Data from: 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 morphological traits that distinguish the two genera and more subtle morphological differences. Using outlier scan approaches, we identify signals of divergent selection between all species pairs with a number of loci showing parallel patterns in replicated contrasts either among genera or male colour types. We then create SNP subsets, which we expect to be characterised to different extents by selection history and neutral processes, and find contrasting population genomic and phylogenomic signals among these datasets. In an attempt to resolve the observed conflicts, we propose at least two intergeneric hybridisation events (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of these five species that would have lead to the evolution of novel trait combinations and new species.MbipiaPundamilia_M2MbipiaPundamilia_M1MbipiaPundamilia_M