Student no:7719196 PhD thesis 2005 Faculty of Science, School of Animal, Plant and Environmental Sciences. / This study aimed to investigate the phylogeny of Cineraria L. to elucidate its position in the tribe Senecioneae (Asteraceae), to delimit its generic and species boundaries, explore species relationships (infrageneric structure) and produce a monograph of the genus. It also aimed to examine its distribution, phytogeographic affinities, levels of rarity and endemism in Cineraria, to identify some of the factors contributing to rarity in Cineraria and to highlight implications for conservation. Phylogenetic analyses were performed using morphological and molecular (DNA sequence) characters to elucidate relationships within the genus and between Cineraria and selected related genera in the subtribe Senecioninae. The phylogenetic species concept was applied - suites of diagnostic characters were used to characterise species. The phenetic approach, using Cluster Analysis and Principal Coordinates Analysis, was applied to investigate variation in two highly variable species, C. deltoidea Sond. and C. lobata L’Hér. Species distributions were mapped and the number of species per degree square was plotted for southern Africa to identify centres of diversity and endemism. Rare species were identified and categorised according to Rabinowitz’s criteria of geographic range, habitat specificity and local population size. Cineraria now has a more homogenous generic concept, characterised as herbs or subshrubs with palmately veined leaves, radiate, calyculate capitula, penicillate style apices and obovate, compressed cypselae with two distinct margins or wings and a substantial carpopodium. Eleven species have been removed from the genus and two new genera, Bolandia Cron and Oresbia Cron & B.Nord. have been established to accommodate three of the species. Two species have been reassigned to and another reinstated in Senecio L. The affinities of five species remain unresolved. Cineraria now comprises 35 species with four new subspecies and two new varieties recognised. Eight species have been placed in synonymy and five new species have been described during this revision. The status of C. deltoidea as a single, highly variable species, widespread throughout the eastern mountains of Africa, has been confirmed. Cineraria lobata has been shown to be a very variable species and the geographic and morphological variation has been formally (and informally) recognised. No infrageneric classification has been applied to Cineraria as a robust phylogeny of all the species has yet to be hypothesised. A southern African origin for Cineraria in the Western and/or Eastern Cape is postulated, based on the current distribution of the sister genus Bolandia and Cineraria mollis DC. iv Cineraria appears to have undergone rapid speciation fairly recently, as indicated by the lack of variation in the molecular data analysed, with reticulate evolution playing an important role in its evolutionary history (as seen by the lack of congruence between the chloroplast and nuclear DNA sequences). The centre of diversity of Cineraria is the KwaZulu-Natal Midlands, part of the Maputaland-Pondoland Centre of endemism in southern Africa. Cineraria has an afromontane affinity, and fifteen species endemic to specific mountains or regions of endemism and five near-endemics have been identified in Cineraria. Eleven species have been shown to be rare (in the sense of low abundance, restricted range and high habitat specificity), however only five are considered to be threatened as indicated by IUCN Red Data Criteria. However, at least seven species are Data Deficient and require further investigation. Causes of rarity in Cineraria are linked to narrow habitat specificity, particularly soil or rock type and/or altitudinal range.

