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Selfish genes, the phenotype paradigm and genome evolution
Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes. Prokaryotic transposable
A kingdom-level phylogeny of eukaryotes based on combined protein data.
The sequences of four of the most broadly taxonomically sampled proteins available are combined to create a roughly parallel data set to that of SSU rRNA, showing strong support for most major groups and several major supergroups.
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
The results illustrate major differences between crenarchaea and euryarchaea, especially for their DNA replication mechanism and cell cycle processes and their translational apparatus.
Prokaryotic evolution in light of gene transfer.
The role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, the implications of these processes for the reconstruction and meaning of "phylogeny," and new views of proKaryotic adaptation and diversification based on gene acquisition and exchange are discussed.
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies
The single-copy gene rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution.
Archaea and the prokaryote-to-eukaryote transition.
This review considers the cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya and the recent use of molecular phylogenetic approaches to reconstructing the tree of life.
Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins.
Phylogenetic analyses of RPB1 sequences strongly support the notion that Microsporidia are not early-diverging eukaryotes but instead are specifically related to Fungi, and reexamination of elongation factors EF-1alpha and EF-2 sequence data show support for an early (Archezoan) divergence of these amitochondriate protists to be weak and likely caused by artifacts in phylogenetic analyses.
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.
The nonparametric bootstrap resampling procedure is applied to the Bayesian approach and shows that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated onbootstrapped character matrices.
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets' plurality signals.