Understanding the processes that have affected the diversification of herbaceous plants is fundamental to understand how flowering plants evolve, how ecosystems form and to predict the effect of climate change and geological events in plant communities. Aiming to create a strong phylogenetic framework where biogeographic and morphological hypothesis can be tested a higher level dated phylogeny of Gesneriaceae was produced. Gesneriaceae is a good study group as it has variable floral morphology, a broad distribution throughout the tropics and subtropics - represented in all non-arid tropical and subtropical hotspots of biodiversity. There are evident differences between lineages in the numbers of species, and it is comparatively well studied compared with other asterid families. In this study a consolidated taxonomic hypothesis of Gesneriaceae is suggested based on a genus level phylogeny, the ages of the main lineages of the family are presented, the effect of geological events are explored, the geographic origin of lineages are suggested and an insight into the effect of floral morphology on the evolution of the family is given. Limiting the taxonomic scope and focusing on a single family should help us better understand how flowering plants diversify.

L'évolution par sélection naturelle se compose d'une succession de trois étapes : mutations, sélection et prolifération. Nous nous intéressons à la description et à la caractérisation du résultat d'une étape de sélection dans une population composée de nombreux variants. Après sélection, cette population va être dominée par les quelques meilleurs variants, ceux qui ont la plus grande capacité à être sélectionnés, ou plus grande « sélectivité ». Nous posons la question suivante : comment est distribuée la sélectivité des meilleurs variants dans la population? La théorie des valeurs extrêmes, qui caractérise les queues extrêmes des distributions de probabilités en terme de 3 classes d'universalités, a été proposée pour répondre à cette question. Pour tester cette proposition et identifier les classes d'universalités rencontrées dans ce genre de problème, nous avons procédé à une sélection quantitative de banques composées de $10^5$ variants d'anticorps grâce à la technique du phage display. Les données obtenues par séquençage à haut débit du résultat de la sélection de nos banques nous permettent d'ajuster la distribution de sélectivités obtenue sur plus de deux décades. / Evolution by natural selection involves the succession of three steps: mutations, selection and proliferation. We are interested in describing and characterizing the result of selection over a population of many variants. After selection, this population will be dominated by the few best variants, with highest propensity to be selected, or highest “selectivity”. We ask the following question: how is the selectivity of the best variants distributed in the population? Extreme value theory, which characterizes the extreme tail of probability distributions in terms of a few universality class, has been proposed to describe it. To test this proposition and identify the relevant universality class, we performed quantitative in vitro experimental selections of libraries of > $10^5$ antibodies using the technique of phage display. Data obtained by high-throughput sequencing allows us to fit the selectivity distribution over more than two decades. In most experiments, the results show a striking power law for the selectivity distribution of the top antibodies, consistent with extreme value theory.

Proposals for the internal relationships and classification of the bostrichoids are currently poorly supported, and almost all are based on morphology alone. This study improves upon on previous phylogenetic analyses of the group by including more taxa using the standard genes for many phylogenetic analyses. Cytochrome C oxidase subunit 1 (CO1), 28S small subunit rRNA, and 16S small subunit rRNA mitochondrial genes were sequenced or obtained from Genbank, then analyzed using parsimony and Bayesian analyses. Topologies differed depending on genes used. A three gene tree and a two gene (28S and CO1) tree both supported relationships in which a basal bostrichid clade was sister to Ptinidae s. s. + anobiids, with another bostrichid clade within the ptinids. Current bostrichid and anobiid subfamilies tested were not supported as monophyletic in any of the trees obtained. Additionally, five new species of spider beetles in the genus Meziomorphum Pic from South Africa are described including M. endrödyi, M. boroveci, and M. nama from the Richtersveld, M. bulla from south-central Namaqualand, and M. cederbergensis from the Cederberg. Genitalia are illustrated for the genus for the first time for six of the 10 species now known. A brief discussion of the evolution of generic morphology and biology as well as the relationships of the genus to other spider beetle groups are also provided. Finally, a revision of the genus Eutaphroptinus is presented. Eutaphroptinus pseudonatalensis is considered a synonym of Eutaphroptinus natalensis. New species records of E. natalensis are also provided, as well as illustrations of the genus.

