M. A. Gilchrist

Quantifying shifts in natural selection on codon usagebetween protein regions: A population genetics approach

This study quantifies shifts in natural selection on codon usage between protein regions using a population genetics approach, revealing a weak relationship between codon usage and protein structure.

Unlocking a signal of introgression from codons in Lachancea kluyveri using a mutation-selectino model

The paper uses a mutation-selection model to analyze codon usage differences between endogenous and introgressed genes in Lachancea kluyveri, revealing distinct mutation biases and improving predictions of protein synthesis rates.

Gene Expression of Functionally-Related Genes Coevolves Across Fungal Species: Detecting Coevolution of Gene Expression Using Phylogenetic Comparative Methods

This study uses phylogenetic comparative methods to detect coevolution of gene expression across 18 fungal species, finding that physically interacting proteins show stronger coevolution signals.

The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)

The paper evaluates gene tree discordance in Blaberidae cockroaches, finding that certain codon models reduce discordance, leading to more robust species trees.

Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach

The paper introduces SelAC, a phylogenetic model that improves tree inference by incorporating stabilizing selection and protein synthesis rates, showing better fit than existing models on yeast data.

Quantifying Codon Usage in Signal Peptides: Gene Expression and Amino Acid Usage Explain Apparent Selection for Inefficient Codons

The paper investigates codon usage in E. coli signal peptides and finds that apparent selection for inefficient codons is explained by amino acid usage and gene expression, not selection.