I investigate use of the simulated annealing heuristic to seek phylogenetic trees judged optimal according to the principle of parsimony. I begin by looking into the central data structure in phylogenetic research, the tree. I discuss why it is usually necessary to employ a heuristic, rather than an exact method, when seeking parsimonious trees. I summarise different heuristic approaches. I explain how to use the program LVB, written to use simulated annealing in the search for parsimonious trees. I use LVB, with different combinations of values for parameters controlling the annealing search, to re-analyse two DNA sequence data matrices, one of 50 objects and one of 365 objects. Equations to estimate suitable control parameters, on the basis of desired run time and quality of result, are fitted to data obtained by these analyses. Future directions of research are discussed.

An experiment involving two treatment groups compared whole wheat diet and refined wheat diet on different sets of mice. Of interest were the differences by treatment of the levels of hundreds of bacteria in the guts of the mice. It was desired to determine the statistical significance of not only the individual bacteria, but also the families of bacteria. These family relationships are represented in a phylogenetic tree, and it was determined helpful to color the branches of bacteria based on the significance of their corresponding families. Calculating these p-values and coloring the branches by hand would not be a quick process. An automated method would greatly increase the efficiency of these calculations. To handle this problem, SigTree, an R package, was written. The p-values for individual bacteria (tips) are combined up the tree using meta-analysis methods, and significance is visualized on a color scale in a revised phylogenetic tree plot. SigTree is able to handle not only the motivating mouse diet experiment, but also experiments that fall into the general framework of having significance tests (and resulting p-values) on each tip in a phylogenetic tree.

Master of Science / Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

Parasites are an important component of every ecosystem, and their interactions with hosts can directly impact the fitness of the host organisms. Despite their significance, it is still largely unknown which host traits predispose a species to increased risk of parasite attack. In the present study, I investigated host and ecological correlates of parasite load in Lake Tanganyikan cichlids using phylogenetic comparative analyses. Specifically, I tested the effect of body size, brain mass, gut length, depth, trophic level, habitat complexity and mating system on parasite prevalence and diversity.  I found that the variation in both average infracommunity richness and parasite prevalence were partly explained by host body mass and habitat complexity. Total parasite diversity, on the other hand, was significantly related to mating behaviour as well as habitat complexity. The comparative analysis presented here is, to the best of my knowledge, the first to investigate determinants of parasite load in Lake Tanganyikan cichlids. As such, my results support several major hypotheses concerning the factors that underlie parasite prevalence and diversity and have broad implications for our understanding of parasite-host interactions.

Phylogenetic structure measures patterns of evolutionary history within communities – are some communities composed of species more distantly or closely related than expected by chance? Due to common descent, closely related species are more ecologically similar, and so degrees of relatedness in a community may be good predictors of its ecology, more so than the number of species. Whether we are speaking of how phylogenetic structure arises as a consequence of ecological processes, or how phylogenetic structure affects the functioning of communities, the role of consumer organisms has received less attention than the role of resources. In this thesis, I ask what are the consequences and causes of phylogenetic structure of a potentially multi-level community, focusing on the underappreciated effects of consumer-resource interactions. In Chapter 2, I show how phylogenetic diversity of plant communities predicts the diversity and abundance of arthropods captured in a long-running biodiversity experiment better than species richness alone. In Chapter 3, I show how phylogenetic diversity and species richness interact to explain herbivore damage at a whole community level. In Chapter 4, I explore how phylogenetic structure of old field plant communities differs in plots of contrasting disturbance history, and speculate as to what factors – such as herbivory – may have contributed to these differences. In Chapter 5, I present a model which incorporates competition – through both resources and consumers of a focal trophic level – and environmental filtering, two factors which are thought to impact phylogenetic structure through their influence on ecological similarity. I show that environmental filtering interacts with competition to determine the coexistence of similar species, and that consumers may have different effects than do resources. My dissertation provides new insight into the importance of consumers in ecological communities, both through their effect on, and through their response to, patterns of evolutionary history in their prey.

Phylogenetic structure measures patterns of evolutionary history within communities – are some communities composed of species more distantly or closely related than expected by chance? Due to common descent, closely related species are more ecologically similar, and so degrees of relatedness in a community may be good predictors of its ecology, more so than the number of species. Whether we are speaking of how phylogenetic structure arises as a consequence of ecological processes, or how phylogenetic structure affects the functioning of communities, the role of consumer organisms has received less attention than the role of resources. In this thesis, I ask what are the consequences and causes of phylogenetic structure of a potentially multi-level community, focusing on the underappreciated effects of consumer-resource interactions. In Chapter 2, I show how phylogenetic diversity of plant communities predicts the diversity and abundance of arthropods captured in a long-running biodiversity experiment better than species richness alone. In Chapter 3, I show how phylogenetic diversity and species richness interact to explain herbivore damage at a whole community level. In Chapter 4, I explore how phylogenetic structure of old field plant communities differs in plots of contrasting disturbance history, and speculate as to what factors – such as herbivory – may have contributed to these differences. In Chapter 5, I present a model which incorporates competition – through both resources and consumers of a focal trophic level – and environmental filtering, two factors which are thought to impact phylogenetic structure through their influence on ecological similarity. I show that environmental filtering interacts with competition to determine the coexistence of similar species, and that consumers may have different effects than do resources. My dissertation provides new insight into the importance of consumers in ecological communities, both through their effect on, and through their response to, patterns of evolutionary history in their prey.

