Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: South Africa is known for its high marine invertebrate diversity but the evolutionary histories of these species are largely unknown. The present study contributes to the growing body of phylogeographic studies of southern African coastal species. The main aim is to better understand the colonization and diversification of South African barnacles. To investigate the phylogeographic pattern in the southern African volcano barnacle, Tetraclita serrata, 410 individuals from 20 sampling localities were analyzed. In addition, to understand the colonization and diversification patterns of South African barnacle species, nine taxa were included in a molecular phylogeny derived from the nuclear gene, 18S rRNA. With only a limited number of 18S sequences available on GenBank, a separate phylogenetic tree, for the mitochondrial gene, was constructed to determine whether the genus Tetraclita is monophyletic. Restricted gene flow in some geographical areas was hypothesized for T. serrata based on oceanic circulation patterns; known biogeographic regions; and features such as the Agulhas Bank, which has shaped the population genetic structure of several other South African marine organisms. The population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (CO1) and nuclear internal transcribed spacer 1 (ITS1) genes. Phylogenetic and population genetic analyses of the CO1 gene revealed two distinct genetic clades with overlapping distributions. The nuclear ITS1 data performed on a subset of individuals drawn from both mtDNA clades revealed a single lineage. The pattern observed can be ascribed to a historical event that may have been responsible for the formation of allopatric lineages that have since come into secondary contact. On the other hand, the pattern observed may be as result of incomplete sorting of nDNA alleles, in which case, given that the two mtDNA clades are not geographically isolated, could be explained by selective pressures acting on the species due to ecological constraints. No clear phylogeographic structure was found within each of these clades and the direction of gene flow of T. serrata individuals can be linked to the oceanographic features found along the South African coast. In contrast to most other South African marine species studied to date, the haplotype network, mismatch distributions and time since expansion suggest that the effective population size of T. serrata was not severely affected by the Last Glacial Maximum. It is proposed that further investigations into the phylogeography of coastal marine species, particularly obligatory sessile species such as barnacles, are required to determine whether the patterns observed in T. serrata is a rare history, or not. Neighbour-joining, maximum parsimony and Bayesian analyses on the CO1 gene provide evidence for the monophyly of the genus Tetraclita; however, Tetraclita species found in South Africa do not share a common ancestry suggesting multiple colonization events. This study has also accidently led to the discovery of an introduced species, Balanus perforatus, native to Europe, and I discuss the potential of the alien becoming invasive on the east coast of South Africa where it was found. / AFRIKAANSE OPSOMMING: Suid-Afrika is bekend vir sy hoë mariene ongewerwelde diversiteit, maar die evolusionêre geskiedenis van hierdie spesies is grootliks onbekend. Hierdie studie is gedoen om by te dra tot die filografiese studies van suider Afrikaanse kus spesies en om die kolonisasie en diversifikasie van die Suid-Afrikaanse eendmossels beter te verstaan. Om die genetiese struktuur van die bevolkings van die vulkaan eendmossel, Tetraclita serrata, wat langs die Suid-Afrikaanse kuslyn voorkom, te bestudeer, was 410 individue van 20 lokaliteite ontleed. Daarbenewens, om die kolonisasie en diversifikasie van Suid-Afrikaanse eendmossels te verstaan, was nege spesies ingesluit in 'n molekulêre filogenie wat gebaseer is op die kern geen, 18s rRNA. Met slegs 'n beperkte aantal 18s DNS volgordes beskikbaar op GenBank,is 'n aparte filogenetiese boom, vir die mitochondriale geen COI, gekonstrueer om te bepaal of die genus Tetraclita monofileties is. Beperkte geen-vloei in sommige geografiese gebiede was verwag vir T. serrrata gebaseer op oseaniese sirkulasiepatrone; bekende biogeografiese streke, en kenmerke soos die Agulhas Bank, wat die filogeografiese struktuur van verskeie ander Suid- Afrikaanse mariene organismes beïnvloed het. Die genetiese struktuurvan die bevolkings is geondersoek met behulp van die mitochondriale sitochroom oksidase subeenheid 1 (COI) en kern interne getranskripeerde spasieërder 1 (ITS1) gene. Geen duidelike bevolkings genetiese struktuur is gevind nie en die rigting van geenvloei van T. serrata individue kan gekoppel word aan die oseanografiese kenmerke wat langs die Suid-Afrikaanse kus voorkom. Filogenetiese en bevolking genetiese ontleding van die COI geen openbaar twee afsonderlike klades maar met oorvleuelende geografiese verspruidings. Die ITS1 data-analise wat uitgevoer was op 'n subset van individue wys op 'n enkele spesie. Die waargenome patroon dui op 'n belangrike historiese verskil tussen die twee klades. 