Phylogenetic and population genetic structure of riverine Astatotilapia cichlid fishes of East Africa.

  • Ling-Lan Hsu

Student thesis: Master's ThesisMaster of Science (MSc)


East African freshwater cichlid fish radiations undergo rapid species diversification and thus contain exceptional species richness and phenotypic diversity. However, the origins of the genetic variants that have undergone divergent selection during these radiations are unclear. Although much of the variation likely stems from standing genetic variation present in shared ancestors, it has been proposed that riverine species could promote the sharing of genetic variation by acting as “gene transporters”. However, supporting this hypothesis would require both dispersal across riverine boundaries, and hybridizations between species at locations where they overlap.

In Chapter 1, I introduce some background knowledge of East African cichlid radiations, and review important research about the evolution and species diversification of East African cichlid, including some hypotheses based on biogeographic evidence. In Chapter 2, I present a study using ddRAD sequencing data to reconstruct the phylogenetic relationships of riverine haplochromines within East Africa, and their close relatives within the Lake Malawi, Tanganyika and Victoria radiations. The results demonstrate clear evidence of the presence of multiple riverine species being present in East Africa, several that apparently lack formal taxonomic identities. The results also reveal very strong population genetic structure both within and among populations of riverine species, but we could find no clear evidence of elevated levels of recent gene flow between sympatric riverine species. However, patterns of coancestry are potentially indicative of historical gene flow among riverine and lacustrine species in the region. Based on the results we conclude that East African rivers harbour an unexpected diversity of cichlid species, and that multiple extant species may have contributed to genetic diversity present within the lake radiations. However, we suggest that limited dispersal among populations coupled within strong assortative mating of these species in sympatry may strongly limit their role as active gene transporters of contemporary genetic diversity.
Date of Award19 Mar 2019
Original languageEnglish
Awarding Institution
  • The University of Bristol
SupervisorMark A Beaumont (Supervisor) & Martin J Genner (Supervisor)

Cite this