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 40 for “"species tree"”.
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Supertree-like methods for genome-scale species tree estimation
… studies is the estimation of evolutionary trees (phylogenies) from genomic data. Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is …
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Inference of parsimonious species phylogenies from multi-locus data
… focus of this dissertation is the inference of species phylogenies, i.e. evolutionary histories of species. Species phylogenies allow us to gain insights into the mechanisms of evolution and to hypothesize past evolutionary events. They also find applications in medicine, for example, the …
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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 computational methods for discordance-aware phylogenomic analysis
Inferring the evolutionary history of a set of species is a key step in many biological and medical research projects, as species trees provide a context in which problems in comparative genomics, biodiversity, phylogeography and epidemiology can be addressed. Recent advances in sequencing …
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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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Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars
… For each system, I applied coalescent-based species tree inference using CASTER (Zhang et al., 2025) and introgression analyses using Dsuite (Malinsky et al., 2021). For the <em>Asterias</em> sea stars system only, I applied admixture dating using linkage disequilibrium decay as implemented …
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Phylogeny Inference in the Presence of Incomplete Lineage Sorting, Gene Duplication and Loss and Hybridization
A species phylogeny captures how a set of extant species split and diverged from 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 …
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Genomic mechanisms underpinning phenotypic diversity in the spiral-horned antelopes (Genus: Tragelaphus)
… argued that they comprise either nine or ten species based on mtDNA and nuclear DNA respectively/chromosomal number difference. With the same mentioned molecular data, there is discordance in their previously reconstructed species tree, placing species in different clades with different …
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Molecular phylogenetics of the North American snake tribe Thamnophiini
… process of genome evolution while the second (species-tree methods) may be overly complex for histories characterized by long divergence times between cladogenesis. Rather than making an a priori determination concerning which of these phylogenetic models to apply to our data, I seek to provide …
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Bayesian Inference of Phylogenetic Networks
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under the MSC, owing mainly to the …
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A Phylogenetic and Environmental Analysis of Brazilian Placosoma Lizards
… were inferred through Bayesian inference and a species tree approach, and reconciled with geographical and climate data. I generated DNA sequences for the nuclear markers DNAH3, PRLR, and SINCAIP, and the mitochondrial markers ND4 and 16S for all species but <em>P. limaverdorum</em> (for which …
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Methods and analysis of genome-scale gene family evolution across multiple species
… 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 evolutionary importance. Performing such an …
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Population genetics and systematics of a species-rich clade of Neotropical reef fishes, the tubeblenny genus Acanthemblemaria
Neotropical coral reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three coral reef fish families endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most …
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Abundance and Nesting Success of Acadian Flycatchers (Empidonax Virescens) at Different Scales of Fragmentation in Illinois, United States of America
… preferred to build their nests in certain tree species, tree species was unrelated to nest concealment and nesting success. Most of the other vegetation variables that were measured at the nest patch and habitat type did not influence nesting success. Local and landscape fragmentation …
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Multi-locus phylogenetic inference of the howler monkey (Alouatta) radiation in South America.
… these analyses, branching patterns among howler species lineages conflict between studies or remain unresolved. Using 14 unlinked non-coding intergenic nuclear regions under both a concatenated Bayesian approach (MrBayes) and a coalescent-based species tree method (*BEAST). I perform a new …
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Evolutionary Relationships Among Duiker Antelope (Bovidae: Cephalophinae)
<p>Duikers are a species rich subfamily of threatened African antelope whose recent origin poses a challenge to the molecular identification of taxa and estimation of their phylogeny. I test the ability of DNA barcodes to identify all taxa within this group. I then use mitochondrial and nuclear …
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The Effect of Seasonal Vegetation Changes on Habitat Suitability and Predation Risk of the Vancouver Island Marmot
… vancouverensis) are a critically endangered species with a small and fragmented population. They live in subalpine meadows, exclusively on Vancouver Island, Canada, but will also colonize logged habitats at lower elevations, which become population sinks for the species. Tree encroachment and …
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Role of subfunctionalized MYB paralogs in the evolution of pigmentation patterning in Clarkia
… complex trait.</p><p>Clarkia is a genus of 42 species that display intricate and widely varied pigmentation patterns on their petals while other species in the family have for the most part unpigmented and unpatterned petals, suggesting that pigmentation patterning first evolved at the origin …
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Fire survival and life histories of Acacia and Dichrostachys species in a South African savanna
The tree-grass mix defines savannas, yet savannas can be defined as ecosystems that move between transition states of grass and bush, the dynamics of which are complex, being affected by a number of biotic and abiotic factors. Recently there has been renewed interest in fire and its role in shaping …
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Using economic factors in managing Appalachian hardwoods for high quality
… factors, many of them economic. Among these are species, tree size, tree quality, logging costs, and market alternatives. This study demonstrates how to incorporate these, using a new microcomputer program with growth projection, YIELD-MS (Hepp, 1986), to find an economically favorable regime for …
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