<p> The higher taxonomic groups within Prokaryotes are presently distinguished mainly on the basis of their branching in phylogenetic trees. In most cases, no molecular, biochemical or physiological characteristics are known that are uniquely shared by species from these groups. Comparative genomic analyses are leading to discovery of molecular characteristics that are specific for different groups of Bacteria and Archaea. These markers include conserved inserts and deletions in universal proteins and lineagespecific proteins, which provide novel means for identifying and circumscribing these groups of prokaryotes in clear molecular terms and for understanding their evolution. Because of their taxa specificities, further studies on these newly discovered molecular characteristics should lead to discovery of novel biochemical and physiological characteristics that are unique to different groups of microbes. The focus of my project was phylogenomic studies for two large prokaryotic group: Actinobacteria and Archaea. My goals were to a) identify molecular markers that are specific to Actinobacteria and Archaea at different taxonomic levels, which will help to understand the phylogenetic relationship within these two major groups; b) understand the functional significance of Actinobacteria-specific proteins. By comparative genomics approach, a number of conserved indels in various proteins (viz. Coxl, GluRS, CTPsyn, Gft, GlyRS, TrmD, Gyrase A, SahH and SHMT) have been identified that are specific for all Actinobacteria and additional indels were found to be unique to its major subgroups, such as Corynebacterineae, Bifidobacteriaceae, etc. In parallel, a large number of proteins were discovered to be restricted to Actinobacteria at different phylogenetic depths. These identified conserved indels and proteins for the first time provide useful markers for defining and circumscribing the Actinobacteria phylum or its subgroups in clear molecular terms. Similar comparative genomic studies have been carried out on Archaea and a vast number of proteins have been identified that are unique to Archaea or its various lineages. Lastly, I have performed functional studies on one of the Actinobacteria-specific proteins (ASPl). The structure of ASPl was determined and structural comparison indicates that the function of this protein might be novel since it does not match any known protein with or without known function. </p> / Thesis / Doctor of Philosophy (PhD)

No description available.

No description available.

No description available.

No description available.

No description available.

The blowflies (Diptera: Calliphoridae) include some of the world‘s most economically significant parasites of livestock. The defining characteristic of blowflies is the need for their larval stages to feed on a proteinaceous substrate, often including the tissues of a living vertebrate host, a process known as myiasis. While the evolution of myiasis has been linked to the development of key adaptations in behaviour and physiology (Stevens et al., 2006), patterns of blowfly evolution suggest that parasitism evolved independently in different blowfly groups after periods of geographic isolation (Stevens et al., 2006). However, understanding the origin and evolution of myiasis in Calliphoridae is restricted by a lack of agreed theories of evolutionary relationships and taxonomic classification (Stevens, 2003). Mitochondrial genes are some of the most widely used molecular markers in insect systematics, yet most studies have utilised only single genes, with few having systematically assessed which if any are best suited for studying particular insect orders. Accordingly, this thesis presents a comprehensive analysis of 62 hexapod mitochondrial genomes, including 55 from Insecta, and assesses the ability of mitochondrial genes to recover currently recognised insect orders as monophyletic groupings. The greatest amount of phylogenetic signal was recovered when all mitochondrial genes were analysed together, regardless of optimality criterion used (PhyML, RaxML, MrBayes). Of the single-gene analyses, COX1 out-performed all other genes, even performing as well as a combined-gene analysis under Bayesian inference. In view of this finding, nucleotide sequence data from COX1 (mitochondrial protein-coding), EF-1α (nuclear protein-coding gene), and 28S (nuclear rRNA) were combined to present one of the most comprehensive multi-gene phylogenetic studies of Calliphoridae to date, resolving many ambiguous relationships, and also including several taxa that have not previously been analysed in molecular phylogenetic studies. Within Calliphoridae, Cochliomyia hominivorax (New World screwworm fly), is widely considered one of the most destructive insect parasites of livestock in the Western hemisphere. While successful eradication programmes using sterile insect technique (SIT) have been completed in North and Central America, and on some Caribbean islands, in some areas SIT has failed. It has been hypothesized that failure of SIT may be related to genetic differentiation between populations of C. hominivorax. Consequently, intra-specific variation using nucleotide sequence data from both mitochondrial (COX1 and 12S) and nuclear (EF-1α) markers, was explored. Phylogenetic analysis of these data confirmed some population substructuring and suggested a South American origin to all Caribbean island populations, with the exception of Cuba. In agreement with previous studies, Cuban populations appeared distinct from all other Caribbean populations; however, our findings do not support a North American origin for Cuba, as has previously been suggested. Finally, this thesis attempted to explore the relationship between antigenic proteins expressed in larvae from species displaying different forms of parasitism, and in doing so assessed the utility of such target proteins as potential candidates for species-specific vaccines and diagnostic tools. However, while this work discovered distinct antigenic profiles for different blowfly species, the ability to characterize specific antigens was fundamentally limited by an apparent lack of homologous proteins in current databases.

One of the restrictions used in all of the works done on phylogenetic invariants for group based models has been that the group be abelian. In my thesis, I aim to generalize the method of invariants for group-based models of DNA sequence evolution to include nonabelian groups. By using a nonabelian group to act one the nucleotides, one could capture the structure of the symmetric model for DNA sequence evolution. If successful, this line of research would unify the two separated strands of active research in the area today: Allman and Rhodes’s invariants for the symmetric model and Strumfels and Sullivant’s toric ideals of phylogenetic invariants. Furthermore, I want to look at the statistical properties of polynomial invariants to get a better understanding of how they behave when used with real, “noisy” data.

Phylogenetic trees represent theoretical evolutionary relationships among various species. Mathematically they can be described as weighted binary trees and the leaves represent the taxa being compared. One major problem in mathematical biology is the reconstruction of these trees. We already know that trees on the leaf set X can be uniquely constructed from splits, which are bipartitions of X. The question I explore in this thesis is whether reconstruction of a tree is possible from subsplits, or partial split information. The major result of this work is a constructive algorithm which allows us to determine whether a given set of subsplits will realize a tree and, if so, what the tree looks like.

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.