The evolutionary relationship between Frankia and actinorhizal plants was evaluated by reconstructing molecular phylogenetic trees from nifH, 16S rDNA, and rbcL nucleotide sequences. Subgroupings in Frankia phylogenetic trees reconstructed from nifH and from 16S rDNA sequences were consistent in terms of plant origins of Frankia strains. Although the branching order of Frankia 16S rDNA and plant rbcL trees were different, subgroupings of Frankia and of plants correlated well in terms of symbiotic partnership. Tree matching, estimated divergence times, and molecular clock hypothesis tests indicated that Frankia clades diverged more recently than plant clades and that actinorhizal symbioses originated more than three times after the plant clades diverged. A phylogenetic tree of Ceanothus species, which are symbiotic partners of Frankia, was reconstructed using ndhF gene sequences. The analysis identified two main clades corresponding to two subgenera: Ceanothus and Cerastes. The analysis also suggested that three monophyletic clades within the subgenus ceanothus can be delimited on the basis of vegetative characters. Based on rbcL sequences, the two subgenera diverged 18-39 million years ago whereas species within each subgenus diverged more recently. These results support the current division of Ceanothus into two monophyletic subgenera and agree with the postulated recent divergence of many species within each subgenus. Specificity between Ceanothus species and their Frankia microsymbionts was evaluated by analysis of DNA in nodules collected from three copopulations of Ceanothus species. Sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiont Frankia are closely related. Nodules were further analyzed by genomic fingerprinting using repetitive sequences and PCR (rep-PCR). A newly designed, direct repeat sequence and a BOX sequence showed that Ceanothus-microsymbiont Frankia exhibited less diversity within each copopulation than among copopulations. Furthermore, geographic separation was a more important factor for divergence of Ceanothus-microsymbiont Frankia than host plant. The population of Ceanothus-infective Frankia in soils under stands of Ceanothus velutinus and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), a non-host plant, were compared. The population sizes were measured using plant bioassay methods with C. velutinus, C. sanguineus, and C. integerrimus as trap plants. Population size in soil under C. velutinus was about 10 times higher than that under the Douglas-fir. Nodulation capacities of the three trap plants were not significantly different. The diversity of Frankia nodulating trap plants was examined using rep-PCR. Results suggested that infective Frankia is not species-specific with regard to the three Ceanothus species used as trap plants and that although the degree of diversity was similar in both soils, the two populations consisted of different Frankia. / Graduation date: 1998

Mitochondria are eukaryotic cellular organelles responsible for power-generation, believed to have come into existence by an endo-symbiontic event where a bacterial cell was incorporated by an un-specified "proto-eukaryote". Phylogenetic analysis have shown that the mitochondrial ancestor was most related to present-day alpha-proteobacteria, although the exact nature of the mitochondrial progenitor remains disputed. In this work, I have used phylogenetic and other methods to investigate the identity of the organism giving rise to mitochondria, by analysing the evolutionary history of select proteins, the events where they have been transfered to the eukaryotic nucleus, and the time-point of mitochondrial establishment. In addition, a search for mitochondrially related organisms in the ocean metagenome was performed, in the hope that something more related to the mitochondrial progenitor than anything previously identified could be found. Previous analysis have shown that a large fraction of mitochondrial proteins does indeed trace their descent to the alpha-proteobacteria, but I found that the amino-acyl tRNA-synthetases display more general bacterial descent, making it likely that these proteins are of a different origin from the mitochondria themselves. While the synthetases are encoded on the nuclear genome, most mitochondria still posses most of the tRNA on their own genomes. In the cases where the tRNA has been lost from the mitochondrial genome, I found that the probability of loss correspond to the evolutionary history of their synthetase. The ocean metagenome represents an order of magnitude more data than previously available, making it suitable for improving the analyses dealing with mitochondrial placement. This large of amount of data was utilised to improve the phylogenetic analyses, showing that previous works might have suffered from artefacts inflating the support for placement of mitochondria with a specific alpha-proteobacterial group. Eukaryotic/mitochondrial radiation was shown to be as old, or older, than radiation of extant alpha-proteobacteria, casting doubt on previous analysis identifying a specific alpha-proteobacterial group as the mitochondrial ancestor.

Cooperation and cheater control have helped shape life as we know it, but there is still much to learn. A eukaryote microbial model organism, like Dictyostelium discoideum , is an excellent system for advancing our understanding. When faced with starvation, multiple genetically distinct clones of D. discoideum aggregate together to form a chimeric fruiting body with a sterile stalk that holds aloft a sorus of hardy reproductive spores. One clone may be able to cheat and form disproportionately more spores, while forcing others to form more stalk. Here we discuss the impact of genetic relatedness on cooperation, and how social actions are temporally organized and can be affected by environmental conditions. First, we documented a potential strategy for facultative cheating within chimeras. We showed that the first cells to starve, and initiate the social stage, cheat cells that starved later. In another paper, we reviewed recent studies of social microbes, which demonstrate the importance of high relatedness in the evolution of cooperation and cheater resistance. In an experimental evolution study, we tested the hypothesis that de novo cheater mutants readily evolve under low relatedness conditions. We found that the majority of our lines evolved to cheat their ancestor. Further, we studied obligate cheaters, which pose a great threat to sociality. They gain a reproductive advantage in chimeras, but cannot cooperate clonally to form fruiting bodies. Wild obligate D. discoideum cheaters have never been documented, but we found that obligate cheaters readily evolved under low relatedness conditions in the laboratory. In another study, we looked at the effects of light level on spore production in D. discoideum and Dictyostelium citrinum . Overall, more spores were produced in the light than in the dark, probably because of reduced movement and cell loss during the motile multicellular slug stage. We found that these effects were species, clone, and environment dependent. Taken together, this work helps us understand how cooperation thrives in nature, despite the threat of cheaters.

