The phenomenon called soil aggregate coalescence occurs at contact-points between aggregates and causes soil strength to increase to values that can inhibit plant root exploration and thus potential yield. During natural wetting and drying, soil aggregates appear to ‘weld’ together with little or no increase in dry bulk density. The precise reasons for this phenomenon are not understood, but it has been found to occur even in soils comprised entirely of water stable aggregates. Soil aggregate coalescence has not been widely observed and reported in soil science and yet may pose a significant risk for crops preventing them from achieving their genetic and environmental yield potentials. This project used soil penetrometer resistance and an indirect tensile-strength test to measure the early stages of aggregate coalescence and to evaluate their effects on the early growth of tomato plants. The early stages of aggregate coalescence were thought to be affected by a number of factors including: the matric suction of water during application and subsequent drainage, the overburden pressure on moist soil in the root zone, the initial size of soil aggregates prior to wetting, and the degree of sodicity of the soil aggregates. Seven mainexperiments were conducted to evaluate these factors. The matric suction during wetting of a seedbed affects the degree of aggregate slaking that occurs, and the strength of the wetted aggregates. The matric suction during draining affects the magnitude of ‘effective stresses’ that operate to retain soil structural integrity as the soil drains and dries out. An experiment was conducted to evaluate the influence of matric suction (within a range of suctions experienced in the field) on aggregate coalescence using soils of two different textures. Sieved aggregates (0.5 to 2 mm diameter) from a coarse-textured and two fine-textured (swelling) soils were packed into cylindrical rings (4.77 cm i.d., 5 cm high) and subjected to different suctions on wetting (near-saturation, and 1 kPa), and on draining (10 kPa on sintered-glass funnels, and 100 kPa on ceramic pressure plates). After one-week of drainage, penetrometer resistance was measured as a function of depth to approximately 45 mm (penetrometer had a recessedshaft, cone diameter = 2 mm, advanced at a rate of 0.3 mm/min). Tensile strength of other core-samples was measured after air-drying using an indirect “Brazilian” crushing test. For the coarse-textured soil, penetrometer resistance was significantly greater for samples wet to near-saturation, despite there being no significant increase in dry bulk density; this was not the case for the finer-textured soils, and it was difficult to distinguish the effects of variable bulk density upon drying from those of the imposed wetting treatments. In both coarse- and fine-textured soils, the tensile strength was significantly greater for samples wet to near-saturation. Thus wetting- and draining-suctions were both found to influence the degree of soil aggregate coalescence as measured by penetrometer resistance and tensile strength. Aggregate coalescence in irrigated crops is known to develop as the growing season progresses. It was therefore thought to be linked to the repeated occurrence of matric suctions that enhance the phenomenon during cycles of wetting and draining. An experiment was conducted to determine the extent of aggregate coalescence in a coarsetextured and two fine-textured (swelling clay) soils during 8 successive cycles of wetting and draining. Sieved aggregates (0.5 to 2 mm diameter) from each soil were packed into cylindrical rings (4.77 cm i.d., 5 cm high) and wetted to near saturation for 24 h. They were then drained on ceramic pressure plates to a suction of 100 kPa for one week, after which penetrometer resistance and tensile strength were measured as described above. The degree of expression of aggregate coalescence depended on soil type. For the coarse-textured soil, repeated wetting and draining significantly increased bulk density, penetrometer resistance and tensile strength. For the fine-textured soil, penetrometer resistance and bulk density did not vary significantly with repeated wetting and draining; on the contrary, there was evidence in these swelling clay soils to suggest bulk density and penetrometer resistance decreased. However, there was a progressive increase in tensile strength as cycles of wetting and draining progressed. The expansive nature of the fine-textured soil appears to have masked the development of aggregate coalescence as measured by penetrometer resistance, but its expression was very clear in measurements of tensile strength despite the reduction in bulk density with successive wetting and draining. Field observations have indicated that aggregate coalescence is first expressed at the bottom of the seedbed and that it develops progressively upward to the soil surface during the growing season. This suggests that overburden pressures may enhance the onset of the phenomenon by increasing the degree of inter-aggregate contact. Soils containing large quantities of particulate organic matter were known to resist the onset of aggregate coalescence to some extent. An experiment was conducted to evaluate the effects of soil organic matter and overburden pressures, by placing brass cylinders of various weights (equivalent to static load pressures of 0, 0.49, 1.47 and 2.47 kPa) on the top of dry soil aggregates (0.5 – 2 mm diameter) having widely different soil organic carbon contents placed in steel rings 5 cm high and 5 cm i.d. With the weights in place, the aggregates were wetted to near-saturation for 24 h and then drained on ceramic pressure plates to a suction