Genetic structure and inversions in the Lake Malawi cichlid radiation

Adaptive radiations produce biodiversity at an accelerated rate. Traditionally, these ‘natural experiments’ have been central to studying the underlying evolutionary processes of adaptation and speciation. The modern synthesis unified evolutionary biology and genetics, fundamentally reorienting life sciences. Recent advances in DNA sequencing have enabled evolutionary research to consider entire genomes, an unprecedented opportunity to study the genetic basis of adaptation and speciation. This thesis focuses on the adaptive radiation of cichlid fishes in Lake Malawi, one of the most dramatic speciation events known in vertebrates. Following a general introduction, I first characterize a new variant callset of 2,198 Malawi cichlids from ~250 species and provide an overview of the genetic structure of the entire radiation. I then describe a new software that employs windowed principal component analysis to examine variation in genetic structure along chromosomes. This method is subsequently used to detect five large polymorphic inversions that segregate within the most species-rich and ecologically diverse lineage of Malawi cichlids. As strong suppressors of recombination, these inversions take up a dual role: they sometimes function as sex determination systems while they are also implicated in ecological adaptation. The final chapter of my thesis focuses on a single genus of rock-dwelling cichlids that repeatedly diversify along a depth gradient. An initial analysis of hundreds of new genomes from various replicate ecomorph pairs across the lake identified a putative inversion that may play a role in repeated diversification. Through this dissertation, I hope to contribute to our understanding of the dynamic genetic processes that underlie the creation of biodiversity through speciation.