R. Bouckaert

How to validate a Bayesian evolutionary model

This paper describes good practices for validating Bayesian models in computational biology and introduces tools to automate validation protocols.

Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme

The paper identifies a functional urzyme, GlyCA, from an arctic fox genome that exhibits enhanced catalytic activity compared to known urzymes, supporting the idea that urzymes represent ancestral catalytic activities in genetic coding.

Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone

This paper uses tertiary-interaction characters to improve structural phylogenetics beyond the twilight zone, achieving accurate results with fast computation.

Triangulation reduces the polygon of error for the history of Transeurasian

The paper addresses critiques of a Transeurasian language and population history study by revising datasets and methods, showing that the original findings remain valid despite objections.

Quantitatively defining species boundaries with moreefficiency and more biological realism

This paper introduces a more efficient and biologically realistic species delimitation method using the multispecies coalescent model and validates it with genomic data.

High-Resolution, Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-modular 'Coupling

The paper uses phylogenetic metrics to show that Class I aminoacyl-tRNA synthetases evolved from a mosaic of genetic sources with modular 'coupling' and identifies a protozyme as the root of the molecular tree.

Adaptive parallel tempering for BEAST 2

This paper introduces an adaptive parallel tempering method for Bayesian phylogenetics in BEAST2 to improve MCMC efficiency by automatically tuning temperatures for better state space exploration.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.