R. E. Lenski

Reduced selection during sweeps lead to adaptive momentum on rugged landscapes

The paper identifies 'adaptive momentum' as a dynamic where selective sweeps reduce purifying selection, allowing populations to explore fitness valleys and access new fitness peaks.

Parasite contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host

This study shows that simple sequence repeats in Bartonella bacteria drive adaptation to specific rodent hosts through frameshift mutations in adhesin genes.

Experimental Test of the Contributions of Initial Variation and New Mutations to Adaptive Evolution in a Novel Environment

This study compares the contributions of initial genetic variation and new mutations to adaptation in E. coli using different starting conditions in a new environment, finding that new mutations eventually contribute more to adaptation.

Parallel evolution of mutational fitness effects over 50,000 generations

The study examines how mutation fitness effects change over 50,000 generations in E. coli, finding parallel evolution of mutation costs and increased essentiality without altering the overall fitness landscape distribution.

Predictability shifts from local to global rules during bacterial adaptation

The study shows that short-term bacterial adaptation is predictable at the gene level, while long-term adaptation follows global statistical patterns.

Idiosyncratic fitness costs of ampicillin-resistant mutants derived from a long-term experiment with Escherichia coli

The paper examines the fitness costs of ampicillin-resistant mutants derived from Escherichia coli, finding significant variation in fitness costs not linked to resistance levels or parental backgrounds.

Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations

This study investigates how periodic bottlenecks affect adaptive evolution in microbial populations, finding that the optimal dilution factor depends on the frequency of beneficial mutations.

Evolution with private resources reverses some changes from long-term evolution with public resources

The paper shows that mutations from evolving under shared resources can enable reversion to ancestral phenotypes when selection shifts to favor numerical yield.

How the footprint of history shapes the evolution of digital organisms

This study investigates how the genomic legacy of prior adaptation (footprint of history) influences subsequent evolution in digital organisms across different environments.

Sustained coevolution of phage Lambda and Escherichia coli involves inner as well as outer membrane defenses and counter-defenses

This paper shows that E. coli and phage Lambda coevolve through interactions at both outer and inner membranes, with E. coli mutating genes to resist phage DNA ejection and phage evolving to bypass these defenses.

Idiosyncratic variation in the fitness costs of tetracycline-resistance mutations in Escherichia coli

The study shows that tetracycline-resistant Escherichia coli mutants have variable fitness costs, independent of resistance level or genetic background.

Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli

This study shows that genetic background influences the genotypic evolution of antibiotic resistance in Escherichia coli, leading to divergent mutational paths despite similar antibiotic treatments.

Maintenance of metabolic plasticity despite relaxed selection in a long-term evolution experiment with Escherichia coli

The paper examines how relaxed selection affects metabolic plasticity in E. coli over 30 years, finding that anaerobic fitness is maintained despite relaxed selection.

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

This study examines the genomic and phenotypic evolution of Escherichia coli in a citrate-only environment, identifying copy-number variations and transposable elements as key factors, while noting persistent physiological mismatches.

Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

This study shows that relaxed antibiotic selection in E. coli leads to increased susceptibility and unpredictable evolvability of resistance when selection is restored.

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

The paper analyzes bacterial genomes from an evolution experiment with horizontal gene transfer, finding that recombination can overwhelm selection by driving donor alleles to fixation without providing selective advantage.

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

The paper examines core gene evolution in E. coli, finding they accumulate more nonsynonymous mutations in lab experiments but are more conserved in nature.