The generation of novel phenotypes in a young radiation of soda lake cichlid fishes

Adaptive radiations are fantastic systems to study the origin of biodiversity as they generate considerable phenotypic and genetic diversity when given ecological opportunity. Alcolapia are small subgenus of four cichlids species each with considerable eco-morphological diversity. Chapter one provides background on adaptive radiations, the history and ecology of Alcolapia and describes polymorphisms within the species flock. Chapter two investigates the phylogenomic relationship of site 14, a population of individuals in the east of Lake Natron that have unusual dental morphologies but mimic A. alcalica and A. latilabris head morphology. RAxML predicts site 14 to be the sister lineage to Lake Natron taxa (100 bs). Furthermore, a genetic PCA, trait measurements, fineRADstructure, RAxML and Dsuite analysis give evidence site 14 contains two morphs which correspond to field categorisations. Furthermore, a GWAS on the two morphs identifies a candidate gene, OSR2, which affects mouse craniofacial and dental development, so may also cause the morphological differences within the head region of site 14 morphs. Further phenotyping of site 14 teeth is needed as previous research indicates they are atypical and reassessment of the size of the Alcolapia flock is required. Chapter three investigates the genetic basis of upturned and terminal morphologies within A. alcalica. A GWAS on mouth orientation, identifies two genes, ANKMY2a and SOSTDC1a which are related to craniofacial development in cichlids. All extremely upturned individuals were female, indicating a sexual basis for this trait and could be related to mouth brooding ability. Further investigation of the ecology of upturned A. alcalica is needed as upturned A. alcalica have been shown to consume fish scales, hinting at cannibalistic behaviour. Chapter four present conclusions and outlines the direction of further research including wider sampling, testing sexual selection for mouth orientation, KO experiments of candidate genes and investigating other polymorphisms.