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Genome-scale approaches to resolving incongruence in molecular phylogenies
The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life.
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
It is shown that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages.
Bayesian estimation of concordance among gene trees.
- C. Ané, B. Larget, D. Baum, Stacey D. Smith, A. Rokas
- Biology, MedicineMolecular biology and evolution
- 9 November 2006
A novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods and introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees.
Inferring ancient divergences requires genes with strong phylogenetic signals
It is argued that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences in vertebrate and metazoan phylogenomic data sets.
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
Dynamics of Pseudomonas aeruginosa genome evolution
- K. Mathee, G. Narasimhan, +17 authors S. Lory
- Biology, MedicineProceedings of the National Academy of Sciences
- 26 February 2008
The complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis patients whose genetic disorder predisposes them to infections by this pathogen suggest that niche adaptation is a major evolutionary force influencing the composition of bacterial genomes.
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus
- Devin R. Scannell, Oliver A. Zill, +6 authors C. T. Hittinger
- Biology, MedicineG3: Genes | Genomes | Genetics
- 1 June 2011
Improved genome sequences of three species of Saccharomyces sensu stricto yeasts are presented, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses, and genetically marked, stable haploid strains are generated for all three species.
Novel information theory-based measures for quantifying incongruence among phylogenetic trees.
Novel measures that use information theory to quantify the degree of conflict or incongruence among all nontrivial bipartitions present in a set of trees are introduced.
Comparing bootstrap and posterior probability values in the four-taxon case.
- M. P. Cummings, S. Handley, Daniel S. Myers, D. Reed, A. Rokas, K. Winka
- Mathematics, MedicineSystematic biology
- 1 August 2003
The results corroborate the findings of others that posterior probability values are excessively high and suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probabilities.
Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution
It is shown that the Abdominal-B (ABD-B) Hox protein directly activates expression of the yellow pigmentation gene in posterior segments, demonstrating how Hox regulation of traits and target genes is gained and lost at the species level and have general implications for the evolution of body form at higher taxonomic levels.