Genomic analyses of gene flow and selection during diversification in Senecio

Diversifying selection and gene flow were traditionally viewed as antagonistic forces, with diversifying selection promoting adaptation and speciation, and gene flow opposing them. However, their roles are far more complex than this. While gene flow can prevent speciation or initiate despeciation, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via hybridisation. The relative frequency of these outcomes, and indeed the frequency of gene flow and diversifying selection in general are largely unknown. This thesis illuminates these questions through evolutionary genomic analyses focussed on a recently diverged group of ragworts (Senecio). The Mediterranean Senecio species-complex contains several cases of hybrid speciation, as well as two species, S. aethnensis and S. chrysanthemifolius, which are a potential case of ecological speciation with gene flow, having adapted to high and low altitude habitats respectively on Mount Etna. However, their demography was previously un-studied. I first show that S. aethnensis and S. chrysanthemifolius diverged recently, at a time that coincides with the growth of Mount Etna to the altitudes which separate the species today, have experienced significant gene flow following their split, and are likely to be sister species, bolstering the hypothesis of ecological speciation. I further demonstrate that gene flow is common in the wider clade, and pinpoint multiple cases of gene flow amongst them. Finally, I identify several genes under positive selection in the clade, and show that the proportion of genes under selection is high relative to many other plant genera. The results further establish Senecio species as an invaluable model system for the study of diversification with gene flow, and suggest that high levels of gene flow and selection are features of their evolution, a situation which may prove to be common in plants.