Two research themes underly our work involving experimental evolution: testing established theories using experimental systems and examining evolving populations using systems level approaches (microarrays, proteomics, metabolomics and sequencing) to uncover patterns of adaptation. 

    Adaptive walks. Testing models of adaptation poses several challenges – not least, the long time scales usually required for adaptation to occur. I circumvent this limitation by building on a laboratory-based study begun by my post-doc advisor (and now collaborator) Richard Lenski (Michigan State University). This study founded 12 replicate populations of E. coli, which have now evolved in a defined environment for over 15 years (~45,000 generations). These populations have allowed researchers to study population level aspects of adaptation. We have worked with collaborators to uncover the specific adaptive mutations that arise and fix in the evolved populations (box below). Adaptive mutations from a focal evolved population have now been introduced into two series of defined strains. One series contains each mutation individually on the ancestral background, the other, contains each mutation sequentially in combination with the other adaptive mutations that were present on the background on which it first arose. These strains represent a unique resource enabling me to trace the adaptive trajectory of an evolving population. Recent work aims to extend the results of the focal population to a series of 96 additional replicate populations. By understanding the influence of interactions between mutations on their selective effects, we hope to build and test a mathematical framework allowing us to predict evolutionary trajectories.

    Expression and adaptation. Adaptation describes the movement of a population toward a phenotype representing the best available fit to the environment. Much theoretical and experimental work has focused on the consequences of adaptation, for example the speed with which adaptive mutations spread in a population Much less is known about the causes of adaptation: the relationship between genotype and phenotype is often left as a ‘black box’ – mutations go in and selective effects come out. An understanding of the genotype-phenotype relationship will allow researchers to ask new types of questions. Can mutations of large effect contribute to adaptation? How do the large number of phenotypic changes (i.e. pleiotropic) caused by most mutations affect adaptation? How does the effect of an adaptive mutation depend on genetic background? I plan to address such questions by extending my previous use of high-dimension phenotypic profiles, applying them to describing and analyzing genetic and phenotypic changes underlying the adaptation of Escherichia coli to a novel environment. 

    Adaptation to fluctuating environments. Many experimental evolution studies have examined the patterns of adaptation followed as populations adapt to simple defined environments. We are extending these studies - just a bit - by including one twist, exposing populations to fluctuating environments. We are currently examining the outcome of these experiments, aiming to test theories predicting how environmental fluctuation should effect the maintenance of genetic diversity. We are also examining some new ideas using these populations. For example, should we expect that populations evolved in fluctuating environments should be selected to increase their ‘evolvability’ - for example by increasing their genomic mutation rate?