A. Eyre-Walker

The silent impact: codon usage bias and protein evolution in bacteria

The paper examines how codon usage bias affects protein evolution in bacteria, finding that selection on codon bias has little influence on non-synonymous polymorphism or substitution patterns.

Recommendations for improving statistical inference in population genomics

The paper discusses challenges in population genomics due to data abundance and highlights best practices for statistical inference and model fitting.

Patterns of selection in the evolution of a transposable element

The paper introduces a method to study natural selection in transposable elements by analyzing the ratio of non-synonymous to synonymous variants in a TE family, finding strong negative selection in Sirevirus retrotransposons.

Site level factors that affect the rate of adaptive evolution in humans and chimpanzees; the effect of contracting population size.

The paper investigates adaptive evolution rates in humans and chimpanzees, finding higher rates at more exposed amino acids and lower rates for dissimilar pairs, but with a shallower slope due to population contraction.

Factors that affect the rates of adaptive and non-adaptive evolution at the gene level in humans and chimpanzees

The paper examines factors affecting adaptive and non-adaptive evolution rates in human and chimpanzee genes, finding significant correlations with recombination, protein length, expression level, and gene age.

Testing the adaptive walk model of gene evolution

The paper tests the adaptive walk model of gene evolution by analyzing population genomic data from Arabidopsis and Drosophila, finding that younger genes have higher molecular adaptation rates and larger physicochemical substitution effects.

A new test suggests that balancing selection maintains hundreds of non-synonymous polymorphisms in the human genome

The paper introduces a new test to detect balancing selection in the human genome and finds over a thousand non-synonymous polymorphisms are maintained by it.

Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

The paper examines mitochondrial DNA diversity in mammals, finding correlations between diversity, range size, and metabolic rate, but not census population size.

Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae

The paper examines how mutation rate, recombination rate, and selection at linked sites influence DNA diversity across homininae genomes, showing their interactions with genetic drift.

Nearly Neutral Evolution Across the Drosophila melanogaster Genome

The paper examines the relationship between effective population size and the proportion of neutral mutations in Drosophila melanogaster using polymorphism data from North American and African lines.

Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?

The paper investigates whether adaptive protein evolution occurs through large or small amino acid substitutions and finds that both adaptive and neutral evolution are dominated by substitutions between similar amino acids.

The Distribution of Bacterial Doubling Times in the Wild

The paper estimates bacterial doubling times in the wild by comparing mutation rates and accumulation rates across species, finding wild doubling times are much longer and vary widely.