of 100 kPa for one week. Bulk density, penetrometer resistance and tensile strength were measured when the samples were removed from the pressure plates and they all increased significantly with increasing overburden pressure in the soil with low organic matter content, but not in the soil with high organic matter content. The amount of tillage used to prepare seedbeds influences the size distribution of soil aggregates produced – that is, more tillage produces finer seedbeds. The size distribution of soil aggregates affects the number of inter-aggregate contact points and this was thought to influence the degree of aggregate coalescence that develops in a seedbed. Previous work has shown that soil organic matter reduces aggregate coalescence and so an experiment was conducted to evaluate the effects of aggregate size and organic matter on the phenomenon. For soils with high and low organic matter contents, aggregate size fractions of < 0.5, 0.5 – 2, 2 – 4, and < 4 mm were packed into soil cores (as above) and wetted to near-saturation then drained to 100 kPa suction as described above. Penetrometer resistance and tensile strength were measured and found to increase directly with the amount of fine material present in the soil cores – being greater in the < 0.5 mm and < 4 mm fractions, and being less in the 0.5 – 2 mm and 2 – 4 mm fractions. In all cases, penetrometer resistance and tensile strength were lower in the samples containing more organic matter. The rate at which soil aggregates are wetted in a seedbed affects the degree of slaking and densification that occurs, and the extent to which aggregates are wetted influences the overall strength of a seedbed. Both wetting rate and the extent of wetting were believed to influence the onset of aggregate coalescence and were thought to be affected by soil organic matter and irrigation technique. An experiment was therefore designed to separate these effects so that improvements to management could be evaluated for their greatest efficacy – that is, to determine whether management should focus on improving irrigation technique or increasing soil organic matter content, or both. The rate of wetting was controlled by spraying (or not spraying) soil aggregates (0.5 – 2 mm diameter) with polyvinyl alcohol (PVA). Samples of coarse- and fine-textured soils were packed into steel rings (as above) and subjected to different application rates of water (1, 10 and 100 mm/h) using a dripper system controlled by a peristaltic pump. Samples were brought to either a near-saturated state or to a suction of 10 kPa for 24 h, and then drained on a pressure plate at a suction of 100 kPa for one week. Measurements of penetrometer resistance and tensile strength were then made as described above. As expected, penetrometer resistance was lower in samples treated with PVA before wetting (slower wetting rates) and in samples held at a greater suction (10 kPa) after initial wetting (greater inter-aggregate strength). The effects were more pronounced in the coarse-textured soil. In both coarse- and fine-textured soils, tensile strengths increased with increasing wetting rate (greatest for 100 mm/h) and extent of wetting (greater when held at near-saturated conditions). The rate of wetting was found to be somewhat more important for promoting aggregate coalescence than the extent of wetting. Because aggregate coalescence often occurs with little or no increase in bulk density, an explanation for the increase in penetrometer resistance and tensile strength is unlikely to be explained by a large increase in the number of inter-aggregate contacts. An increase in the strength of existing points of inter-aggregate contact was therefore considered in this work. For inter-aggregate bond strengths to increase, it was hypothesized that small increases in the amount of mechanically (or spontaneously) dispersed clay particles, and subsequent deposition at inter-aggregate contact points could increase aggregate coalescence as measured by penetrometer resistance and tensile strength. An experiment was devised to manipulate the amount of spontaneously dispersed clay in coarse- and fine-textured soils of high and low organic matter content. The degree of sodicity of each soil was manipulated by varying the exchangeable sodium percentage (ESP) of soil aggregates (0.5 – 2mm) above and below a nominal threshold value of 6. Dry aggregates were then packed into steel rings (as above) and subjected to wetting near saturation, then draining to a suction of 100 kPa for one week as described above. Measurements were then taken of penetrometer resistance and tensile strength, both of which were affected by ESP in different ways. In the coarse-textured soil, sodicity enhanced aggregate slaking and dispersion, which increased bulk density. While penetrometer resistance also increased, its effect on aggregate coalescence could not be separated from a simple effect of increased bulk density. Similarly, the effect of sodicity on aggregate coalescence in the fine-textured soil was confounded by the higher water contents produced by greater swelling, which produced lower-than-expected penetrometer resistance. Measurements of tensile strength were conducted on air-dry samples, and so the confounding effects of bulk density and water content were eliminated and it was found that tensile strength increased with sodicity in both coarse- and fine-textured soils. The presence of dispersed clay was therefore implicated in the development of aggregate coalescence in this work. Finally, a preliminary evaluation of how the early stages of aggregate coalescence might affect plant growth was attempted using tomatoes (Gross lisse) as a test