Thesis (Ph. D.)--University of Chicago, Committee on Evolutionary Biology, March 2001. / Includes bibliographical references. Also available on the Internet.

Recent scholarship has suggested that transformist ideas had a wider currency in Edinburgh in the first half of nineteenth century than had previously been acknowledged. The first objective of this study is to delve deeper into the reception of transformist theories there in the years 1790 to 1844. The main figures whose theories on the transmutation of species were discussed in contemporary sources are Carl Linnaeus (1707–1778), George-Louis Leclerc, Conte de Buffon (1707–1788), Erasmus Darwin (1731–1802), Jean-Baptiste Lamarck (1744–1829) and Étienne Geoffroy Saint-Hilaire (1772–1844); this study therefore concentrates on the reception of their work. The principle Edinburgh contexts in which the reception of their theories is explored are the University of Edinburgh, the extra-mural medical schools and the city’s various learned societies and scientific journals, although the opinions of all those in Edinburgh known to have discussed transformism in this period are considered. The sources examined reveal that transformist theories were largely received with interest. Discussion of them was generally confined to scientific, or naturalistic, arguments, except in the cases of some Evangelical natural historians, who rejected them outright on theological grounds. This thesis also explores how some thinkers in Edinburgh went beyond discussing received ideas about transformism and developed their own theories, synthesising the work of earlier thinkers. The most important of these were Robert Edmond Grant (1793– 1874), Robert Jameson (1774–1854), Robert Knox (1791–1862) and Henry H. Cheek (1807–33). This thesis also explores the genesis of the later transformist theory of Robert Chambers (1802–71), the anonymous author of Vestiges of the Natural History of Creation (1844), to establish to what extent he may have been influenced by the earlier transformists of the 1820s and 30s. Events in Edinburgh in the 1820s also had a wider resonance for the history of evolutionary ideas in Britain, as Charles Darwin (1809–1882) was a student at the University of Edinburgh between 1825 and 1827. It has long been suspected that his experiences in Edinburgh had a larger part to play in the development of his theory of evolution than he later cared to admit. Careful to avoid associating himself with the more speculative theories of earlier transformist thinkers, Darwin made little mention of them in his published writings. We already know, however, that Darwin had a close relationship with Grant during his time in Edinburgh and must have been familiar with his transformist ideas. This thesis aims to show to what extent the intellectual environment that Darwin found himself in was suffused with the idea of the transmutation of species. In broad outline, it can be concluded that transformism was much less controversial in Edinburgh in the first half of the nineteenth century than might be supposed from the prevailing historiography and had a significant number of sympathisers and adherents.

Explaining why cooperation exists despite the persistent advantage of cheats has been the focus of much theoretical and empirical attention in biology. Using the bacterium Pseudomonas aeruginosa as a model system for the evolution of cooperation, I investigate two distinct phenomena which may develop our understanding of how cooperation is maintained; 1) tag-based cooperation and diversity; and 2) environmental heterogeneity. The first investigates how diversity in cooperative systems may be a response to the selective pressure exerted by cheating, and how cheats may then regulate communities to maintain diversity: I demonstrate that in competition, tag-based cooperation is able to evade parasitism, provided the public-good is only accessible to producer strains, i.e., the cheat possesses the “wrong” tag. I also demonstrate that cheats can have a marked influence on diversity: In a community of two producer strains with different tags, if a third cheater strain is introduced, it will drive both its own producer and itself extinct. I do not find that the presence of cheats maintains diversity in either structured or unstructured environments, and discuss the possible causes of this. In the second topic of this thesis, I investigate the effect of environmental heterogeneity in resource availability, through space and time, on the evolution of cooperation. Environmental heterogeneity is a ubiquitous feature of natural landscapes, yet its effect on the evolution of cooperation has not been extensively studied. I demonstrate that resource availability heterogeneity, in both time and space, acts to maintain cooperation at higher levels than homogeneous environments of the same total resource value. This effect is due to the covariance between productivity and the cost of cooperation: high resource availability periods and spaces are highly productive, and also incur a relatively lower cost of cooperation.

