Data from: Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)

Studying hybrid zones that form between morphologically cryptic taxa
offers valuable insights into the mechanisms of cryptic speciation and the
evolution of reproductive barriers. Although hybrid zones have long been
the focus of evolutionary studies, the awareness of cryptic hybrid zones
increased recently due to rapidly growing evidence of biological diversity
lacking obvious phenotypic differentiation. The characterization of
cryptic hybrid zones with genome-wide analysis is in its early stages and
offers new perspectives for studying population admixture and thus the
impact of gene flow. In this study, we investigate the population genomics
of the Myotis nattereri complex in one of its secondary contact zones,
where a putative hybrid zone is formed between two of its cryptic
lineages. By utilizing a whole genome shotgun sequencing approach, we aim
to characterize this cryptic hybrid zone in detail. Demographic analysis
suggests that the cryptic lineages diverged during the Pliocene,
approximately 3.6 million years ago. Despite this ancient separation, the
populations in the contact zone exhibit mitochondrial introgression and a
considerable amount of mixing in nuclear genomes. The genomic structure of
the populations corresponds to geographic locations and the genomic
admixture changes along a geographic gradient. These findings suggest that
there is no effective hybridization barrier between both lineages,
nevertheless their population structure is shaped by dispersal barriers.
Our findings highlight how such deeply diverged cryptic lineages can still
readily hybridize in secondary contact.