J. Masel

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.

Background selection from unlinked sites causes non-independent evolution of deleterious mutations

The paper shows that background selection from unlinked sites reduces neutral genetic diversity more than linked sites, and explains underdispersion of deleterious load without requiring epistasis.

A Mechanistically Integrated Model of Exploitative and Interference Competition over a Single Resource Produces Widespread Coexistence

The paper develops a model integrating exploitative and interference competition, showing interference can promote coexistence without requiring specific conditions previously thought necessary.

Human deleterious mutation rate slows adaptation and implies high fitness variance

The paper shows that high human deleterious mutation rates slow adaptation and increase fitness variance, but also suggest that increased mutation rates can speed adaptation.

The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

The paper introduces a new Codon Adaptation Index (CAIS) to measure selection effectiveness in vertebrates and shows that more adapted species have protein domains with higher intrinsic structural disorder.

The effectiveness of selection in a species affects the direction of amino acid frequency evolution

The paper examines how effective selection in species influences amino acid frequency evolution, finding that preferred amino acids are less costly to synthesize and use GC-rich codons, explaining 85% of variance in preferences.

Differential retention of Pfam domains creates long-term evolutionary trends

The paper shows that differential retention of protein domains with specific structural properties drives long-term evolutionary trends in Pfam domains.

Substitution load revisited: a high proportion of deaths can be selective

The paper revisits Haldane's Dilemma by analyzing substitution load and selective deaths in Arabidopsis thaliana, finding a higher proportion of selective deaths than previously thought.

Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses

The paper shows that evolutionary accessibility, not just functionality, determines which regulatory motif evolves to generate protein pulses, with I1FFLs being more accessible under most conditions.

Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful

The paper investigates which random peptides are less harmful by analyzing their amino acid composition and fitness effects in E. coli.

Universal and taxon-specific trends in protein sequences as a function of age

The paper analyzes protein sequence trends across species age, finding universal hydrophobic clustering reduction but taxon-specific structural disorder patterns in young domains.

Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

The paper shows mutation-biased adaptation can occur in asexual populations despite clonal interference, depending on mutation rate and selection coefficient differences.

Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences

The paper investigates how readthrough errors in yeast genes influence the evolution of coding sequences by selecting against deleterious cryptic polypeptides.

High transcriptional error rates vary as a function of gene expression level

The paper examines transcriptional error rates in E. coli and S. cerevisiae, finding a relationship between gene expression levels and error rates for non-CU errors in E. coli but not in S. cerevisiae.

Evolution rapidly optimizes stability and aggregation in lattice proteins despite pervasive landscape valleys and mazes

This study develops a biophysically-grounded model of protein evolution showing that despite rugged fitness landscapes with valleys and mazes, adaptive paths can still reach high fitness.

Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection

The paper models how different mechanisms stabilize genetic polymorphism under fluctuating selection in Drosophila, finding that reversal of dominance has the strongest effect.

Directional selection rather than functional constraints can shape the G matrix in rapidly adapting asexuals

The paper shows that directional selection, not functional constraints, shapes the G matrix in asexual populations through linkage disequilibrium rather than pleiotropy.

A shift in aggregation avoidance strategy marks a long-term direction to protein evolution

The paper shows that older genes have more interspersed hydrophobic residues compared to younger genes, indicating a long-term evolutionary trend toward reducing aggregation risk.

Density-dependent selection and the limits of relative fitness

The paper shows that density-independent relative fitnesses can accurately describe strong density-dependent selection under certain conditions, using a novel model with ecologically intuitive traits.

Gene birth contributes to structural disorder encoded by overlapping genes

The paper investigates how gene birth contributes to structural disorder in overlapping genes, finding that recent de novo gene birth explains 32% of the increased intrinsic structural disorder in viral genes.

Drift barriers to quality control when genes are expressed at different levels

The paper shows that population size affects the evolution of gene expression error control strategies, with smaller populations favoring global error reduction and larger populations allowing for more localized error tolerance.