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A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.
Most current models of sequence evolution assume that all sites of a protein evolve under the same substitution process, characterized by a 20 x 20 substitution matrix. Here, we propose to relax this… Expand
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within… Expand
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the… Expand
Tunicates and not cephalochordates are the closest living relatives of vertebrates
Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate… Expand
Phylogenomics and the reconstruction of the tree of life
As more complete genomes are sequenced, phylogenetic analysis is entering a new era — that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of… Expand
Phylogenomics Revives Traditional Views on Deep Animal Relationships
The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence… Expand
Computing Bayes factors using thermodynamic integration.
In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the… Expand
A general comparison of relaxed molecular clock models.
- T. Lepage, D. Bryant, H. Philippe, N. Lartillot
- Biology, Medicine
- Molecular biology and evolution
- 1 December 2007
Several models have been proposed to relax the molecular clock in order to estimate divergence times. However, it is unclear which model has the best fit to real data and should therefore be used to… Expand
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g.,… Expand
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
BackgroundThanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support… Expand