Since Darwin proposed that all species on the earth have evolved from a common ancestor, evolution has played an important role in understanding biology. While the evolutionary relationships/histories of genes are represented using trees, the genomic evolutionary history may not be adequately captured by a tree, as some evolutionary events, such as horizontal gene transfer (HGT), do not fit within the branches of a tree. In this case, phylogenetic networks are more appropriate for modeling evolutionary histories. In this dissertation, we present computational algorithms to reconstruct phylogenetic networks from different types of data. Under the assumption that species have single copies of genes, and HGT and speciation are the only events through the course of evolution, gene sequences can be sampled one copy per species for HGT detection. Given the alignments of the sequences, we propose systematic methods that estimate the significance of detected HGT events under maximum parsimony (MP) and maximum likelihood (ML). The estimated significance aims at addressing the issue of overestimation of both optimization criteria in the search for phylogenetic networks and helps the search identify networks with the ``right" number of HGT edges. We study their performance on both synthetic and biological data sets. While the studies show very promising results in identifying HGT edges, they also highlight the issues that are challenging for each criterion. We also develop algorithms that estimate the amount of HGT events and reconstruct phylogenetic networks by utilizing the pairwise Subtree-Prune-Regraft (SPR) operation from a collection of trees. The methods produce good results in general in terms of quickly estimating the minimum number of HGT events required to reconcile a set of trees. Further, we identify conditions under which the methods do not work well in order to help in the development of new methods in this area. Finally, we extend the assumption for the genetic evolutionary process and allow for duplication and loss. Under this assumption, we analyze gene family trees of proteobacterial strains using a parsimony-based approach to detect evolutionary events. Also we discuss the current issues of parsimony-based approaches in the biological data analysis and propose a way to retrieve significant estimates. The evolutionary history of species is complex with various evolutionary events. As HGT contributes largely to this complexity, accurately identifying HGT will help untangle evolutionary histories and solve important questions. As our algorithms identify significant HGT events in the data and reconstruct accurate phylogenetic networks from them, they can be used to address questions arising in large-scale biological data analyses.

Hybridization is an important mechanism in diversification. It often makes taxonomy difficult. Lack of strong supported intrageneric classification in genus Pteris (Pteridaceae) could be caused by natural hybridization. Most hybridization documnted in Pteris was based on limited evidence. This study focuses on Pteris cadieri complex, the taxon with putative hybridization. The species complex displayed significant morphological variation and was associated with hybrid origin. Reproductive biology revealed variation in spore number per sporangium, spore size, spore shape and apogamous reproduction, which imply its hybrid origin. Cytology analysis using chromosome counting and flow cytometry identified diploids, triploids, and tetraploids. CpDNA and nuclear DNA supported that Pteris cadieri complex is hybrid origin: paternal and maternal lineages were inferred and 11 taxa were identified. Furthermore, comparing materials form Hainan and Taiwan, , it is clear that the species complex is composed by taxa arisen from multiple hybridization. Systematic inconsistency existed between chloroplast and nuclear phylogenies in Pteris impled that other taxa might have involved in hybridization events, in addition to the Pteris cadieri complex. Hybridization may be very common in Pteris. To infer intrageneric taxonomy of Pteris, effect of reticulate evolution should never be neglected. Finally, based on morphological and evolutionary traits, the taxonomy of Pteris cadieri complex is revised. There are Pteris cadieri Christ, Pteris dimorpha Copel. var. dimorpha, Pteris dimorpha var. plumbea (Christ) Y.-S. Chao, H.-Y. Liu & W.-L. Chiou, Pteris grevilleana Wall. ex Agardh var. grevilleanan, Pteris grevilleana Wall. ex Agardh var. ornata Alderw., and Pteris hainanensis Ching.

