A population genomics perspective on wolf-dog hybridization

European wolf populations persisted in southern refugia during the Late Pleistocene and experienced severe demographic bottlenecks followed by recent recovery. Consequently, extant populations such as the Dinaric-Balkan, Iberian, and Italian wolves retain reduced genetic diversity and elevated inbreeding. In parallel with population expansion, increasing anthropogenic pressures and spatial overlap with domestic dogs have promoted recurrent wolf-dog hybridization (WDH). While recent studies have begun to explore the potential adaptive effects of dog introgression, the consequences of WDH on genomic diversity patterns from a population-genomic perspective remain poorly understood. Here, we evaluate the effects of WDH on genomic diversity using an extensive whole-genome dataset of Dinaric-Balkan, Iberian, and Italian wolf populations. Such dataset included both non-admixed wolves and a uniquely representation of recently admixed individuals, spanning first to fourth generation backcrosses. Our findings show that dog introgression consistently increases genomic diversity and reduces inbreeding across all three refugial wolf populations, with WDH acting functionally as gene flow into historically bottlenecked populations. These apparent benefits are, however, accompanied by a significant increase in genetic load – particularly in its masked component. Overall, our results highlight a trade-off associated with anthropogenic hybridization: gains in genetic diversity and reduced inbreeding versus the accumulation of deleterious variation that may pose a latent risk under future population contractions or renewed fragmentation.