A series of studies was carried out in order to ascertain some of the ecological determinants of the foraging and caching behaviour of heteromyid rodents (kangaroo rats, Dipodomys, and pocket mice, Chaetodipus). The results show that heteromyids are sensitive to cues of predation while they are foraging. They put more effort into foraging under the safety of cover and in the dark of the new moon, when risk of predation from visually hunting predators is low. They also modulate their selectivity in relation to cues of predation risk, requiring a better pay-off(a more valuable food) as risk increases. The kangaroo rats and pocket mice compete for resources, and the pocket mice are at an aggressive disadvantage to the kangaroo rats at primary resource patches. However, the pocket mice compensate at least partially for their loss by engaging in cache pilferage. Finally, a study of the scatter caching decisions made by kangaroo rats demonstrates that they adaptively modulate cache spacing by placing more valuable seeds into caches that are more widely spaGed. This differential spacing leads to decreased probability that pilferers conducting area-localised search after encountering one cache will be able to locate further caches. The results are discussed in relation to current theory and empirical findings. / Thesis / Doctor of Philosophy (PhD)

For almost every organism there are large gaps in our knowledge about the processes that leads to speciation. The changes an organism undergoes before divergence has occurred have remained a mystery, as it is difficult to say whether or not a species is going to diverge and when. To investigate this unknown the European whitefish (Coregonus lavaretus) and the northern pike (Esox lucius) were studied, as they produce a repeatable and predictable pattern of speciation in sympatry. To investigate the changes in phenotypes and behaviour in whitefish that precedes divergence, two lake populations were examined, Gräsvattnet and Ringsjön. Gräsvattnet was used as a control, with a population of whitefish but an absence of pike, whereas Ringsjön has a population of whitefish that invaded from Gräsvattnet and a pike population. The presence of pike presumably exerts divergent selection on the whitefish population. Fish and zooplankton were surveyed in both lakes from 1970 to the present day, which allows us to compare how whitefish populations and their resources change in the presence and absence of pike. The results found in Ringsjön show; (1) a change in habitat use, (2) a change in diet from pelagic to benthic, (3) an increase in the relationship between individual body size and diet and (4) a decrease in average size over the course of the study. (1)The presence of pike is believed to have forced the whitefish into the pelagic which could be seen in the result, with an increase in individuals caught in the pelagic. (2) The change in diet is thought to be caused by a resource competition created by individuals being forced to use the pelagic. Although insignificant this led to an overall reduction in zooplankton abundance by almost 40% which could have intensified competition. The resource competition could then have been intensified further by the change in composition of zooplankton relative abundance. (3) The increase in relationship between individual body size and diet is thought to increase due to the resource competition between smaller and larger individuals in the pelagic. Smaller individuals are better competitors than larger individuals for pelagic resource which could have led to the larger individuals switching to a more benthic diet. (4) The decrease in average size is thought to be caused by negative selection for larger individuals. Larger individuals have switched to a more benthic diet, and although the individuals are larger they still face the risk of predation in the littoral zone as they have not outgrown the gape size of the pike. This could have led to the average size reduction that may be the first steps in speciation, and ultimately leading to the divergence of two morphs by sympatric speciation in Ringsjön. In Gräsvattnet over the course of the study there were few and small changes in whitefish size, zooplankton relative abundance in the diet and in the environment. The results in Gräsvattnet could however suggest resource competition for benthic resources. Although resource competition is thought to be an important factor in the speciation of whitefish, without predation pressure no speciation occurs. This result could suggest the importance of predation pressure in the speciation of whitefish.

Plasmodium falciparum (P. falciparum) infection modulates the response of innate immune cells. The aim of this work was to study the impact of P. falciparum infection and P. falciparum-derived molecules on the response of dendritic cells (DC) and monocytes. In paper I we investigated the effects of natural hemozoin (nHZ), a P. falciparum-derived molecule, on the phenotype and functionality of DC. We found that exposure to nHZ impaired the capacity of DC to mature. Paper II is a follow-up on paper I, where the underlying transcriptional events preceding the nHZ-induced impairment of DC maturation were investigated. More specifically, we examined the involvement of certain transcription factors, subunits of chromatin remodeling complexes and histone modifications in the regulation of DC maturation. Our findings suggest that nHZ-exposure of DC does not lead to recruitment or enrichment of molecules needed for transcriptional activation. In paper III we investigated P. falciparum effects in vivo in sympatric ethnic groups with differential susceptibility towards P. falciparum infection living in Burkina Faso. The aim of this study was to establish the transcriptional networks underlying the relatively better protection against P. falciparum infection observed in the Fulani ethnic group compared to other sympatric ethnic groups. Our findings reveal differential gene expression in monocytes of infected Fulani compared to uninfected Fulani and the difference concerned multiple classes of genes including signal transduction, immunological responses and chromatin remodelers. The results provide new aspects on molecules and regulatory mechanisms that are involved in the relatively more protective response against P. falciparum infection. Taken together, the work presented in this thesis leads to a deeper understanding of the P. falciparum-induced modulation of responses of innate immune cells and the underlying mechanisms possibly regulating those responses. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.</p>

京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第19853号 / 情博第604号 / 新制||情||105(附属図書館) / 32889 / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 守屋 和幸, 教授 大手 信人, 教授 荒井 修亮 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

No description available.

