W. R. Shoemaker

Macroecological patterns in experimental microbial communities

This study shows that macroecological patterns observed in natural microbial communities also emerge in controlled lab experiments and can be modeled using the Stochastic Logistic Model.

Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

This study uses the Stochastic Logistic Model to predict microbial biodiversity across taxonomic and phylogenetic scales, showing that ecological interactions are necessary to explain diversity patterns at different scales.

Coevolution with a seed bank

This study shows that dormancy creates a seed bank that reduces coevolutionary dynamics between hosts and parasites by preserving genetic diversity and buffering population dynamics against phage infection.

A macroecological perspective on genetic diversity in the human gut microbiome

The paper tests if an ecological model predicts genetic diversity patterns across human hosts for 22 gut microbes, finding it explains allele frequency distributions and prevalence.

Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis

This study shows that seed banks in Bacillus subtilis increase genetic diversity and alter mutation trajectories over 700 days, while not changing negative selection but affecting the direction of molecular evolution.

Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

The paper analyzes strain-level dynamics in the human gut microbiome and finds that strain abundances follow macroecological laws similar to species-level patterns, indicating ecological stability at the strain level.

Comparative Population Genetics in the Human Gut Microbiome

The paper explores comparative population genetics in the human gut microbiome to identify evolutionary trends and functional categories under different selection pressures.

Molecular evolutionary dynamics of energy limited microorganisms

This study examines how energy limitation affects molecular evolutionary dynamics across diverse microorganisms over 1,000 days, finding it influences mutation spectra and evolutionary direction but not consistently across phylogenetic groups.

Microbial population dynamics and evolutionary outcomes under extreme energy-limitation

This study examines microbial survival and evolution under extreme energy limitation, finding that bacteria can persist for decades and adapt through mutation and scavenging.

Predicting Parallelism and Quantifying Divergence in Experimental Evolution

The paper develops a statistical framework to identify genes involved in divergent evolution by modeling mutation counts as a Skellam distribution.

Evolution with a seed bank: the population genetic consequences of microbial dormancy

This paper examines how microbial dormancy, through seed banks, influences population genetic processes and macroevolutionary dynamics by reviewing theory, simulations, and analysis of speciation and extinction rates.