B. H. Good

Linkage equilibrium between rare mutations

The paper introduces a theoretical framework to analyze homoplasy caused by recombination, showing how it depends on mutation rates, selection, drift, and allele frequencies.

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

Predicting the First Steps of Evolution in Randomly Assembled Communities

The paper predicts early evolutionary steps in randomly assembled microbial communities by analyzing mutation fitness and coexistence probabilities.

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

This study investigates gut microbiome colonization dynamics after antibiotic use, finding prolonged delays in microbial transmission and ecological barriers to colonization.

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

The paper creates a mutant fitness compendium for Bifidobacterium breve to identify molecular factors affecting colonization and host-microbe interactions.

Evolution of Evolvability In Rapidly Adapting Populations

This study develops a mathematical framework to predict the fate of genetic variants that modify future mutation rates and benefits in rapidly adapting populations, showing how competition between mutations can influence selection for evolvability modifiers.

Limited codiversification of the gut microbiota with humans

The paper reanalyzes data on human-microbe coevolution and finds that correlations between human and microbial phylogenies are often weaker than expected, suggesting limited codiversification.

Dynamics of bacterial recombination in the human gut microbiome

The paper quantifies recombination rates and patterns in the human gut microbiome using sequenced fecal samples, revealing heterogeneities and the role of natural selection in variant spread.

Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking

The paper quantifies in vivo evolutionary forces in gut bacteria by analyzing transposon libraries in gnotobiotic mice, revealing positive selection on hidden mutations and diverse fitness tradeoffs.

Quantifying the Local Adaptive Landscape of a Nascent Bacterial Community

The paper quantifies the adaptive potential of a bacterial community by measuring gene knockout fitness effects across different genetic backgrounds and ecological conditions.

Eco-evolutionary feedbacks in the human gut microbiome

The paper shows that short-term evolution of gut microbiota is linked to shifts in ecological structure, with feedbacks emerging from resource competition models.

Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota

The paper develops a population genetic framework to model evolutionary dynamics in spatial microbial growth, showing that well-mixed models can capture key dynamics despite spatial variation.

Population genetics of polymorphism and divergence in rapidly evolving populations

This paper extends the traveling wave framework to intermediate regimes of mutation fitness effects, deriving new expressions for fixation probabilities and site frequency spectra.

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

The paper shows that resource competition models can replicate species abundance time series statistics across diverse microbiotas, suggesting resource competition drives community dynamics.

Linkage disequilibrium between rare mutations

This paper develops a forward-time framework to predict linkage disequilibrium between neutral and deleterious mutations based on their frequencies, recombination rates, and fitness costs.

Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

The paper tracks bacterial evolution and transmission in mice using barcoded E. coli strains, showing rapid selection and migration effects on microbiota composition.

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

This study uses linked-read sequencing to track genetic and ecological changes in a human gut microbiome during antibiotic treatment and recovery.

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

This study examines evolutionary dynamics of gut bacteria within and across hosts, finding rapid genetic changes within hosts and challenges to standard population genetic models.

Directional selection limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

The paper models how directional selection and ecological diversification interact in microbial communities competing for substitutable resources, showing they reach a balance where ecotype diversity is constrained by fitness differences.

The effect of strong purifying selection on genetic diversity

This study analyzes the dynamics of neutral and deleterious mutations under strong purifying selection using a forward-time approach, revealing distortions in the site frequency spectrum that can mimic population expansions or positive selection.