Abstract
Progress along the speciation continuum is characterized by increasing genome-wide divergence between incipient species. Much of our understanding of genome-wide divergence patterns comes from studies on host plant ecotypes in phytophagous insects. Divergent ecological adaptation, with gene flow between ecotypes, differentiates a minority of loci under selection and those physically linked while homogenizing the rest of the genome. Furthermore, the genomic architecture of traits under host-related selection have been found to be localized in the genome, as e.g. certain host crypsis traits of Timema cristinae and diapause traits on chromosomal structures such as inversions as observed in Rhagoletis pomonella. Here the generality of the above mentioned genome-wide divergence pattern on the European cherry fruit fly, Rhagoletis cerasi was tested. The wide distribution range and its adaptability to two drastically different host plant families makes R. cerasi a suitable system for studies of genome-wide divergence with gene flow. A genomic approach was used to compare flies collected from four locations with co-occurring Prunus avium and Lonicera xylosteum host plants. Expected differences in SNP Fst distribution patterns were found when comparing same-host allopatric populations and different-host sympatric populations. SNP Fst outlier scans of these two groups resulted in different groups of SNPs showing signs of selection, with the allopatric populations resulting in fewer outliers due to higher background Fst values. Linkage disequilibrium (LD) among allopatric outliers was the same as among all SNPs, while outliers under sympatric host related selection exhibited significantly higher LD. Our data indicates genomic localization of SNPs under host-related selection.