In this research, the necessity of understanding and using bioinformatics is demonstrated using the enzyme aspartate transcarbamoylase (ATCase) as the model enzyme. The first portion of this research focuses on the use of bioinformatics. A partial sequence of the pyrB gene found in Enterococcus faecalis was submitted to GenBank and was analyzed against the contiguous sequence from its own genome project. A BLAST (Basic Local Alignment Search Tool; Atschul, et al., 1990) was performed in order to hypothesize the remaining portion of the gene from the contiguous sequence. This allowed a global comparison to other known aspartate transcarbamoylases (ATCases) and once deduced, a translation of the sequence gave the stop codon and thus the complete sequence of the open reading frame. When this was complete, upstream and downstream primers were designed in order to amplify the gene from genomic DNA. The amplified product was then sequenced and used later in phylogenetic analyses concerning the evolution of ATCase. The second portion of this research involves taking multiple ATCase nucleotide sequences and performing phenetic and phylogenetic analyses of the archaea and eubacter families. From these analyses, ancestral relationships which dictate both structure and function were extrapolated from the data and discussed.

The hawkweed subgenus Hieracium s. str. is notoriously known for its extreme morphological variability and variation in ploidy levels that is associated with differences in modes of reproduction. Extensive past hybridization is supposed for the subgenus, but recent hybridization was evidenced only in few cases. The subgenus attracts the attention of botanists already for more than a century. Therefore the species diversity is largely examined and the taxonomy of the subgenus is well elaborated, although several contradictory taxonomic concepts exist. However the relationships among the species are unknown and haven't been studied yet. The investigation of these relationships from a phylogenetic perspective using molecular approaches was the main aim of the presented thesis. Basic species (both diploid and polyploid), representing morphologically unique taxa, that are supposed to be the basic evolutionary units of the subgenus were studied. The sequences of two intergenic spacers of the cpDNA (trnT-trnL and trnV-ndhC) and the external transcribed spacer of the nuclear ribosomal DNA (nrDNA ETS) were analyzed. Moreover, three new low-copy nuclear markers with higher variability than nrDNA and cpDNA markers were developed and their suitability for phylogenetic studies in Hieracium s. str. was...

Doctor of Philosophy / Division of Biology / Carolyn J. Ferguson / The genus Lappula Moench is a diverse group of herbaceous plants in the large, cosmopolitan family Boraginaceae. Over sixty species are recognized in Eurasia; many are found in cold deserts, steppes, and semi-deserts of Central Asia. Fewer species were described from western North America, and compared with the Asian species they are poorly known. Various North American taxa have been placed into synonomy under Eurasian species, and complex patterns of variation have made species circumscription challenging. The goal of this dissertation was to explore phylogenetic relationships between North American and Eurasian species and to revise the taxonomy of the North American species. A molecular phylogenetic study was initiated in order to infer patterns of relationships among the North American species relative to Eurasian diversity. Samples were collected from throughout the western United States and from Siberia. Additional samples of Eurasian species were taken from herbarium specimens. Sequences were generated for three DNA regions (the ITS region of the nuclear ribosomal DNA, and chloroplast intergenic spacers trnS-trnG and rpl32-trnL) and phylogenies were generated using parsimony and Bayesian analyses. Results were in general agreement among all analyses. The genus Lappula was recovered as a monophyletic group, with the exception of the morphologically anomalous L. sessiliflora (Boiss.) Gürke, which was sister to the genus Rochelia Rchb. The native North American species of Lappula and L. redowskii (Hornem.) Greene formed a clade. Samples of L. squarrosa (Retz.) Dumort., a Eurasian steppe plant with a wide introduced range in North America, grouped with samples from Eurasia. Sampled species of Hackelia Opiz, a genus sometimes treated as part of Lappula, formed a clade separate from the Lappula species sampled here. Herbarium and field studies resulted in a revised taxonomy for the North American Lappula. Nomenclatural problems were resolved; nine native species and four varieties were recognized along with the introduced Eurasian species L. squarrosa.

Over the last few decades, phylogenetics has emerged as a very promising field, facilitating a comparative framework to explain the genetic relationships among all the living organisms on earth. These genetic relationships are typically represented by a bifurcating phylogenetic tree — the tree of life. Reconstructing a phylogenetic tree is one of the central tasks in evolutionary biology. The different evolutionary processes, such as gene duplications, gene losses, speciation, and lateral gene transfer events, make the phylogeny reconstruction task more difficult. However, with the rapid developments in sequencing technologies and availability of genome-scale sequencing data, give us the opportunity to understand these evolutionary processes in a more informed manner, and ultimately, enable us to reconstruct genes and species phylogenies more accurately. This thesis is an attempt to provide computational methods for phylogenetic inference and give tools to conduct genome-scale comparative evolutionary studies, such as detecting homologous sequences and inferring gene families. In the first project, we present FastPhylo as a software package containing fast tools for reconstructing distance-based phylogenies. It implements the previously published efficient algorithms for estimating a distance matrix from the input sequences and reconstructing an un-rooted Neighbour Joining tree from a given distance matrix. Results on simulated datasets reveal that FastPhylo can handles hundred of thousands of sequences in a minimum time and memory efficient manner. The easy to use, well-defined interfaces, and the modular structure of FastPhylo allows it to be used in very large Bioinformatic pipelines. In the second project, we present a synteny-aware gene homology method, called GenFamClust (GFC) that uses gene content and gene order conservation to detect homology. Results on simulated and biological datasets suggest that local synteny information combined with the sequence similarity improves the detection of homologs. In the third project, we introduce a novel phylogeny-based clustering method, PhyloGenClust, which partitions a very large gene family into smaller subfamilies. ROC (receiver operating characteristics) analysis on synthetic datasets show that PhyloGenClust identify subfamilies more accurately. PhyloGenClust can be used as a middle tier clustering method between raw clustering methods, such as sequence similarity methods, and more sophisticated Bayesian-based phylogeny methods. Finally, we introduce a novel probabilistic Bayesian method based on the DLTRS model, to sample reconciliations of a gene tree inside a species tree. The method uses MCMC framework to integrate LGTs, gene duplications, gene losses and sequence evolution under a relaxed molecular clock for substitution rates. The proposed sampling method estimates the posterior distribution of gene trees and provides the temporal information of LGT events over the lineages of a species tree. Analysis on simulated datasets reveal that our method performs well in identifying the true temporal estimates of LGT events. We applied our method to the genome-wide gene families for mollicutes and cyanobacteria, which gave an interesting insight into the potential LGTs highways. / <p>QC 20161010</p>

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.

Esta tese de doutorado versa sobre relações filogenéticas, evolução e biogeografia das espécies do gênero Ramphastos, representado pelos tucanos. / This PhD thesis is about phylogenetics, evolution and biogeography of the species of the genus Ramphastos (toucans).

O presente trabalho trata da revisão taxonômica e análise filogenética do gênero Armitermes Wasman, 1897 (Termitidae, Nasutitermitinae), que até esta revisão contava com 12 espécies: A. armiger, A. cerradoensis, A. euamignathus, A. gnomus, A grandidens, A. holmgreni, A. lane, A. manni, A. minutus, A. peruanus, A. projectidens e A. teevani, ocorrendo em toda Região Neotropical. Nesse trabalho, além da proposta de quatro espécies novas e duas sinonímias (A. cerradoensis com A. euamignathus e A. projectidens com A. manni), também se realizou uma análise filogenética e o resultado corrobora a criação de quatro novos gêneros, propostos com base no estudo da morfologia. Todos os soldados foram descritos e ilustrados, além das mandíbulas e tubo digestivo do operário e da casta do alado, quando disponível. Também foram incluídas chaves dicotômicas, baseadas na casta do soldado, para identificação das espécies dos gêneros propostos, além de mapas com a distribuição geográfica das espécies. / The present work deals with the taxonomic revision of the genus Armitermes Wasman, 1897 (Termitidae, Nasutitermitinae), which counts 12 species at the moment: A. armiger, A. cerradoensis, A. euamignathus, A. gnomus, A. grandidens, A. holmgreni, A. lanei, A. manni, A. minutus, A. peruanus, A. projectidens and A. teevani, occurring in all Neotropics. In this work, besides the proposal of four new species and two new synonymies (A. cerradoensis with A. euamignathus and A. projectidens with A. manni), a phylogenetic analysis was accomplished and its results used to support the proposal of four new genera based on morphology. All soldiers were described and illustrated, the mandibles and digestive tract of the worker and the imago caste, when available. Dichotomous keys based on soldiers were also included, for identifying the species of the genera proposed, as well as maps with the geographical distribution of species.

A musculatura esquelética representa um dos principais complexos anatômicos dos vertebrados, contudo, esta fonte de informação é escassamente estudada em alguns grupos de peixes, com o conhecimento atual limitado em observações de aspectos superficiais da musculatura de poucas espécies ou descrições sucintas de componentes miológicos pontuais. Este cenário ilustra o conhecimento em dois importantes grupos de Ostariophysi (Teleostei), os Gymnotiformes e os Siluriformes. Os estudos anatômicos nestas ordens acompanham a tendência dos esforços em outros grupos de Teleostei e apresentam uma ênfase excessiva na osteologia. Outros complexos anatômicos relevantes, como os miológicos, permanecem amplamente desconhecidos. O presente estudo foi concebido objetivando preencher a lacuna no conhecimento da musculatura dorsolateral da cabeça em Gymnotiformes e Siluriformes. Cada ordem é tratada em um capítulo separado, incluindo seções descritivas, comparativas e filogenéticas. O capítulo 1 descreve e ilustra os músculos faciais de 83 espécies de Gymnotiformes. As descrições são acompanhadas por uma análise comparativa destinada a estabelecer relações de homologia. As conclusões nessa parte do estudo estão resumidas em uma lista nomenclatural, incluindo 15 músculos, e os respectivos nomes válidos, mais 18 sinônimos. O estudo anatômico comparativo identificou 56 caracteres miológicos discretos que foram analisados com metodologia filogenética. A topologia resultante da árvore, baseada exclusivamente em caracteres mitológicos, concorda com muitas hipóteses de relacionamentos anteriormente propostas para Gymnotiformes. Em uma segunda análise, os caracteres derivados da miologia foram concatenados com uma matriz fenotípica maior, que inclui caracteres de várias fontes diferentes. Os resultados das análises concatenadas demonstram que os caracteres de miologia facial são altamente informativos para os relacionamentos em Gymnotiformes, especialmente para grupos mais inclusivos. O Capítulo 2 oferece o mesmo tipo de estudo que o Capítulo 1, mas desta vez aplicado a Siluriformes, um grupo muito maior e mais complexo. Uma análise comparativa abrangente dos músculos dorsolaterais da cabeça dos Siluriformes é oferecida, com descrições detalhadas e ilustrações dos músculos faciais de 124 espécies em 39 famílias da ordem. Inúmeros problemas de homologia e nomenclatura são identificados e resolvidos, com a lista sinônima resultante contendo 215 nomes para 44 músculos válidos. Conforme feito para Gymnotiformes, a informação comparativa é organizada em 67 caracteres miológicos. Esses caracteres foram concatenados com um banco de dados morfológico disponível e resultaram em um conjunto de novas sinapomorfias em Siluriformes e discussões sobre novas evidências para os relacionamentos na ordem. Os resultados apresentados neste estudo compreendem na síntese do conhecimento da miologia facial dos Gymnotiformes e Siluriformes através da documentação detalhada dos principais grupos e subgrupos destas ordens. A padronização nomenclatural dos componentes musculares, bem como a proposição de novos caracteres oriundos da miologia, fornecem base para investigações futuras sobre a detecção de potenciais sinais filogenéticos oriundos deste complexo anatômico, além de estimular contribuições direcionadas para a busca em fontes de informações ainda inexploradas em Gymnotiformes e Siluriformes. / Skeletal musculature is among the most important anatomical complexes of vertebrates, however, this source of information is barely explored in most groups of fishes, with knowledge restricted to superficial features in a few species or brief descriptions of specific muscles. Such is the case in two of the most important groups of freshwater fishes, Gymnotiformes and Siluriformes. Anatomical studies in those orders have followed the usual trend in Teleostei, with an inordinate emphasis on osteology. Other relevant anatomical systems, such as myology, remain mostly unknown. The present study attempts to fill this gap by focusing on the head musculature Gymnotiformes and Siluriformes. Each order is treated in a separate chapter, including descriptive, comparative and phylogenetic sections. Chapter 1 describes and illustrates the facial muscles of 83 gymnotiform species. The descriptions are accompanied by a comparative analysis intended to establish relationships of homology. The conclusions in that portion of the study are summarized in a nomenclatural list including 15 muscles and respective valid names, plus 18 synonyms. The comparative anatomical study identified 56 discrete myological characters which were analyzed with phylogenetic methodology. The resulting tree topology, based exclusively on myological characters, agrees with many previously-proposed hypotheses of relationships for Gymnotiformes. In a second analysis, characters derived from myology were concatenated with a larger phenotypic matrix including characters from several different sources. Results of the concatenated analyzes demonstrate that facial myological characters are highly informative for relationships of Gymnotiformes, especially for more inclusive groups. Chapter 2 offers the same kind of study as Chapter 1, but this time applied to Siluriformes, a much larger and more complex group. A comprehensive comparative analysis of the myological components of the dorsolateral head muscles of the Siluriformes is offered, with detailed descriptions and illustrations of the facial muscles of 124 species in 39 families of the order. Countless homology and nomenclatural problems are identified and resolved, with the resulting synonymic list containing 215 names for 44 valid muscles. As done for Gymnotiformes, comparative information is organized into 67 discrete myological characters. Those characters were concatenated with a previously-available morphological database, and resulted in a set of new synapomorphies within Siluriformes and discussions about new evidences for relationships within the order. Results presented herein comprise the synthesis of the knowledge of the facial myology of Gymnotiformes and Siluriformes through the detailed documentation of the main groups and subgroups of these orders. The nomenclatural standardization of muscles, as well as the proposition of new characters form the myology, provide the basis for future investigations on potential phylogenetic signals from this anatomical complex, in addition to motivating contributions directed to the search in sources of information unexplored in Gymnotiformes and Siluriformes.

The extant medically and socially important cobras have been the subject to several comparative taxonomic studies since the 1940s, but still lack an inclusive and thorough phylogenetic tree. With recent major advancements in phylogenetic analysis, it is now common to use multiple independent loci for studying the phylogenetic relationships within groups. For the first time, 27 from the 29 identified Naja species, alongside 5 putative new or elevated species had 4426 base pairs across 1701 sequences of mitochondrial and nuclear DNA sequence data analysed. The results continue to support the monophyletic core cobra clade encompassing the genera Walterinnesia, Aspidelaps, Hemachatus, Pseudohaje and Naja (1.0 Bayesian posterior probability (BPP)), in addition to the grouping of four monophyletic subgenera within Naja. The group of African spitting cobras, Afronaja, is positioned as the sister group to the rest of the genus. Moderate support (0.8 BPP) is found for the grouping of the Asian cobras, Naja, with the African non-spitting cobras, Ureaus. The closest relative to the genus Naja is Pseudohaje goldii, a genus and species never before included in phylogenetic analysis, followed by the sister taxa Hemachatus haemachatus. The king cobra continues to be positioned outside the core cobra group, sister to Hemibungarus calligaster. The results support the hypothesis of three independent origins of spitting, once in the monotypic Hemachatus haemachatus, once within the subgenus Afronaja, and the final origin within the Asian cobras, subgenus Naja. The relationships found were broadly consistent with previous studies, with the additional inclusion of more species creating the most comprehensive cobra phylogeny to date. Further molecular analysis, specifically species delimitation, must be undertaken to ascertain the position of the 5 putative new species included in this study.

Fast-evolving RNA viruses are a leading cause of morbidity and mortality among human and animal populations, contributing significantly to both global health and economic burden. The advent and revolution of high-throughput sequencing has empowered phylogenetic analyses with increasing amounts of temporally and spatially sampled viral data. Moreover, the parallel advancement in molecular evolution and phylogenetic methods has provided investigators with a unique opportunity to gain detailed insight into the evolutionary and epidemiological dynamics of emerging viral pathogens. Using state-of-the-art statistical approaches, this thesis addresses some of the important but controversial questions in viral emergence. Chapter 2 introduces a new framework to quantify and investigate reassortment events in influenza A viruses. By developing a computationally efficient algorithm to calculate the largest common subtree for a pair of tree sets, which are estimated from diffe rent parts of the genome for the same taxa set, the level of phylogenetic incongruency due to reassortment can be appropriately ascertained. Chapters 3, 4 and 5 investigate the evolutionary origins of three diff erent viruses: the novel emergence and cross-species transmission of SARSCoV, the genesis and dissemination of the unique HCV circulating recombinant form, and the ancient divergence of all influenza viruses, respectively. Moreover, Chapter 4 presents an improved statistical framework, which provides more precise evolutionary estimates, by utilizing the hierarchical bayes approach to investigate recombination events in emerging RNA viruses. The last empirical study, presented in Chapter 6, applies the recently developed Bayesian phylogeography models to a large viral sequence dataset sampled from southern Viet Nam to examine the fine-scale spatiotemporal dynamics of endemic dengue in Southeast Asia. The work presented here reflects both the advancements made in sequencing technology and statistical phylogenetics, along with some of the challenges that remain in studying the emergence of fast-evolving RNA viruses. This thesis proposes new and improved solutions to these evolutionary problems, such as incorporating non-vertical evolution (i.e. homologous recombination and reassortment) into the phylodynamic framework, with the aim of facilitating future investigations of emerging viral diseases.