Towards a genomic resolution of the Phengaris alcon species complex

Abstract

Abstract Taxonomic entities below the species level often pose difficulties for conservation practice, especially when they are ecologically distinct from the nominal species. Genomic tools provide the opportunity to study and potentially resolve such cryptic diversity. The Alcon blue butterfly Phengaris alcon species complex is such a cryptic example, comprising different ecotypes or even subspecies, one of them is the high elevation taxon P. rebeli from the European Alps. We sequenced a first reference genome for Phengaris alcon. Furthermore, we generated whole genome resequence data for individuals of three Swiss ecotypes, i.e., the low elevation P. alcon, the mid elevation and high elevation Alpine P. rebeli and integrated genomic data from across Europe to study the relationship among these ecotypes. At a European scale, our results suggest that biogeography and the evolutionary context of diversification of the P. alcon complex is more multifaceted than previously suggested, falling in the range of more recent ecological speciation. In Switzerland, the three ecotypes were genetically isolated with only limited current gene flow between them. Past gene flow, however, could have given rise to the mid elevation ecotype. Our findings emphasise that high elevation P. rebeli should be treated as a distinct species. Our study highlights how the availability of reference genome assemblies allows to address so far open taxonomic questions in conservation research and that broadscale studies are needed to understand the biogeographic history of apparent diversification.