Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly Maculinea alcon. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologically — specimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters.

The work was supported by the Swiss National Science Foundation (grant PP00P3_144870), a Sciex PostDoc Fellowship (14.002), BNF project of the Bern University, Switzerland, the Spanish Ministerio de Economía y Competitividad (Project CGL2016-76322-P (AEI/FEDER, UE), and the European Union's Seventh Framework programme for research and innovation under the Marie Skłodowska-Curie grant agreement No 609402-2020 researchers: Train to Move (T2M) postdoctoral fellowship to R. Vodă. V. D. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme (project no. 625997). Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum provided under the programme "Projects of Projects of Large Research, Development, and Innovations Infrastructures" (CESNET LM2015042), is greatly appreciated.