<p>The <italic>Polypodium vulgare<italic> complex (Polypodiaceae) comprises a well-studied group of fern taxa whose members are cryptically differentiated morphologically and have generated a confusing and highly reticulate species cluster. Once considered a single species spanning much of northern Eurasia and North America, <italic>P. vulgare<italic> has been segregated into approximately 17 diploid and polyploid taxa as a result of cytotaxonomic work, hybridization experiments, and isozyme studies conducted during the 20th century. Despite considerable effort, however, the evolutionary relationships among the diploid members of the <italic>P. vulgare<italic> complex remain poorly resolved, and several taxa, particularly allopolyploids and their diploid progenitors, remain challenging to delineate morphologically due to a dearth of stable diagnostic characters. Furthermore, compared to many well-studied angiosperm reticulate complexes, relatively little is known about the number of independently-derived lineages, distribution, and evolutionary significance of the allopolyploid species that have formed recurrently. This dissertation is an attempt to advance systematic knowledge of the <italic>Polypodium vulgare<italic> complex and establish it as a "model" system for investigating the evolutionary consequences of allopolyploidy in ferns. </p><p>Chapter I presents a diploids-only phylogeny of the <italic>P. vulgare<italic> complex and related species to test previous hypotheses concerning relationships within <italic>Polypodium<italic> sensu stricto. Analyses of sequence data from four plastid loci (<italic>atpA<italic>, <italic>rbcL<italic>, <italic>matK<italic>, and <italic>trnG-trnR<italic>) recovered a monophyletic <italic>P. vulgare<italic> complex comprising four well-supported clades. The <italic>P. vulgare<italic> complex is resolved as sister to the Neotropical <italic>P. plesiosorum<italic> group and these, in turn, are sister to the Asian endemic <italic>Pleurosoriopsis makinoi<italic>. Divergence time analyses incorporating previously derived age constraints and fossil data provide support for an early Miocene origin for the <italic>P. vulgare<italic> complex and a late Miocene-Pliocene origin for the four major diploid lineages of the complex, with the majority of extant diploid species diversifying from the late Miocene through the Pleistocene. Finally, node age estimates are used to reassess previous hypotheses, and to propose new hypotheses, about the historical events that shaped the diversity and current geographic distribution of the diploid species of the <italic>P. vulgare<italic> complex. </p><p>Chapter II addresses reported discrepancies regarding the occurrence of <italic>Polypodium calirhiza<italic> in Mexico. The original paper describing this taxon cited collections from Mexico, but the species was omitted from the recent <italic>Pteridophytes of Mexico<italic>. Originally treated as a tetraploid cytotype of <italic>P. californicum<italic>, <italic>P. calirhiza<italic> now is hypothesized to have arisen through hybridization between <italic>P. glycyrrhiza<italic> and <italic>P. californicum<italic>. The allotetraploid can be difficult to distinguish from either of its putative parents, but especially so from <italic>P. californicum<italic>. These analyses show that a combination of spore length and abaxial rachis scale morphology consistently distinguishes <italic>P. calirhiza<italic> from <italic>P. californicum<italic> and confirm that both species occur in Mexico. Although occasionally found growing together in the United States, the two species are strongly allopatric in Mexico, where <italic>P. californicum<italic> is restricted to coastal regions of the Baja California peninsula and neighboring Pacific islands and <italic>P. calirhiza<italic> grows at high elevations in central and southern Mexico. The occurrence of <italic>P. calirhiza<italic> in Oaxaca, Mexico, marks the southernmost extent of the P. vulgare complex in the Western Hemisphere.</p><p>Chapter III examines a case of reciprocal allopolyploid origins in the fern <italic>Polypodium hesperium<italic> and presents it as a natural model system for investigating the evolutionary potential of duplicated genomes. In allopolyploids, reciprocal crosses between the same progenitor species can yield lineages with different uniparentally inherited plastid genomes. While likely common, there are few well-documented examples of such reciprocal origins. Using a combination of uniparentally inherited plastid and biparentally inherited nuclear sequence data, we investigated the distributions and relative ages of reciprocally formed lineages in <italic>Polypodium hesperium<italic>, an allotetraploid fern that is broadly distributed in western North America. The reciprocally-derived plastid haplotypes of <italic>Polypodium hesperium<italic> are allopatric, with populations north and south of 42&#730; N latitude having different plastid