The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A ( diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

Genome size in plants varies greatly; in angiosperms this variability can make a 2400- fold difference. This is why the subject of many studies is the attempt to explain these differences in various contexts. One of these is the phylogenetic viewpoint, which studies the relationships between genome size and different taxonomic groups. Many studies have been published so far which explore the plants of the temperate zone; there are however very few studies investigating genome size in tropical plants. For this reason, the subject of this thesis is the analysis of genome size in the pantropical family Costaceae Nakai. This family presently includes seven genera: Monocostus K.Schum., Dimerocostus Kuntze, Costus L., Paracostus C.D.Specht, Chamaecostus C.D.Specht & D.W.Stev, Hellenia Retz. and Tapeinochilos Miq., counting altogether about 300 species. The family is sister to the family Zingiberaceae, which has been notably better explored due to its economic importance. One of the aims of this thesis was a partial revision of the phylogeny published by Specht (2006). Molecular methods were used to analyse the phylogenetic relationships; these methods included classical sequencing of the trnL-F region and next-generation sequencing, where probes designed in advance were used to obtain the targeted genes....

Les virus à ARN - à l'exception des rétrovirus - représentent plus de 200 pathogènes humains et/ou vétérinaires majeurs. Ils sont pour la plupart considérés comme émergents, durant les dernières années ils ont été retrouvés au-delà de leur territoire d'origine, dans de nouvelles régions du monde. Les plus connus de ces virus sont le virus du West Nile, le virus chikungunya, la grippe, le coronavirus SRAS, l'entérovirus 71 (agent responsable de la fièvre aphteuse), les virus de la dengue, l'hépatite C virus, le virus de la fièvre hémorragique de Crimée Congo, le virus de la vallée du Rift, l'encéphalite japonaise et plusieurs entérovirus humains. En terme de mortalité et morbidité ils sont à l'origine de plus 100 millions de cas par an et la menace a tendance à augmenter. Ces statistiques sont démoralisantes quand on considère les immenses progrès de la médecine et de la science durant ces dernières dizaines d'années. Les recherches présentées dans ma thèse portent sur le genre Flavivirus, au sein duquel on retrouve le virus de la fièvre jaune, un pathogène humain responsable d'épidémies majeures en Afrique et en Amérique latine durant les 300 à 400 dernières années. Ce virus est toujours responsable d'épidémies majeures en Afrique malgré un vaccin très bien toléré et des plus efficaces. On assiste au même scénario avec le virus de l'encéphalite japonaise en Inde. / Without including the retroviruses, there are in excess of 200 RNA viruses that are recognised human and/or animal pathogens, many of which are considered to be emerging viruses because during recent years they have dispersed beyond their original territories causing epidemics in new regions of the World. The more well known of these emerging viruses include, West Nile virus, chikungunya virus, influenza virus, SARS coronavirus, EV71 virus (the aetiological agent of hand foot and mouth disease), dengue virus, hepatitis C virus, Crimean Congo haemorrhagic fever virus, Rift Valley fever virus, Japanese encephalitis virus and many human enteroviruses from a variety of genera. The combined global morbidity and mortality figures for these viruses add up to 100s of millions per year and the current trend appears to be upwards. This is a depressing statistic when one considers the amazing medical and scientific achievements that we have witnessed during the past decades. The studies described in my thesis were focused on the genus Flavivirus the type species of which is yellow fever virus, another terrifyingly virulent human pathogen that has caused so much suffering in Africa and Latin America during the past 300 to 400 years. This virus continues to cause major epidemics in Africa despite the availability of one of the safest and most effective vaccines with which to control infections due to yellow fever virus. Indeed similar comments can be made in the context of the flavivirus Japanese encephalitis virus in India.