Phylogenetic structure measures patterns of evolutionary history within communities – are some communities composed of species more distantly or closely related than expected by chance? Due to common descent, closely related species are more ecologically similar, and so degrees of relatedness in a community may be good predictors of its ecology, more so than the number of species. Whether we are speaking of how phylogenetic structure arises as a consequence of ecological processes, or how phylogenetic structure affects the functioning of communities, the role of consumer organisms has received less attention than the role of resources. In this thesis, I ask what are the consequences and causes of phylogenetic structure of a potentially multi-level community, focusing on the underappreciated effects of consumer-resource interactions. In Chapter 2, I show how phylogenetic diversity of plant communities predicts the diversity and abundance of arthropods captured in a long-running biodiversity experiment better than species richness alone. In Chapter 3, I show how phylogenetic diversity and species richness interact to explain herbivore damage at a whole community level. In Chapter 4, I explore how phylogenetic structure of old field plant communities differs in plots of contrasting disturbance history, and speculate as to what factors – such as herbivory – may have contributed to these differences. In Chapter 5, I present a model which incorporates competition – through both resources and consumers of a focal trophic level – and environmental filtering, two factors which are thought to impact phylogenetic structure through their influence on ecological similarity. I show that environmental filtering interacts with competition to determine the coexistence of similar species, and that consumers may have different effects than do resources. My dissertation provides new insight into the importance of consumers in ecological communities, both through their effect on, and through their response to, patterns of evolutionary history in their prey.

Phylogenetic structure measures patterns of evolutionary history within communities – are some communities composed of species more distantly or closely related than expected by chance? Due to common descent, closely related species are more ecologically similar, and so degrees of relatedness in a community may be good predictors of its ecology, more so than the number of species. Whether we are speaking of how phylogenetic structure arises as a consequence of ecological processes, or how phylogenetic structure affects the functioning of communities, the role of consumer organisms has received less attention than the role of resources. In this thesis, I ask what are the consequences and causes of phylogenetic structure of a potentially multi-level community, focusing on the underappreciated effects of consumer-resource interactions. In Chapter 2, I show how phylogenetic diversity of plant communities predicts the diversity and abundance of arthropods captured in a long-running biodiversity experiment better than species richness alone. In Chapter 3, I show how phylogenetic diversity and species richness interact to explain herbivore damage at a whole community level. In Chapter 4, I explore how phylogenetic structure of old field plant communities differs in plots of contrasting disturbance history, and speculate as to what factors – such as herbivory – may have contributed to these differences. In Chapter 5, I present a model which incorporates competition – through both resources and consumers of a focal trophic level – and environmental filtering, two factors which are thought to impact phylogenetic structure through their influence on ecological similarity. I show that environmental filtering interacts with competition to determine the coexistence of similar species, and that consumers may have different effects than do resources. My dissertation provides new insight into the importance of consumers in ecological communities, both through their effect on, and through their response to, patterns of evolutionary history in their prey.

Master of Science / Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

>Magister Scientiae - MSc / Determination of CXCR4-usage patterns is essential in establishing suitability of CCR5 antagonist prescription in HIV-1 infected individuals to prevent treatment failure. Previous studies have suggested a switch to CXCR4-usage to be far less common in subtype C, yet recent studies have reported between 30 - 50% CXCR4-usage in this subtype. However, CXCR4-usage in subtype C is poorly characterised. Furthermore, the reliability of available genotypic algorithms is unknown for subtype C sequences. In this study, a comparative analysis of the predictive ability of several subtype B-modeled genotyping algorithms in subtype C tropism determination was undertaken. A total of 731 HIV-1 subtype C V3 sequences with phenotypically determined coreceptor tropism were collated from several sources. Datasets of 349 CCR5, 25 CXCR4 exclusive and 31 R5X4 (Dual) sequences were submitted to 11 various tropism prediction tools. The best performing tool was used to determine the tropism of 12,121 subtype C V3 sequences with unknown phenotypes, in order to characterise the prevalence and method of CXCR4 usage in HIV-1 subtype C. We determined that geno2pheno with a false positive rate of 5% is the best approach for predicting CXCR4-usage in subtype C sequences with an accuracy of 94% (89% sensitivity and 99% specificity). Contrary to what has been reported for subtype B, the optimal approaches for prediction of CXCR4-usage in sequence from viruses that use CXCR4 exclusively, also perform best at predicting CXCR4-use in dual-tropic viral variants. Furthermore, we find that a switch to CXCR4 usage is seen in subtype C for well over 20 years and has occurred consistently over time. At 5%, the frequency of CXCR4-usage in subtype C database records is lower than previous reports for both subtype C and B. The Geno2pheno coreceptor tool may be used as a reliable genotypic predictor in clinical settings to establish the viability of CCR5-antagonist therapies using drugs such as Maraviroc and provides a rapid and cost effective alternative to phenotypic testing in resource limited areas. A switch to CXCR4-usage in subtype C is constant but lower when compared to subtype B, a finding which may have broad implications for the design of intervention and treatment strategies for HIV-1 subtype C.