The thousands of haplochromine cichlid fish species in the great lakes of the African rift valley constitute some of the most dramatic vertebrate evolutionary radiations. This presentation will cover analysis of >300 whole-genome sequences spanning three evolutionary timescales: 1) unpublished results covering over 85 species and all the proposed major evolutionary lineages of Lake Malawi; 2) a phylogeographic study connecting Lake Malawi to other East African lake and riverine haplochromines; 3) speciation in Massoko - a small crater lake in the Malawi catchment (Malinsky et al., 2015).
Key results include the finding that the maximum genome wide divergence of Lake Malawi cichlids is of a similar level as for species from Victoria (surprising given that the Victoria radiation is thought to be at least 10x younger). We also see strong signatures of gene-flow between the great lakes, likely mediated by riverine fish. To assist time calibration, we estimated the mutation rate from parents-child trios (preliminary estimate: ~0.6x10e-8 per bp per generation). In Lake Malawi, the average genome phylogeny shows differences to standard taxonomy, with instances of repeated phenotypic specialization. A large amount of genetic variation is shared across species, with pairwise Fst between 5% and 65% (diversity within species 0.05-0.1%, divergence between species 0.1-0.3%). Because of the shared variation, local phylogeny varies across the genome. In part this is expected due to incomplete lineage sorting, but we also see evidence for gene-flow between separate branches of the Malawi phylogeny. In coding sequences, we see strong evidence of selection in the visual system, including genes not previously studied in cichlids. A detailed study into a specific case of speciation and selection has been carried out for Lake Massoko. To obtain a similar level of detail for pairs of Malawi species, we recently collected 1400 more Lake Malawi samples from ~250 species.