Divergence in the face of gene flow is perhaps the most wildly disputed subject among researchers through time. The debate is an old one and we find its origin as far back as the era of Darwin. The theories dealing with sympatric and parapatric speciation, its processes and ecological conditions, are numerous and the empirical data supporting the ideas is constantly growing. However, the reach of a consensus almost seem as distant as ever. Two fundamental prerequisites can be identified for the evolution of divergence with gene flow, the act of disruptive selection, and the development of assortative mating. A set of models in which speciation with gene flow seem particularly likely is when a shift occurs in host preference in phytophagous insects and mating takes place on the host. In the work behind this thesis, the role of assortative mating in the initial stages of sympatric and parapatric speciation has been studied, as has the interaction between assortative mating and inbreeding and how it effects speciation in small sympatric populations, an aspect not much attended to earlier in the literature. My results show that assortative mating based on resource preference, can evolve rapidly upon secondary contact, and even in parapatric populations with a migration rate of 8% (13-15 individuals) per generation. However for assortative mating to be maintained selection against hybrids is needed. My results also suggests that small inbred populations have a hard time coping with strong assortative mating an as a consequence tend to relax their mating preferences to avoid inbreeding depression. Based on these results, I advocate for the importance of considering not only assortative mating in itself, but also the joint effects of assortative mating and inbreeding when dealing with theories of speciation with gene flow.

Apresenta-se nesta tese os resultados de aplicações do formalismo da Mecânica Estatística em dois problemas independentes. O primeiro diz respeito a um modelo para Evolução do Acasalamento Preferencial no processo de Especiação Simpátrica; enquanto que o segundo refere-se ao desenvolvimento de um algoritmo de aprendizado por meio de Inferência Aproximativa. No problema biológico estudado, cada indivíduo em um modelo de agentes é composto por dois traços. Enquanto um é responsável pela ecologia do indivíduo, o outro dita uma aparência física descorrelacionada com a adaptabilidade. Esses traços são expressos por diferentes loci que estão ligados entre si por uma taxa de recombinação. O modelo inclui também a possibilidade de evolução da preferência sexual dos indivíduos. Foi construído para esse modelo um diagrama de fases no espaço dos parâmetros que descrevem o ambiente como, por exemplo, quantidades de recursos e deficiência do indivíduo híbrido. Foram encontradas três fases de equilíbrio: (i) emergência de Acasalamento Preferencial; (ii) extinção de um dos alelos do locus responsável pela ecologia e (iii) equilíbrio Hardy-Weinberg. Foi verificado que o acasalamento preferencial pode emergir ou mesmo ser perdido (e vice-versa) em resposta a mudanças no ambiente. Além disso, o sistema apresenta memória característica típica de transições de primeira ordem, o que permitiu a descrição desse sistema biológico por meio do arcabouço da Mecânica Estatística. Em relação à Inferência Aproximativa, está-se interessado na construção de um algoritmo de aprendizado supervisionado por meio da técnica de Propagação de Expectativas. Mais especificamente, pretende-se inferir os parâmetros que compõem um Perceptron Professor a partir do conjunto de pares - entradas e saídas - que formam o conjunto de dados disponíveis. A estimativa desses parâmetros será feita pela substituição de uma distribuição Posterior original, geralmente intratável, por uma distribuição aproximativa tratável. o algoritmo Propagação de Expectativas foi adotado para a atualização, passo a passo, dos termos que compõem essa distribuição aproximativa. Essa atualização deve ser repetida até que a convergência seja atingida. Utilizando o Teorema do Limite Central e o método de Cavidade, foi possível obter um algoritmo genérico e que apresentou desempenho bastante evidente em dois modelos estudados: o modelo do Perceptron Binário e o modelo do Perceptron Gaussiano, com desempenho ótimo em ambos os casos. / This thesis presents applications of the framework of Statistical Mechanics to two independent problems. The first corresponds to a computational model for the evolution of Assortative Mating in the Sympatric Speciation process; and the second a learning algorithm built by means of a Bayesian Inference approach. In the biological problem each individual in an agent-based model is composed of two traits. One trait, called the ecological trait, is directly related with the fitness; the other, called the marker trait, has no bearing on the fitness. The traits are determined by different loci which are linked by a recombination rate. There is also the possibility of evolution of mating preferences, which are inherited from the mother and subject to random variations. The study of the phase diagram in the spa e of parameters describing the environment (like carrying capacity and disruptive selection) reveals the existence of three phases: (i) assortative mating; (ii) extinction of one allele from ecological loci; and (iii) Hardy-Weinberg equilibrium. It was verifed that the assortative mating an emerge or even be lost (and vice-versa) acording with the environmental hanges. Moreover, the system shows memory of the initial condition, characterising a hysteresis. Hysteresis is the signature of first order phase transition, which allows the description of the system by means of the Statistical Mechanics framework. In relation to the Bayesian Inference, a supervised learning algorithm was constructed by means of the Expectation Propagation approach. The idea is to estimate the parameters which compose a Teacher Perceptron by the substitution of the original posterior distribution, intra table, by a tractable approximative distribution. The step-by-step update of the terms composing the approximative distribution was performed by using the Expectation Propagation algorithm. The update must be repeated until the convergence ocurrs. Using the Central Limit Theorem and the Cavity Approah, it was possible to get a generic algorithm that has shown a very good performance in two application scenarios: The Binary Perceptron Model and the Gaussian Perceptron Model.

