In this thesis, I study a radiation of brood-parasitic finch species, the indigobirds and whydahs (genus Vidua), that occur across Africa. Host colonisation is tightly linked to speciation in Vidua because of their remarkable capacity to imprint on their hosts, with mating traits and host preferences being influenced by the parasite's early environment. The challenge of explaining why the radiation has diversified to the extent it has therefore simplifies to understanding why only certain potential host species have been successfully colonised. Following on from the introduction (Chapter 1), I begin by critically examining the logic with which mimicry in the natural world can be conceptually organized (Chapter 2). This creates a “mimicry landscape” in which to situate the mimetic adaptations of hosts exhibited by Vidua. The framework can be used to contrast and draw parallels between these and other mimetic adaptations present in the natural world. In Chapter 3, I review the literature on begging call mimicry and development across all avian brood parasite species. I outline the conditions under which we expect begging call mimicry to evolve, and when we expect it to develop primarily through genetic or environmental cues. This provides clear predictions for what we expect to occur in Vidua finches, which are tested in Chapters 4 and 5. In Chapter 4, I quantify the mimicry of host nestlings by Vidua in detail. I provide the first quantitative evidence that Vidua nestlings mimic the begging calls and show for the first time that Vidua are imperfect mimics of their hosts. In Chapter 5, I simulate the colonisation of a new host by transferring Vidua eggs into the nest of a new host species. I monitor Vidua survival in the foreign host environment and test several hypotheses about what explains differences in chick survival. I find that Vidua survive poorly in the new nest environment and that they do not show adaptive plasticity in begging calls or head movements. This poor survival occurs despite there being minimal differences in the diets each host species feeds their young. Finally, in Chapter 6, I carry out a comparative analysis on the evolution of estrildid mouth markings. Estrildid finches are the hosts of Vidua and so provide the landscape of potential ecological niches that Vidua may colonise and adapt to. I demonstrate that the host family shows strong phylogenetic signal in mouth marking traits, and find no evidence that ecological factors such as light environment or predation pressure has shaped estrildid mouth marking evolution. The work in this thesis highlights how difficult successfully colonising new hosts is for Vidua finches. Vidua must mimic hosts in multiple traits (mouth markings, begging calls, head movements) to obtain sufficient amounts of food from host parents. Overall, habitat filters, the complex and diverse begging displays of estrildid nestlings, the discriminatory behaviour of estrildid parents against mismatching chicks and the lack of adaptive plasticity in begging displays by Vidua together help explain why the Vidua radiation consists of only 19 species rather than many more or fewer.

The evolution of snakes (Squamata: Serpentes) represents a major transition in squamate reptiles and involves extensive modifications in the body plan. Functional morphology and phylogeny are integrated to discuss adaptive morphological traits in the origin of snakes and in the evolution of the venom-injecting apparatus among lizards, which is convergent with that in snakes. The focus of these analyses is to determine how to best optimize morphological traits on the phylogeny and to use character distribution in terminal taxa to estimate ecological adaptation in ancestral nodes. To study the locomotion transition from lizards to snakes, 45 virtual models of the squamate bony labyrinth in the inner ear were reconstructed. The results show morphological diversifications of the vestibular region among burrowers, generalists and marine swimmers. The vestibule is enlarged in fossorial species, and reduced in marine snakes and the marine lizard Platecarpus coryphaeus. To quantify the morphological differences and provide tractable methods to reconstruct locomotion in ancestral snakes, I performed three-dimensional geometric morphometric analysis of the 45 samples, using six landmarks and 22 semilandmarks. ANOVA tests on the Procrustes coordinates supported differences among fossorial, generalist, and aquatic locomotion categories. Phylogenetic signal was insignificant in the Procrustes coordinates. Using a phylogeny with the 44 extant samples as terminal taxa, I reconstructed shape coordinates of all internal nodes. Reconstructed shape of the vestibular region of key ancestral nodes in snakes preferred a terrestrial origin for crown-group snakes. Morphological proxies used in this study can be applied to stem snakes to estimate locomotion. Methodologically, this study provides a novel approach to resolve the question whether snakes become limbless on land or in the oceans. Evolution of the venom-injection apparatus in lizards is discussed, based on new material of Estesia mongoliensis. A total-evidence phylogenetic analysis of anguimorph lizards is performed with 86 anguimorph taxa coded to 435 morphological characters and four genes. The matrix includes eight new morphological characters. The total-evidence phylogeny suggests that Estesia Mongoliensis is a basal monstersaur whose crown groups are Heloderma, the only living venomous lizards. Presence of tooth flanges with venom grooves is recognized as a new monstersaurian synapomorphy in this study. Estesia mongoliensis has venom grooves comparable to extant Heloderma, but has a deeper root-to-tip groove in the caudal tooth carina, revealing morphological variations of lizard venom delivery apparatus that are not recorded in extant species.

