A. J. Drummond

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.

LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses

This paper introduces a new model specification language, LPhy, for phylogenetic analyses to improve reproducibility and clarity in model descriptions.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

This paper introduces a new evolutionary model, FBD-MSC, that integrates genealogical and fossilization processes to improve divergence time estimates in Caninae.

Accounting for errors in data improves timing in single-cell cancer evolution

This study improves timing accuracy in single-cell cancer evolution by modeling errors in single-cell DNA sequencing data using BEAST2, showing that error accounting shifts divergence times forward and reduces overestimation of phylogenetic diversity.

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.

Bayesian Inference of Species Networks from Multilocus Sequence Data

This paper introduces a Bayesian method to infer species networks and gene trees from multilocus sequence data, demonstrating its ability to detect reticulate evolution in spruce species.