A study of the marine dinoflagellate Glenodinium foliaceum is presented which attempts to provide information on the process of host-endosymbiont integration in a unicellular system that may be of relevance to current hypotheses on chloroplast evolution. An experimental ultrastructural review of G. foliaceum supports the proposal that the chloroplasts and supernumerary nucleus belong to a morphologically reduced, endosymbiotic chromophyte. DAPI staining shows that the endosymbiont nucleus is fragmented in some cells and appears to be randomly divided by the host's cleavage furrow at cytokinesis. A quantification of the intensity of mithramycin fluorescence from single cells by flow cytometry suggests that both nuclei synthesize their ENA in synchrony. Protocols are outlined for isolating the chloroplasts and dinoflagellate nucleus from G. foliaceum and a method is given for fractionating whole cell lysates to prepare chloroplast, host nuclear, and endosymbiont nuclear DNAs. It is estimated that the symbiont and dinoflagellate nuclei contain about 34 pg and 40 pg of ENA respectively. There is no evidence of amplified genesized ENA molecules in the symbiont nucleus. The results of preliminary re-association experiments show only the presence of highly repeated ENA and sequences of intermediate repetitiveness in total cell ENA, which together comprise about half the genome. The chloroplast DNA is shown to a molecular weight of approximately 103 kb by restriction endonuclease analysis but an attempt to localize the rbc S gene in either the chloroplast or nuclear DNAs using a cloned pea ENA probe proved unsuccessful. Two other anomalously pigmented dinoflagellates, Gyrodinium aureolum and Gymnodinium galatheanum, are demonstrated to lack endosymbionts by electron and fluorescence microscopy, but the atypical ultrastructural or cytological characters of their chloroplasts are considered to indicate an endosymbiotic origin. The possibility that Glenodinium foliaceum could evolve into a similar uninucleate species is discussed in relation to the conservation of genetic information for nuclear-encoded, chloro-plast proteins.

<p> This study examines how the different behavioral, environmental and physiological factors might be influencing the essential physiological trait of erythrocyte mean cell diameters (MCD). At present no other study has explored the effects of these factors. Erythrocyte MCD for 153 species were collected from recent literary sources and compared to erythrocyte MCDs collected by Gulliver (1875), genome sizes and spleen sizes were also collected from a variety of literary sources. This data was analyzed using R with phylogenetic generalized least square analyses against several different behavioral, environmental and physiological factors. From these analyses, I found that as mammal mass and length increase the erythrocyte MCD also increases and as mammals move into higher elevations and warmer climates erythrocyte MCD decreases. All other behavioral, environmental, and physiological factors did not have an influence on erythrocyte MCD. These data did not support hypotheses previously offered by the other studies done on erythrocytes. Further research needs to be conducted on this topic because other factors that influence erythrocyte MCD may still exist that were not examined in this study.</p><p>

