Experimental evolution is a powerful method for testing fundamental questions in evolution and ecology. I will present work showing that high-throughput sequencing methods can provide insights into the eco-evolutionary dynamics in experiment populations yeast. In this first study, we carry out whole population sequencing at multiple time points, allowing the tracking of the dynamics of each mutation as it arises during adaptation. Using this sequencing-across-time approach, we reveal that that multiple co-evolving populations emerge spontaneously within evolving lineages. In our yeast experiments, recombination between co-existing sub-populations does not cause the breakdown of the stable co-existence of multiple yeast types. While long-term evolution experiments such as these produce insights, these experiments in laboratory settings are removed from the actual conditions that microbes experience in nature. In an effort to bridge useful experimental models with complex microbial ecologies, we are carrying out long-term evolution experiments with yeast in co-culture with model bacterial species. I will also present data from these on-going experiments.