Metagenomics has provided insight into the constituents of a variety of populations and ecosystems. In fact, often the only information we have on the members of an ecological community is their genome sequence. We are reasonably adept at detecting functions possessed by individuals, but can we use sequence data to determine the dynamics of evolution and ecology within these communities?
Experimental populations of microbes provide a great model system to address this question. Here I describe experiments in yeast and E. coli using time resolved sequencing to detect eco-evolutionary dynamics within evolving populations.
In yeast we study the spontaneous evolution of frequency dependence, and show how gene flow can allow the persistence of niche specific genotypes, even while newly arising mutations fix across the microcosm. I will also present new work from a long term E. coli evolution experiment, where our whole population sequencing at every 500 generations of a 60,000 generation experiment reveals the surprising prevalence of ecotype proliferation.