plant. Seeds were planted in aggregates (0.5 – 4 mm) of a coarse- or fine-textured soil packed in steel rings. These were wetted at a rate of 1 mm/h to either near-saturation (for maximum coalescence) or to a suction of 10 kPa (for minimum coalescence) and held under these conditions for 24 h. All samples were then transferred to a ceramic pressure plate for drainage to 100 kPa suction for one week. Samples were then placed in a growth-cabinet held at 20C with controlled exposure to 14 h light/day. Germination of the seeds, plant height, and number and length of roots were observed. Germination of the seeds held at near-saturation in both coarse- and fine-textured soils was delayed by 24 h compared with seeds held at 10 kPa suction. Neither the number nor the length of tomato roots differed significantly between the different treatments and soils. In the coarse-textured soil, however, the total root length over a period of 14 days was somewhat greater in the uncoalesced samples than in the coalesced samples, but this difference was not statistically significant. These results suggest that aside from delaying germination, aggregate coalescence may not have a large effect on early growth of tomato plants. However, this is not to say that detrimental effects may not be manifest at later stages of plant growth, and this certainly needs to be evaluated, particularly because aggregate coalescence increase with repeated cycles of wetting and draining. In conclusion, the primary findings of the work undertaken in this thesis were: • Rapid wetting of soil aggregates to near-saturation enhanced the onset of soil aggregate coalescence as measured by (in some cases) penetrometer resistance at a soil water suction of 100 kPa, and (in most cases) tensile strength of soil cores in the air-dry state. The rate of wetting appeared to be more important in bringing on aggregate coalescence than how wet the soil eventually became during wetting. This means reducing the rate at which irrigation water is applied to soils may reduce the onset of aggregate coalescence more effectively than controlling the total amount of water applied – though both are important. The literature reports that aggregate coalescence occurs in the field over periods of up to several months, involving multiple wetting and draining cycles, but the work here demonstrated that this can occur over much shorter time periods depending on conditions imposed. • Aggregate coalescence occurred in coarse-textured soils regardless of whether the bulk density increased during wetting and draining. In finer-textured soils, the response to wetting conditions varied and was complicated by changes in bulk density and water content due to swelling. • Small overburden pressures enhanced the onset of aggregate coalescence, but these effects were diminished in the presence of high soil organic matter contents. • Finer aggregate size distributions (which are often produced in the field by excessive tillage during seedbed preparation) invariably led to greater aggregate coalescence than coarser aggregate size distributions. The effects of aggregate size were mitigated to some extent by higher contents of soil organic matter. • Sodicity enhanced aggregate coalescence as measured by tensile strength, but when penetrometer resistance was measured in the moist state, the effects were masked to some extent by higher water contents generated by swelling and dispersion. This work suggests that tensile strength (in the air dry state) may be a more effective measure of aggregate coalescence than penetrometer resistance. • Early plant response to aggregate coalescence was not large, but the response may become magnified during later stages of growth. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1297583 / Thesis (Ph.D.) -- School of Earth and Environmental Sciences, 2007

Made available in DSpace on 2016-06-02T20:21:24Z (GMT). No. of bitstreams: 1 3224.pdf: 2177320 bytes, checksum: 89cae5d787c7083f95c6ec6ff9f87e2a (MD5) Previous issue date: 2010-08-31 / Financiadora de Estudos e Projetos / The genus Anastrepha which is endemic to the Neotropical region has big economic importance to cause great losses in fruit production. We studied three species of the cryptic group fraterculus: Anastrepha fraterculus, A. obliqua and A. sororcula. Although no single marker is able to distinguish these species, some morphological and behavioral markers are able to distinguish them. There is evidence that these markers do not match the patterns of genetic variation and divergence of these flies. We investigated the role of genes related or not to reproduction in the speciation of these flies. We used a cDNA library of the reproductive tissues of females of A. fraterculus, to isolate expressed genes from those tissues. From a framework of divergence population genetics, we estimated relevant demographic parameters that reported the genetic architecture of speciation in this group. To study the separation of these species, we used gene trees as a framework to be compared and to infer eventual species trees. We amplified 12 genes isolated from the cDNA library. The analysis of population divergence and levels of polymorphism were made in DNAsp and showed high levels of polymorphism for the vast majority of loci. Neutrality tests reveal that only Fs Fu was significantly negative for the combination of species here considered. These results indicate a possible evidence of population expansion on this group of species. These data were corroborated by the values of ancestral and current theta estimated from the analysis undertaken on the software IMa2 program. These analysis also showed relevant levels of migration in some contrasts, but