Documenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterflies Heliconius melpomene and Heliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.
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