Evolutionary history and interspecific gene flow in six <i>Coenonympha</i> butterfly species in Europe

Abstract Recently diverged species often exhibit incomplete reproductive barriers, leading to potential hybridisation where their ranges overlap. Distinguishing the effects of past hybridisation and incomplete lineage sorting from contemporary secondary gene flow in species evolution remains challenging, yet it is critical in conservation biology. To investigate species boundaries and the diversification history of six closely related Coenonympha butterflies, we analysed their genomic diversity using ddRADseq data from 140 individuals sampled in two broad geographical regions (the Alps and the Southern Urals) where species distributions overlap. We tested for hybridisation amongst species and contrasted various divergence scenarios, incorporating gene flow and hybrid speciation. In addition to the known gene flow history between the pearly heath C. arcania and the alpine heath C. gardetta , which led to the formation of two currently allopatric hybrid species ( C. darwiniana and C. cephalidarwinia ) in the Alps, we identified signatures of post‐speciation gene flow between C. arcania and both the Russian heath C. leander and the scarce heath C. hero at a period of increased amplitude of the Pleistocene climatic oscillations, around 800,000 years ago. Amongst these species, the least genetically diverse is C. hero , which is the only species protected by a high conservation status. Our findings reveal widespread secondary gene flow within this butterfly group, yet the six species remain well‐differentiated genetically and morphologically, even in regions where their distributions overlap, suggesting ancient rather than current gene flow. This highlights the need for broadscale studies to better understand the biogeographical and ecological context of species diversification.