The Pleistocene species pump past its prime: evidence from European butterfly sister species

The Pleistocene glacial cycles had a profound impact on the ranges and genetic make-up of organisms. Whilst it is clear that the current contact zones between sister taxa are secondary and have formed during the last interglacial, it is unclear when the taxa involved began to diverge. Previous estimates are unreliable given the stochasticity of genetic drift and the contrasting effects of incomplete lineage sorting and gene flow on gene divergence. We use genome-wide transcriptome data to estimate divergence for 18 sister species pairs of European butterflies showing either sympatric or contact zone distributions. We find that in most cases species divergence was initiated before the Pleistocene, substantially earlier than assumed previously, and that post divergence gene flow is restricted to contact zone pairs, although they are not systematically younger than sympatric pairs. This suggests that contact zones are not limited to early stages in the speciation process, but can involve notably old taxa.