We investigate stellar models for main-sequence and horizontal-branch stars constructed using the Carson opacities and make comparisons with models based on the Cox-Stewart opacities. A Henyey code based on the prescription of Kippenhahn et al (1967) is used for most of the calculations of stellar structure and evolution. In the equation of state we treat ionisation equilibrium and non-relativistic degeneracy for separate temperature-density regimes. The opacity is obtained by 4-dimensional linear interpolation in the Carson opacity tables. Nuclear energy generation rates are taken from Fowler et al (1975) and neutrino losses from the approximation due to Beaudet et al (1967). Electron-screening factors are from Reeves (1965). The standard local mixing-length theory of Bohm-Vitense (1958) is used to treat non-adiabatic convection, although some models are calculated with modifications due to Deupree et al (1979, 1980). We neglect semi convection. The Carson opacities have only a small effect on the position of ZAHB models, but this may be metallicity dependent. The drop in the hydrogen- shell luminosity due to the helium-core expansion during HB evolution is greater than that obtained with the Cox-Stewart opacities. Allowing for the inclusion of semi convection and convective overshooting, we find that adoption of the Carson opacities leads to a reduction of approximately 25% in the HB lifetimes. For a given range of values for the masses and envelope helium abundances of stars on a synthetic HB, the width in effective temperature is increased, and in luminosity the width is decreased. The dependence of the core luminosity on the falling core helium abundance is increased by approximately 16%. Studies of main-sequence stars lead to agreement with Stothers' (1974a, 1974b, 1976) results for homogeneous models constructed with the Carson opacities. The evolution of main-sequence stars of intermediate mass is unaffected by the change in the opacity. Two evolutionary sequences (for 1 Mo stars) suggest that the main-sequence lifetimes of low mass stars may be reduced by as much as 30%. Combined with a shift in the ZAMS position this will move isochrones for low mass stars towards lower effective temperatures and densities. If studies of red-giant evolution indicate little change in the luminosity level of the horizontal branch, globular cluster ages determined from the position of the main-sequence turnoff point may be substantially reduced (possibly by as much as 50%). This could save a conflict between observed values for globular cluster ages and a value for the Hubble constant of 90. Studies of the apsidal motion constant, k2, for evolved MS stars shows that the discrepancy between observed values of k1 for eclipsing binary systems and theoretical values obtained from homogeneous stellar models may be resolved by considering the evolution of the binary components. CO Lac is an exception to this result, but analysis of the observations suggests that a redetermination of the orbital semi-amplitudes may resolve the conflict.

Submitted by Johnsson Rodrigo (r.johnsson@gmail.com) on 2013-08-29T04:57:23Z No. of bitstreams: 1 CAMILA.pdf: 4295274 bytes, checksum: 3b6ba55df2f36928304a61d910553c85 (MD5) / Approved for entry into archive by Alda Lima da Silva(sivalda@ufba.br) on 2013-09-03T18:19:01Z (GMT) No. of bitstreams: 1 CAMILA.pdf: 4295274 bytes, checksum: 3b6ba55df2f36928304a61d910553c85 (MD5) / Made available in DSpace on 2013-09-03T18:19:01Z (GMT). No. of bitstreams: 1 CAMILA.pdf: 4295274 bytes, checksum: 3b6ba55df2f36928304a61d910553c85 (MD5) / FAPESB / Os cassidulóides têm proporcionado grandes desafios aos taxonomistas que tentam classificá-los, provavelmente por se tratar de um grupo artificial. Estudos filogenéticos da ‘ordem’ resultaram em topologias com baixa resolução devido à falta de informação acerca de alguns táxons e sinais de exaustão de caracteres ao longo da evolução de suas famílias. Dentre elas, a família Cassiulidae é composta por cinco a seis gêneros e pouco se sabe sobre o relacionamento entre seus gêneros, visto que análises ao nível de ordem incluíram poucas espécies desta família. Neste trabalho foram realizadas análises cladísticas para propor uma hipótese de relações filogenéticas entre os gêneros da família Cassidulidae. A análise principal incluiu 16 cassidulídeos e 33 caracteres morfológicos. As análises seguintes tiveram como objetivo verificar a influência dos dados faltantes e da inclusão de táxons fósseis na topologia encontrada. Cada uma das três análises resultou em uma única árvore mais parcimoniosa, em geral, bem resolvida. As relações de parentesco foram: (Eurhodia relicta (demais Eurhodia) + ((Australanthus + Cassidulus malayanus) + (Paralampas (Cassidulus + Rhyncholampas)))). Tanto a quantidade de dados faltantes quanto a exclusão de espécies fósseis não afetaram negativamente a resolução da árvore. Os resultados obtidos indicaram a necessidade de estudar a taxonomia, principalmente, dos gêneros Eurhodia, Cassidulus e Rhyncholampas e a exclusão de Cassidulus malayanus e Eurhodia relicta dos seus respectivos gêneros. Possíveis ocorrências de processos heterocrônicos foram detectadas, a exemplo da evolução do gênero Rhyncholampas por peramorfose e do gênero Paralampas por pedomorfose. Os cassidulídeos provavelmente se originaram no Cretáceo Tardio e novidades não foram adicionadas à sua evolução. Como resultado, processos heterocrônicos devem ter desempenhado um papel importante na diversificação da família. Evidências de processos heterocrônicos obtidas a partir da análise atual foram discutidas. Finalmente, um cenário paleobiogeográfico dos cassidulídeos foi proposto, com origem Tetiana e dispersão inicial, seguida por expansão e vicariância. / Salvador

