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Microbial populations display an enormous range of variation in gene content, genome structure, and sequence, but our understanding of its significance is limited. What does this variation reveal about the mechanisms governing genome evolution, and to what extent does it contribute to organismal fitness? How do ecological parameters interact with evolutionary forces such as mutation, recombination, migration, and selection in establishing patterns of variation? To what extent are patterns replicated, and which develop stochastically?

Metagenomics, which refers to the study of genomic sequence obtained from a mixed population, is a powerful tool to address these questions. It has provided significant insights into the structure and function of microbes in the environment, but to date, most metagenomic studies of microbial communities have collected snapshots of data at a particular point in space and time. The power of metagenomics as a tool to measure rates and dynamics of fundamental evolutionary processes in natural systems remains largely unexplored.

The Simmons Lab uses a combination of manipulative experiments on microbial communities and high-throughput sequencing to interrogate the evolutionary dynamics and ecological significance of naturally occurring genetic variation.