particularly among species which are more distant in the tree from the other two. However, the same analyses performed amongst species pairs fail to reveal high levels of migration rate among species, though t e theta values were close to those estimated in the analysis with all three species together. We also tested for the presence of selection at different loci, using the program PAML and obtained evidence of positive selection for three genes CG7203, CG8064 and MLC, whereas the gene CG7009 showed evolution by a mild purifying selection. The haplotype networks showed the grouping of haplotypes of the species for five of the 12 genes CG7009, CG8064, Elp, TCTP and Cyclophylin. CG7009 revealed possible species specific markers for A. sororcula. We carried out the deep coalescence analysis in the program MESQUITE, comparing gene trees simulated with real trees for each gene locus, placing the species as an outgroup for each tree model and obtained significant results, which would be compatible to simulated scenarios only for the genes V Cyclophylin and TCTP. The tree obtained by minimizing the deep coalescence estimated showed that A. sororcula is farther from the other two species of the genus Anastrepha. It is necessary, however, a larger investigation of different genes, particularly genes with higher evolutionary rates and an expansion of the samples of these species to consider geographical distribution and assist in studies of speciation of this group. / O gênero Anastrepha, endêmico da região Neotropical, tem grande importância econômica por causar grandes prejuízos na produção de frutos. Neste trabalho, estudamos três espécies do grupo críptico fraterculus: Anastrepha fraterculus, A. obliqua e A. sororcula. Apesar de não haver um único marcador capaz de diferenciar essas espécies, alguns marcadores morfológicos e comportamentais, são capazes de distinguí-las. Há evidências de que esses marcadores não correspondam aos padrões de variação e divergência genética dessas moscas. Investigamos o papel de diversos genes nucleares na especiação dessas moscas. Usamos uma biblioteca de cDNAs do aparelho reprodutivo de fêmeas de A. fraterculus, para a amplificação de genes expressos desse tecido. A partir de um quadro de divergência genética populacional, estimamos parâmetros demográficos relevantes que informaram a arquitetura genética da especiação neste grupo. Para estudar a separação dessas espécies, utilizamos árvores de genes como base e as comparamos com árvores de espécies. Foram amplificados 12 genes expressos na biblioteca de cDNAs. As análises de divergência populacional e nível de polimorfismo foram feitas no DNAsp e mostraram valores bem altos do nível de polimorfismo para a grande maioria dos loci e os testes de neutralidade foram significativos apenas para Fs de Fu. Esses resultados indicam uma possível expansão populacional das espécies estudadas. Estes dados foram corroborados pelos valores de q das análises realizadas pelo programa IMa2, que também mostrou uma taxa de migração alta entre a espécie mais distante na árvore para uma das outras duas. No entanto, as mesmas análises feitas com as espécies par a par não revelaram uma taxa de migração significativa entre as espécies, os valores de t e theta foram próximos dos obtidos para as análises com as espécies juntas. Fizemos também testes para detectar a presença de seleção nos diferentes loci, usando o programa PAML e obtivemos indício de seleção positiva para três genes CG7203, MLC e CG8064; o gene CG7009, no entanto, mostrou evoluir por uma seleção purificadora branda, pois não rejeitamos somente o primeiro dos dois testes. As redes haplotípicas, feitas no TCS, mostraram o agrupamento dos haplótipos das espécies para cinco dos 12 genes CG7009, CG8064, Elp, TCTP e Cyclophylin. Para o CG7009 notamos possíveis marcadores específicos para A. sororcula. Realizamos, pelo programa MESQUITE, análises de coalescência profunda comparando árvores de genes simuladas com árvores de genes reais para cada locus, colocando uma das espécies como grupo externo em cada modelo de árvore e III obtivemos resultados significativos apenas para os genes Cyclophylin e TCTP. A árvore obtida pela minimização das coalescências profundas mostrou que A. sororcula se encontra mais distante das outras duas espécies do gênero Anastrepha. Faz-se necessária, no entanto, uma investigação maior de diferentes genes, particularmente genes com taxas evolutivas mais altas e uma expansão das amostras destas espécies para considerar sua distribuição geográfica e auxiliar nos estudos da especiação deste grupo.

La coalescence intervient dans de nombreuses situations physiques, naturelles ou industrielles, de la microphysique des nuages à la stabilité des émulsions ou l’assèchement des pétroles. Dans toutes ces situations, il est crucial de comprendre les mécanismes physiques en jeu, de manière pouvoir influencer la coalescence, la favoriser ou au contraire l’inhiber, selon les besoins. Dans cette thèse, nous étudions la coalescence dans l’air entre deux gouttes attachées et décomposons le processus global en quatre étapes : l’approche avec drainage du film d’air entre les gouttes, le perçage des interfaces, l’ouverture du pont résultant de ce perçage, les oscillations amorties conduisant à l’équilibre de la goutte résultante. Les théories décrivant les étapes 1, 2 et 4 font intervenir des modèles hydrodynamiques continus, se plaçant à une échelle macroscopique. Cependant, à l’articulation entre les deux premières étapes, intervient le perçage des interfaces, processus gouverné par des forces dont la portée correspond à une échelle de quelques dizaines de nanomètres. Une des difficultés les plus