T. Latrille

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

This paper introduces a neutrality index combining within- and between-species variation to detect diversifying selection on quantitative traits, applied to brain and body mass in mammals.

Improved estimation of molecular evolution coupling stochastic simulations and deep learning

This paper combines stochastic simulations with deep learning to estimate molecular evolution parameters, achieving higher accuracy than traditional likelihood-based methods under complex rate variation patterns.

Gene expression is the main driver of purifying selection in large penguin populations

The paper shows gene expression drives purifying selection in penguin populations, with highly expressed genes experiencing stronger selection pressures.

Estimating the proportion of beneficial mutations that are not adaptive in mammals

The paper estimates the proportion of beneficial mutations in mammals that are not adaptive, finding they account for 15-45% of all beneficial mutations in 24 of 28 populations.

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.

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.

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.