We are an experimental evolution lab. We use bacteriophages (esp. ϕX174) as model organisms to study evolutionary dynamics and the influence of ecological variables on these. Please find below a brief description of our lab's approaches and activities. Students, please look at the teaching menu for local and external resources.
To explore adaptation, we need an approach that holds most factors constant. In our lab we have built apparatus (e.g., the chemostat opposite) and refined protocols (e.g., qPCR assays) to control and measure the effects of high mutation rates or fluctuating environments on fitness and other phenotypes in evolving bacteriophage populations.
As well as examining phenotypes, we quantify genetic variation in evolving populations. We use next-generation sequencing to detect polymorphisms from population samples and have developed several approaches to the analysis of these data (esp. related to variant calling).
We also work with individual-based simulations of viral evolution. We do this to explore dynamics that are difficult to predict using analytical approaches (for example owing to epistasis or changing recombination frequencies).
