A significant number of proteins function as multimeric structures, most commonly as dimers. One of the primary mechanisms by which proteins evolve is through gene duplication and mutations of the resulting duplicated gene. The evolution of dimeric proteins after gene duplication is of interest because it can form three types of dimer: two homodimers and a heterodimer. Point mutations that occur in the interface of dimers would affect their binding strength and might change their path in the evolution. Here we designed an evolutionary model for protein dimerization after gene duplication. In this work, we have used dimers' PDB structures to construct the network of contacts between amino acids in the interface. Several pairwise energy contact matrices were examined to find reasonable interface binding energies. Using the population genetics theory, we defined a selection criteria based on dimer interface strength and let them evolve as the mutations happen. We observed that the dimer structures are bound to be in the mostly homodimer state or mostly heterodimer state, and there are few occasions that we have all three types of structures as strong dimers. We anticipate three fates for the dimer protein's evolution after gene duplication, neofunctionalization, subfunctionalization, and loss of the gene. A loss of function in homodimer structures might eventually lead to a subfunctionalization since the two interfaces are different. On the other hand, if a heterodimer loss happens, we would have two strong homodimer structures so both neofunctionalization and subfunctionalization might still happen. In the first case, one could gain a new function while the other homodimer performs the protein's old function. In the latter case, the two separate homodimers could each assume different parts of the full function of the original gene (which is the definition of subfunctionalization). / Thesis / Master of Science (MSc) / A large fraction of proteins are found to exist as dimers composed to two identical subunits. If the gene for the single subunit is duplicated, three types of dimers can emerge, two homodimer structures and a heterodimer structure. Gene duplication is a major driving force of evolution as it can allow the proteins to perform new tasks. Here we define a model to understand the evolution of dimeric proteins as they undergo mutations in their interface, changing their stickiness to each other. We find that evolution favours the dimers to either be homodimer or heterodimer, but not both at the same time. When there are two homodimers, one of them can acquire a new function (which is known as neofunctionalization). When there is a heterodimer, both genes are now required to do the orginal job of a single gene (which is known as subfunctionalization). These mechanism provide two possible reasons why the duplicate gene cannot subsequently be deleted from the genome.

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This thesis is a study of the evolution and development of the flagellate green algae. The first part is a comparative study of the evolution of body size, multicellularity and segregated soma. The allometry of morphological characters, development, life history and the life cycle are also considered. The second part is an experimental test of the potential role of mutation as a determinant of the course of evolution. Mutation is directional for all the characters studied. The variances and covariances created by mutation are compared to those of 30 species of Volvocaceae; the correspondence between the two depends upon the characted examined. In the third part, the growth of germ cells grown with and without a soma is compared. The response to nutrient concentration of cells grown with an intact soma is steeper than that of cells grown without a soma. This result demonstrates a physiological advantage of soma in Volvox, attributable to a division of labour between 'source' and 'sink'.

<p>This thesis explored species-level phylogenetic relationships of the African cycad genus Encephalartos, which is one of the eleven genera of cycads. The genus is confined to Africa and comprises approximately 65 species, 38 of which are found naturally in South Africa. The phylogenetic studies on Encephalartos to date still result in many unresolved polytomies so it is not possible to fully understand the relationships between different taxa. In this study, AFLPs were used together with DNA sequencing to reconstruct the phylogenetic relationships of the genus. This study was the first to be presented with aims of resolving the relationships of Encephalartos using AFLPs together with DNA sequences.</p>

<p>This thesis explored species-level phylogenetic relationships of the African cycad genus Encephalartos, which is one of the eleven genera of cycads. The genus is confined to Africa and comprises approximately 65 species, 38 of which are found naturally in South Africa. The phylogenetic studies on Encephalartos to date still result in many unresolved polytomies so it is not possible to fully understand the relationships between different taxa. In this study, AFLPs were used together with DNA sequencing to reconstruct the phylogenetic relationships of the genus. This study was the first to be presented with aims of resolving the relationships of Encephalartos using AFLPs together with DNA sequences.</p>