Late Miocene climatic swings triggered incipient postglacial speciation of flightless Calosoma beetles in Western Balkan sky islands
Restriction of gene flow through allopatry can be a major driver of diversification, especially in mountainous frameworks. Highland endemic lineages are therefore an ideal system to study the impact of past climatic and tectonic events on glacial and postglacial genomic signatures. The flightless species Calosoma (Callisthenes) pentheri is endemic from the Western Balkan highlands. This taxon is represented by two subspecies with subtle morphological variation and a clear disjunct geographic distribution. The status of both lineages as subspecies or distinct species has been debated in the past and current evidence supporting either of these hypotheses remains tenuous. We report the first phylogeographic examination of this species in the Western Balkans using 63 contemporary and historical specimens representing both lineages across their geographic ranges, as well as a new high-fidelity genome generated using long-read sequencing. Genomic data was generated using hybridization capture of RAD-derived probes and high-throughput sequencing consisted of up to 10,794 single nucleotide polymorphisms and 2,278 loci for population genomic and phylogenomic analyses. Based on this data, we demonstrate a clear genomic delineation between the two lineages in line with their allopatric distribution along Western Balkan highlands. Our analyses clearly suggest that these two lineages are distinct species that diverged in the late Miocene. The diversification of these two species in the Western Balkans was likely driven by vicariance in sky island glacial refugia fuelled by climatic oscillation during the Miocene.