N. Lartillot

The evolution of GC-biased gene conversion by means of natural selection

This study shows that GC-biased gene conversion (gBGC) evolves under weak stabilising selection and can increase population load, suggesting it may have been positively selected in humans.

Genome streamlining: effect of mutation rate and population size on genome size reduction

This study uses computational models to show that population size and mutation rate interact to determine genome size and coding density in bacteria.

Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

The paper develops a theoretical model to explore the evolutionary dynamics of meiotic recombination, focusing on the role of PRDM9 and its symmetric binding in driving hotspot turnover and selection pressures.

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

This study shows that genes and sites under adaptation detected at the phylogenetic scale are also under adaptation at the population-genetic scale using mutation-selection codon models.

The birth-death diffusion leading to present-day Mammal diversity

This paper introduces a new model to estimate diversification rates in mammals, finding that speciation rates increased 10-20 My before the K-Pg extinction.

Phylogenomic Analysis of Protein-Coding Genes Resolves Complex Gall Wasp Relationships

This paper uses phylogenomic analysis of protein-coding genes to resolve relationships among gall wasps, finding that Cynipidae is not monophyletic and proposing its division into three families.

Compositionally constrained sites drive long branch attraction

This study introduces a method to address phylogenetic bias caused by compositional heterogeneity and shows it reduces long branch attraction artifacts in metazoan datasets.

An improved codon modeling approach for accurate estimation of the mutation bias

The paper introduces an improved codon model that accurately estimates mutation bias by treating fixation rates as a tensor rather than a scalar, disentangling mutation and selection effects.

Reconstructing the history of variation in effective population size along phylogenies.

This paper introduces a framework to reconstruct the history of effective population size (Ne) across phylogenies and tests nearly-neutral theory predictions using primate data, finding Ne and mutation rate vary significantly.

A theoretical approach for quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

The paper derives a theoretical model to predict how changes in effective population size and protein expression level affect the ratio of non-synonymous to synonymous substitution rates (ω), and finds weak responses to these factors.

Inferring long-term effective population size with Mutation-Selection models

This paper introduces an extended mutation-selection model to infer long-term effective population size trends and life-history traits from phylogenetic data, finding that Ne variation is narrow across species.

Universal probabilistic programming offers a powerful approach to statistical phylogenetics

This paper demonstrates that universal probabilistic programming languages can effectively solve phylogenetic analysis by generating efficient inference algorithms and applying them to bird phylogenies.

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

The paper reconstructs body mass evolution in Cetartiodactyla using phylogenomic data and finds body mass affects substitution rates and GC-content dynamics.