Genomic data, part 1, of "Secondary contact rather than co-existence – Erebia butterflies in the Alps"

Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. While such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species Erebia cassioides and E. tyndarus in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology in order to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past. Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why co-existence between these butterflies may currently not be possible.123 BAM files, out of total 235, containing the RAD sites used in the manuscript. The second set of 112 BAM files for the remaining samples is deposited under 10.5281/zenodo.7041545 due to size limitations, it can also be found under the same project title as this one, part 2. RAD site locations (in bed format) were extracted from Lucek et al. 2020 (NCBI BioProject Accession: PRJNA640280). Each individual has its own BAM file, aligned against a Erebia ligea reference genome (NCBI GCA_917051295.2). File names indicate the field IDs, and correspond to table S1 of the manuscript