Benjamin H. Good

Prehistoric Global Migration of Vanishing Gut Microbes With Humans

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.

Rapid evolution can select for fitness tradeoffs in fluctuating environments

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.

Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics

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.

Modeling the Synergetic Dynamics of B cells and TFH cells in Germinal Center Reactions

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.

Community coalescence reveals strong selection and coexistence within species in complex microbial communities

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

Dynamics of local B cell migration during affinity maturation in the human tonsil

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

Ecological diversification in rapidly evolving populations

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.

Dynamics of dN/dS within recombining bacterial populations

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.

Gut microbe-derived lactic acid optimizes host energy metabolism during starvation

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

Low-dimensional genotype-fitness mapping across divergent environments suggests a limiting functions model of fitness

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.

Direct and indirect selection in a proofreading polymerase

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.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

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.

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.