Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic...

Garry oak (Quercus garryana Douglas ex. Hook) is a white oak (Quercus sect. Quercus) with a geographic range extending from southwestern BC to south-central California. It is the only native white oak in BC and Washington, and is the northernmost species of the California Floristic Province-Pacific Northwest white oak clade. I used molecular methods to address the following questions: 1) What are the patterns of genetic variation within Garry oak? 2) How do these patterns vary geographically, and how did the spatial distribution of the gene lineages come to occupy its current geographical range? 3) Does Garry oak show evidence of genetic interaction with other white oak species in western North America? 4) Is there morphological or genetic evidence to support the three described varieties of Garry oak? I obtained samples of Garry oak from 117 localities over its geographic range, as well as samples of two other California white oaks (Q. lobata and Q. douglasii) and a Rocky Mountain species (Q. gambelii). Analyses of DNA sequence data from four plastid DNA regions revealed 24 distinct molecular variants (haplotypes) in Garry oak. These show a strong south-to-north decrease in genetic diversity, consistent with post-glacial northward expansion. Haplotypes present in the northern part of the range provide evidence of two separate northward migrations, only one of which reached the northern range limit of Garry oak in BC. I found that Garry oak shared plastid DNA haplotypes with two other white oak species, indicating that it hybridizes with other oaks in the southern part of its range. The nuclear ribosomal ITS phylogeny showed poor resolution, but both cpDNA and nrDNA may indicate that Q. garryana is more closely related to the white oaks of central North America than was previously thought. My findings also suggest that the three currently recognized varieties of Garry oak (var. garryana, breweri and semota) are not well differentiated genetically, but show morphological variation at the regional level. This study shows the phylogeographic patterns within Q. garryana. In addition, it contributes to conservation efforts in Garry oak ecosystems by indicating regions of high genetic diversity in Garry oak, including genetically unique populations that may be especially worthy of preservation. / Graduate

<em>Cladophora</em> is a widespread freshwater filamentous cholorophyte genus and is frequently observed in eutrophic waters where it can produce large nuisance blooms. These blooms can have direct impacts on water intake for power generation, irrigation canals and can be aesthetically unpleasant. Much of the ecological and physiological studies on <em>Cladophora</em> have assumed that the populations of this genus in North America belong to the species <em>Cladophora glomerata</em>. However, this has never been tested despite that it is well documented that identifying freshwater <em>Cladophora</em> to the species level is difficult due morphological variability under different ecological conditions. In addition, the species epithets for freshwater <em>Cladophora</em> are based on European collections and it is not clear if these should be applied to North America. This study examines approximately 40 collections of <em>Cladophora</em> from the Laurentian Great Lakes and 43 from various locations in North America ranging from the Northwest Territories to Puerto Rico. Initially we determined the nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron and observed sequence divergence to be low (0-3%), demonstrating an inability for this marker to resolve species delineation as divergence of this region was low. Amplification of the inter-simple sequence repeat (ISSR) regions were used to analyze microsatellite motif frequency throughout the genome to evaluate the biogeography relationships, including diversity, of freshwater <em>Cladophora</em> sp. five different primers were used on 70 individuals. UPGMA analyses of the presence/absence of bands demonstrate that each of the Great Lake populations separate into groups according to the Lake they were initially sampled from. However, collections from North America are highly variable and do not form well supported biogeographic clades. In addition, these collections appear to be distinct from type cultures of freshwater <em>Cladophora</em> from Europe. Supplementary morphological analysis using suggested taxonomically valid criterion (length and diameter of main axis, ultimate branch, and apical cell) none were able to differentiate Great Lake populations.

