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Genome-scale approaches to resolving incongruence in molecular phylogenies
One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate theExpand
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The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genomeExpand
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The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
Dating Wood Rot Specific lineages within the basidiomycete fungi, white rot species, have evolved the ability to break up a major structural component of woody plants, lignin, relative to theirExpand
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Inferring ancient divergences requires genes with strong phylogenetic signals
To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolvingExpand
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Bayesian estimation of concordance among gene trees.
Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited.Expand
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Dynamics of Pseudomonas aeruginosa genome evolution
One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immuneExpand
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Novel information theory-based measures for quantifying incongruence among phylogenetic trees.
Phylogenies inferred from different data matrices often conflict with each other necessitating the development of measures that quantify this incongruence. Here, we introduce novel measures that useExpand
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The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus
High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of SaccharomycesExpand
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Comparing bootstrap and posterior probability values in the four-taxon case.
Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently usedExpand
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework toExpand
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