CHOX1

Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on the changes in developmental mechanisms that explain present and past morphological diversity, and thus opens an important bridge between biology and paleontology.

During the module, we will discuss, based on articles, several evolutionary issues that are useful for Evo-Devo approaches: the question of homology, the question of the establishment and evolution of repeated structures, the genetic basis of development and the links between genome evolution and shape evolution. We will illustrate these notions from examples taken from metazoans and the green lineage, and will apply them to the scale of large current groups but also to populations.

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Phylogeny is a quest for evolutionary clues. The aim of this module is to recall the existence of gene phylogenies in species phylogenies, the ways of representing evolutionary histories in the form of trees, and the challenge of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the heart of the knowledge of this course. The distance methods allow to underline the difficulties of separating homology and homoplasy, and the necessity to build models of character evolution. The cladistic approach with maximum parsimony allows to illustrate on the one hand the use of bootstrap to estimate the strength of the nodes of phylogenies, and on the other hand the impact of taxonomic sampling to detect multiple substitutions.

The probabilistic approaches are presented and further developed. The attraction artifact of long branches leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to approach the calculation of the likelihood, the estimation of the parameters of the models by optimality, the construction of different models of character evolution, as well as the comparison of models. Bayesian inference introduces the distinction between density and optimality approaches. It then shows the a priori use of probability densities, the estimation of a posteriori distributions of model parameters given the data, their approximation by Markov chains with Monte Carlo techniques and Metropolis coupling (MCMCMC), the ignition and convergence phases, and the computation and interpretation of the posterior probabilities of trees and clades. The importance of DNA, RNA and protein sequence evolution models and their improvement is stressed.

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