Made available in DSpace on 2016-04-28T20:15:35Z (GMT). No. of bitstreams: 1 2009 - Raquel de Oliveira Simoes.pdf: 2148721 bytes, checksum: 7408aa4a20471b27145d83c2bea4886a (MD5) Previous issue date: 2009-01-28 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The objective of this study was to describe the composition and structure of helminthes community comparing the helminthes community component and infracommunity from sympatric rodents Akodon spp. and Oligoryzomys nigripes in the Atlantic Forest and in the different fragments size and the Parque Nacional da Serra dos ?rg?os (PARNA SO reserve. One hundred and fifty-six specimens of Akodon spp. and fifty-seven of Oligoryzomys nigripes were collected in Teres?polis, being 38 rodents in 4 small fragments (30 Akodon spp. and 8 O. nigripes), 58 in 4 medium fragments (43 Akodon spp. and 15 O. nigripes), 87 in 4 large fragments (67 Akodon spp. and 20 O. nigripes) and 30 in PARNASO (16 Akodon spp. e 14 O. nigripes). The stydy was done for two years (2004- 2005). The animals were necropsied and the viscera and cavities examined to helminthes parasites. A total of eighteen helminthes species were collected: 15 from Akodon spp. and12 from O. nigripes. Nine species were common for both rodents. The rodent Akodon spp. showed a higher richness than O. nigripes. A low degree of similarity between the helminthes infracommunities from Akodon spp. and O. nigripes was detected, although these rodents species live in coexistence. The terrestrial and arboreal behavior of O. nigripes and terrestrial behavior of Akodon spp. would determine this difference between both parasite communities. Probably, with the share of soil resource boths species of rodents could disseminate or be infected by the parasite. The prevalence of Stilestrongylus aculeata and mean abundance for Stilestrongylus eta increased, respectively, in small, medium and large fragments in Akodon spp.. The rodent O. nigripes showed high prevalence rate and mean abundance values for Stilestongylus lanfrediae (over 86%) regardless of the fragments size studied. The difference in mean richness for Akodon spp. and O. nigripes in different fragments size and PARNASO were not significant. There were variations between the helminthes infracommunities for the two species of rodent in different fragments size and PARNASO. These differences may also be related to the environmental changes that can produce both positive and negative effects on the transmission of helminthes parasites. / O objetivo deste trabalho foi descrever a composi??o e estrutura da comunidade helm?ntica comparando a comunidade componente e a infracomunidade dos helmintos das popula??es de roedores simp?tricos Akodon spp. e Oligoryzomys nigripes na Mata Atl?ntica e os diferentes tamanhos de fragmentos e a reserva do Parque Nacional da Serra dos ?rg?os (PARNASO). Cento e cinq?enta e seis esp?cimes de Akodon spp. e cinq?enta e sete de O. nigripes foram coletados no munic?pio de Teres?polis, sendo 38 roedores em 4 fragmentos pequenos (30 Akodon spp. e 8 O. nigripes), 58 em 4 fragmentos m?dios (43 Akodon sp p. e 15 O. nigripes), 87 em 4 fragmentos grandes (67 Akodon spp. e 20 O. nigripes) e 30 no PARNASO (16 Akodon spp. e 14 O. nigripes). O estudo foi feito durante dois anos (2004- 2005). Os animais foram necropsiados tendo suas v?sceras e cavidades tor?cica e abdominal examinadas para recupera??o de helmintos parasitos. Um total de 18 esp?cies de helmintos foram coletados: 15 em Akodon spp. e 12 em O. nigripes. Nove esp?cies foram comuns aos dois roedores. O roedor Akodon spp. teve uma maior riqueza parasit?ria do que O. nigripes. Um baixo grau de similaridade entre as infracomunidades de helmintos de Akodon spp. e O. nigripes foi observado, embora sejam esp?cies que coexistam. O comportamento terrestre e arbor?cola de O. nigripes e apenas terrestre de Akodon spp. poderia determinar essa diferen?a entre as duas comunidades de helmintos parasitos. Provavelmente, ao compartilharem os recursos do solo, ambas as esp?cies podem se infectar ou disseminar o parasita. A preval?ncia para Stilestrongylus aculeata e a abund?ncia m?dia para S. eta aumentaram, respectivamente, nos fragmentos pequenos, m?dios e grandes no Akodon spp.. O roedor O. nigripes apresentou elevada taxa de preval?ncia e valores de abund?ncia m?dia para S. lanfrediae (acima de 86%) independente do tamanho dos fragmentos estudados. A diferen?a na riqueza m?dia de Akodon spp. e O. nigripes nos diferentes tamanhos de fragmentos e no PARNASO n?o foi significativa. Houve varia??es entre as infracomunidades de helmintos das duas esp?cies de roedores nos diferentes tamanhos de fragmentos e PARNASO, podendo essas diferen?as estarem relacionadas com as altera??es ambientais causadas pela fragmenta??o que podem produzir tanto efeitos positivos como negativos na transmiss?o dos helmintos parasitos.

