Os dados obtidos neste trabalho contribuem para o conhecimento da família Gymnophthalmidae, acrescentando dados genéticos de três novos genes para a tribo Ecpleopodini e descrição de 11 novos cariótipos para a família, pertencentes às tribos Ecpleopodini, Heterodactylini, Iphisiini e Gymnophthalmini. As análises filogenéticas obtidas para a tribo Gymnophthalmini pretenderam investigar o posicionamento de Scriptosaura Catimbau, espécie descrita recentemente que apresenta 2n=48, que foi recuperada como grupo irmão de Nothobachia ablephara, relacionados ainda à Calyptommatus. Já em Ecpleopodini, as análises foram realizadas para a investigação das relações filogenéticas entre os gêneros da tribo e do posicionamento de Kaieteusosauros hindsi. Foi recuperado o monofiletismo da tribo e do clado composto pelos gêneros Anotosaura, Dryadosaura (2n=44, 20M+24m) e Colobosauroides (2n=44, 20M+24m), entretanto, as relação entre os demais gêneros, inclusive de Kaieteurosaurus, não puderam ser estabelecidas e, com base nos dados citogenéticos, nota-se o predomínio de cariótipos com divisão entre macro e microcromossomos. Apesar de a família Gymnophthalmidae apresentar uma elevada diversidade cariotípica, as tribos Heterodactylini e Iphisiini apresentaram um cariótipo altamente conservado, sendo que as oito espécies descritas apresentam cariótipos compostos por 42 cromossomos com divisão clara entre macro e microcromossomos (18M+24m) e Ag-RONs em um par de microcromossomos. Os motivos que contribuem para a manutenção deste número diplóide nessas tribos ainda deverão ser investigados, mas aparentemente, este pode ser o cariótipo ancestral para a subfamília Gymnophithalminae e teria originado a diversidade cariotípica da tribo Gymnophthalmini por ocorrência de eventos de fissão e fusão cêntrica. Novos estudos cariotípicos e moleculares devem ser conduzidos para estabelecimento de tendências cromossômicas e evolutivas na tribo Ecpleopodini, que parece apresentar uma divergência rápida e simultânea, e para um melhor conhecimento da família que apresenta uma diversidade cromossômica elevada e sistemática longe de estar bem estabelecida. / This study contributes to knowledge of the family Gymnophthalmidae, adding new genetic data of three genes for the tribe Ecpleopodini and description of 11 new karyotype for the family, belonging to the tribes Ecpleopodini, Heterodactylini, Iphisiini and Gymnophthalmini. Phylogenetic analysis for the tribe Gymnophthalmini aimed to investigate the position of Scriptosaura Catimbau, recently described species which has 2n = 48 and was recovered as sister group of Nothobachia ablephara, both related to Calyptommatus. In Ecpleopodini, the analysis was performed to investigate the phylogenetic relationships among genera of the tribe and the placement of the species Kaieteusosauros hindsi. It was recovered the monophyly of the tribe and a clade composed of the genera Anotosaura, Dryadosaura (2n = 44, 20M+24m) and Colobosauroides (2n = 44, 20M+24m), however, the relationship among other genera, including Kaieteurosaurus, could not be established and, based on cytogenetic data, it can be seen the predominance of karyotype with a division into macro and microchromosomes. Although the family gymnophthalmids exhibit a high karyotypic diversity, the tribes and Heterodactylini Iphisiini showed a conservative karyotype, and the eight described species present karyotypes composed of 42 chromosomes with a clear division between macro and microchromosomes (18M +24 m) and Ag-NORs in a pair of microchromosomes. The reasons that contributed to the maintenance of this diplod number in the two tribes are still to be investigated, but apparently, this may be the ancestral karyotype for the subfamily Gymnophithalminae and may have originated the karyotypic diversity in the Gymnophthalmini for a series of fission events centric. New karyotypic and molecular studies should be conducted to establish trends in chromosomal and evolution in the tribe Ecpleopodini, which seems to have a simultaneous and rapid divergence, and to a better understanding of the family that has a high diversity and systematic chromosome far from well established.