M.Sc. / Africa's cycads (66 species and 2 subspecies in two endemic genera: Encephalartos and Stangeria) are extremely endangered with four species extinct in the wild and 80% threatened (CR, EN, or VU) with all included in CITES Appendix 1. Although South Africa has some of the world’s strictest cycad legislation, these plants are still under threat from illegal collection for horticulture and medicine especially where they are seized in an unidentifiable condition. Currently developed legislation demands accurate identification for permit issue. Ex situ conservation of genetic and locality based diversity is paramount. Furthermore, taxonomically many species of unknown origin are difficult to identify especially when diagnostic characters are absent. Species delimitation and numbers are uncertain with field observations often contradicting current understanding. DNA barcoding can assist with all the above-mentioned scenarios. In the current study all proposed DNA barcoding regions (matK, rbcLa, psbA-trnH, and nrITS) along with several additional regions were tested on ~350 samples from which a phylogeny of 63 of the 65 Encephalartos species was also constructed. Results show general good amplification and sequencing success of proposed barcoding regions, although a shift to specialist primers was made in several cases. Genetic variation however was extremely low as is resolution at species level, even when multi-locus barcodes were employed. Results obtained from the phylogenetic analyses show an increase in resolution at both species and higher levels compared to previous work and as such several new groupings are delimitated. Each species grouping is characterised by shared, derived morphological, ecological, and geographic characters and when compared to previous phylogenetic studies are supported to some extent. The current study provides the first step towards a much-needed monograph and revision of the entire genus Encephalartos.

Orientador: Virgínia Bodelão Richini-Pereira / Resumo: O Zika virus (ZIKV) é um flavivírus transmitido por mosquito que causa Febre Zika e está associado às Malformações Congênitas e Síndrome de Guillain-Barré integrando a lista de agentes etiológicos que são um problema de saúde pública internacional. Apresentamos uma investigação sorológica e molecular do ZIKV em amostras humanas na região de Bauru do estado de São Paulo, Brasil a fim de contribuir na determinação dos primeiros casos de infecção de ZIKV nos locais do estudo. Foi realizada a investigação sorológica por técnica de imunocromatografia em 2000 amostras Dengue virus negativas referentes aos anos de 2014-2016, sendo 159 (7,9%) positivas para ZIKV, evidenciando que a circularização do ZIKV na região de estudo teve início em 2014. Foi investigado pela técnica de Reação em Cadeia da Polimerase quantitativa por transcrição reversa a presença de ácido ribonucleico (RNA) do ZIKV nas 159 amostras positivas a nível sorológico. Porém o RNA viral não foi detectável. Esse resultado negativo quanto a molecular a partir de soro reforça a possibilidade de aderência do ZIKV em eritrócitos. Esses achados levantam o questionamento se outros membros do gênero Flavivirus possuem o mesmo potencial. Para complementar os dados realizamos uma análise filogenética da espécie ZIKV. Com o propósito de geração de hipóteses referentes a sua dinâmica de distribuição no Brasil. Para tal utilizamos os bancos de dados, algoritmos e parâmetros presentes nos softwares Virus Pathogen Resource e MEGA7. ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Zika virus (ZIKV) is a mosquito-borne flavivirus that causes Zika Fever and is associated with Congenital Malformations and Guillain-Barré Syndrome, which has been declared an international public health problem by the World Health Organization. We conduct a serological and molecular investigation of ZIKV in human samples in the Bauru region of the state of São Paulo, Brazil, in order to contribute to the determination of the first cases of ZIKV infection in the study sites. Serological investigation was made by immunochromatography technique performed in 2000 Dengue virus negative samples referring to the years 2014-2016, 159 (7.9%) was positive for ZIKV, evidencing that the circularization of ZIKV in the region of study began in 2014. The presence of ZIKV ribonucleic acid (RNA) in the 159 serologically positive samples was investigated by the Quantitative Reverse Polymerase Chain Reaction technique. All did not show detectable RNA. This molecular negative result from serum enhances the possibility of ZIKV adhesion in erythrocytes. These findings raise the question of whether other flaviviruses have the same potential. We also performed a phylogenetic analysis of the ZIKV species. With the purpose of generating hypotheses referring to its distribution dynamics. For this we use the databases, algorithms and parameters present in the software Virus Pathogen Resource and MEGA7. Our evidence allows us to infer that the ZIKV presents a possible adaptation in the Northeast Region ... (Complete abstract click electronic access below) / Mestre

Simaba, as traditionally and currently circumscribed, is the largest genus in the Simaroubaceae and is mostly restricted to tropical South America with a few species extending northward into Central America. The genus encompasses a large morphological heterogeneity, expressed in the vegetative and reproductive morphology, and many of its species are narrow endemics, most of them poorly known. Our phylogenetic analyses based on DNA sequence data from two nuclear ribosomal spacer regions (ITS and ETS) and three plastid regions (rps16 intron, and intergenic spacers psbA-trnH and trnL-trnF), including a comprehensive sampling of species of Simaba and closely related genera, show that Simaba as traditionally circumscribed is not monophyletic, with taxa segregated into two strongly supported but distinct clades. Also, we performed ancestral character reconstructions to identify morphological characters that could serve as synapomorphies for major clades. Based on the results of the phylogenetic analyses performed, a division of Simaba s.l. into two distinct genera is here proposed. The clade composed by species of Simaba sect. Tenuiflorae Engl., which includes the type species of Simaba, is here proposed to be recognized as Simaba sensu stricto, while the species of Simaba formerly included in S. sect. Grandiflorae Engl. and S. sect. Floribundae Engl. form a distinct lineage that will be recognized as members of another genus, Homalolepis Turcz., a taxon currently treated in synonymy of Simaba. As here circumscribed, Simaba s.s. comprises approximately 10 species distributed mostly in the Amazonian region, and Homalolepis comprises 28 species with mostly extra-Amazonian distribution, mainly in the cerrado and Atlantic forest domains. In addition to molecular data support, several morphological characters corroborate the recognition of the two clades as distinct lineages. We provide a synopsis of Simaba s.s., including an emended description of the genus, the description of four new species, complete nomenclature for each accepted species, including new lectotypifications. We also present a taxonomic treatment of Homalolepis, with a key for two sections and species, data on nomenclatural types, including new lectotypifications and one epitype, complete synonymy, full morphological descriptions, including two new species, etymology of species names, common names and uses, illustrations and photos of live specimens, as well as comments on phenology, taxonomy and nomenclature. Distribution maps are provided for each species, along with biogeographical and ecological comments / Simaba, como tradicionalmente circunscrito, é o maior gênero de Simaroubaceae e é principalmente restrito à América do Sul tropical, com algumas espécies que se estendem para o norte na América Central. O gênero engloba uma grande heterogeneidade morfológica, expressa tanto na morfologia vegetativa quanto reprodutiva, e muitas de suas espécies são endêmicas, estreitamente distribuídas, muitas delas ainda pouco conhecidas. Nossas análises filogenéticas baseadas em dados de sequências de DNA de duas regiões espaçadoras ribossômicas nucleares (ITS e ETS) e três regiões plastidiais (rps16 intron e espaçadores intergênicos psbA-trnH e trnL-trnF), incluindo uma amostragem abrangente de espécies de Simaba e gêneros proximamente relacionados, mostra que Simaba como tradicionalmente circunscrito não é monofilético, com os táxons segregados em dois clados fortemente sustentados e distintos. Também realizamos reconstruções de caracteres ancestrais para identificar caracteres morfológicos que poderiam servir como sinapomorfias para os principais clados. Com base nos resultados das análises filogenéticas realizadas, uma divisão de Simaba s.l. em dois gêneros distintos é aqui proposta. Propomos aqui que o clado composto pelas espécies de Simaba sect. Tenuiflorae Engl., que inclui a espécie-tipo de Simaba, seja reconhecido como Simaba sensu stricto, enquanto as espécies de Simaba anteriormente incluídas em S. sect. Grandiflorae Engl. e S. sect. Floribundae Engl. formam uma linhagem distinta que será reconhecida como um outro gênero, Homalolepis Turcz., um táxon atualmente tratado em sinonímia de Simaba. Como aqui circunscrito, Simaba s.s. compreende aproximadamente 10 espécies distribuídas majoritariamente na região Amazônica, e Homalolepis compreende 28 espécies com distribuição predominantemente extra-Amazônica, principalmente nos domínios do Cerrado e da Floresta Atlântica. Além da sustentação dada pelos dados moleculares, vários caracteres morfológicos corroboram o reconhecimento desse dois clados como linhagens distintas. Apresentamos aqui uma sinopse de Simaba s.s., incluindo uma descrição emendada do gênero, a descrição de quatro novas espécies, nomenclatura completa de cada espécie aceita, incluindo novas lectotipificações. Apresentamos também uma revisão taxonômica de Homalolepis, com chave para duas seções e espécies, dados sobre tipos nomenclaturais, incluindo novas lectotipificações e designação de um epítipo, sinonímia completa, descrições morfológicas, incluindo descrição de duas espécies novas, etimologia de nomes de espécies, nomes comuns e usos, ilustrações e fotos de espécimes vivos, bem como comentários sobre fenologia, taxonomia e nomenclatura. São fornecidos mapas de distribuição de cada espécie, juntamente com comentários biogeográficos e ecológicos

