the captive breeding population
(T2). The model consistently predicts T1 after T2, estimated here to be
19.3 generations (~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.