Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modeling indicated that the two species diverged with gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F_ST) and sequence divergence (d_XY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.

The final filtered SNP data was in the VCF file- DP3g70maf00MD10.SNP.recode.vcf

Perl script for calculating site Dxy and example input can be found in Calc_Dxy.zip

Perl script for calculating Tajima's D and example input can be found in Cal_TajimaD.zip

All tested demographic models in the paper are defined in the file dadi_define_model.py

R code for generating Manhatann plot for the population statisitcs can be found in the file plot_statistics.R