EU CHOICE DARWIN Profile 2

The module explores the theoretical and empirical advances in recent research in evolutionary genetics through several key issues:

- Topic 1: Genetic Burden and the Evolution of Reproductive Systems: Recombination, Sexual/Asexual Reproduction, Self-Fertilization/Cross-Fertilization

- Topic 2: Kinship structures and their evolutionary consequences: kin selection, group selection, the evolution of cooperation, and sex ratios

- Topic 3: Long-term interactions between species: parasitism, mutualism, coevolution

- Topic 4: Traces of evolutionary history in genomes; genomics of adaptation.

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The primary objective of this course is to provide students with all the skills necessary to understand and apply the concepts and methods underlying the quantitative study of population phenomena. The main methods for analyzing and modeling these phenomena will be addressed from both a theoretical (formal calculations) and practical (statistics, simulations) perspective, using examples that explore different phylogenetic scales (microbial dynamics, invasive species, human demography), spatial (from local to global) and temporal (transient and steady-state regimes, eco-evolutionary coupling), with particular attention paid to heterogeneity (spatial, genetic, or phenotypic) and randomness (stochasticity, uncertainties) characteristic of populations or inherent in their study.

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The objective of this teaching unit is to demonstrate that biological diversity serves a functional purpose:

1) for various groups of organisms: plants, insects, aquatic organisms, vertebrates, and

2) at different organizational scales (from organisms to ecosystems). The course aims to explain how to approach this functional aspect of diversity for the more than 10 million organisms present on the planet’s surface, using examples from highly and minimally anthropized environments.

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Phylogeny is a search for evolutionary clues. The goal of this module is to highlight the existence of gene phylogenies within species phylogenies, the methods for representing evolutionary histories as trees, and the concept of positional molecular homology through sequence alignment. The principles of phylogenetic inference methods are at the core of this course unit. Distance-based methods highlight the difficulties in distinguishing between homology and homoplasy, as well as the need to construct models of character evolution. The cladistic approach based on maximum parsimony illustrates, on the one hand, the use of bootstrapping to estimate the robustness of phylogenetic nodes and, on the other hand, the impact of taxonomic sampling on the detection of multiple substitutions.

Probabilistic approaches are introduced and then explored in greater depth. The long-branch attraction artifact leads to the introduction of probabilistic reasoning. The maximum likelihood method allows us to address the calculation of likelihood, the estimation of model parameters using optimality criteria, the construction of various models of character evolution, and the comparison of models. Bayesian inference, in turn, introduces the distinction between density-based and optimality-based approaches. It then covers the a priori use of probability densities, the estimation of posterior distributions of model parameters based on the data, their approximation using Markov chains with Monte Carlo and Metropolis coupling (MCMCMC), the initialization and convergence phases, and the calculation and interpretation of posterior probabilities for trees and clades. The importance of evolutionary models for DNA, RNA, and protein sequences and their refinement is emphasized.

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Evo-devo is an evolutionary approach to developmental genetics. This discipline seeks to shed light on changes in developmental mechanisms that explain current and past morphological diversity, thereby bridging the gap between biology and paleontology.

Throughout this module, we will use articles to discuss several evolutionary topics relevant to Evo-Devo approaches: the concept of homology, the origin and evolution of repetitive structures, the genetic basis of development, and the links between genomic evolution and morphological evolution. We will illustrate these concepts using examples from metazoans and the green lineage, and apply them at the level of major modern groups as well as at the population level.

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