genomes. Biogeographic information and previously estimated ages for the diversification of its diploid progenitors, lends support for middle to late Pleistocene origins of <italic>P. hesperium<italic>. Several features of <italic>Polypodium hesperium<italic> make it a particularly promising system for investigating the evolutionary consequences of allopolyploidy. These include reciprocally derived lineages with disjunct geographic distributions, recent time of origin, and extant diploid progenitor lineages. </p><p>This dissertation concludes by demonstrating the utility of the allotetraploid <italic>Polypodium hesperium<italic> for understanding how ferns utilize the genetic diversity imparted by allopolyploidy and recurrent origins. Chapter IV details the use of high-throughput sequencing technologies to generate a reference transcriptome for <italic>Polypodium<italic>, a genus without preexisting genomic resources, and compare patterns of total and homoeolog-specific gene expression in leaf tissue of reciprocally formed lineages of <italic>P. hesperium<italic>. Genome-wide expression patterns of total gene expression and homoeolog expression ratios are strikingly similar between the lineages--total gene expression levels mirror those of the diploid progenitor P. amorphum and homoeologs derived from <italic>P. amorphum<italic> are preferentially expressed. The unprecedented levels of unbalanced expression level dominance and unbalanced homoeolog expression bias found in <italic>P. hesperium<italic> supports the hypothesis that these phenomena are pervasive consequences of allopolyploidy in plants.</p> / Dissertation

Orientador: João Semir / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T09:13:52Z (GMT). No. of bitstreams: 1 Oliveira_RenataSouzade_D.pdf: 18742422 bytes, checksum: 60b13be02b7671ce99e0f011e441ee1e (MD5) Previous issue date: 2012 / Resumo: O gênero Hippeastrum Herb. pertence à família Amaryllidaceae, subfamília Amaryllidoideae. Compreende cerca de 50 espécies, distribuídas na América do Sul, sendo no Brasil representado por 27 espécies e 11 nomes duvidosos. Hippeastrum Herb. revelou-se como um grupo monofilético nos últimos trabalhos de filogenia com dados moleculares e caracteriza-se principalmente pelo número cromossômico básico x=11, folhas geralmente loriformes, inflorescência com brácteas espatais livres, flores zigomorfas, seis estames em quatro comprimentos diferentes e corona geralmente presente. O presente estudo apresenta revisão bibliográfica, com o levantamento das espécies de Hippeastrum ocorrentes no Brasil, chave de identificação, descrições e mapas de distribuição. Hippeastrum é tradicionalmente subdividido em cinco subgêneros caracterizados por atributos florais, muitos dos quais de delimitação controversa. Foram investigadas as relações entre as espécies brasileiras e testou-se o monofiletismo dos subgêneros com base em dados de sequência de DNA. Para isto, diversos marcadores de DNA plastidial foram testados; mesmo os mais polimórficos (trnH-psbA e trnK-matK) forneceram poucos dados e incongruentes com dados de rDNA (ITS e 5S-NTS). Dados de rDNA possibilitaram o reconhecimento e análise de indivíduos heterozigotos, com padrões condizentes com eventos de hibridização, que podem ser observados em populações de espécies simpátricas. As incongruências, recombinações e compartilhamento de haplótipos foram explorados por meio de "networks". Os subgêneros revelaram-se polifiléticos; os atributos morfológicos utilizados para seu reconhecimento, bem como para as diferentes espécies, estão associados as síndromes e biologia da polinização. Com auxílio da análise discriminante e reconstrução de estado ancestral, averiguou-se a correlação de atributos florais, principalmente morfométricos, com a delimitação de espécies e grupos revelados pelas inferências filogenéticas. As espécies são bem delimitadas por atributos florais, mas os clados testados não foram corroborados pela morfologia, reafirmando a hipótese de que os eventos evolutivos estão ligados à proximidades geográfica e que os estados de caracteres acompanham as pressões de polinização. A reconstrução do estados dos caracteres revelou que a corona em placas é uma sinapomorfia do clado formado por H. aulicum e H. calyptratum. Além disso detectou-se sobreposições morfológicas entre espécies de Hippeastrum e gêneros próximos, tornando difícil uma delimitação morfológica precisa dos grupos / Abstract: The genus Hippeastrum Herb. belongs to family Amaryllidaceae, subfamily Amaryllidoideae, and comprises about 50 species, distributed in South America; in Brazil is represented by 27 species and 11 doubtful names. Hippeastrum Herb. revealed as a monophyletic group in recent studies of phylogeny with molecular data; it is characterized by cromossomic basic number x=11, leaves usually loriform, free bracts in inflorescence, zygomorphic flowers, six stamens with four different lengths, and corona usually present. This work presents a bibliographic