A fibropapilomatose é uma neoplasia caracterizada pela formação de múltiplos tumores que acomete, mais frequentemente, a espécie de tartaruga marinha Chelonia mydas. Estudos recentes apontam o Chelonid herpesvirus 5 (ChHV5) como o provável agente etiológico dessa doença, embora a associação com ambientes antropogenicamente alterados parecem contribuir para o desenvolvimento da doença. Nesse estudo, biópsias de tumores e secreções de tartarugas verdes capturadas no litoral do Estado de São Paulo, Brasil, foram submetidas a análises histológicas e moleculares visando detectar e caracterizar ChHV5. Em 45,5 % dos casos, os achados histopatológicos revelaram células epiteliais balonizantes com corpúsculos de inclusão intranucleares. ChHV5 foram detectados nas biópsias de pele e oculares dos animais e em secreções oculares e saliva por PCR. A análise das sequências parciais do gene da polimerase do ChHV5 detectadas revelou duas sequências gênicas distintas entre si. A análise filogenética indicou que as amostras brasileiras são similares às amostras de ChHV5 do grupo filogeográfico do Atlântico, compartilhando o mesmo clado que amostras provenientes do Golfo da Guiné e de Porto Rico, sugerindo um possível fluxo dos vírus entre essas três regiões. / Fibropapillomatosis is a neoplastic disease characterized by the formation of multiple tumors affecting different species of sea turtles and, most often, Chelonia mydas. Recent studies indicate that Chelonid herpesvirus 5 (ChHV5) is the etiological agent of this disease, though its association with anthropogenically altered environments also appears to contribute to disease expression and tumor formation. In this study, tumor biopsy and secretions from green turtles captured off the coast of São Paulo State, Brazil, were used in histological and molecular analyses to detect and characterize ChHV5. In 45.5 % of cases, the tumor histopathological findings revealed ballooning degeneration with intranuclear inclusion bodies. ChHV5 was detected using polymerase chain reaction on the animals skin, ocular tumor biopsies, and ocular and oral secretions. The analysis of the detected ChHV5 sequences revealed two distinct genetic sequences together. Phylogenetic analysis indicated that Brazilian samples were similar to ChHV5 samples described for the Atlantic phylogeographic group and are therefore part of the same clade as the Gulf of Guinea and Puerto Rico samples. This similarity suggests a possible flow of the virus between these three regions.

O florestamento dos campos do sul da América do Sul incluindo os campos do Pampa estão mudando a paisagem local e levando a mudanças nas populações de aves. O conhecimento sobre o efeito do florestamento sobre a avifauna dos campos do sul da América do Sul é bastante limitado à riqueza e composição de espécies. Além de preencher lacunas considerando diferentes índices para avaliar respostas das comunidades de aves ao florestamento dos campos (Capítulos 2 e 3), nesta tese nós também avaliamos se Áreas de Preservação Permanente localizadas dentro de plantações de eucalipto são funcionais para a avifauna local, fazendo uma comparação com áreas de campo pastejado (Capítulo 1). No capítulo 1 nós registramos uma diferença na composição de espécies entre as áreas devido principalmente às mudanças na altura e densidade da vegetação. Nos capítulos 2 e 3 nós avaliamos diferentes componentes da diversidade (taxonômica, filogenética e funcional) considerando possíveis efeitos do florestamento dos campos sobre estes Nossos resultados demonstram respostas diferenciadas entre os componentes, enquanto o florestamento leva a uma redução na diversidade taxonômica, diversidade filogenética e funcional não demonstram respostas negativas. No capítulo 2 no entanto, nós observamos que o florestamento dos campos conduz a uma perda de distintividade evolutiva, beneficiando desta forma linhagens que se diversificaram recentemente. No capítulo 3 apesar da redução na diversidade taxonômica não houve uma redução na diversidade funcional em áreas plantadas. Já a associação de alguns atributos funcionais com as áreas pós-corte, indica a plasticidade de algumas espécies que retornam para essas áreas logo após o corte dos plantios.De modo geral nossos resultados indicam que a manutenção de mosaicos de campo de diferentes alturas maximiza a biodiversidade local de aves e destaca a importância da proteção de áreas campestres. Além disso, vimos que considerar diferentes componentes da diversidade que incorporam informações sobre as espécies são importantes pois podem informar por exemplo, quantas extinções uma comunidade pode suportar até que funções importantes sejam perdidas, afetando assim a estabilidade dos ecossistemas. / The afforestation of southern grasslands of South America including the Pampa grasslands are changing the local landscape and leading to reduction of bird populations. Knowledge about the effect of afforestation on the avifauna of the southern South American grasslands is limited to richness and composition of species. In addition to filling gaps considering different indices to evaluate responses of the bird communities to the afforestation of the grasslands (Chapters 2 and 3), in this thesis we also evaluated whether Permanent Preservation Areas located within eucalyptus plantations are functional for the local avifauna, making a comparison with grazed grasslands areas (Chapter 1). In Chapter 1 we recorded a difference in species composition between areas due mainly to changes in height and density of vegetation. In chapters 2 and 3 we evaluated different components of diversity (taxonomic, phylogenetic, and functional), considering possible effects of grasslands afforestation on them. Our results demonstrate differentiated responses among components, while afforestation leads to a reduction in taxonomic diversity, phylogenetic and functional diversity do not demonstrate negative responses In chapter 2 however, we observe that grasslands afforestation leads to a loss of evolutionary distinctiveness, thus benefiting species that have diversified recently. In chapter 3, despite the reduction in taxonomic diversity, there was no reduction in functional diversity in planted areas. Furthermore, the association of some functional traits with the post-cut areas indicates the plasticity of some species that return to these areas soon after cut the plantations. In general our results indicate that the maintenance of grasslands mosaics of different heights maximize the local biodiversity of birds and highlight the importance of the protection of grasslands areas. In addition, we have seen that considering different components of diversity that incorporate information on species is important because they can tell, for example, how many extinctions a community can support until important functions are lost.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22282号 / 理博第4596号 / 新制||理||1659(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 朝倉 彰, 准教授 下村 通誉, 教授 曽田 貞滋 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.

