published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

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

Thesis (Ph. D.)--Stanford University, 2008. / Submitted to the Department of Biology. Copyright by the author. Includes bibliographical references (p. 183-205). Also available online.

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Thesis (Ph. D.)--University of Hong Kong, 1995. / Includes bibliographical references (leaves 267-316).

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Les suspensivores ont la tâche importante de séparer les particules de l'eau. Bien qu'une grande gamme de morphologies existe pour les structures d'alimentation, elles sont pratiquement toutes constituées de rangées de cylindres qui interagissent avec leur environnement fluide. Le mécanisme de capture des particules utilisé dépend des contraintes morphologiques, des besoins énergétiques et des conditions d'écoulement. Comme nos objectifs étaient de comprendre ces relations, nous avons eu recours à des études de comparaison pour interpréter les tendances en nature et pour comprendre les conditions qui provoquent de nouveaux fonctionnements. Nous avons utilisé la dynamique des fluides numérique (computational fluid dynamics, CFD) pour créer des expériences contrôlées et pour simplifier les analyses. Notre première étude démontre que les coûts énergétiques associés au pompage dans les espaces petits sont élevés. De plus, le CFD suggère que les fentes branchiales des ptérobranches sont des structures rudimentaires, d'un ancêtre plus grande. Ce dernier point confirme l'hypothèse qu'un ver se nourrit par filtration tel que l'ancêtre des deuterostomes. Notre deuxième étude détermine la gamme du nombre de Reynolds number critique où la performance d'un filtre de balane change. Quand le Re est très bas, les différences morphologiques n'ont pas un grand effet sur le fonctionnement. Cependant, une pagaie devient une passoire lorsque le Re se trouve entre 1 et 3,5. Le CFD s’est dévoilé être un outil très utile qui a permis d’obtenir des détails sur les microfluides. Ces études montrent comment la morphologie et les dynamiques des fluides interagissent avec la mécanisme de capture ou de structures utilisées, ainsi que comment des petits changements de taille, de forme, ou de vitesse d'écoulement peuvent conduire à un nouveau fonctionnement. / Suspension feeders have the important task of separating particles from the liquid medium surrounding them. Although a wide range of morphologies exist for feeding structures, essentially all consist of arrays of cylinders interacting with their fluid environment. The particle capture mechanism employed depends on morphological constraints, energy requirements, and flow conditions, therefore our objectives were to understand these relationships through comparison studies to interpret trends in nature and to understand the conditions in which novel functioning arises. Our studies used computational fluid dynamics (CFD) to create controlled experiments and to simplify analyses. The first study demonstrates the unfeasibly high energetic costs of pumping in small and medium pharynx sizes of hemichordates, implying the gill pores of pterobranchs are likely vestigial structures from a larger ancestor. This last point further supports the hypothesis of an acorn worm as the ancestor to all deuterostomes. Our second study determined the critical Reynolds number (Re) range where barnacle filters transition from a paddle to a sieve. At very low Re, morphological differences have no major effect on functioning and filters behave as paddles, however, at Re 1 - 3.5, these differences dictate when a paddle becomes a sieve. CFD proved to be a very useful tool for simplifying studies and providing detailed microfluidics. These studies demonstrate how morphology and fluid dynamics interact to dictate the capture mechanisms or appendages employed and how simple changes in size, shape, or flow speed can lead to novel functioning.