review, a inventory of Hippeastrum species that occur in Brazil, identification key, descriptions and distribution maps. Hippeastrum Herb. is typically divided into five subgenera, characterized by floral attributes, many with controversial delimitation. The relationship between Brazilian species and the monophyly of its subgenera based on DNA sequence data were investigated. Various plastid DNA markes were tested; even the most polymorphic ones (trnH-psbA and trnK-matK) provided little evidence and are incongruente whith rDNA (5S-NTS). The rDNA data allow the recognition and analysis of heterezygous individuals, with patterns consistente with hybridization events, which can be observed in populations of sympatric species. Incongruence, recombination, and sharing of haplotypes were explored with networks. Subgenera are polyphyletic; morphological attributes used for their recognition, as well as for different species, are associated with syndromes and pollination biology. With discriminant analysis and reconstruction of ancestral state, the correlation of floral traits, particularly morphometric, with the delimitation of species and groups revealed by phylogenetic inferences were investigated. The species are clearly discriminate by their floral traits, but the clades tested were not corroborated by the morphology, confirming the hypothesis that the evolutionary events related to geographic proximity and the characters arose from the pressures of pollination. The reconstruction of character states revealed that the corona in plaques is a synapomorphy of the clade formed by H. aulicum and H. calyptratum. In addition, morphological superposition between Hippeastrum species and correlated genera was found, making it difficult a accurate morphological delimitation of groups / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

[pt] Um politopo convexo é semiregular se todas as suas faces forem regulares e o grupo de isometrias agir transitivamente sobre os vértices. A classificação dos politopos semiregulares inclui algumas famílias infinitas, algumas exceções em dimensão baixa e uma família, os politopos de Gosset, que está definida para dimensão entre 3 e 8. Certos grupos de isometrias de R(n) gerados por reflexões são chamados grupos de Coxeter. A classificação dos grupos de Coxeter inclui três famílias infinitas, algumas exceções em dimensão menor ou igual a 4 e os grupos excepcionais E(6), E(7) e E(8). O grupo E(n) é o grupo das isometrias do politopo de Gosset em dimensao n. Nesta dissertação construiremos os grupos de Coxeter En, os politopos de Gosset e indicaremos a relação destes objetos com os reticulados e as álgebras de Lie também conhecidos como E(n). / [en] A convex polytope is semiregular if all its faces are regular and the group of isometries acts transitively over vertices. The classification of semiregular polytopes includes a few infinite families, some low dimensional exceptions and a family, the Gosset polytopes, which is defined for dimension 3 to 8. Certain groups of isometries of R(n) generated by reflections are called Coxeter groups. The classification of finite Coxeter groups includes three infinite families, some exceptions in dimension 4 or lower and the exceptional groups E(6), E(7) and E(8). The group En is the group of isometries of the Gosset polytope in dimension n. In this dissertation we construct the Coxeter groups En, the Gosset polytopes and indicate the relationship of these objects with the lattices and Lie algebras which are also known as E(n).

In culture, exposure to penicillin and other stressors induce chlamydiae to enter a non-infectious but viable state termed persistence. Chlamydiae may reenter their normal developmental cycle after stressor removal. Though aberrant RB similar to those present in culture models of persistence have been observed within infected tissues, the existence of persistent chlamydiae has not been definitively demonstrated in vivo. As a result, the role of persistent organisms in pathogenesis is undefined. In order to establish an experimentally tractable model of in vivo persistence, Chlamydia muridarum vaginally-infected mice were gavaged with either water or amoxicillin (amox). Vaginal swabs were collected for chlamydial titration and RNA isolated for quantification of pre-16s rRNA. Uterine tissue was analyzed by transmission electron microscopy (TEM). Although amox-treatment reduced vaginal shedding by >99%, C. muridarum pre-16s rRNA accumulation was unchanged by treatment. These data indicate that the amox-exposed organisms were viable but not infectious. Furthermore, TEM analyses demonstrated that inclusions in amox-treated animals contained primarily large, aberrant RB, but those observed in untreated control animals were normal. Collectively, these data suggest that amoxicillin treatment induces C. muridarum to enter the persistent state in vivo. This model also represents the first experimentally tractable animal model of chlamydial persistence.

