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Gascuel O.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics | Steel M.,University of Canterbury
Systematic Biology | Year: 2014

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rates become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, that, depending on the tree and branch length distribution, reconstructing these changes (i.e., reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony- and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification. [Ancestral state prediction; character evolution; majority rule; Markov model; maximum likelihood; parsimony; phylogenetic tree.] © The Author(s) 2014. Source

Richa R.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics
Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | Year: 2010

In the context of minimally invasive cardiac surgery, active vision-based motion compensation schemes have been proposed for mitigating problems related to physiological motion. However, robust and accurate visual tracking is a difficult task. The purpose of this paper is to present a hybrid tracker that estimates the heart surface deformation using the outputs of multiple visual tracking techniques. In the proposed method, the failure of an individual technique can be circumvented by the success of others, enabling the robust estimation of the heart surface deformation with increased spatial resolution. In addition, for coping with the absence of visual information due to motion blur or occlusions, a temporal heart motion model is incorporated as an additional support for the visual tracking task. The superior performance of the proposed technique compared to existing techniques individually is demonstrated through experiments conducted on recorded images of an in vivo minimally invasive CABG using the DaVinci robotic platform. Source

Lartillot N.,University of Montreal | Lartillot N.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics | Rodrigue N.,Agriculture and Agri Food Canada | Rodrigue N.,University of Ottawa | And 2 more authors.
Systematic Biology | Year: 2013

Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity.However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version ofPhyloBayes,implementing the Dirichletprocess mixture models aswell as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org. [Bayesian inference; Dirichlet process; mixture models; phylogenetics; phylogenomics.] © The Author(s) 2013. Source

Lartillot N.,University of Montreal | Lartillot N.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics
Molecular Biology and Evolution | Year: 2013

According to the nearly-neutral model, variation in long-term effective population size among species should result in correlated variation in the ratio of nonsynonymous over synonymous substitution rates (dN/dS). Previous empirical investigations in mammals have been consistent with this prediction, suggesting an important role for nearly-neutral effects on protein-coding sequence evolution. GC-biased gene conversion (gBGC), on the other hand, is increasingly recognized as a major evolutionary force shaping genome nucleotide composition. When sufficiently strong compared with random drift, gBGC may significantly interfere with a nearly-neutral regime and impact dN/dS in a complex manner. Here, we investigate the phylogenetic correlations between dN/dS, the equilibrium GC composition (GC*), and several life-history and karyotypic traits in placental mammals. We show that the equilibrium GC composition decreases with body mass and increases with the number of chromosomes, suggesting a modulation of the strength of biased gene conversion due to changes in effective population size and genome-wide recombination rate. The variation in dN/dS is complex and only partially fits the prediction of the nearly-neutral theory. However, specifically restricting estimation of the dN/dS ratio on GC-conservative transversions, which are immune from gBGC, results in correlations that are more compatible with a nearly-neutral interpretation. Our investigation indicates the presence of complex interactions between selection and biased gene conversion and suggests that further mechanistic development is warranted, to tease out mutation, selection, drift, and conversion. © The Author 2012. Source

Guindon S.,University of Auckland | Guindon S.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics
Systematic Biology | Year: 2013

The accuracy and precision of species divergence date estimation from molecular data strongly depend on the models describing the variation of substitution rates along a phylogeny. These models generally assume that rates randomly fluctuate along branches from one node to the next. However, for mathematical convenience, the stochasticity of such a process is ignored when translating these rate trajectories into branch lengths. This study addresses this shortcoming. A new approach is described that explicitly considers the average substitution rates along branches as random quantities, resulting in a more realistic description of the variations of evolutionary rates along lineages. The proposed method provides more precise estimates of the rate autocorrelation parameter as well as divergence times. Also, simulation results indicate that ignoring the stochastic variation of rates along edges can lead to significant overestimation of specific node ages. Altogether, the new approach introduced in this study is a step forward to designing biologically relevant models of rate evolution that are well suited to data sets with dense taxon sampling which are likely to present rate autocorrelation. © 2012 The Author(s). Source

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