<em>Cladophora</em> is a widespread freshwater filamentous cholorophyte genus and is frequently observed in eutrophic waters where it can produce large nuisance blooms. These blooms can have direct impacts on water intake for power generation, irrigation canals and can be aesthetically unpleasant. Much of the ecological and physiological studies on <em>Cladophora</em> have assumed that the populations of this genus in North America belong to the species <em>Cladophora glomerata</em>. However, this has never been tested despite that it is well documented that identifying freshwater <em>Cladophora</em> to the species level is difficult due morphological variability under different ecological conditions. In addition, the species epithets for freshwater <em>Cladophora</em> are based on European collections and it is not clear if these should be applied to North America. This study examines approximately 40 collections of <em>Cladophora</em> from the Laurentian Great Lakes and 43 from various locations in North America ranging from the Northwest Territories to Puerto Rico. Initially we determined the nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron and observed sequence divergence to be low (0-3%), demonstrating an inability for this marker to resolve species delineation as divergence of this region was low. Amplification of the inter-simple sequence repeat (ISSR) regions were used to analyze microsatellite motif frequency throughout the genome to evaluate the biogeography relationships, including diversity, of freshwater <em>Cladophora</em> sp. five different primers were used on 70 individuals. UPGMA analyses of the presence/absence of bands demonstrate that each of the Great Lake populations separate into groups according to the Lake they were initially sampled from. However, collections from North America are highly variable and do not form well supported biogeographic clades. In addition, these collections appear to be distinct from type cultures of freshwater <em>Cladophora</em> from Europe. Supplementary morphological analysis using suggested taxonomically valid criterion (length and diameter of main axis, ultimate branch, and apical cell) none were able to differentiate Great Lake populations.

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

To improve fungal identification using a single DNA sequence, I introduce the Barcode Similarity Group (BSG) defined as a cluster of sequences that share greater than or equal to a threshold amount of genetic similarity with each other. As a test case, I created 393 BSGs from 2463 Cortinarius ITS sequences using a 94% similarity cut-off value in DOTUR. Some BSGs may contain multiple species. The BSG database was used to label environmental sequences, find misidentified or mislabeled sequences, and find potential cryptic species and novel species. Expert taxonomists will be needed to perform detailed morphological and phylogenetic studies to identify the individual species within each BSG. The main advantage of using BSGs is that it clusters together sequences using total genetic relatedness and does not rely on any taxonomy for identification. A website was created where the RDP Classifier is used to classify a query sequence into a BSG.

Orientador: Ana Maria Goulart de Azevedo Tozzi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-09T03:16:51Z (GMT). No. of bitstreams: 1 Meireles_JoseEduardodeCarvalho_M.pdf: 5457639 bytes, checksum: 2254e34efd86c3760ca5a245abf9eaf6 (MD5) Previous issue date: 2007 / Resumo: Poecilanthe (Leguminosae, Papilionoideae, Brongniartieae) é em gênero sul-americano que inclui atualmente dez espécies. A heterogeneidade morfológica e química encontrada em Poecilanthe dificulta sua circunscrição e coloca em dúvida sua monofilia. Além disso, limites interespecíficos imprecisos e falta de chave de identificação dificultam o reconhecimento das espécies. Este trabalho tem como objetivos testar a monofilia de Poecilanthe e estabelecer as relações entre suas espécies, bem como revisar a taxonomia do gênero. Para tanto, uma análise filogenética de máxima parcimônia baseada em caracteres morfológicos e seqüências de ITS/5.8S (nrDNA) foi realizada. Como subsídio para a análise cladística, foi feito um estudo sobre a morfologia das sementes e embriões de Poecilanthe, que resultou no reconhecimento de quatro padrões distintos de morfologia. Os resultados da filogenia mostram que Poecilanthe não é um gênero monofilético, sendo composto por três clados parafiléticos em relação à tribo. Estes três clados foram caracterizados morfologicamente e considerados como gêneros distintos. Poecilanthe é recircunscrito para incluir apenas as espécies extra-amazônicas (Poecilanthe s.s.), compreendendo então seis espécies. O gênero Amphiodon é restabelecido, e P. ovalifolia combinada neste. Um gênero novo é descrito para incluir P. amazonica e P. hostmannii. Cada um destes gêneros foi tratado taxonomicamente, constando em cada tratamento descrições, ilustrações e chave para a identificação das espécies / Abstract: The genus Poecilanthe (Leguminosae, Papilionoideae, Brongniartieae) currently comprises ten South-American species. The morphological and chemical diversity that is found within this genus renders its circumscription imprecise and brings Poecilanthe¿s monophyly into question. This work aims to test the monophyly of Poecilanthe and to revise the taxonomy of the genus. A parsimony analysis based on both morphological and ITS/5.8S data was carried out. In order to provide characters to the cladistic analysis, the morphology of the seeds and embryos of Poecilanthe was analyzed, and resulted in the identification of four different morphological patterns. The phylogeny does not support Poecilanthe as monophyletic, but resolves three different well-supported lineages that are paraphyletic with respect to the tribe. These clades are morphologically characterized and ranked at the generic level. Poecilanthe is recircumscribed to include the six extra-Amazonian species only. The genus Amphiodon is reinstated and P. ovalifolia is combined. Poecilante amazonica and P. hostmannii are segregated into a new genus. Each genus was revised and descriptions, illustrations and identification key for the species are presented. / Mestrado / Biologia Vegetal / Mestre em Biologia Vegetal

