Analysis of genomic divergence landscape in recurrently hybridising Chironomus sister taxa suggests stable steady-state between mutual gene-flow and isolation. Divergence landscape in Chironomus

By virtue of steadily accumulating evidence, divergence with gene-flow is now a recognised mode of speciation. Current models suggest that diverging lineages inevitably become completely reproductively and genomically isolated. We tested this hypothesis by analysing the divergence landscape between two recurrently hybridising sister species of non-biting midges, Chironomus riparius and C. piger. Using a principal component based method, we estimated that 28.44% of the genome were mutually isolated, containing 49.4% of the annotated genes. These genes were enriched for processes and structure requiring close molecular collaboration. Divergence landscape was fragmented, distributed throughout the genome and isolation regions on average 30 kb small. Evidence for recent divergent selection processes was scarce, while traces of purifying selection were abundant in the isolated regions. Comparing the observed distribution of divergence time estimates with coalescence simulations implies that most of divergence happened during a short time span about 4.5 mio generations ago. We suggest that the observed steady-state equilibrium between mutual gene-flow and isolation is due to seasonal hybridisation, high migration rates and high Ne favouring rapid purification. Our findings thus extent the speciation with gene flow paradigm with evidence for long diverged “good” sister species that nevertheless share large parts of their genomes.