O gênero Astyanax é um dos mais especiosos da ordem Characiformes. Suas mais de 100 espécies distribuemse por praticamente toda a região Neotropical e habitam os mais diversos ambientes, como regiões montanhosas, trechos lóticos e leitos de rios, porções lênticas ou lagunares e nascentes. Durante cerca de trinta anos estes peixes têm sido alvo de estudos cromossômicos, que os caracterizaram como um grupo com grande diversidade citogenética. Recentemente, o advento de técnicas de citogenética molecular e de estudos empregando marcadores de DNA tem produzido novos dados sobre a biologia evolutiva do grupo, e possibilitado a revisitação de antigos problemas do gênero, como sua difícil classificação taxonômica. No presente trabalho buscouse a caracterização citogenética e a análise de segmentos do mtDNA (seqüências parciais das regiões dos genes ND2 e ATPase6/8) de diferentes espécies e populações de Astyanax, com a finalidade de contribuir para o reconhecimento de padrões e processos evolutivos no gênero. Foram analisados exemplares provenientes das bacias hidrográficas dos rios São Francisco, Tietê, Paranapanema, MogiGuaçu, Iguaçu, Paraíba do Sul, Ribeira de Iguape e Guapimirim. Os resultados forneceram panoramas filogeográficos e estabeleceram relações evolutivas entre as espécies analisadas, utilizando dados associados de duas classes diferentes de marcadores genéticos. Através da aplicação de técnicas citogenéticas clássicas e moleculares são apresentados dados cariotípicos de A. altiparanae, A. aff. bimaculatus, A. bockmanni, A. aff. fasciatus, A. hastatus, A. mexicanus e A. ribeirae. Nos estudos filogenéticos foram utilizadas, adicionalmente às seqüências das espécies acima citadas, dados provenientes de Astyanax sp.B, A. giton, A. intermedius, A. lacustris, A. aff. scabripinnis, Bryconamericus iheringii, Mimagoniatis microlepis e Roeboides occidentalis. Foram ainda incluídas nas análises seqüências do mtDNA de haplótipos diferentes de A. mexicanus e A. bimaculatus retirados da literatura. Para as diferentes populações amostradas dos grupos A. altiparanae, A. aff. bimaculatus e A. aff. fasciatus, foram efetuadas análises filogeográficas associadas a dados cromossômicos. As análises cromossômicas e moleculares do sistema de drenagem do Leste e de bacias circunvizinhas apresentadas no presente trabalho forneceram dados adicionais para o entendimento da biologia evolutiva do gênero Astyanax. iv Outra contribuição do presente estudo foi a inferência das relações evolutivas de algumas das mais bem estudadas espécies do gênero Astyanax, que a despeito da sua importância ecológica e de constituírem um modelo para estudos cromossômicos e evolutivos, ainda não apresentam estudos filogenéticos amplos. Ainda, a associação de dados cromossômicos e moleculares forneceu um panorama interessante sobre as relações evolutivas em algumas espécies do gênero, bem como sobre os processos e padrões evolutivos presentes nos Astyanax. / Astyanax is one of the species-richest genera within the order Characiformes. More than 100 representatives are widespread throughout nearly all the Neotropical region, inhabiting an array of environments, such as mountain areas, lotic and lentic river portions, lake systems and headwaters. This fish group has been a target of chromosomal studies for over 30 years, showing a remarkable cytogenetic diversity. Recently, the advances in molecular cytogenetics and DNA marker studies have provided new data about the evolutionary biology in this group, allowing revisiting former issues in species of this genus, such as their problematic taxonomical classification. In the present work, we attempted to obtain a cytogenetic characterization and analyze mtDNA segments (partial sequences of the genes ND2 and ATPase6/8) of different species and populations of Astyanax, in order to identify the evolutionary patterns and processes within the genus. Specimens from São Francisco, Tietê, Paranapanema, Mogi-Guaçu, Iguaçu, Paraíba do Sul, Ribeira de Iguape and Guapimirim hydrographic basins were collected. The results revealed phylogeographic scenarios and enabled us to establish the evolutionary relationships among the analyzed species, by associating data from two distinct classes of genetic markers. Through classic and molecular cytogenetic techniques, we present karyotypic data in A. altiparanae, A. aff. bimaculatus, A. bockmanni, A. aff. fasciatus, A. hastatus, A. mexicanus and A. ribeirae. For the phylogenetic studies, we also used, besides those sequences of the species abovementioned, data from the species Astyanax sp.B, A. giton, A. intermedius, A. lacustris, A. aff. scabripinnis, Bryconamericus iheringii, Mimagoniatis microlepis e Roeboides occidentalis. In the mtDNA analyses, sequences from the mtDNA of A. aeneus, and different haplotypes of A. mexicanus and A. bimaculatus available in the literature were included as well. Phylogeographic analyses coupled with chromosomal data were performed for the distinct populational samples in the groups A. altiparanae, A. aff. bimaculatus and A. aff. fasciatus. Both molecular and chromosomal analyses along Eastern drainage systems and nearby basins carried out in the present work provided additional information to the understanding of the evolutionary biology in the genus Astyanax. Another contribution of the present work refers to the inference on the evolutionary vi relationships in some of the most intensively studied species in the genus Astyanax, that, despite of their ecological importance and their role as a model for chromosomal and evolutionary studies, still lack more complete phylogenetic approaches. Furthermore, the association between chromosomal and molecular data revealed an interesting panorama about the evolutionary relationships in some species of this genus, as well as the evolutionary processes and patterns identified within Astyanax.

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.