Demographic history and evidence for gene flow among six European Coenonympha butterfly species. Coenonympha evolutionary history

Recently diverged species often exhibit incomplete reproductive barriers, leading to potential hybridization where their ranges overlap. Distinguishing the effects of past hybridization from contemporary secondary gene flow in species evolution remains a significant challenge, yet it is critical in conservation biology. To investigate species boundaries and the diversification history of six closely related Coenonympha butterflies, we analyzed genomic diversity using ddRADseq data from 140 individuals from the six species across their geographical ranges in Europe. We tested for evidence of interspecific gene flow and evaluated various divergence scenarios, incorporating gene flow and hybrid speciation. In addition to the known gene flow history between C. arcania and C. gardetta, which led to the formation of two allopatric hybrid species (C. darwiniana and C. cephalidarwinia) in the Alps, we identified post-speciation gene flow occuring between C. arcania and both C. leander and C. hero through secondary contact at a period of increased amplitude of the Pleistocene climatic oscillations. Among these species, the least genetically diverse is the Scarce heath C. hero, which is the only species protected by a high conservation status. However, all species, including the widespread C. arcania, have experienced sharp population declines since the mid-Holocene. An exception is the eastern population of C. hero, which has maintained a stable but low effective population size. These findings highlight pervasive secondary gene flow in this butterfly group during late Pleistocene climatic oscillations.