Inferring the biogeography and demographic history of an endangered butterfly in Europe from multilocus markers

The genetic structure of a species is influenced by its history and by current gene flow. Using a population genomics approach, we infer the demographic history of the false ringlet (Coenonympha oedippus) in Europe based on 1594 genome-wide double digest restriction site associated DNA sequencing loci from 96 individuals (32 localities) sampled throughout the fragmented species range. In contrast to the weak geographical structure in mitochondrial DNA, a clear nuclear differentiation was observed between the westernmost Atlantic localities, those from the western Alps and all other sampled localities. Mountain ridges were the main factor explaining population divergence at the European scale, while isolation by distance was found at a regional scale. We applied Approximate Bayesian Computation in a coalescent framework to infer past and contemporary demographic parameters. The best scenario suggested a first divergence between French and all other European populations around 66000 years ago, such that the species survived the Last Glacial Maximum in at least two distinct areas separated by the Alps. This scenario fits species distribution modelling identifying variation of suitable areas with past climatic modifications. The Atlantic and western Alps lineages separated about 6000 years ago. Strong population decline was inferred in these lineages during historical time, in agreement with multiple records of recent decline of this species in Europe.