Multiple genomic ancestries in the broom hare mark the complex biogeographic history of hares in the Iberian Peninsula

Pleistocene climatic fluctuations have often driven range shifts and hybridization among related species, leaving present-day genomic footprints. In the Iberian Peninsula, repeated and transient post-glacial contacts among hare species has left extensive mitochondrial DNA traces, but the genomic correlates and underlying biogeographic scenarios are still incompletely understood. Here, we study genome admixture in the broom hare, Lepus castroviejoi, endemic to the Cantabrian region, using its non-Iberian sister species, L. corsicanus, for contrast. Coalescent analyses of 10 genomes estimate that these species remained isolated since their divergence around 50,000 years ago, consistent with their current allopatry. Further analyses with 25 additional genomes indicate that small fractions of the L. castroviejoi genome originate from L. granatensis, L. timidus, and L. europaeus (0.72%, 0.08%, and 0.04%, respectively). Introgression dating based on tract lengths suggests L. granatensis was already admixed with L. timidus when it hybridized with L. castroviejoi, which could explain granatensis-timidus ancestry tract junctions detected in L. castroviejoi. Genomic segments with such junctions contain genes enriched for cell signaling and olfactory receptor activity, suggesting functional drivers facilitating genetic exchange. This research demonstrates that genomic ancestry inferences can reveal complex multiway admixture histories, which can be used to illuminate complex past biogeographic events.