No description available.

J'étudie la formation du système vasculaire des feuilles des plantes à l'aide de modèles mathématiques. L'hypothèse de canalisation d'une phytohormone, l'auxin, stipule que l'auto activation de son transport entre les cellules crée des chemins préférentiels qui se différencieront plus tard en système vasculaire. J'entreprends une analyse numérique de modèles de canalisation sur une grande matrice et parviens à créer des motifs branchés dans lesquels circule l'auxin. Une analyse de stabilité d'un modèle simplifié nous éclaire sur les raisons de la formation de ces motifs et l'impossibilité de créer un réseau réticulé. La majorité des plantes ayant un système vasculaire réticulé, je modifie le modèle de façon à obtenir ce type de réseau. En ajoutant une variable biologiquement plausible je parviens à créer un réseau réticulé dans lequel l'auxin circule uniformément. Enfin, je discute des relations entre la formation du système vasculaire et de la spirale de phyllotaxie.

This thesis comprises studies of the phylogenetic relationships in the flowering plant clade Potentilleae in Rosaceae. The relationships were elucidated by using DNA sequence data from the nuclear genome as well as from the plastid genome. In particular, the focus of the studies was the investigation of allopolyploidy, i.e. speciation as a result of hybridization and subsequent chromosome doubling. A phylogenetic method was used for identifying allopolyploidy through comparison of trees resulting from the analyses of different DNA sequences. Five sub-clades were investigated. First, both the sister clades that together contain all of Potentilleae: Fragariinae and Potentilla. Secondly, three subclades of Fragariinae, namely Alchemilla in wide sense, Sibbaldia and relatives, and Fragaria. The aim was to unravel the phylogenetic relationships, including instances of allopolyploidy. Classification issues were discussed in relation to the phylogenetic results. The split between Potentilla (=Potentillinae) and Fragariinae received better support than in previous studies. The phylogeny of Fragariinae was found to be consistent with classifying ten genera: Alchemilla in wide sense (incl. Aphanes and Lachemilla), Comarum, Sibbaldia, Sibbaldianthe, Sibbaldiopsis, Chamaerhodos, Drymocallis, Dasiphora, Potaninia, Fragaria, and also including a few orphan Potentilla species. The segregated genera Ivesia, Horkelia, Horkeliella and Duchesnea were found to be nested within Potentilla, corroborating earlier studies, while the segregated genus Argentina (P. anserina and close relatives) showed an ambiguous position. Plastid and nuclear (ribosomal) phylogenies were compared and incongruences were detected as potential instances of allopolyploid speciation. Five strongly supported incongruences were detected in Fragariinae and four of them were considered to be potentially caused by allopolyploidy. In addition, five supported incongruences were found in Potentilla. Alchemilla in the wide sense was found to contain four major clades, African Alchemilla, Eurasian Alchemilla, Lachemilla and Aphanes. Both Lachemilla and Aphanes were nested within Alchemilla and it was suggested that the name Alchemilla should be used in the wide sense, i.e. including both the genera Lachemilla and Aphanes. The genus Sibbaldia as commonly classified was shown to be polyphyletic in five different places in Potentilleae. Three Sibbaldia clades ended up in Fragariinae and two in Potentilla. A phylogeny of Fragaria, based on a nuclear low/single copy DNA region was estimated. The gene copy phylogeny was used to construct a reticulate tree hypothesizing allopolyploid speciation events. The evolution of Fragaria was shown to have been shaped by polyploidy. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.