Data from: 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.