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A Simple and Robust Statistical Test for Detecting the Presence of Recombination
TLDR
A new statistic, Φw, is developed that can be used to test for recombination and is suggested to be one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.
TLDR
The results suggest that the complexity of the pattern of substitution of real sequences is better captured by the CAT model, offering the possibility of studying its impact on phylogenetic reconstruction and its connections with structure-function determinants.
Tunicates and not cephalochordates are the closest living relatives of vertebrates
TLDR
It is shown that phylogenetic analyses of the genome sequencing of the appendicularian Oikopleura dioica provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates.
Phylogenomics and the reconstruction of the tree of life
TLDR
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
TLDR
Three recent large-scale phylogenomics studies, which deal with the early diversification of animals, produced highly incongruent findings despite the use of considerable sequence data, suggesting that merely adding more sequences is not enough to resolve the inconsistencies.
Computing Bayes factors using thermodynamic integration.
TLDR
The present article proposes to employ another method, based on an analogy with statistical physics, called thermodynamic integration, which is applied to the comparison of several alternative models of amino-acid replacement, indicating that modeling pattern heterogeneity across sites tends to yield better models than standard empirical matrices.
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
TLDR
This study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies and suggests that urochordates are more closely related to vertebrates than are cephalochordates.
A general comparison of relaxed molecular clock models.
TLDR
This work reimplemented most of the already existing models, including the popular lognormal model, as well as various prior choices for divergence times (birth-death, Dirichlet, uniform), in a common Bayesian statistical framework, and proposes a new autocorrelated model, called the "CIR" process, with well-defined stationary properties.
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
TLDR
The CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment.
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