Gegenstand der Arbeit ist eine umfassende Charakterisierung von Struktur und Funktion des G-Protein-gekoppelten Rezeptors GPR34 auf genomischer, mRNA und Proteinebene, die mögliche Rückschlüsse auf physiologische Funktionen oder den natürlichen Agonisten zulassen. Dazu wurde die genomische Organisation des GPR34 in Mensch, Maus und Ratte analysiert und festgestellt, dass neben der intronlosen kodierenden Sequenz auch der 5´-Bereich des GPR34 mit seiner nicht-kodierenden Intron-Exon-Struktur stark konserviert ist. Es wurden in der Ratte und der Maus mindestens zwei, beim Menschen ein putativer Transkriptionsstart identifiziert. Beim Menschen konnte ein kryptisches Intron innerhalb der kodierenden Sequenz des GPR34 gefunden werden, was zu einer Verkürzung des N-Terminus um 47 Aminosäuren führt. Auf der Transkriptionsebene wurde der GPR34 und der GPR34-like Rezeptor im Haushuhn (Gallus gallus) und die GPR34-Expression in der Ratte mittels quantitativer RT-PCR analysiert und die ubiquitäre Gewebeverteilung des Rezeptors bestätigt. Beim menschlichen GPR34 konnte festgestellt werden, dass die fünf putativen Translationsstarts innerhalb der kodierenden Sequenz auch als solche funktionstüchtig sind und der zweite Translationsstart bevorzugt genutzt wird. Die genetische Variabilität des GPR34 in der menschlichen Population ist sehr gering. Es konnte innerhalb einer weltweiten DNA-Probensammlung nur ein einziges Mal eine Mutation in der kodierenden Sequenz lokalisiert werden. Mithilfe des während dieser Arbeit entstandenen Mausmodelles ist eine weitere Charakterisierung der physiologischen Relevanz des GPR34 möglich.

Among mammals, primates are exceptional for their large brain size relative to body size. Relative brain size, or encephalization, is particularly striking among humans and their direct ancestors. Since the human-chimp split 5 to 7 million years ago, brain size has tripled in the human lineage (Wood & Collard 1999). The focus of this doctoral work is to investigate some of the cell biological mechanisms responsible for this increase in relative brain size. In particular, the processes that regulate symmetric cell division (ultimately generating more progenitors), the constraints on progenitor proliferation, and how neural progenitors have overcome these constraints in the process of primate encephalization are the primary questions of interest. Both functionally analyses in the mouse model system and comparative neurobiology of rodents and primates are used here to address these questions. Using the mouse model system, the cell biological role of the Aspm (abnormal spindle-like microcephaly associated) protein in regulating brain size was investigated. Specifically, Aspm function in symmetric, proliferative divisions of neuroepithelial (NE) cells was analyzed. It was found that Aspm expression in the mouse neuroepithelium correlates in time and space with symmetric, proliferating divisions. The Aspm protein localizes to NE cell spindle poles during all phases of mitosis, and is down-regulated in cells that undergo asymmetric (neurogenic) cell divisions. Aspm RNAi alters the division plane in NE cells, increasing the likelihood of premature asymmetric division resulting in an increase in non-NE progeny. At least some of the non-NE progeny generated by Aspm RNAi migrate to the neuronal layer and express neuronal markers. Importantly, whatever the fate of the non-NE progeny, their generation comes at the expense of the expansion of the proliferative pool of NE progenitor cells. These data have contributed to the generation of an hypothesis regarding evolutionary changes in the regulation of spindle orientation in vertebrate and mammalian neural progenitors and their impact on brain size. Specifically, in contrast to invertebrates that regulate the switch from symmetric to asymmetric division through a rotation of the spindle (horizontal versus vertical cleavage), asymmetric NE cell division in vertebrates is accomplished by only a slight deviation in the cleavage plane away from the vertical, apical-basal axis. The requirement for the precise alignment of the spindle along the apical-basal axis in symmetric cell divisions may have contributed to selection on spindle “precision” proteins, thus increasing the number of symmetric NE cell division, and contributing to brain size increases during mammalian evolution. Previous comparative neurobiological analyses have revealed an increase in basally dividing NE cells in the brain regions of highest proliferation and in species with the largest brains (Smart 1972a,b; Martinez-Cerdeno et al. 2006). The cell biological characteristics of these basally dividing cells are still largely unknown. We found that primate basal progenitors, similar to rodent apical progenitors, are Pax6+. This suggests that primate basal progenitors may share other properties with rodent apical progenitors, such as maintenance of apical contact. Our previous finding that artificial alteration of cleavage plane in NE cells affects their ability to continue proliferating supports the hypothesis that the apical membrane and junctional complexes are cell fate determinants (Huttner & Kosodo 2005). As such, the need to maintain apical membrane contact appears to be a constraint on proliferation (Smart 1972a,b; Smart et al. 2002). Together, these data favor the hypothesis that primate basally dividing cells maintain apical contact and are epithelial in nature.

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xiv, 131 p.; also includes graphics. Includes abstract and vita. Advisor: David L. Haury, College of Education. Includes bibliographical references (p. 97-104).

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy