Phylogenetic analysis is used in all branches of biology by inferring evolutionary trees. Applications include designing more effective drugs, tracing the transmission of deadly viruses, and guiding conservation and biodiversity efforts. Most analyses rely on effective heuristics for obtaining accurate trees. However, relatively little work has been done to analyze quantitatively the behavior of phylogenetic heuristics in tree space. This is important, because a better understanding of local search behavior can facilitate the design of better heuristics, which ultimately leads to more accurate depictions of the true evolutionary relationships. In order to access and analyze the tree search space, we implement an effec- tive local search heuristic. Having an effective heuristic that can open the space is important, since no search heuristic in this field can effectively provide data collec- tion control. So we have implemented and estimated a search heuristic, Simple Local Search or SLS, that works reasonably well in the space. Our investigations led to several interesting observations about the behavior of a search heuristic and the tree search space. We studied the correlation of tree features of search path trees, where tree features refer to the parsimony score, the Robinson- Foulds distance and the homoplasy measure. Most importantly from the results, parsimony score was highly correlated with Robinson-Foulds distance only in trees that lie on the search path to a local optimum. We also note that the scores of neighborhoods along search paths improve together, as a local search progresses. Correlations of tree features of search path trees are particularly useful in char- acterizing and controlling a search path. This paper proposes one possible stopping criterion to maximize the tree search results while minimizing computational time tested on three biological datasets using the correlation between the parsimony score and the RF distance value of search path trees. Also, the observation that scores of a neighborhood on a search path improve together gives us a significant amount of flexibility in selecting the next pivot of a search without losing performance. Eventually, our long-term goal is developing an effective search heuristic that can deal with large scale tree space in reasonable time. Improved knowledge about the tree search space and the search heuristic can provide a reasonable starting point toward the goal.

Preliminary phylogenetic analyses of Passalidae and the genus Popilius are presented based on 207 characters for the family level part of this study and 232 characters for the generic portion. The strict consensus and successive approximation trees show that the New World passalid fauna is monophyletic, and that Popilius is paraphyletic and intertwined with several closely related, also paraphyletic, genera (at least Heliscus, Odontotaenius and Petrejoides). An unrooted analysis of Popilius identified four species groups, two that are monophyletic, one that is probably paraphyletic (more closely related to Petrejoides than to other members of Popilius) and one for a distinct species, the single specimen of which was not available for examination. New character systems were investigated and the metendosternite, eversible internal sac of the male genitalia, prostheca of the right mandible, epipharynx, and hypopharynx provided useful characters to supplement those traditionally used. A new autapomorphy for the family is reported, an organ on the inner surface of both elytral humeri. The structure has a membranous covering and appears to contact an apophysis on the base of the wing. Its position and structure suggest that it may be a sound receptor. A rigorous investigation of the relationships among the genera closely related is required to define generic boundaries and identify the out-group taxa most appropriate for the analysis of the component taxa.

The internal transcribed spacer region (ITS) from fourteen samples of Sclerospora graminicola was amplified using a nested PCR. These regions of the rDNA were amplified by a combination of conserved primers (ITS 1 and 6 and ITS 3 and 4). These products were cloned into a puc-4 vector and transformed into E.coli competent cells. The inserts from transformants were isolated, then sequenced by the Gene Technologies Lab, Texas A& M University. The sequences produced were and aligned with the ITS2 region of other known Oomycete fungi( Peronospora, Phytophthora and Pythium) using CLUSTALX. Phylogenetic relationship among sequences from Indian and African samples was examined using a consensus bootstrap parsimony tree. All the samples from India, Mali, Nigeria and Niger, with the exception of Niger 4, formed a monophyletic group with the Oomycetes ( Peronospora, Phytophthora and Pythium). The three samples Niger 4, BFaso 2 and BFaso 17 from Burkina Faso shared a close relationship with the outgroup Cladosporium herbareum.

Elatostema J.R.Forst. & G.Forst. (Urticaceae) is a taxonomically problematic genus of approximately 300 species that is widespread throughout the tropical, subtropical and sub-temperate regions of Africa through to SE Asia, Australasia to Polynesia. Morphological and molecular analyses were conducted to evaluate the infra-familial classification of the Urticaceae, to test the monophyly of Tribe Elatostemeae, to define generic limits of Elatostema and assess its relationship within the tribe, and to examine the current infrageneric grouping within Elatostema. Phylogenetic analyses based on choloroplast DNA sequences of rbcL and trnL-F do not provide support for the monophyly of Urticaceae, because of the position of Poikilospermum (currently Cecropiaceae) within the tribe Urticeae. Although the status of Cecropiaceae is equivocal, there is support for the inclusion of this family in the Urticaceae, with Cecropia and Coussapoa (Cecropiaceae) having close affinities to the Boehmerieae and Parietarieae. The phylogenetic position of Myriocarpa is unresolved, but is excluded from the Boehmerieae, as currently classified. The Elatostemeae is paraphyletic with Pilea placed sister to the Urticeae. Evaluation of the infrageneric classification of Elatostema, based on phylogenetic analyses of both morphological and molecular data (trn and ITS) does not support the current subgeneric classification as proposed by Schr??ter and Winkler (1935, 1936). The analyses support two main infrageneric grouping: (1) a group consisting of Elatostema subg. Pellionia and Procris, and (2) a group consisting of the remaining members of Elatostema (including E. griffithianum ??? subg. Pellionia). The molecular data are regarded as a more accurate estimate of the phylogeny than provided by morphology, with molecular data having a higher Rescaled Consistency Index on the most parsimonious trees, together with a much greater level of resolution and support than that of the morphological analyses.

An evolutionary tree represents the relationship among a group of species, DNA or protein sequences, and play fundamental roles in biological lineage research. A high quality tree construction relies heavily on optimal multiple sequence alignment (MSA), which aligns three or more sequence simultaneously to derive the similarity. On the other hand, a good tree can also be used to guide the MSA process. Due to the high computational cost to conduct both the MSA and tree construction, parallel approaches are exploited to utilize the enormous amount of computing power and memory housed in a supercomputer or Linux cluster. In this paper, first of all, a divide and conquer based parallel algorithm is designed and implemented to perform optimal three sequence alignment using reduced memory cost. Secondly, all internal nodes of a phylogenetic tree resulting from a parallel Maximum-likelihood inference software are labeled using the parallel MSA. Such tree node labeling process is carried out from top down and is also parallelized to fully utilize the numerous cores and nodes in a high performance computing facility.

Phylogenetic footprints are short pieces of noncoding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are collinear:  they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining collinear cliques, and finally the insertion of the noncollinear ones at “reasonable” positions. We show that solving the footprint sorting problem requires the solution of the “Minimum Weight Vertex Feedback Set Problem”, which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for data sets of interest. The remaining steps of the sorting process are straightforward:  computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sublists. As an application we show that the rat has a slighly increased insertion/deletion rate in comparison to the mouse genome.

Emerging and re-emerging diseases have increased worldwide in incidence in the past decades. Of these emerging diseases 60.3% are caused by zoonotic pathogens of which 22.8% are arboviruses or arthropod borne viruses. Arboviruses are transmitted by hematophagous insects, especially moquitoes. Multiple factors such as human population growth, climate change and adaptations of certain Aedes mosquito vector species to urban environments and anthropophilic have been attributed to causing this rise in arboviral infections. In Southern Africa, zoonotic arboviruses belonging to the families Flaviviridae (genus Flavivirus), Togaviridae (genus Alphavirus), and those in the order Bunyavirales, family Phenuiviridae: (genus Phlebovirus) and Peribunyaviridae (genus Orthobunyaviruses), have proven, in the past, to be of both medical and veterinary importance. Recent detection of neurological cases in South Africa, most likely, due to flaviviruses, alphaviruses and orthobunyaviruses in the Simbu serogroup, has rekindled interest in these zoonotic diseases. This interest is also warranted because of lack of recent information on arboviral prevalence in mosquito species, distributions, abundance, and ecology, especially of Aedes species, the likely primary vectors of these arboviruses in Southern Africa. To update this lack of information, this study t reports on zoonotic arboviruses circulating in selected areas in the north-eastern provinces of South Africa in mosquitoes with a focus on Aedes. Many Aedes species are morphologically quite difficult to identify especially when they are old, and scales rubbed off in the process of trapping. To aid in the identification of Aedes in this study we provide molecular barcodes for Aedes species occurring in in South Africa and define their phylogenetic relationship with other mainly Afrotropical Aedes mosquitoes based on the cytochrome oxidase I gene sequences. The first Chapter provides a comprehensive review of the literature and describes the importance of arboviruses worldwide and in South Africa, highlighting the role of Aedes mosquitoes as vectors. In Chapter 2, what is known about the broad patterns of Aedes mosquito species diversity, abundance, and distribution in different habitats across selected sites in five different provinces in South Africa is described. The sites selected were chosen because of evidence of neurological cases in humans and animals in recent years likely due to arboviral infections. In total, 61,737 adult mosquitoes were collected from January 2014 to May 2018, using three kinds of carbon dioxide baited trap types About 16% (11,440) were Aedes species, of which, 14 species were recognised or suspected vectors of mosquito-borne diseases because of positive infections, including Aedes mcintoshi which was the most abundant Aedes species captured. The effect of the climatic conditions on the mosquito population dynamics were also investigated. Aedes species were present in the sites following the peak of the rainfall and were mostly captured in temperatures between 18°C and 27°C. Chapter 3 focuses on determining the blood meal source present in engorged Aedes mosquitoes sampled to give an assessment of blood feeding tendencies that would serve useful to determine their vector status. Aedes species were identified feeding on a broad range of livestock, and wildlife, only two specimens were identified as feeding on avian species.Chapter 4 focuses on interpretations of cytochrome oxidase subunit 1 (COI) gene sequences to identify Aedes species in South Africa and to analyse the relationship among the species. A total of 52 COI sequences were aligned representing 21 Aedes species. In several cases these were the first African aedine species uploaded in NCBI GenBank. Neomelaniconion species clustered together, except for Ae. aurovenatus. Finally, the data also suggested that Ae. cumminsii present in South Africa belongs to the subspecies ssp. mediopunctatus. In Chapter 5 results of arboviral infections in Culicidae mosquitoes captured from the selected sites, particularly Aedes species is provided. Arboviral infection or prevalence screening was performed using multiple genus specific polymerase chain reactions (PCR). Alphavirus and Orthobunyavirus were detected in different Culicidae genera, including Aedes, Culex, Anopheles and Mansonia. There were no isolations of pathogenic flaviviruses in mosquitoes. The only alphaviruses detected in mosquitoes were Middelburg, Sindbis and Ndumu viruses during the period of the study. Shuni virus was the only member of Orthobunyavirus genus, detected. Even though, the main aim was to identify pathogenic viruses, several insect-specific viruses belonging to Alphavirus and Flavivirus genera were also detected and these are described in Chapter 6. The numerous arboviruses detected in Culicine mosquitoes, including Aedes species, demonstrate that some species are likely maintaining natural cycling of these arboviruses. Noteworthy, is that mosquito species positive for arboviruses are often the most abundant in the selected sampling locations and that these species blood feed mostly on the larger vertebrates present in the area. Outbreaks possibly occur when the prevalence of certainmosquito species are high due to favourable climatic conditions. Highest arbovirus detections occurred in peri-urban, rural, and conservation areas, indicating that livestock and wildlife likely play an important role in the amplification of these arboviruses. This study highlights the importance of a continues mosquito-based surveillance for arboviruses in South Africa, and the role that Aedes species might be playing in the circulation of these arboviruses. Surveillance for the species that tested positive for pathogenic arboviruses during the arbovirus season may act as an early warning system and can also help to avoid spill over in animals and humans in the area surveyed. / Thesis (PhD)--University of Pretoria, 2020. / Centres for Disease Control and Prevention National Research Foundation / Medical Virology / PhD / Unrestricted

Living organisms are under selection not only for one, but also for several inheritable characters at the same time. Well-sampled and well-supported phylogenies are necessary for the studies of character evolution and their history. The poison frogs (Dendrobatidae) are a well-known example of aposematism in anurans. They include ~270 species of Neotropical frogs with aposematic (toxic and conspicuous) and non-defended (palatable and cryptic) species. The origin of aposematism in poison frogs is puzzling, because of its predicted low probability of establishment due to the prey's increased conspicuousness. Previous studies suggested a single origin of toxicity and warning coloration. By expanding taxon sampling of the group, I reexamined the phylogenetic correlation between the origins of toxicity and warning coloration. I found four or five independent origins of aposematism; by using simulations, I rejected hypotheses of one, two, or three origins of aposematism (P < 0.002). I also found that diet specialization is linked with the evolution of aposematism and has evolved independently at least two times. Poison frogs are endemic to the Neotropic, which is one of the Earth's largest reservoir of biodiversity. I reconstructed the biogeography of the poison frog clade and rejected an Amazonian center-of-origin in favor of a model expanding over the Neotropics. I inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. Poison frogs have significant variation on their physiological characteristics. I measured resting and active metabolic rates of 54 species. I traced metabolic measurements along aposematism, diet specialization, molecular rates, and body mass. I found a synergistic and co-adapted functionality of active metabolic rates with all previous traits that is perhaps the consequence of the increase in complexity in most biological systems. My thesis has expanded the knowledge of the biology, phylogenetic history, and biogeography of the poison frogs. / text

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