Andrew L. Wheeler

Partitioning amino acid substitution models by structure improves fit and meaningfully differentiates exchangeability values, but does not improve gene tree inference

The paper partitions amino acid substitution models by protein structure, improving model fit but not gene tree inference in mammals.

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

This study introduces CLOAK, an MSA cleaning algorithm that improves gene tree inference by removing alignment errors while preserving informative residues.

Tryptophan became part of the universal genetic code post-LUCA

The paper investigates whether tryptophan was present in LUCA by analyzing the evolution of tryptophanyl-tRNA synthetase and finds that W usage originated in Bacteria with later horizontal transfer to Archaea.

Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains

The paper infers the order of amino acid recruitment into the genetic code by analyzing ancestral protein domain frequencies, finding smaller amino acids were added earlier and metal-binding/sulfur-containing amino acids earlier than previously thought.