B. Boussau

Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus

This study examines the evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus, showing male-biased genes emerge first and positive selection affects some SBGs.

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

This paper uses machine learning and phylogenetic reconciliation to estimate the evolutionary timeline of Bacteria, linking transitions to aerobic lifestyles to the Great Oxidation Event.

Evaluation of methods to detect shifts in directional selection at the genome scale

This study evaluates six methods for detecting directional selection shifts using simulations and shows Pelican performs well compared to codeml in most conditions.

Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

Phyloformer uses a transformer-based network to predict pairwise evolutionary distances from multiple sequence alignments, enabling accurate and faster phylogenetic tree reconstruction compared to traditional methods.

Adaptation to host cell environment during experimental evolution of Zika virus

This study identifies genetic adaptations in Zika virus during experimental evolution in host cells, revealing increased infectivity and resistance to TLR3-induced restriction.

Relative time constraints improve molecular dating

This study introduces a method to improve molecular dating by combining fossil calibrations with relative age constraints, showing significant improvements in estimating node ages using simulations and empirical data.

Nucleotide Usage Biases Distort Inferences of the Species Tree

This study shows that nucleotide usage biases, like GC-bias, systematically underestimate genetic distances in species trees, affecting molecular dating of fruit fly populations.

Accurate detection of convergent amino-acid evolution with PCOC

The paper introduces PCOC, a method to detect convergent amino-acid evolution by identifying shifts in amino acid preferences rather than exact substitutions, showing improved performance on simulations and plant protein alignments.

Gene transfers, like fossils, can date the Tree of Life

The paper uses lateral gene transfer patterns to date the Tree of Life, showing they are as informative as fossils for microbial lineages.