Limited recent introgression and ancient shared ancestry in Ethiopian wolves (Canis simensis)

Hybridization between domestic and wild species is an increasing conservation concern, as continued introgression could lead to genomic extinction. The Endangered Ethiopian wolf (Canis simensis) is thought to be threatened by hybridization with free-roaming domestic dogs (C. familiaris) and African golden wolves (C. lupaster), particularly in human-dominated landscapes. Phenotype-based assessments during two field seasons in 1989 and 1991 have suggested that 8-17% of individuals in the Bale Mountains show signs of admixture, but the extent and timing of gene flow remain unresolved. This study analyzed 27 whole genomes, including nine Ethiopian wolves that showed no obvious signs of admixture, collected in 2003, to quantify patterns of introgression among African canids. Population structure analyses identified limited signals of hybridization, with most Ethiopian wolves forming a distinct genetic cluster. Although two related Ethiopian wolves exhibited subtle but significant excess allele sharing with African golden wolves, the overall genomic data provide little support for strong recent or directional introgression. Linkage disequilibrium decay analyses suggest an admixture event occurring approximately 800 generations ago; however, estimates of timing and admixture proportion were not robust, indicating substantial uncertainty in the precise parameters. Forward-in-time simulations indicate that, despite currently limited introgression, continued small population sizes could facilitate gradual genomic replacement over evolutionary timescales. Therefore, hybridization may become increasingly important under sustained demographic decline.