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Several morphological and mitochondrial lineages of the alpine ringlet butterfly species  Erebia pronoe  have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1α, RPS5) gene sequences and compared them with sequences from the sister species  Erebia melas . Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with  Wolbachia  strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the  E. pronoe-melas  complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in  E. melas  and  E. pronoe glottis  can be explained by different ages of  Wolbachia  infections with different  Wolbachia  strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of  E. pronoe glottis  in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.

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Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure