Ecological speciation with gene flow followed initial large-scale geographic speciation in the enigmatic afroalpine giant senecios (Dendrosenecio).

Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The geographic and ecological isolation of the afroalpine vegetation fragments on the East African mountain tops makes them an excellent system to study speciation. The initial diversification within the afroalpine endemic genus Dendrosenecio was shown to occur via allopatric divergence among four isolated mountain groups, but the potential role of ecological speciation within these groups and the role of gene flow in speciation remained uncertain. Here we extend the sampling of Dendrosenecio and use phylogenomics to assess the importance of gene flow in the diversification of the genus. Then, population genomics, demographic modelling and habitat differentiation analyses are used to study ecological speciation in two sister species occurring on Mount Kenya. We found that two sympatric sister species on Mt Kenya occupy distinct microhabitats, and our analyses support that they originated in situ via ecological speciation with gene flow. In addition, we obtained signals of admixture history between mountain groups. Taken together, these results suggest that geographic isolation shaped main lineages, while ecologically mediated speciation occurred within a single mountain.