Habitat loss and climate change are major factors implicated in the decline of bumble bees worldwide. These factors may be particularly acute in regions subject to climatic extremes such as seasonal drought. Combining methods from pollinator research and phylogenetic community ecology, I investigated the impacts of seasonal drought on plant phenology and bumble bee community ecology across gradients of disturbance and soil moisture in a semi-arid ecosystem. Seasonal fluctuations in floral resources coincided with significant phylogenetic clustering in plant communities, with decreasing plant diversity observed under conditions of increasing drought stress. In the late season, modified wet areas supported higher floral resource availability and greater bumble bee abundances as compared to dry woodlands, though wetlands were also an important source of late season floral resources. Despite these local effects, however, the areal extent of natural vs modified matrix habitat accounted for the majority of variation in models explaining bumble bee abundances. Modified matrix habitat was negatively associated, and natural matrix habitat positively associated, with the occurrence of bumble bee workers in June and late-flying queens in July and August. Results provide insight into the temporal niche dynamics of entomophilous flowering plants in this system, and emphasize the importance of conserving natural habitat diversity in efforts to promote resilient plant-pollinator communities. This study also provides evidence for the local extinction of Bombus occidentalis Greene, 1858 and Bombus suckleyi Greene, 1860 from Galiano Island, BC, Canada, as well as the island’s recent colonization by Bombus vosnesenskii Radoszkowski, 1862. / Graduate

The statistical analysis of phylogenetic footprints in the two known horn shark Hox clusters and the four mammalian clusters shows that the shark HoxN cluster is HoxD-like. This finding implies that the most recent common ancestor of jawed vertebrates had at least four Hox clusters, including those which are orthologous to the four mammalian Hox clusters.

<div>Model-based clustering, with its flexibility and solid statistical foundations, is an important tool for unsupervised learning, and has numerous applications in a variety of fields. This dissertation focuses on nonparametric Bayesian approaches to model-based clustering under structural restrictions. These are additional constraints on the model that embody prior knowledge, either to regularize the model structure to encourage interpretability and parsimony or to encourage statistical sharing through underlying tree or network structure.</div><div><br></div><div>The first part in the dissertation focuses on the most commonly used model-based clustering models, mixture models. Current approaches typically model the parameters of the mixture components as independent variables, which can lead to overfitting that produces poorly separated clusters, and can also be sensitive to model misspecification. To address this problem, we propose a novel Bayesian mixture model with the structural restriction being that the clusters repel each other.The repulsion is induced by the generalized Matérn type-III repulsive point process. We derive an efficient Markov chain Monte Carlo (MCMC) algorithm for posterior inference, and demonstrate its utility on a number of synthetic and real-world problems. <br></div><div><br></div><div>The second part of the dissertation focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A classic example of such problems, which is also the focus of our work, is the phylogenetic tree with nodes often representing biological species. The structure of this problem refers to the hierarchical structure of the populations. Clustering of the populations in this problem is equivalent to identify branches in the tree where the populations at the parent and child node have significantly different distributions. We construct a nonparametric Bayesian model based on hierarchical Pitman-Yor and Poisson processes to exploit this, and develop an efficient particle MCMC algorithm to address this problem. We illustrate the efficacy of our proposed approach on both synthetic and real-world problems.</div>

>Magister Scientiae - MSc / Molecular methods were used to investigate the microbial diversity and community structure of ammonia-oxidizing bacteria (AOB) associated with the roots of the Proteaceae plant family. The identification of ammonia oxidizing bacteria in this ecosystem is of particular interest since Proteaceae are adapted to acidic, low nutrient (e.g. nitrogen) soils. The ammonia monooxygenase operon was used as a molecular marker to identify ammonia-oxidizing bacteria associated with the proteoid roots of the three Proteaceae members and compared to non-plant associated soil. PCR amplification using primer sets targeting the ammonia monooxygenase gene (amoA subunits) were used to construct a clone library. Sequence diversity was determined by RFLP analysis of amoA to identify major groups of AOB of the ~-subclass of Proteobacteria in total community DNA, and DNA sequencing and phylogenetic analysis were also applied. DGGE analysis was performed to determine the community structure and distribution of ammonia-oxidizing bacteria in plant-associated and non-plant associated soils. The AOB genotypic diversity was similar in the plant-associated samples and non-plant associated soil. All AOB phylotypes belonged to Nitrosospira species and clustered with Nitrosospira cluster 3. The abundance of the amoA was quantified to be approximately 4.2 x 107 copies/g of dry soil, using a real-time PCR assay. These data suggest that the Nitrosospira species are the dominant phylotypes in that environment. This investigation provides new insights into the relationships between plants and ammonia-oxidizing bacteria in natural Fynbos ecosystems.