Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

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 (FST) and sequence divergence (dXY) 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.