Joanna Masel

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.

Rare variants drive high variance in human ancestral fitness at mutation-selection-drift balance

The paper estimates human genetic load variation due to rare and ultra-rare deleterious mutations, showing significant ancestral fitness differences between individuals.

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.

Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation

The paper compares the effects of mutational drought and meltdown on extinction risk in small populations, finding mutational drought is more significant in stable and changing environments.

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.

nQMaker: estimating time non-reversible amino acid substitution models

nQMaker estimates time non-reversible amino acid substitution models and rooted phylogenetic trees from protein sequence alignments, showing improved model fit across diverse datasets.

Biomarkers for aging identified in cross-sectional studies tend to be non-causative

This study shows cross-sectional aging biomarker studies are biased toward non-causal factors, but this bias can be corrected using mortality correlates from longitudinal studies.

Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

The paper shows that feed-forward loops and diamond motifs evolve as signal filters, with dynamics rather than topology being key under intrinsic noise.