Characterizing the genomic architecture of divergence along the speciation continuum in the Rhagoletis pomonella species complex

The process of genomic differentiation along the speciation continuum, in the presence of ongoing gene flow, has become a focus of research in ecological speciation over the past decade. Many questions remain unanswered, because we lack the ability to observe a single speciation event from incipient divergence at a small number of ecologically significant loci (with homogenization of the rest of the genome due to ongoing gene flow) to genome –wide differentiation and complete reproductive isolation. Therefore, we look to recent and ongoing radiations, occurring in the face of gene flow, and displaying a spectrum of divergence and gene flow among member taxa. The Rhagoletis pomonella complex is an ideal radiation, because it allows for comparisons along the speciation continuum, from host race to “good species.” In addition to the well-known apple and hawthorn host races, the R. pomonella species complex comprises three other named species, R. mendax, R. zephyria, and R. cornivora, as well as up to two undescribed species, and an isolated hawthorn infesting R. pomonella population in the Mexican highlands. Here, we present data from a RAD-seq study of differentiation among these members of the R. pomonella species complex. While largely supporting previously defined relationships among taxa within this complex, we show an accumulation of genetic divergence over time. Our results could shed light on the process of genomic differentiation during speciation with gene flow, particularly the recently proposed process of “genome-wide congealing.”