The thousands of haplochromine cichlid fish species found in the African rift valley great lakes and surrounding rivers constitute perhaps the most dramatic vertebrate evolutionary radiation. Lake Malawi contains over 500 morphologically and ecologically diverse species that have separated within the last million years or so. In this presentation we will relate recently published results on the sympatric separation of two A. calliptera ecomorphs in Lake Massoko, a small crater just north of Lake Malawi (Malinsky et al, Science, 2015), to results from unpublished whole genome sequences of over 150 fish from over 85 species in the main Lake Malawi.
In the Lake Malawi sequences we observe a large amount of shared variation segregating across species, with pairwise Fst varying from 5% to 65% (diversity within species 0.05-0.1%, divergence between species 0.1-0.3%). The average phylogeny shows numerous differences to the standard taxonomy, with multiple instances of repeated phenotypic specialization across the phylogeny. As in Massoko, we see evidence of selection in the visual system, and we are testing loci selected in Lake Massoko for signs of independent repeated selection within Lake Malawi. Because of the shared variation the gene phylogeny varies across the genome. In part this is expected due to incomplete lineage sorting, but using D statistics we also see evidence for gene flow between separate branches of the species phylogeny, and are looking for evidence of selection acting on this gene flow.
We recently collected 1500 more samples from ~250 species to enable more detailed studies into speciation and selection. Finally, we are making all our sequences openly available, to enable others already working on the evolution of Malawi cichlids to also study the genetic sources of phenotypic diversity in this rich system, and are also collaborating with the Genome10K initiative to establish reference genome sequences more broadly to cover vertebrate diversity.