Hylodidae is composed of 46 species distributed in three genera: Crossodactylus (14 spp), Hylodes (25 spp), and Megaelosia (7 spp). These torrent-frogs are diurnal and associated with riverine habitats throughout the Atlantic Rain Forest. The high degree of habitat specificity observed in this group seems to be associated with an extremely conservative external morphology; however, other sources of evidence have been proved useful to distinguish species. My study was designed to review the status of the current hylodid systematics, performing a total evidence analysis that represents as many species (and populations) as possible; confirm the monophyly of currently valid nominal taxa; investigate the evolutionary history of some morphological characters; and reconstruct biogeographical changes in the distribution of hylodids. My total evidence analysis included morphological (293 characters) and molecular data (four mitochondrial and five nuclear genes) for up to 371 hylodid terminals plus 45 outgroups, and resulted in 713 most parsimonious trees. I recovered Hylodidae and its compounding genera as monophyletic, and recognized 58 lineages within this family. Three synapomorphies were identified for Hylodidae based on vocal sac morphology (external double vocal sac, internal double vocal sac, and opening of the m. interhyoideus through which the diverticulum passes). Analysis of the distribution of hylodids revealed the origin of this frog family in the East Atlantic river basin, with subsequent allopatric speciation in adjacent basins / Hylodidae é composta por 46 espécies distribuídas em três gêneros: Crossodactylus (14 spp), Hylodes (25 spp) e Megaelosia (7 spp). Essas rãs-de-corredeiras são diurnas e associadas à ambientes encachoeiradas ao longo da Mata Atlântica. O alto nível de especificacidade à esses habitats observado nesse grupo parece estar relacionado com a morfologia externa extremamente conservada; entretanto, outras fontes de evidências tem provado ser úteis para distinção de espécies. Meu estudo foi designado para revisar o status atual da sistemática dos hilodídeos através de uma análise de evidência total que representa o máximo de espécies (e populações) possíveis; confirmar o monofiletismo dos taxa válidos atualmente; avaliar a história evolutiva de alguns caracteres; e reconstruir mudanças biogeográficas na distribuição de Hylodidae. Minha análise de evidência total incluiu dados morfológicos (293 caracteres) e moleculares (quatro genes mitocondriais e cinco genes nucleares) para 34371 terminais de hilodídeos mais 45 terminais de grupo externo, resultando em 713 árvores mais parcimoniosas com 32.405 passos. Eu recuperei Hylodidae e todos os seus gêneros como monofiléticos e reconheci 59 linhagens dentro da família. Três sinapomorfias putativas foram identificadas para Hylodidae baseadas na morfologia do saco vocal (saco vocal externo duplo, saco vocal interno duplo e abertura no m. interhyoideus por onde o divertículo passa). Análises da distribuição dos hilodídeos revelaram a origem de Hylodidae na bacia Atlântico Leste com subsequentes especiações alopátricas em bacias subjacentes

Master’s Dissertation University of the Witwatersrand Faculty of Humanities School of Literature, Language and Media (SLLM), 2016 / The two aims of this study are, first, to use lexical items to generate networks which represent relationships between various members of the Germanic language family, and second, to examine the effects of different lexical coding strategies on the placement of language nodes in these networks. This is done using old and modern Germanic languages, as well as items from reconstructed Proto-Germanic. The data was coded using amino acid codes. The median-joining phylogenetic networking program Network has been used to process the data and to generate a series of networks under various conditions. Two semantic conditions were used, a strict and a lax, and three strategies were employed to handle missing data. The generated networks were then compared with each other and also with recognised classifications of the Germanic languages. The results indicated a general three-way division in the family, although there was variation at lower levels of classification. The results also indicated the degree to which choice of lexical item and coding strategy could influence results. The study shows that more research into the utility of such quantitative methods in linguistics is required. / GR2017

