Phylogenomic discordance and ancestral variation in rapidly radiating felids

Phylogenetic discordance, where genetic and phenotypic signals conflict, challenges our understanding of evolutionary histories in rapidly radiating species. In this study, we investigated these dynamics in the felid genera Otocolobus, Prionailurus, and Felis, focusing on Pallas's cat (Otocolobus manul), to elucidate how genetics and natural selection shape rapid radiations. Comparative morphological analyses and whole-genome comparisons among these cats, combined with whole-genome resequencing, reveal a complex evolutionary history shaped by extensive ancestral incomplete lineage sorting (ILS) together with ancient introgression. Despite its predominantly Prionailurus-like genome background, Pallas's cat shares marked cranial and ecological similarities with Felis species inhabiting arid environments. These similarities may reflect the contribution of standing ancestral variation together with later habitat-associated selection. Genes associated with craniofacial development, lipid metabolism, and fur development were enriched among candidate regions and may have contributed to the Pallas's cat's observed phenotypic differentiation. Our findings suggest that ancestral genomic variation retained in discordant genealogical backgrounds may provide material for later ecological selection.