importantes dans l’étude de la coalescence est celle de l’intégration des processus ayant lieu à un niveau moléculaire, dans une théorie du continuum dont l’échelle caractéristique est bien supérieure. L’objectif est de faire le lien entre les différentes échelles : y a-t-il des interactions entre les processus se produisant à ces différentes échelles ? Pour répondre à cette question, nous développons trois axes de travail, engageant chacun une échelle caractéristique. L’un est l’étude, au niveau macroscopique du micromètre, de l’ouverture du pont liquide. Grâce à une caméra rapide, plusieurs régimes d’écoulement sont mis en évidence. Les modèles théoriques existants concernent essentiellement le régime visqueux, et aucun modèle complet ne décrit le régime purement inertiel. Nous explorons expérimentalement ce régime et décrivons la forme et la longueur du pont, à l’aide d’ondes capillaires. Nous mettons en évidence l’existence de deux lignes de très forte courbure, que nous appelons singularités, qui naissent sur le lieu de perçage des interfaces et se propagent presque sans déformation de part et d’autre. Ces singularités, conditionnées par la tension superficielle, moteur de la coalescence, façonnent la forme du pont liquide et donc l’écoulement dans ce dernier. Nous proposons un modèle simple d’écoulement inertiel, basé sur la forme du pont liée à ces singularités. Ce modèle permet de mieux comprendre les rôles des forces hydrodynamiques et de la courbure dans l’évolution temporelle de la largeur du pont. Un autre axe est une étude expérimentale par Microscope à Force Atomique, qui permet de décrire les forces responsables de la coalescence à l’échelle nanométrique, les déformations des gouttes intervenant à cette échelle et leur rôle dans la rupture des interfaces. Les mesures de forces entre goutte et flaque, puis entre deux gouttes sont effectuées avec un AFM principalement en mode dynamique de Modulation de Fréquence. Elles permettent de mettre en évidence une distance seuil de déclenchement de l’instabilité hydrodynamique responsable de la coalescence et de mesurer cette distance en fonction des propriétés physiques du liquide et du rayon des gouttes. Un diagramme de coalescence est proposé, qui permet de prévoir la valeur de la distance de déclenchement de la coalescence et le rôle des déformations d’interfaces à l’échelle nanométrique. Enfin, les oscillations du pont liquide, générées par la coalescence, sont étudiées, les modes et fréquences propres sont calculés numériquement par la méthode des éléments finis, puis comparés aux valeurs expérimentales mesurées à partir des films acquis par caméra rapide.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-08-30T17:12:19Z No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-08-31T13:03:24Z (GMT) No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-08-31T13:03:24Z (GMT). No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-06-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Eugenia dysenterica is a plant species from Cerrado that is widely distributed throughout the biome. Previous studies showed that natural populations of species have a high genetic structure, suggesting that historical changes in the geographic distribution and habitat fragmentation may have affected its genetic differentiation. In this context, studies of phylogeographic and landscape genetics are needed to understand which factors influence the distribution of genetic diversity of the species. In the first chapter we used the statistical phylogeography integrated to modeling analysis to reconstruct the demographic history and dispersal routes of E. dysenterica lineages and investigated the Quaternary climate change effects on its spatial pattern of genetic diversity. In the second chapter, we evaluated if habitat loss and fragmentation affect genetic diversity and connectivity in the species. Our results suggest that the central region of the Cerrado biome is probably the center of distribution of E. dysenterica and the spatial pattern of its genetic diversity may be the outcome of population stability through periods of the Quaternary. Moreover, also indicate that habitat fragmentation may be related to the increase in differentiation and a decrease of genetic diversity in these populations. / Eugenia dysenterica é uma espécie de planta nativa do Cerrado que apresenta ampla distribuição ao longo do bioma. Estudos anteriores revelam que populações naturais da espécie apresentam alta estruturação genética, sugerindo que mudanças históricas na distribuição geográfica e a fragmentação do habitat podem ter afetado o padrão de diferenciação genética da espécie. Nesse contexto, estudos filogeográficos e de genética da paisagem se fazem necessários para entender os fatores responsáveis pela distribuição da diversidade genética da espécie. No primeiro capítulo foi utilizada a filogeografia estatística integrada às análises de paleomodelagem para acessar a história demográfica da espécie e compreender como as mudanças climáticas do Quaternário influenciaram sua distribuição geográfica e estrutura genética. No segundo capítulo, procura-se responder como a perda de habitat e fragmentação pode influenciar a diversidade genética e conectividade das populações da espécie no Cerrado. Os resultados apresentam evidências de que a origem de dispersão dos haplótipos analisados se deu na região central do bioma e que mudanças ocorridas durante o Pleistoceno, provavelmente, resultaram no padrão de distribuição da diversidade genética observado. Além disso, indicam que a fragmentação do habitat pode estar relacionada com o aumento da diferenciação e diminuição da diversidade genética nas populações estudadas.

