This thesis represents a critical taxonomical review of the fungal genus Cryphonectria sensu lato. An appropriate taxonomy for this group is of great importance because it includes many well known tree pathogens such as the chestnut blight fungus Cryphonectria parasitica and the Eucalyptus canker pathogen Cryphonectria cubensis. The many taxonomic changes introduced in studies presented in this thesis have largely arisen as a result of DNA sequence comparisons for Cryphonectria spp. that show that Cryphonectria sensu lato is comprised of different lineages, strongly supported by robust morphological characteristics. New taxa, of which many are pathogenic, have also been discovered. The expanded number of species of Cryphonectria and related genera as well as the consideration of large numbers of isolates has furthermore made it possible to establish a broad view of the group at the super-generic level. The first part of the thesis deals with studies on Cryphonectria cubensis. A new genus Chrysoporthe is described for C. cubensis sensu lato. Two additional species are also described for phylogenetic sub-clades previously known as C. cubensis. These include Chrysoporthe austroafricana, representing all isolates from South Africa, and an anamorphic species described in the new genus Chrysoporthella as Chrysop. hodgesiana, which is currently only known from Colombia on native Tibouchina spp. Isolate collections from several new host genera for Chr. cubensis are also characterized. Collections from Eucalyptus in Cuba, now representing the epitype of Chr. cubensis, also define the type of Chr. cubensis as residing in the South American sub-clade. Another new species, Chrysoporthe inopima from Tibouchina lepidota in Colombia is described as well as a new species Chrysoporthe doradensis for isolates from Eucalyptus spp. in Ecuador. A new family Cryphonectriaceae is described in this thesis for Cryphonectria, Chrysoporthe and Endothia. Genera in this family are united by orange stromatic tissue, with the pigments colouring purple in 3% KOH and yellow in lactic acid. The existence of this new family confirms the close relationship of Cryphonectria and morphologically similar genera. A proposal to conserve the name Cryphonectria against the new type C. parasitica is presented. This is required because Cryphonectria gyrosa, the currently accepted type, was erroneously used as type. The conservation of Cryphonectria against C. parasitica made it possible to describe the new genus Amphilogia for C. gyrosa. Amphilogia also includes a second species from New Zealand described as Amphilogia major, although no isolates currently exist for this species. New genera for existing Cryphonectria spp., as well as newly discovered fungi are presented in this thesis. The new genus Rostraureum is established for a fungus pathogenic on Terminalia ivorensis in Ecuador. This fungus also represents a new species, Rostraureum tropicale. Cryphonectria longirostris, originating from Puerto Rico, Trinidad and Tabago, is also transferred to Rostraureum. A fungus morphologically similar to Chrysoporthe on native Tibouchina, Miconia and exotic Eucalyptus spp. in Colombia, is described as Aurapex penicillata gen. sp. nov. Cryphonectria havanensis is transferred to the new genus Microthia. Cryphonectria coccolobae also resides in this genus based on morphology, although its phylogenetic relationship to C. havanensis could not be confirmed due the absence of isolates. A new fungus was discovered during surveys for C. coccolobae on Coccoloba uvifera in Florida, which is described in the new genus Ursicollum as U. fallax. Phylogenetic analyses in this study also clearly distinguish Cryphonectria eucalypti from Cryphonectria, and this fungus is thus transferred to the new genus Holocryphia. A minireview is presented at the end of the thesis and discusses the new taxonomic concepts developed for Cryphonectria during this thesis, and recent studies by other authors. The review describes how this new taxonomic scheme has changed our view and understanding of the distribution and ecology of Cryphonectria sensu stricto from what it has traditionally been seen. The final part of the thesis is written in the form of a monograph. It contains background information of all the species, including many pathogens, currently known in Cryphonectria and allied genera. The majority of these have recently been described, some in this thesis, and this chapter thus contains all recent information pertaining to them. It is intended that this monograph should be useful as a manual, enabling users to work with and isolate these fungi and to identify the different taxa based on morphology and phylogenetic relationships. The studies presented in this thesis greatly change the taxonomy of Cryphonectria sensu lato, which is now seen as representing a large number of genera and species in a new family. Many would argue that Cryphonectria is still monophyletic, but the different lineages shown by DNA sequence comparisons are morphologically inordinately diverse, and clearly represent different genera. Studies presented in this thesis further suggest that additional genera await description from diverse geographical areas and ecological niches. The studies presented in this thesis will hopefully provide a foundation against which these new taxa can be compared and will improve our understanding of tree diseases. / Thesis (PhD)--University of Pretoria, 2009. / Microbiology and Plant Pathology / Unrestricted

RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing technologies [1]. A plethora of tools have been developed to analyze and visualize the transcriptome data from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] [3]. This allows for analysis of most reads produced by the experiments, but these tools typically discard reads that do not match well with the reference genome. This additional information could reveal important insight into the experiment and possible contributing factors to the condition under consideration. We introduce PARSES, a pipeline constructed from existing sequence analysis tools, which allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition.

Submitted by Mario BC (mario@bc.ufrpe.br) on 2016-06-28T12:14:06Z No. of bitstreams: 1 Ewerton Pereira de Oliveira.pdf: 3097383 bytes, checksum: 9fa977ae687b83d00d6da838bc685cb5 (MD5) / Made available in DSpace on 2016-06-28T12:14:06Z (GMT). No. of bitstreams: 1 Ewerton Pereira de Oliveira.pdf: 3097383 bytes, checksum: 9fa977ae687b83d00d6da838bc685cb5 (MD5) Previous issue date: 2015-07-30 / Sagital otoliths were analyzed trying to identify possible relationships among shape groups and environmental, biological and taxonomical variables of fishes. Five hundred otoliths images of different species were obtained. Cluster analysis by Ward's criterion was used in order to form similar otolith groups based on their shapes. This method was applied at two different times: 1) using a matrix of normalized Fourier coefficients, obtained by Fourier Elliptical analysis and Euclidean distance as similarity measure; and 2) using a similarity matrix produced by "TO distance ". Thirteen otolith morphotypes, validated by the silhouette graph, were obtained from both procedures. However, "TO distance" was more efficient, getting more heterogeneous shapes among groups and homogeneous shapes within them. Based on the groups obtained from “TO Distance”, simple correlation analysis was carried out to investigate the relationship among otolith shapes and fish variables. Results showed that the variables related to sulcus acusticus, such as position, depth and shape, were the most significant, getting a percentage of explanation of 100% of the total variability among shape groups. It follows that the results presented here can help to explain how otolith shape varies in function of fish species characteristics. / Otólitos sagita foram analisados buscando identificar possíveis relações entre os grupos de forma do mesmo com as características ambientais, biológicas e taxonômicas de peixes. Quinhentas imagens de otólitos sagita de espécies diferentes foram obtidas sendo estas imagens associadas a um arquivo com informações biológicas, ambientais e taxonômicas dos otólitos. A análise de agrupamento, através do critério de Ward, foi utilizada com o objetivo de formar grupos de otólitos semelhantes quanto a sua forma. Este método foi aplicado em dois momentos distintos, o primeiro utilizando a matriz dos coeficientes de Fourier normalizados, obtidos pela análise de Fourier Elíptica, tendo a distância Euclidiana como indicador de similaridade entre os otólitos e o segundo momento utilizando uma matriz de similaridade produzida pelo “TO distance”, onde foram estabelecidos 13 morfotipos de otólitos quanto a sua forma, estes validados por meio do gráfico da silhueta. Foi possível identificar que o “TO distance” mostrou ser uma medida de similaridade eficiente na separação das imagens, obtendo morfotipos mais heterogêneos entre os grupos e mais homogêneos dentro deles. A análise de correspondência simples mostrou que as variáveis relacionadas aos sulcos acústicos, como posição, profundidade e forma da cauda foram as que mais se destacaram, obtendo um percentual de explicação de 100% da variabilidade total dos dados para as duas dimensões juntas. Os resultados obtidos pelos métodos multivariados facilitaram a interpretação das inter-relações entre os treze grupos e as categorias das variáveis, mostrando como a forma dos otólitos e suas características podem influenciar na vida das espécies.

The ground beetles are one of the most worthwhile model groups of organisms for the indication of quality of environment due to their advantages such as simple identification, well known ecology of most species and described distribution. In this thesis I present the suitability of assemblages of ground beetles to evaluate the conservation value in two types of environment: (1) open forest in medium and lower altitudes, (2) post-mining biotopes as quarries and black coal dumps. I also discuss possible limitation of ground beetles as valid bioindicators and I recommend multi-taxonomical approach in ecological studies.

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