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Showing 1 to 13 of 13 for “"Species Trees"”.
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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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Enumeration Results On Leaf Labeled Trees
<p>ENUMERATION RESULTS ON LEAF LABELED TREES,Virginia P. Johnson In evolutionary biology, it is common practice to represent the evolution of species, populations, and organisms with graphs, called phylogenetic or species trees. These are rooted leaf-labeled trees where non-root internal vertices …
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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 phylogenetic approaches to problems in microbial genomics
… algorithm GAnG, which can construct prokaryotic species trees from thousands of distinct gene trees. GAnG analysis of archaeal gene trees supports hypotheses that the Nanoarchaeota diverged from the last ancestor of the Archaea prior to the Crenarchaeota/Euryarchaeota split.
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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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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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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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Effects of pine invasions on ground-dwelling ants on the southern slopes of the Swartberg Mountains
Ant and plant assemblages in patches of Pinus species trees in mountain fynbos and renosterbos (Elytropappus rhinocerotis) shru.bland were investigated in order to detennine whether there were differences in ant and plant species richness, abundance and cover between patches of pines and the …
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Diversity and species overlap of Botryosphaeriaceae on some trees of Anacardiaceae in disturbed and undisturbed ecosystems in South Africa
… disturbances through human activities influence species diversity and distribution of fungi in the Botryosphaeriaceae. The current study explored Botryosphaeriaceae species diversity on native and non-native tree species of Anacardiaceae found in disturbed and undisturbed ecosystems, as well as …
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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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Identification and functional characterization of microRNA regulatory elements in Brassicaceae
… and studied. In 16 phylogenetically related species within Brassicaceae, we analyzed the microRNA promoter sequences and identified overall conserved cREs in microRNA390 promoter regions, and accompanied with functional characterization, we obtained a good view of microRNA390 regulatory …
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Efficient and scalable algorithms for phylogenomics and overlapping communities
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-02-04 without embargo terms