Orientadores: Sérgio Furtado dos Reis, Sergio Ivan Perez / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T14:03:24Z (GMT). No. of bitstreams: 1 Costa_CarolinaLemesNascimento_M.pdf: 1856991 bytes, checksum: 0333e9b5415ace1df307eb389ef0260c (MD5) Previous issue date: 2014 / Resumo: Mudanças climáticas são fenômenos responsáveis por influenciar dinâmicas de populações ao longo da história evolutiva das espécies. Quando mudanças no clima ocorrem de maneira abrupta suas consequências podem ser refletidas na distribuição, no tamanho e na persistência das populações sob o efeito destas mudanças. O Quaternário foi uma época caracterizada por mudanças climáticas rápidas e intensas. Estimar a demografia histórica de populações nesta escala de tempo é uma forma de avaliar como flutuações no clima influenciaram populações ancestrais. Dados genéticos nos permitem recuperar informação sobre o tamanho populacional em escalas de tempo amplas e buscar associações entre flutuações no tamanho das populações e variações no clima. A demografia histórica de populações do peixe de água doce Poecilia vivipara habitantes da planície Quaternária do norte do Rio de Janeiro foi estimada com o objetivo de avaliar se fenômenos em escalas de tempo ancestrais deixaram uma assinatura no genoma dos indivíduos de populações contemporâneas. Subsequentemente, foi avaliado se as assinaturas genéticas são reflexo de respostas populacionais às variações climáticas intensas ocorridas no Quaternário. Para estimar a demografia histórica de P. vivipara, utilizou-se o método Skyline-Plot Bayesiano (BSP), sendo o gene mitocondrial citocromo b o marcador molecular analisado. A dinâmica populacional ancestral de P. vivipara revelou uma mudança de regime nos últimos 75 mil anos, que pode estar associada direta ou indiretamente às variações climáticas do Quaternário. Flutuações no nível do mar, geradas pelas mudanças climáticas do Quaternário, podem estar relacionadas com as flutuações no tamanho populacional de P. vivipara. Estudos incluindo outras regiões do genoma e com maior detalhamento sobre variações climáticas locais podem contribuir para gerar estimações mais confiáveis da história populacional de P. vivipara e sua potencial relação com eventos climáticos / Abstract: Paleoclimatic changes are responsible to influence population dynamics through the evolutionary history of species. When climatic changes occur suddenly its consequences can be reflected in the distribution, size and persistence of populations. The Quaternary was a time of massive climatic changes. The estimation of the demographic history of populations at such timescales allows the assessment of how climatic fluctuations have influenced ancestral populations. Genetic data are available and allow recovering information about population sizes in wide timescales and searching for associations between population size fluctuations and climatic change. The historical demography of freshwater fish Poecilia vivipara populations inhabiting the Rio de Janeiro Northern Quaternary Plain was estimated aiming to evaluate if phenomena in ancestral timescales leaves a signature in the genomes of its modern representatives. Subsequently, we evaluate if the genetic signatures are the result of population responses to massive climatic changes occurred in Quaternary. The Bayesian Skyline-Plot (BSP) was utilized to estimate the demographic history of P. vivipara, with the mitochondrial gene cytochrome b as molecular marker. The ancestral population dynamics of P. vivipara revealed a regime change in the last 75,000 years, which can be direct or indirectly associated to Late Quaternary climatic variations. Sea level fluctuations, generated by Quaternary climatic changes, could be related to population size fluctuations of P. vivipara. Studies including other genome regions and with more details about local climatic variations can create more reliable estimations of the P. vivipara population history and its potential relationship with climatic events / Mestrado / Biodiversidade Animal / Mestra em Biologia Animal

Cette thèse se place dans le cadre de l'analyse des forces évolutives qui génèrent les polymorphismes et les divergences entre les génomes d'une même espèce. Le cadre théorique utilisé dans la majorité des domaines de l'évolution moléculaire est la théorie neutraliste, proposée par Motoo Kimura en 1968. Ce modèle est caractérisé par les hypothèses de neutralité, de taille constante de la population étudiée, et de panmixie. Dans un premier temps nous avons cherché à comprendre comment ce cadre théorique est utilisé en pratique et quelles peuvent être les conséquences de ces hypothèses sur les inférences et les prédictions faites dans ce cadre théorique. Pour cela nous avons mené deux études confrontant des données à des méthodes existantes d'inférence démographique. Une première étude a montré que les méthodes utilisées fréquemment pour l'inférence démographique microbienne, basées sur la reconstruction d'un arbre phylogénétique unique, sont biaisées par la sélection, la recombinaison et les biais d'échantillonnage. Nous avons ensuite comparé plusieurs méthodes d'inférence démographique en les appliquant à une population humaine africaine, les Yoruba. Cette étude a montré les limites d'une méthode existante, et elle illustre le problème d'identifiabilité des histoires démographiques lorsque l'inférence est basée sur le spectre de fréquence. Enfin, dans un troisième temps nous avons analysé plusieurs jeux de données de polymorphisme génétique avec un modèle de référence alternatif à coalescences multiples avec démographie. Nous avons comparé comment le modèle de référence actuel et ce modèle alternatif pouvaient expliquer les données observées de diversité génétique. / The general setting of this thesis is the analysis of evolutionary forces that generate polymorphisms and divergence between genomes within a species. The theoretical framework used in the majority of disciplines of molecular evolution is the neutral theory, formulated by Motoo Kimura in 1968. This model is characterized by the hypotheses of neutrality, constant population size and panmixia. First, we investigated how this theoretical framework is used in practice and what are the consequences of these hypotheses on the inferences and predictions made in this framework. To this end, we carried out two studies confronting existing demographic inference methods with data. A first study demonstrated that methods frequently used for bacterial demographic inference, based on a single reconstructed phylogenetic tree, are biased by selection, recombination and sampling bias. We then compared several demographic inference methods, by applying them to an African human population, the Yoruba. This study showed the limits of an existing method, and illustrates the issue of identifiability of demographic histories, when the inference is based on the site frequency spectrum. Finally, in a third study we analyzed several genetic polymorphism datasets with an alternative reference model comprising multiple mergers and demography. We compared how the current reference model and this alternative model can explain the observed genetic diversity.

