Date of Award

Spring 1998

Project Type


Program or Major


Degree Name

Doctor of Philosophy

First Advisor

Thomas D Kocher


The cichlid species "flocks" which are endemic to the East African Rift Valley are characterized by frequent lineage splitting events which have led to the rapid evolution of high levels of taxonomic diversity. Changes in water level cause these habitat patches to be chronically unstable, hypothetically speeding the process of genetic differentiation through the combined effects of genetic drift and selection. Allele frequencies at four simple sequence repeat loci indicate low levels of gene flow in two rock dwelling fish species, Melanochromis auratus and Labeotropheus fuelleborni, collected from the Nankumba Peninsula in southern Lake Malawi. Small interruptions in habitat cause low, but statistically significant genetic differentiation among populations. The highest levels of interpopulation heterogeneity were observed between populations separated by deep troughs of open water. Differences in habitat usage cause the absolute magnitude of interpopulation heterogeneity to be higher among M. auratus populations than among L. fuelleborni populations. A correlation exists between allelic diversity at a locus and the relative age of a habitat, suggesting that mild bottlenecks are associated with colonization. Simulation studies indicate that the level of differentiation observed among these populations is unlikely to be merely an artifact of modest sample sizes and highly polymorphic loci.

Philopatry alone is not sufficient to drive speciation. Populations must become reproductively isolated as well. A series of mate choice experiments indicated that mate recognition is nearly perfect among the congeners M. auratus and M. heterochromis. When F$\sb1$ hybrid females were included in these experiments, they preferentially mated with hybrid males.

An estimate of the relationships among Lake Tanganyika and Lake Malawi species was obtained by surveying the genome for SINE (retrotransoposon) insertions by using a modified AFLP protocol which incorporates a SINE specific primer. The resulting phylogeny estimate was consistent with other molecular and morphological data sets for the older lineages in Lake Tanganyika, and indicated that the Lake Malawi species flock has a common ancestor with the Tanganyikan tribe Tropheini. Resolution among the Lake Malawi species was poor due to the incomplete lineage sorting which is characteristic of this extremely rapidly evolving lineage.