Population divergence shaped by natural selection is central to evolutionary ecology research and has been in focus since Darwin formulated “The origin of species”. Still, the process of adaptive divergence among sympatric populations is poorly understood. In this thesis I studied patterns of adaptive divergence among subpopulations of pike (Esox lucius) that are sympatric in the Baltic Sea but become short-term allopatric during spawning and initial juvenile growth in freshwater streams. I also examined causes and consequences of phenotypic variation among individuals within subpopulations to evaluate the contribution of natural selection to population divergence.   I first investigated homing behaviour and population structures of pike to assess the potential for adaptive divergence among sympatric pike that migrate to spawn in different streams. Mark-recapture data suggested that migrating pike displayed homing behaviour and repeatedly returned to the same stream. Analyses of microsatellite data revealed partial reproductive isolation among subpopulations spawning in different streams. These subpopulations, however, were truly sympatric during the life-stage spent in the Baltic Sea.   To address whether short-term allopatry has resulted in adaptive divergence among sympatric subpopulations I combined observational, experimental and molecular approaches. Observational data showed that subpopulations differed in morphological and life-history traits and common-garden experiments suggested that differences were, at least in part, genetically based. Moreover, QST-FST comparisons indicated that genetically based phenotypic differences has been driven by divergent selection, and a reciprocal translocation experiment showed that phenotypic variation represented local adaptations to spawning habitats. Finally, longitudinal and cross-sectional comparisons among individuals revealed associations between phenotypes, performance and fitness components.   In conclusion, my thesis illustrates how short-term allopatry due to migratory behaviour can result in adaptive divergence among sympatric subpopulations. These findings advance the understanding of evolutionary processes at the finest spatiotemporal scale and illustrate that local adaptations can arise in environments with high connectivity.  The results also emphasise that fine spatial scale population structures must be taken into consideration in management and conservation of biodiversity in the Baltic Sea.

The theory of "genomic islands of speciation" has been extensively debated during the last decade. This thesis not only supports this theory, but provides evidence that challenges previous beliefs on the level of admixture between species. The recently published Heliconius melpomene genome project reported apparent genomic paraphyly of H. pardalinus with regard to H. elevatus (Heliconius Genome Consortium 2012). Here, we investigate this pair of butterfly species more fully, firstly by using whole-genome resequence data, and secondly by analyzing additional geographic populations of both species, as well as outgroup taxa. Using a nuclear whole-genome phylogenetic analysis we also confirm that H. elevatus is paraphyletic. The genome-wide phylogenetic signal in H. pardalinus and H. elevatus does not indicate expected mutual monophyly of each species as it seems strongly distorted by a high level of admixture. However, several regions of the genome remain differentiated and do show the presumably original phylogenetic signal with mutual monophyly of H. pardalinus and H. elevatus. The genomic background is so homogenized that its level of differentiation (FST ~ 0.03) virtually implies panmixia. The pattern of a high level of homogenization across the genome with several regions of differentiation was consistent with a number of other statistics such as absolute divergence Dxy, nucleotide polymorphism π, number of fixed differences and with a sliding window phylogeny. The identified genomic islands of divergence comprise genes responsible for wing-patterning and chemosensation in Heliconius and some of these genes are found to be under positive selection, suggesting possible candidates of speciation.