'n Geskiedkundige gebeurtenis was dalk verantwoordelik vir die vorming van twee evolusionêre lyne wat sederdien sekondêre kontak het. Aan die ander kant, kan die patroon waargeneem word as gevolg van die onvolledige sortering van nDNA allele, in welke geval, gegee dat die twee mtDNA clades nie geografies geïsoleer is nie, dit verduidelik kan word deur selektiewe druk wat op die spesie was as gevolg van fisiologiese of ekologiese beperkings. Die statistiese parsimonie netwerk, ongelyksoortige verspreidings en tyd sedert die bevolkingsuitbreiding dui daarop dat T. serrata die laaste ysagtige maksimum tydperk oortleef het. Tot op hede het geen Suid- Afrikaanse mariene spesies so 'n patroon gewys nie. So, verdere ondersoeke in die filogeografie van die kus mariene spesies, veral verpligte sittende spesies soos eendmossels, word vereis om te bepaal of die patroon waargeneem in T. serrata 'n seldsame geskiedenis het, of nie. Buur-aansluiting, maksimum parsimonie en Bayesian afleiding op die CO1 geen het bewyse verskaf vir die monofiletiese afkoms van die genus Tetraclita, maar Tetraclita spesies wat in Suid Afrika gevind is, deel nie ‘n gemeenskaplike afkoms nie, wat weer bewyse verskaf vir verskeie kolonisasie gebeure. Hierdie studie het gelei tot die ontdekking van 'n eksotiese spesie, Balanus perforatus, inheems aan Europa, en die potensiaal van die indringer om ontwykend te raak aan die ooskus van Suid-Afrika waar dit gevind is word bespreek. / The South African National Research Foundation (NRF) and Stellenbosch University

Mussels are important ecological engineers on intertidal rocks where they create habitat that contributes substantially to overall biodiversity. They provide secondary substratum for other free-living, infaunal or epifaunal organisms, and increase the surface area for settlement by densely packing together into complex multilayered beds. The introduction of the alien invasive mussel Mytilus galloprovincialis has extended the upper limit of mussels on the south coast of South Africa, potentially increasing habitat for associated fauna. The aim of this study was to describe the structure of mussel beds, the general biodiversity associated with multi- and monolayered mussel beds of indigenous Perna perna and alien M. galloprovincialis, and to determine the relationship between mussels and epibiotic barnacles. This was done to determine the community structure of associated macrofauna and the role of mussels as biological facilitators. Samples were collected in Plettenberg Bay, South Africa, where M. galloprovincialis dominates the high mussel zone and P. perna the low zone. Three 15 X 15 cm quadrats were scraped off the rock in the high and low zones, and in the mid zone where the two mussel species co-exist. The samples were collected on 3 occasions. In the laboratory mussel-size was measured and sediment trapped within the samples was separated through 75 μm, 1 mm and 5 mm mesh. The macrofauna was sorted from the 1 mm and 5 mm sieves and identified to species level where possible. The epibiotic relationship between mussels and barnacles was assessed by measuring the prevalence and intensity of barnacle infestation and the condition index of infested mussels. Multivariate analysis was used on the mean abundance data of the species for each treatment (Hierarchical clustering, multidimensional scaling, analysis of similarity and similarity of percentages) and ANOVA was used for most of the statistical analyses. Overall, the results showed that tidal height influences the species composition and abundance of associated fauna. While mussel bed layering influenced the accumulation of sediments; it had no significant effect on the associated fauna. Time of collection also had a strong effect. While there was an overlap of species among samples from January, May and March, the principal species contributing to similarity among the March samples were not found in the other two months. The outcomes of this study showed that low shore mussel beds not only supported a higher abundance and diversity of species, but were also the most structurally complex. Although the condition index of mussels did not correlate to the percentage cover of barnacle epibionts, it was also evident that low shore mussels had the highest prevalence. The levels of barnacle infestation (intensity) for each mussel species were highest where it was common and lowest where it was least abundant. This is viewed as a natural artefact of the distribution patterns of P. perna and M. galloprovincialis across the shore. Mussels are more efficient as facilitators on the low mussel zone than the high mussel zone possibly because they provide habitats that are more effective in protecting the associated macrofauna from the effects of competition and predation, than they are at eliminating the effects of physical stress on the high shore. Although mussels create less stressful habitats and protect organisms from the physical stress of the high shore, there are clear limitations in their ability to provide ideal habitats. The biological associations in an ecosystem can be made weak or strong depending on the external abiotic factors and the adaptability of the affected organisms.