Chaire Modélisation Mathématique et Biodiversité

Little is known about the diversity of beneficial mutations, including their number, their molecular and functional heterogeneity, and the dynamics of their interactions. To address these issues, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting over 600 different beneficial sites. Few mutations were shared precisely among the replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered the primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar outcomes. The high degree of replication in our experiment allowed us to infer the pervasive presence of epistasis among beneficial mutations. Epistatic interactions shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.

We consider a diploid population with birth and death rates depending on a parameter, the so-called system size. If the rates depend weakly on the type of the individual, in the limit of large system size, we obtain fast convergence to constant population size and Hardy Weinberg equilibrium. On the time scale of the order of the system size we derive the Wright Fisher diffusion with selective drift. The results are based on joint work with Hans Metz (Leiden).

Language diversification is a random process similar in many ways to biological evolution. We model the diversification of so-called "core" lexical data by a stochastic process on a phylogenetic tree. We focus on the Indo-European language family. The age of the most recent common ancestor of these languages is of particular interest and issues of dating ancient languages have been subject to controversy. We use Markov Chain Monte Carlo to estimate the tree topology, internal node ages and model parameters. Our model includes several aspects specific to language diversification, such as rate heterogeneity and the data registration process, and we show that lexical borrowing does not bias our estimates. We show the robustness of our model and analyse two independent data sets to estimates the age of Proto-Indo-European. (Joint work with Geoff Nicholls.)
Références

All complex life forms that grow beyond microscopic scales are multicellular. Multicellularity and differentiation are fundamental organizational themes in development, and have played a key role in the evolution of life. How does one study the deep evolutionary transitions that led to these traits? In this talk, I use bacteria as a case study to understand the origins of multicellularity in simple life forms. I summarize results from phylogenetic reconstruction and genome comparisons, theoretical models of population dynamics, strain isolation, and laboratory experiments that shed light on different aspects of the evolution of multicellularity and cellular differentiation.