A. F. Moutinho

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.

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.

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.

The impact of protein architecture on adaptive evolution

The paper analyzes how protein architecture influences adaptive evolution by examining Drosophila and Arabidopsis data, finding that surface accessibility and functional classes drive adaptive substitutions.