The thesis is focused on phylogeny of the family Torymidae (Hymenoptera: Chalcidoidea) and evolution of their life-strategies. The study consists of general introduction to the phylogeny and classification of the family Torymidae chapter, four published papers in international journals and one manuscript prepared for submission. Firstly, our aim was to figure out the phylogenetic position of Torymidae as well as the position of other chalcidoid families inside superfamily Chalcidoidea (paper I and II). The supermatrix of sequencies of two ribosomal genes (18S rDNA and 28S rDNA) were developed for 649 species of chalcidoid taxa. However, family Torymidae was considered as polyphyletic group with the subfamily Megastigminae unrelated to the subfamily Toryminae (paper I). Monophyly of Torymidae was corroborated in another study (paper II) focused on molecular and morphological characters. We used a web-based, systematics workbench mx database for scoring 233 characters of 300 members of all chalcidoid families. Contrary to our previous only DNA-based study, we revealed also potential sister relationships of Torymidae with Ormyridae+Colotrechninae or Cerocephalinae+Diparinae respectively. Other paper (paper V) was focused on detailed study of Torymidae phylogeny. A total of 5 genes (18S rDNA, 28S rDNA,...

Orientador: Itamar Alves Martins / Banca: Fernando Rodrigues da Silva / Banca: Rogério Pereira Bastos / Banca: Denise de Cerqueira Rossa-Feres / Banca: Cynthia Peralta de Almeida Prado / Resumo: Os sinais acústicos dos anuros são excelentes padrões de comportamento para estudos comparativos. Atualmente, as hipóteses filogenéticas que explicam a evolução do canto em anuros se dividem. Uma frente sugere que espécies próximas filogeneticamente tendem a ter o canto mais similar do que o esperado ao acaso, predizendo que espécies mais próximas filogeneticamente tendem a ter o canto mais similar. Outro ramo indica que diferenças nas características do hábitat afetam as propriedades acústicas do canto minimizando as interferências ambientais. Essas forças, assim, podem atuar em oposição. O objetivo geral deste estudo foi analisar as influências filogenéticas e ambientais nos parâmetros acústicos do canto de anúncio de 28 espécies de anuros do gênero Physalaemus. No capítulo 1, Os parâmetros bioacústicos espectrais e temporais dos cantos são comparados qualitativa e quantitativamente para avaliar se influenciam a segregação dos cantos e para determinar o grau de similaridade entre os cantos dessas espécies crípticas no grupo P. cuvieri. No capítulo 2, discutimos a relação entre os parâmetros acústicos e o tipo de hábitat ocupado pelas espécies e, a similaridade entre os cantos de anúncio de 28 espécies do gênero Physalaemus que ocupam áreas abertas e ambiente de mata. E, no capítulo 3, Nosso objetivo foi comparar e sinalizar as transformações nos parâmetros espectrais e temporais do canto de anúncio para três táxons de espécies do gênero Physalaemus através de árvores filogenéticas. A similaridade dos parâmetros bioacústicos dos cantos não é relacionada com a distribuição geográfica das espécies. As espécies alopátricas demonstram maior similaridade do canto do que as espécies simpátricas. Nas espécies simpátricas analisadas, P. cuvieri, P. ephippifer e P. fischeri... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The acoustic signals of frogs are excellent standards of behavior for comparative studies. Currently, the phylogenetic hypotheses that explain the evolution of singing in Anurans are divided. A front suggests that phylogenetically close species tend to have the calls more similar than expected by chance, predicting that phylogenetically closest species tend to have the most similar. Another branch indicates that differences in habitat characteristics affect the acoustic properties of the minimizing environmental interferences. These forces, therefore, can act in opposition. The overall objective of this study was to analyze the phylogenetic and environmental influences in the acoustic parameters of the advertisement call of 28 species of Anurans belonging to the genus Physalaemus. In Chapter 1, the spectral and temporal bioacoustics parameters of the calls are compared qualitatively and quantitatively to assess whether they influence the segregation of calls and to determine the degree of similarity between the calls of these cryptic species in P. cuvieri group. In Chapter 2, we discussed the relationship between the acoustic parameters and the type of Habitat occupied by the species and, the similarity between the advertisement call of 28 species of the Physalaemus genus occupying open areas and forest environment. And in Chapter 3, our objective was to compare and flag the transformations in the spectral and temporal parameters of the advertisement call for the three taxa of the Physalaemus genus through phylogenetic trees. The similarity of bioacoustics parameters of the calls is not related to the geographic distribution of the species. Allopatric species show greater similarity of corner than the sympatric species. In sympatric species analyzed, P. cuvieri, P ephippifer and P. fischeri, there is overlap of spectral parameters, as... (Complete abstract click electronic access below) / Doutor