Paleogenomic insights into reduced gene flow between Felis species in Eastern Europe throughout the Holocene

Hybridisation between the European wildcat (Felis silvestris) and the rapidly expanding domestic cat population is an important conservation concern. Recent paleogenomic data indicate that hybridisation has become more common only recently, though past hybridization occurred between European wildcats and African wildcats (F. lybica lybica), ancestors of domestic cats. To investigate this, 23 specimens from eastern Europe, dated from the Late Pleistocene to the Early Medieval period were analysed. Our results show that all specimens predating the Roman period harboured 85%–90% F. silvestris nuclear ancestry, even when carrying mitochondrial haplotypes characteristic of F. l. lybica. These findings suggest that the phylogeographic structure of the modern F. silvestris population was likely established early in the Holocene, following postglacial expansion. This study highlights the complexity of hybridisation and domestication events, indicating that ancient introgression may persist in the genomes of modern European wildcats and be misinterpreted as evidence of recent hybridisation.