Population genomic signatures of divergent adaptation, gene flow, and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

Adaptive radiations are an important source of biodiversity, and are often characterized by many speciation events in very short succession. It has been proposed that the high speciation rates in these radiations may be fuelled by novel genetic combinations produced in episodes of hybridisation among the young species. The role of such hybridisation events in the evolutionary history of a group can be assessed by comparing the phylogenetic relationships inferred from different subsets of loci. Here, we use a genome-wide sampling of SNPs identified within restriction site associated DNA (RAD) tags to investigate the genomic consistency of patterns of shared ancestry and adaptive divergence among five sympatric cichlid species of two genera, Pundamilia and Mbipia, which form part of the massive adaptive radiation of cichlids in the East African Lake Victoria. Species pairs differ along several axes: male nuptial colouration, feeding ecology, depth distribution, as well as the morphologica...