Data from: Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Maintenance of genetic distinction in the face of gene flow is an
important aspect of the speciation process. Here, we provide a detailed
spatial and genetic characterization of a hybrid zone between two
subspecies of the European rabbit. We examined patterns of allele
frequency change for 22 markers located on the autosomes, X-chromosome,
Y-chromosome, and mtDNA in 1078 individuals sampled across the hybrid
zone. While some loci revealed extremely wide clines (w>=300 km)
relative to an estimated dispersal of 1.95-4.22 km/generation, others
showed abrupt transitions (w = 10 km), indicating localized genomic
regions of strong selection against introgression. The subset of loci
showing steep clines had largely coincident centers and stepped changes in
allele frequency that did not co-localize with any physical barrier or
ecotone, suggesting that the rabbit hybrid zone is a tension zone. The
steepest clines were for X and Y chromosome markers. Our results are
consistent with previous inference based on DNA sequence variation of
individuals sampled in allopatry in suggesting that a large proportion of
each genome has escaped the overall barrier to gene flow in the middle of
the hybrid zone. These results imply an old history of hybridization and
high effective gene flow, and anticipate that isolation factors should
often localize to small genomic regions.