Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 25 for “"Phylogenetic methods"”.
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Traits and Trees: Exploring the edges of phylogenetic methods
Phylogenetic methods are central to the study of biology and in recent years more formal techniques involving computational methods have been developed and widely applied. While these have focused on building the Tree of Life from molecular data, other approaches have extended to phenotypes, …
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Using a complex model of sequence evolution to evaluate and improve phylogenetic methods
The performance of phylogenetic methods was evaluated by testing their success in recovering the true tree from computer simulated data. Data were generated on a variety of tree shapes under a complex model of sequence evolution based on the work of Aaron Halpern and William Bruno. Parameters of …
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Towards an Edition of Troilus and Criseyde: The Work, Authorial Versions, and Digital Tools
… of Geoffrey Chaucer’s Troilus and Criseyde using phylogenetic methods. It has three main goals: (1) to show that phylogenetic methods can illuminate the relationships within the textual tradition, (2) to challenge the “three-version” theory that has influenced Troilus scholarship for over a …
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Phylogeographic structure of the Atlantic pupfish, Cyprinodon variegatus (Cyprinodontidae), along the eastern coast of North America: Evidence from mitochondrial nucleotide sequences
… parsimony, distance, and maximum likelihood phylogenetic methods to analyze the control region data. The cytochrome-b sequence data supported this monophyletic northern clade, although their utility for this analysis is marginal. Little evidence was found for the existence of a hybrid zone. …
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Problems in Pedigrees and Phylogenies
… the units of observation. We discuss statistical methods for various problems within both settings. We begin with heritability estimation using pedigree data, with an ordinal outcome trait. We discuss the use of the threshold model for heritability estimation, exploring the consequences of model …
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Speciation and diversification of the beetle tribe Cratopini on the islands of the South West Indian Ocean area.
… approach that employed both population genetic methods and phylogenetic methods to gain a broad understanding of the evolution of the group. Questions addressed range from aspects of the ecology of individual species to the relationships within islands amongst morphospecies and finally to the …
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Novel phylogenetic approaches to problems in microbial genomics
… phylogenies. In this thesis, I present three new phylogenetic methods for gaining insight into how microbes evolve. In Chapter 1, I introduce the algorithm AdaptML, which uses strain ecology information to identify genetically- and ecologically-distinct bacterial populations. Analysis of 1000 …
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Genomic Evolution in the Oomycetes
… species. Using comparative genomic, network, and phylogenetic methods, this thesis reports the identification of lineage and species-specific expansions of effectors. Despite their ubiquity and the threat that oomycetes pose to global food security, there is a lack of dedicated tools to analyse …
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The evolution of parental care in insects
… and benefits of insect parental care. I use phylogenetic methods to test large-scale hypotheses, and field studies to test proximate hypotheses. Initially I look at the evolution of variation in the sex performing care, reconstructing transitions across insect evolutionary history. Consistent …
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Phylogenomic supertrees: integration of maximal data and assessment of input tree shape.
… previously that some commonly used supertree methods are biased with respect to the tree shape they produce (Wilkinson et al., 2005). However, since some supertree methods (e.g. matrix representation with parsimony; MRP) have an inherent phylogenetic component, the observed shape …
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Proximate And Evolutionary Insights Into The Epigenetics Of Posttraumatic Stress Disorder
… in PTSD development. In the second, I utilize phylogenetic methods to infer and characterize the evolutionary history of genetic loci necessary for the epigenetic regulation of PTSD, revealing that this capacity may have ancient origins. In the third, I test, and fail to provide evidence for, …
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A cause for consilience: Utilizing multiple genomic data types to resolve problematic nodes within Arthropoda and Ecdysozoa
… long periods of divergent evolution. Phylogenetic signal to resolve the relationships of these lineages is diluted, increasing the likelihood of recovery of phylogenetic artifacts. In an attempt to resolve the relationships within Ecdysozoa, consilience of three independent …
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Inferring tumour evolution from single-cell and multi-sample data
… This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-cell sequencing technologies have promised to reveal tumour heterogeneity at a much higher resolution, but single-cell …
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Ancestral structures in population genetics and a generalisation to birth-death processes with catastrophes
… more precisely, mutation fluxes) estimated via phylogenetic methods relative to those observed in pedigree studies.<br /><br /> We then establish a connection between the pLD-ASG and the killed ancestral selection graph (k-ASG), a different genealogical structure used to determine the type …
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Physiological and behavioural responses to temperature and humidity in fossorial amphibians
… behaviour of fossorial amphibians. By combining phylogenetic methods and laboratory experiments, my chapters address the topics of energetics, hydroregulation, thermoregulation, and overwintering emergence. First, I tested the prevailing hypothesis that fossorial amphibians should have reduced …
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The origin and evolution of the ribosome
… structure and function of macromolecules into phylogenetic analyses. Macromolecular structure is more evolutionarily conserved than sequence due to constraints arising from the intricate structure-function relationship. Tracing the evolution of the structural elements of the ribosome, namely …
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Identifying dryinidae (hymenoptera) - auchenorrhyncha (hemiptera) host associations using phylogenetics
… periods, usually with limited success. Molecular phylogenetic methods provide an alternative to expand knowledge of dryinid host breadth by DNA sequencing of host attached parasitoid larvae. For this study, 142 late-stage dryinid larvae were removed from parasitized individuals of Auchenorrhyncha …
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Dung beetle radiations in Madagascar
… tribes using several gene regions and different phylogenetic methods. Evolution of closely related species and among populations of the same species was examined with haplotype networks. The Malagasy Canthonini consists of three large lineages, while Helictopleurina forms a monophyletic group. …
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Mitochondrial and chromosomal genomics in type 2 diabetes
… a combination of bioinformatics and experimental methods we identified several genes and non-coding sequences within Niddm71 that likely play a role in insulin secretion and mitochondrial function. To investigate the role of mtDNA variants on the susceptibility of T2D we sequenced complete …
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