Intracellular symbionts are widespread among arthropods, particularly within insects. Obligate symbiotic associations are known to have originated multiple times between the arthropods feeding on nutrient-poor diets and bacteria from various groups. However, exact phylogenetic positions and relationships among these symbiotic lineages are mostly unclear or vague. This thesis consists of an exemplary case study on the most symbiont-rich bacterial group, Enterobacteriaceae, already published in BMC Biology. It uses advanced phylogenetic tools and extended taxonomic sample to establish phylogenetic relationships among individual symbiotic lineages and their phylogenetic affinity to freeliving relatives. To provide it with broader background, the publication is accompanied by a review on general evolutionary forces influencing origin and maintenance of intracellular symbiosis in arthropods. Apart from overviewing the current known diversity of the symbiotic bacteria, it also points out specific drawbacks in inferring symbionts phylogeny and consequences that can phylogeny have on our understanding of intracellular symbiosis.

Adaptive evolution is the process by which natural selection, acting on variation within a population, promotes the survival of individuals that are more successful at reproducing and contributing to future generations. Evolutionary processes in microbes occur at the intersection of population genetics, natural selection, and underlying mechanistic constraints, to give rise to the repertoire of adaptation observed in nature. Understanding microbial adaptive evolution is of critical importance for human health for example, through the emergence of pathogenicity and antibiotic resistance. Moreover, the stability and function of natural and artificial ecosystems is contingent on the evolving interactions between microbes, and between microbes and the environment. We present a modelling framework, based on the theory of adaptive dynamics, to investigate how cellular resource allocation trade-offs affect the adaptation process. We used resource-consumer theory, which explicitly models the interactions between cells and their environment, together with matrix models of structured populations, to implement phenotype-determined cellular strategies of resource allocation between mutually exclusive processes. We then analyse the outcome of competitions between different phenotypes across environmental and competitive conditions. We applied our methods to the evolution of strategies (phenotypes) for resource allocation between two competing cellular process in microbial populations growing in chemostat-like environments. We calculated the adaptively stable strategies for several models and showed how state-structured population models can be mapped to simpler chemostat models on invariant manifolds. We then extended our analysis to the case where a limiting nutrient may be utilized using two alternative metabolic pathways. We described how the total population fitness of a metabolic strategy can be constructed from the individual decisions of its constituent members. We developed numerical methods to simulate and analyse general models of adaptive dynamics using principles from graph theory and discrete Markov processes. The methods were used to explore the evolution of nutrient use strategies for microbial populations growing on two and three substitutable nutrients. We highlight the importance of the ancestral phenotype in channelling the adaptation process, which, together with the choice of the mutational kernel, influences the adaptively stable strategies and modes of co-existence. In a related finding, we show how some phenotypes are adaptively stable only in the presence of a competitor lineage that modifies the environment in a manner that permits another phenotype to invade. Our methods also reveal instances where historical contingency and chance have an important effect on determining the stable nutrient use strategies. Finally, we demonstrate the existence of adaptively stable periodic solutions whereby, under some conditions, phenotype successions are cyclical. Our work builds on the foundation of adaptive dynamics theory to provide a general framework for analysing models of microbial adaptation. We focused on understanding the implications of underlying constraints and cellular resource allocation trade-offs in the context of adaptive evolution.

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