J. L. Payne

Protein evolvability under rewired genetic codes

This study investigates how rewired genetic codes affect protein evolvability by analyzing adaptive landscapes under various genetic codes.

Mutation and selection induce correlations between selection coefficients and mutation rates

The paper analyzes the joint distribution of selection coefficients and mutation rates under the SSWM regime, showing that correlations can arise even without initial correlations.

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

The paper investigates environment-dependent epistasis in gene regulatory networks using synthetic biology in E. coli, finding that it increases phenotypic diversity through nonlinear interactions.

On the incongruence of genotype-phenotype and fitness landscapes

This paper studies how selection for low or intermediate phenotypic values creates incongruence between genotype-phenotype and fitness landscapes, showing that fitness landscapes can be more rugged but still support adaptive evolution.

Linking host plants to damage types in the fossil record of insect herbivory

The paper evaluates methods for linking insect damage types to host plants in fossil records, finding beta diversity and rarefaction of interactions to be more reliable than other metrics.

Generating and testing hypotheses about the fossil record of insect herbivory with a theoretical ecospace

The paper develops a theoretical ecospace framework to analyze insect herbivory in the fossil record and demonstrates a reliable method for estimating damage type diversity.

The adaptive potential of non-heritable somatic mutations

This paper shows non-heritable somatic mutations can promote adaptive evolution by enabling germline genotypes to explore fitness landscapes through somatic genotypic exploration.

Mutation bias shapes the spectrum of adaptive substitutions

The paper analyzes how mutation bias affects the spectrum of adaptive substitutions in three species using statistical models and simulations.

Little evidence the standard genetic code is optimized for resource conservation

The paper challenges claims that the standard genetic code is optimized for nitrogen and carbon conservation, showing these optimizations are either sensitive to null models or confounded by other known properties.

SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution

The paper uses proteomic data to show that paralogues influence protein complex evolution through co-expression patterns and functional divergence.

Mutation bias interacts with composition bias to influence adaptive evolution

The paper studies how mutation bias and composition bias interact to influence adaptive evolution using empirical genotype-phenotype landscapes from eukaryotic transcriptional regulation.

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

The paper shows transition bias drives antibiotic resistance mutations in Mycobacterium tuberculosis, suggesting mutation supply, not selection, is the cause.