Made available in DSpace on 2016-06-02T19:32:14Z (GMT). No. of bitstreams: 1 6751.pdf: 1090624 bytes, checksum: f2bfa0137477a5e0146bbb71ea1ac963 (MD5) Previous issue date: 2015-02-12 / Universidade Federal de Minas Gerais / The zonation of rocky shores results from the action of physical and chemical factors and of biological interactions within the benthic assemblages, being a good model to investigate factors that structure biological communities. In the present study, the objective was to evaluate the processes influencing a particular zonation pattern in sheltered rocky shores of Southeastern Brazil. The intermediate and lower midlittoral in these environments is a zone mainly formed by bare rock, or biofilm, presenting only few individuals of the barnacle Tetraclita stalactifera or other filtering-feeding species, whereas the upper midlittoral is dominated by the barnacle Chthamalus bisinuatus. In this way, we first evaluated the variation in these communities at three spatial scales (within shores, between shores and between regions), to identify the extension of the pattern (Chapter 1). Then, we carried out two experiments to test the assumptions that 1) the pattern would be determined by biofilm action, which would be distinct in the two zones and thus influence barnacle recruitment differentially; 2) the pattern would be determined by higher barnacle mortality in the lower zone, probably caused by higher predation pressure in this zone (Chapter 2). Our results allowed us to conclude that the main source of variation in the communities studied was usually at small spatial scales, meaning that the structuring processes in these communities would also occur at small scale. Barnacle recruitment during the study was excessively low and not correlated with different heights on the midlittoral, whereas the biofilm was more abundant in the lower midlittoral. In this midlittoral zone, barnacles showed higher mortality than in the upper midlittoral, evidencing strong effects of differential mortality structuring the community, although few predators were sampled in the studied areas. Thus, the present study contributes to our understanding of structuring processes in subtropical sheltered rocky shores, generating a reference framework on the system studied and subsidizing studies on environmental impacts. / A zonação em costões rochosos é resultante da atuação de fatores físico-químicos e de interações biológicas sobre as assembleias bentônicas, caracterizando-se como um bom modelo para investigar os fatores que estruturam as comunidades biológicas. Neste trabalho, o objetivo foi avaliar processos envolvidos com um padrão de zonação particular em costões rochosos abrigados do sudeste brasileiro. O mesolitoral médio e inferior nesses ambientes constitui-se de uma zona majoritariamente formada por rocha nua, ou biofilme, apresentando apenas poucos indivíduos da craca Tetraclita stalactifera ou outros filtradores, enquanto o mesolitoral superior é dominado pela craca Chthamalus bisinuatus. Dessa forma, nós primeiro avaliamos a variação nas comunidades desses costões em três escalas espaciais (dentro de costão, entre costões e entre regiões), a fim de identificar a extensão do padrão (capítulo 1). Em seguida, elaboramos dois experimentos para testar as hipóteses de que 1) o padrão seria determinado pela ação do biofilme, o qual seria distinto nas duas zonas e influenciaria o recrutamento de cracas diferencialmente; 2) o padrão seria determinado por maior mortalidade de cracas na zona inferior, provavelmente causado por maior pressão de predação nessa zona (capítulo 2). Nossos resultados permitiram concluir que a principal fonte de variação nas comunidades estudadas geralmente ocorre em pequena escala espacial, indicando que os processos estruturadores dessas comunidades também devem ocorrer em pequena escala. O recrutamento de cracas durante o estudo foi excessivamente baixo e não correlacionado com as diferentes alturas do mesolitoral, enquanto o biofilme se mostrou mais abundante no mesolitoral inferior. Nesta porção do mesolitoral, as cracas apresentaram maior mortalidade do que na região superior, evidenciando forte efeito da mortalidade diferencial na estruturação das comunidades, apesar de terem sido amostrados poucos predadores nas áreas estudadas. Assim, este estudo permitiu colaborar com o conhecimento dos processos estruturadores em costões rochosos abrigados subtropicais, gerando um quadro de referência sobre o sistema estudado e subsidiando possíveis estudos sobre impactos ambientais.

Les suspensivores ont la tâche importante de séparer les particules de l'eau. Bien qu'une grande gamme de morphologies existe pour les structures d'alimentation, elles sont pratiquement toutes constituées de rangées de cylindres qui interagissent avec leur environnement fluide. Le mécanisme de capture des particules utilisé dépend des contraintes morphologiques, des besoins énergétiques et des conditions d'écoulement. Comme nos objectifs étaient de comprendre ces relations, nous avons eu recours à des études de comparaison pour interpréter les tendances en nature et pour comprendre les conditions qui provoquent de nouveaux fonctionnements. Nous avons utilisé la dynamique des fluides numérique (computational fluid dynamics, CFD) pour créer des expériences contrôlées et pour simplifier les analyses. Notre première étude démontre que les coûts énergétiques associés au pompage dans les espaces petits sont élevés. De plus, le CFD suggère que les fentes branchiales des ptérobranches sont des structures rudimentaires, d'un ancêtre plus grande. Ce dernier point confirme l'hypothèse qu'un ver se nourrit par filtration tel que l'ancêtre des deuterostomes. Notre deuxième étude détermine la gamme du nombre de Reynolds number critique où la performance d'un filtre de balane change. Quand le Re est très bas, les différences morphologiques n'ont pas un grand effet sur le fonctionnement. Cependant, une pagaie devient une passoire lorsque le Re se trouve entre 1 et 3,5. Le CFD s’est dévoilé être un outil très utile qui a permis d’obtenir des détails sur les microfluides. Ces études montrent comment la morphologie et les dynamiques des fluides interagissent avec la mécanisme de capture ou de structures utilisées, ainsi que comment des petits changements de taille, de forme, ou de vitesse d'écoulement peuvent conduire à un nouveau fonctionnement. / Suspension feeders have the important task of separating particles from the liquid medium surrounding them. Although a wide range of morphologies exist for feeding structures, essentially all consist of arrays of cylinders interacting with their fluid environment. The particle capture mechanism employed depends on morphological constraints, energy requirements, and flow conditions, therefore our objectives were to understand these relationships through comparison studies to interpret trends in nature and to understand the conditions in which novel functioning arises. Our studies used computational fluid dynamics (CFD) to create controlled experiments and to simplify analyses. The first study demonstrates the unfeasibly high energetic costs of pumping in small and medium pharynx sizes of hemichordates, implying the gill pores of pterobranchs are likely vestigial structures from a larger ancestor. This last point further supports the hypothesis of an acorn worm as the ancestor to all deuterostomes. Our second study determined the critical Reynolds number (Re) range where barnacle filters transition from a paddle to a sieve. At very low Re, morphological differences have no major effect on functioning and filters behave as paddles, however, at Re 1 - 3.5, these differences dictate when a paddle becomes a sieve. CFD proved to be a very useful tool for simplifying studies and providing detailed microfluidics. These studies demonstrate how morphology and fluid dynamics interact to dictate the capture mechanisms or appendages employed and how simple changes in size, shape, or flow speed can lead to novel functioning.