VCF file for experimental and natural populationsThis is the VCF file for the experimental and natural population comparisons. To test for differentiation genome wide among sympatric populations, we contrasted our apple7 and haw7 groups; for a response to selection in our experiment, we compared haw7 and haw30. Haw or apple represents the host plant from which the flies were collected; the number - 7 or 30 - represents the pre-winter warm period experienced by larvae/pupae prior to overwintering to match that found in nature on haw or apple plants. See txt file to match individual MID labels in the VCF file with the experimental group they were part of.snps.ScottSelection.05-400-20.filteredHwe0.05.wOutApple30.cleaned.vcfR_pomonella_denovo_assemblyThis file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details.LatestRadFakeGenome.cut.fa.txtR. pomonella Linkage MapLinkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans.MapLinearOrderAllChrom.txt

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence.