Abstract

Our genomes are both the product of evolution, and the medium through which evolution acts. Modern genomics allows us to observe directly the consequences of evolution acting on genetic variation, to study the processes that give rise to the diversity of life. I will discuss our studies on one of the largest recent adaptive radiations, of over 500 species of cichlid fish in Lake Malawi, which have diverged within the last million years. These species demonstrate enormous variation in morphology, diet, behaviour and ecology, although the mean genetic divergence between species is just 0.2%, only twice the diversity within modern humans. Over the last five years we have started to investigate the genetic history and structure of the radiation by whole genome sequencing samples from over 300 species/populations. There is not a simple tree-like phylogeny but rather evidence of hybridisation at the base of the radiation and also at multiple points since. In several cases this was associated with adaptive introgression of functional variation, for example between deeply diverged deep water clades. Sequences of over 600 samples from two recently diverging A. calliptera ecomorphs from the satellite crater lake Masoko reveal 50-100 genomic “islands” of genetic divergence in a background of very low population separation (4% Fst). We have begun to use these data to map loci involved in specific traits by genome wide association. Most strikingly, we have identified two competing XY sex determination loci, suggesting a possible role for rapid evolution of sex determination in supporting adaptive speciation.