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 16 of 16 for “"Gene trees"”.
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Improving gene trees without more data
Species tree and gene tree estimation from sequence data are two steps in many biological analyses. Computational challenges and limited amount of data often make estimating highly accurate phylogenetic trees a difficult task. Moreover, gene alignments used to estimate trees on individual loci …
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Novel phylogenetic approaches to problems in microbial genomics
… 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 marine …
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Large scale phylogenomic estimation
… - the science of calculating evolutionary trees from genomic data - is an important biological problem. As the amount of genomic data in biological datasets increases, new methods are needed to analyze this data. Cutting edge analyses may utilize genomes from tens of thousands of species. I …
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Molecular phylogenetics of the North American snake tribe Thamnophiini
Advancements in phylogenetic theory and methodology coupled with improvements in computational and sequencing technology facilitate study of the divergence and diversification patterns of life. I apply our current understanding to further explore the relationships and evolution of the North …
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Methods and analysis of genome-scale gene family evolution across multiple species
… datasets. In this work, I explore how evolution generates the diversity of life we see in modern species, specifically the evolution of new genes and functions. By reconstructing the history of the diverse sequences present in modern species, we can improve our understanding of their function and …
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Biogeography of Isolepis subgenus Fluitantes (C.B. Clarke), Muasya (Cyperaceae): niche conservatism, long distance dispersal and hybridization
… and provides a useful study group to assess the general validity of published biogeographical trends. Furthermore, the cooccurrence of several closely related species in the Cape floristic region allows geographical and ecological patterns to be used for inference of speciation processes in the …
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Unravelling the Origins and Evolution of the Animal Kingdom using Genomics
… including comparative genomics (e.g., gene loss/gain, non-coding regions, synteny, etc),gene family evolution, and their evolutionary relationships using genome-wide data. No study to date has compared all the wealth of genomic data available to understand theevolution of the Animal …
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Statistical estimation problems in phylogenomics and applications in microbial ecology
… data according to evolution, with orthologous genes grouped together and stored as a multiple sequence alignment and phylogenetic tree. First we consider the related problem of estimating the population-level phylogeny of a group of species based on the alignments and phylogenies of several …
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Adaptive radiation and speciation in African weakly-electric fish
… the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its …
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Differential Selection Pressure Among Duplicated Genes In Teleosts
Gene and genomic duplications provide organisms with new genetic material subject to selection. Using myo5, rab11, and rab27 gene families as models, I examined the evolutionary rate differences among duplicated genes and whether selective forces (e.g. purifying selection or positive selection) …
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Phylogenomic analysis of hemimetabolan insects with emphasis on the hemipteran suborder Auchenorrhyncha and the superorder Paraneoptera
… researchers to seek additional sources of phylogenetic information. The past two decades have seen an extraordinary expansion in the availability of genome-scale data from non-model organisms including insects due to increasing availability and affordability of high-throughput sequencing …
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The evolution and diversity of noncanonical microbial nitrogen metabolisms
… domains conserved in Proteobacterial nirS. Phylogenetic domain mapping reveals that this gene resulted from a chimeric domain fusion in ancestral Chloroflexi. I also identify an underreported variant of nitric oxide reductase (eNOR) within Chloroflexi MAGs, and provide a detailed phylogeny of …
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Inference of parsimonious species phylogenies from multi-locus data
… In the traditional method for inferring species trees from genetic data, we sequence a single locus in species genomes, reconstruct a gene tree, and report it as the species tree. Biologists have long acknowledged that a gene tree can be different from a species tree, thus implying that this …
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Phylogeny Inference in the Presence of Incomplete Lineage Sorting, Gene Duplication and Loss and Hybridization
… their most recent common ancestral species. A gene tree captures the evolutionary history of an individual gene or, more generally, non-recombining genomic region. A very complex relationship exists between the phylogeny of a set of species and the trees of genes in the genomes of those …
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Phylogenetic Studies of Pasteuria penetrans Looking at the Evolutionary History of Housekeeping Genes and Collagen-like Motif Sequences.
… using the concatenation of forty housekeeping genes, two subsets of these involving twenty-eight taxa and twenty-seven genes, with and without indels removed, and each gene individually. Through the application of maximum likelihood, maximum parsimony, and Bayesian methods on these datasets, P. …
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Tick-borne haemoparasite occurrence and Anaplasma bovis strain diversity in eastern rock sengis (Elephantulus myurus)
… been fully investigated. In addition, the phylogenetic position of the described A. bovis-like strain is unclear as genetic data are currently limited to the highly conserved 16S rRNA gene and studies are constrained by difficulties with cultivation of tick-borne Anaplasmataceae. The aim of the …