This study investigates the linguistic relationship between Southern and Northern Ndebele. The focus is on the historical background of the two main South African Ndebele groups, covering various linguistic aspects, such as phonology, morphology, lexicography and spelling rules. The research reveals that, despite the fact that Southern and Northern Ndebele share a common name and historical background, the death of the Ndebele ancestral chief, Musi, at KwaMnyamana, which caused this nation to split into Southern and Northern Ndebele, resulted in the two Ndebele languages. As this study shows, these differ substantially from each other. The two Ndebele languages are examined, phonologically, in Chapters Three and Four revealing demonstrable phonological differences. Southern Ndebele, for instance, has several sounds (e.g., click sounds) that do not occur in its northern counterpart, while Northern Ndebele contains a number of non-Nguni sounds (e.g., interdentals) that do not occur in Southern Ndebele. Phonologically, Southern Ndebele, like other Zunda Nguni languages, employs the voiced lateral alveolar fricative phoneme /z/ [z] (e.g., izifo ‘diseases’), whereas Northern Ndebele, like other Tekela Nguni languages, uses the ejective interdental explosive /t/ [t’] (e.g., tifo ‘diseases’). Morphophonologicallly, the so-called denasalition feature that both languages manifest in their primary and secondary nasal compounds (i.e., Classes 9 and 10 noun class prefixes) occurs in almost opposing ways. In Southern Ndebele, the nasal /n/ resurfaces in all noun class prefixes of Class 10 nouns, while in Northern Ndebele, it occurs only in the noun class prefixes with monosyllabic stems or stems beginning with a voiced or semi-voiced consonant. This morphophonological feature (denasalisation) has spread to other grammatical environments, such as adjectival concords, inclusive quantitative pronouns and all formatives with the nasal compound ng [g] , in Northern Ndebele. The two languages also reveal that there are differences in assimilation, syllabification, palatalization, vowel elision, vowel substitution, consonantalization, glide insertion and labialization. Chapters Five to Eight focus on morphological differences. Here, the two Ndebele languages show differences in the various word categories: nouns, pronouns, qualificatives, copulatives, adverbs, moods, tenses, verbs, auxiliary verbs, conjunctives and ideophones. For instance, whereas Southern Ndebele noun class prefixes, like other Nguni languages – such as isiZulu and isiXhosa – comprises the pre-prefix + basic prefix + stem (e.g., u-mu-ntu ‘person’ a-ba-ntu ‘people’), in Northern Ndebele, this word category comprises the basic prefix + stem like Sotho languages (e.g., mu-nru ‘person’ ba-nru ‘people’). In addition, while the noun class prefix of Class 8 in Southern Ndebele contains a nasal before polysyllabic noun stems (e.g., iinkhova ‘owls’), in Northern Ndebele, Class 8 noun class prefixes contain no nasal (e.g., tikxabula ‘shoe’). Lexically, the most salient differences are that, although the two Ndebele languages share similar Nguni vocabulary, they have been unequally influenced by the neighbouring Sotho languages. Most importantly, despite the fact that both Ndebele languages have borrowed words from Northern Sotho and Setswana, Northern Ndebele has borrowed many more terms than Southern Ndebele. Lastly, in line with the Southern Ndebele (2008) and Northern Ndebele (2001) Spelling Rules, this investigation observes that the two Ndebele languages differ radically. In Southern Ndebele, for instance, there are numerous language aspects that have spelling rules governing their encryption, but in Northern Ndebele no rules exist as yet for such aspects. The findings reveal that Southern and Northern can be regarded as two distinct languages that deserve autonomous development even though they trace their origin from the same historical source. / Thesis (DLitt)--University of Pretoria, 2010. / African Languages / unrestricted

Cette thèse étudie des modèles de populations branchantes appelés arbres de ramification, dans lesquels les individus évoluent indépendamment les uns des autres, ont des durées de vie indépendantes, identiquement distribuées (non nécessairement exponentielles), et donnent naissance à taux constant au cours de leur vie. On enrichit ces modèles en supposant que chaque individu porte un type et peut subir à la naissance une mutation, qui lui confère un nouveau type. On démontre dans le premier chapitre des résultats théoriques de convergence en loi pour des processus de Lévy bivariés sans sauts négatifs. Ces résultats sont ensuite exploités dans le deuxième chapitre pour établir un principe d'invariance pour l'arbre généalogique des populations décrites ci-dessus, enrichi de leur historique mutationnel, dans une asymptotique de grande taille de population. Enfin, on étudie dans le troisième chapitre la structure généalogique et le spectre de fréquence par site (nombre de mutations portées par un nombre donné d'individus) d'échantillons uniformes dans des populations branchantes critiques dont la limite d'échelle est un arbre brownien (par exemple, des arbres de naissance et mort critiques). Des perspectives d'applications de ces résultats à la génétique des populations sont présentées dans le quatrième chapitre. / This thesis studies branching population models called splitting trees, where individuals evolve independently from one another, have independent and identically distributed lifetimes (that are not necessarily exponential), and give birth at constant rate during their lives. We further assume that each individual carries a type, and possibly undergoes a mutation at her birth, that changes her type into a new one. In the first chapter, we prove convegence results for bivariate Lévy processes with non negative jumps. These theoretical results are used in the second chapter to establish an invariance principle for the genealogical tree of the populations described above, enriched with their mutational history, in a large population size asymptotic. Finally we study in the third chapter the genealogical structure and the site frequency spectrum (number of mutations carried by a given number of individuals) for uniform samples in critical branching populations whose scaling limit is a Brownian tree (e.g., critical birth-death trees). Possible future applications of these results to population genetics are presented in the fourth chapter.

