Biology subjects

Didier, G.

Publications and source records attributed to Didier, G..

4 recordsLinked to original sources

bioRxiv2018

Exact distribution of divergence times under the birth-death-sampling model

Dating the tree of life is a task far more complicated that only determining the evolutionary relationships between species. It is therefore of interest to develop approaches able to deal with undated phylogenetic trees. The main result of this work is a method to compute probabilities of undated phylogenetic trees under piecewiseconstant-birth-death-sampling models by constraining some of the divergence times to belong to given time intervals and by allowing diversification shifts on certain clades. The computation is quite fast since its time complexity is quadratic with the size of the tree topology and linear with the number of time constraints and of "pieces" in the model. The interest of this computation method is illustrated with three applications, namely, O_LIto compute the exact distribution of the divergence times of a tree topology with temporal constraints, C_LIO_LIto directly sample the divergence times of a tree topology, and C_LIO_LIto test for a diversification shift at a given clade. C_LI

evolutionary biology↗

bioRxiv2017

Parsimonious identification of evolutionary shifts for quantitative characters

Detecting shifts in the rate or the trend of a character evolution is an important question which has been widely addressed. To our knowledge, all the approaches developed so far for detecting such shifts from a quantitative character strongly involved stochastic models of evolution.\n\nWe propose here a novel method based on an asymmetric version of the linear parsimony (aka Wagner parsimony) for identifying the most parsimonious split of a tree into two parts between which the evolution of the character is allowed to differ. To this end, we evaluate the cost of splitting a phylogenetic tree at a given node as the integral, over all pairs of asymmetry parameters, of the most parsimonious cost which can be achieved by using the first parameter on the subtree pending from this node and the second parameter elsewhere. By testing all the nodes, we then get the most parsimonious split of a tree with regard to the character values at its tips.\n\nA study of the partial costs of the tree enabled us to develop a polynomial algorithm for determining the most parsimonious splits and their evolutionary costs. Applying this algorithm on two toy examples shows that using more than one asymmetry parameter does not always lower parsimonious costs. By using the approach on biological datasets, we obtained splits consistent with those identified by previous stochastic approaches.

evolutionary biology↗

bioRxiv2017

Detecting Molecular Basis Of Phenotypic Convergence

Convergence is the process by which several species independently evolve similar traits. This evolutionary process is not only strongly related to fundamental questions such as the predictability of evolution and the role of adaptation, its study also may provide new insights about genes involved in the convergent character. We focus on this latter question and aim to detect molecular basis of a given phenotypic convergence. After pointing out a number of concerns about detection methods based on ancestral reconstruction, we propose a novel approach combining an original measure of the extent to which a site supports a phenotypic convergence, with a statistical framework for selecting genes from the measure of their sites. First, our measure of \"convergence level\" outperforms two previous ones in distinguishing simulated convergent sites from non-convergent ones. Second, by applying our detection approach to the well-studied case of convergent echolocation between dolphins and bats, we identified a set of genes which is very significantly annotated with audition-related GO-terms. This result constitutes an indirect evidence that genes involved in a phenotypic convergence can be identified with a genome-wide approach, a point which was highly debated, notably in the echolocation case (the latest articles published on this topic were quite pessimistic). Our approach opens the way to systematic studies of numerous examples of convergent evolution in order to link (convergent) phenotype to genotype.

evolutionary biology↗

bioRxiv2016

Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost).\n\nA formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony.\n\nThis study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated to the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

evolutionary biology↗