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 a..., , # Data from: Multiple genomic ancestries in the broom hare mark the complex biogeographic history of hares in the Iberian Peninsula

Dataset DOI: [10.5061/dryad.xd2547dtv](10.5061/dryad.xd2547dtv)

## Description of the data and file structure

Fasta file of a hare pseudo-reference genome, built based on the whole genome re-sequencing dataset from the original paper using an iterative mapping approach (Sarver et al., 2017) and using the European rabbit (*Oryctolagus cuniculus*) reference genome as template (OryCun2.0).

### Files and variables

#### File: AncestralHare_3it.v2.gatk.iteration3.consensus.FINAL.fa.gz

**Description:** Fasta file.

## Access information

Data was derived from the following source:

Next-generation sequencing data from Lepus castroviejoi, Lepus corsicanus, Lepus granatensis, Lepus europaeus, Lepus timidus, and Lepus americanus. Pseudo-reference built based on the European rabbit reference genome (OryCun2.0).,