What we do:
A lot of what we know about evolution has been figured out from the observations of naturalists, examinations of the fossil record, and math. Experimental evolution is a relatively new and complementary way of investigating evolution. Microbes grow and divide very quickly, providing a powerful means for directly observing thousands of generations of evolution as they happen. This allows for direct tests of evolutionary theory and explorations of what is possible- often leading to unexpected discoveries. In order to figure out what has been going on in our evolving populations, we do a lot of whole-genome sequencing - we have an Oxford Nanopore Sequencing suite in the lab. We also use the tools of molecular genetics to build the strains we want to evolve or to test functional hypotheses generated by sequencing our evolved strains. For a better understanding of what we have done, take a look at our publications.
Connecting experimental model systems with the reality of complex microbiomes
In current work, we are finding ways to build more complex experimental evolution systems so that we can bring our experiments closer to the reality of microbial evolution.
1. Coevolution: almost no microbial species evolves in isolation, so we are running co-evolution experiments so that we can track the genetics of adaptation in multiple species as they adapt to co-existence.
2. Horizontal Gene Transfer: 1000's of sequenced genomes show us that horizontal gene transfer is really important, yet running experiments that incorporate HGT has proven difficult. We are running experimental populations that can adapt by HGT as well as spontaneous mutation.