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal native to the Andean region of South America and a staple crop for subsistence farmers in the altiplano of Bolivia and Peru. Downy mildew is the most significant disease of quinoa caused by the pathogen Peronospora farinosa f.sp. chenopodii Byford. This disease greatly impacts quinoa crops with yield losses up to 99%. As fungicides are expensive for farmers, the development of resistant cultivars appears to be the most efficient means for controlling downy mildew. The quinoa germplasm bank contains high amounts of genetic diversity, some of which exhibit mildew resistance. Methods for evaluating mildew severity are important for finding resistant genotypes that are useful in breeding programs. The main objectives of this study were to evaluate and investigate downy mildew resistance in quinoa through several different methods. A simple inoculation method was developed for downy mildew disease assessment by placing a damp piece of cheesecloth on a leaf, pipetting a known spore solution onto the cloth, and subjecting the plants to specific humidity cycles in a growth chamber. After inoculation of five quinoa-breeding lines in a growth chamber, accession 0654 was found to be the most resistant, while genotypes NL6 and Sayana showed moderate resistance. Each of these genotypes displayed some potential for resistance breeding programs. Investigation of the growth and development of P. farinosa through resistant and susceptible quinoa genotypes revealed fewer sporangiophores, hyphal strands, and haustoria among leaf tissues of accession 0654 than in the susceptible Chucapaca cultivar. Peronospora farinosa growth was detected in leaf, petiole, and stem tissues with polymerase chain reaction (PCR) using ITSP primers designed from the internal transcribed spacer (ITS) region of the pathogen. Scanning electron microscopy (SEM) also revealed that P. farinosa penetrated stomata via appressoria, secreted extracellular matrices during sporangia germination, grew intercellularly in leaf and petiole tissues, and exited leaf tissue through stomata. Future research requiring knowledge of resistant quinoa genotypes, P. farinosa growth and development, or inoculation methods for large numbers of small quinoa plants would benefit from this report.

Molecular and morphologic studies were used to determine the evolution, classification and differentiation of Nymphaea odorata. Molecular analyses of the nuclear internal transcribed spacer (ITS) region, the chloroplast trnL-F region, and inter-simple sequence repeat (ISSR) markers determined the variation present between and within two species of Nymphaea. The ITS region resulted in a phylogeny depicting strong separation between species (N. mexicana and N. odorata) and some separation between N. odorata's subspecies. The ITS region contained polymorphisms, which upon SAHN clustering and principle coordinate (PCOA) and minimum spanning tree (MST) analyses produced groups similar to the clades in the ITS phylogeny. Sixteen accessions were chosen for trnL-F analysis, where a subspecies-specific molecular marker was found. In most accessions the marker confirmed the original subspecies classification. Molecular analyses using ISSRs characterized among population variation in N. odorata and N. mexicana using five primers. ISSR markers among populations were highly variable within a species and were used in UPGMA, PCOA and MST analysis, which resulted in separation between the subspecies. Both univariate and multivariate analyses were performed on quantitative and qualitative morphological characters. An analysis of variance resulted in six morphological characteristics that were statistically significant (P< 0.05), the majority being leaf blade characteristics. Multivariate statistics of principle component analysis and discriminate analysis resulted in groups for each subspecies, both emphasized the importance of quantitative leaf blade characteristics. Overall, both morphology and molecular characteristics supported the classification of subspecies for ssp. odorata and ssp. tuberosa, due a lack of strong segregation of characteristics. / Master of Science

No description available.