Benjamin H. Good

The paper compares gut microbiomes of Tsimane and Hadza populations to show that many microbes co-migrated with humans globally, but are now vanishing in industrialized populations.

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

This study develops a theory to predict how rapidly adapting populations select for fitness tradeoffs in fluctuating environments, showing that mutations with larger tradeoffs can be favored despite lower geometric mean fitness.

This study shows that gut microbiome recovery after antibiotics is path-dependent, shaped by ecological and evolutionary dynamics including strain sweeps, genetic changes, and phage activity.

The paper develops a population dynamics model of B and TFH cells in germinal centers, showing reciprocal stimulation regulates their ratio and balances affinity maturation speed with B cell diversity.

The paper studies intra-species diversity in microbial communities by competing gut strains, finding strong selection and coexistence due to biotic interactions.

This study shows that B cells in human tonsils migrate locally during affinity maturation at a consistent rate, contributing to diversity while balancing selection.

The paper studies ecological diversification in rapidly evolving microbial populations, showing that priority effects drive the formation of distinct ecotypes and alter long-term metabolic structure.

The paper models dN/dS dynamics in recombining bacterial populations, showing recombination explains most of the decline in dN/dS and reveals weak selection at many coding sites.

This study identifies lactic acid from gut microbes as a key factor improving Drosophila survival during starvation by enhancing oxidative phosphorylation.

The paper uses yeast mutants to show that fitness can be predicted by low-dimensional genotype-phenotype-fitness maps across environments, supporting a limiting functions model of fitness.

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

This study examines the evolution of mutation rates in proofreading polymerases by controlling direct and indirect selection, revealing dynamic evolutionary features and trade-offs between mutation rates and short-term fitness.

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

The paper estimates phage population dynamics and lifestyle in the human gut using integrated data, finding a low lysis rate and high genome-to-genome ratio suggesting temperate phage dominance.

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