PhD (Tshivenda) / Senthara ya M.E.R. Mathivha ya Nyambo dza Afrika kha Vhutsila na Mvelele / Tshivenḓa is one of African languages spoken in the Northern parts of South Africa and some parts of Zimbabwe. This proposal focuses on a study of selected phonological processes involving Tshivenḓa vowels. The Tshivenḓa phonological processes involving vowels under this study include vowel elision/deletion, vowel epenthesis, vowel coalescence, vowel nasalisation, vowel harmony, vowel raising and glide formation. In this regard, consonants are not part and parcel of this study. Furthermore, the study enriches the phonology of Tshivenḓa with more phonological processes thereby adding on the existing literature. The study also attempts to motivate and encourage Tshivenḓa speaking people and those who are interested in the language to have a clear understanding of phonological processes which occur in Tshivenḓa. The theoretical framework underpinning this study is the Optimality Theory (OT). The study will be carried out through phonological analysis, that is, field work and word list. Secondary sources will also be used for data collection.

Ein neues, verallgemeinertes Modell für Blasenkoaleszenz und –zerfall wurde entwickelt. Es basiert auf physikalischen Überlegungen und berücksichtigt verschiedene Mechanismen, die zu Blasenkoaleszenz und –zerfall führen können. In einer ausführlichen Literaturrecherche wurden zunächst die verfügbaren Modelle zusammengestellt und analysiert. Es zeigte sich, dass viele widersprüchliche Modelle veröffentlicht wurden. Keins dieser Modelle erlaubt die Vorhersage der Entwicklung der Blasengrößenverteilungen entlang einer Rohrströmung für einen breiten Bereich an Kombinationen von Volumenströmen der Gas- und der Flüssigphase. Das neue Modell wurde ausführlich in einem vereinfachten Testsolver untersucht. Dieser erfasst zwar nicht alle Einzelheiten einer sich entlang des Rohres entwickelten Strömungen, erlaubt aber im Gegensatz zu den CFD-Simulationen eine Vielzahl von Variationsrechnungen zur Untersuchung des Einflusses einzelner Größen und Modelle. Koaleszenz und Zerfall kann nicht getrennt von anderen Phänomenen und Modellen, die diese widerspiegeln, betrachtet werden. Es bestehen enge Wechselwirkungen mit der Turbulenz der Flüssigphase und dem Impulsaustausch zwischen den Phasen. Da die Dissipationsrate der turbulenten kinetischen Energie ein direkter Eingangsparameter für das neue Modell ist, wurde die Turbulenzmodellierung besonders genau untersucht. Zur Validierung des Modells wurde eine TOPFLOW-Experimentalserie zur Luft-Wasser-Strömungen in einem 8 m langen DN200-Rohr genutzt. Die Daten zeichnen sich durch eine hohe Qualität aus und wurden im Rahmen des TOPFLOW-IIVorhabens mit dem Ziel eine Grundlage für die hier vorgestellten Arbeiten zu liefern, gewonnen. Die Vorhersage der Entwicklung der Blasengrößenverteilung entlang des Rohrs konnte im Vergleich zu den bisherigen Standardmodellen für Blasenkoaleszenz und -zerfall in CFX deutlich verbessert werden. Einige quantitative Abweichungen bleiben aber bestehen. Die vollständigen Modellgleichungen sowie eine Implementierung über „User-FORTRAN“ in CFX stehen zur Verfügung und können für weitere Arbeiten zur Simulation polydisperser Blasenströmungen genutzt werden.