Research
Our approach is to study the process by which new genotypes and species arise through evolutionary time. To do this, we follow the emergence and fate of biodiversity directly in populations of microorganisms evolving in the laboratory. The small size and short generation times of many microbes means that we can design experiments to answer questions about the processes of adaptation and diversification that would otherwise be impossible with larger organisms. Evolutionary diversification involves two processes. The first is adaptation. The second is the process of diversification itself that gives us two (or more) recognizably distinct populations or species.
Genetics of adaptation
Adaptation is a subject about which we know surprisingly little. There is no great mystery why: adaptation requires beneficial mutations, those that increase fitness relative to an existing wild type, which are typically extremely rare and so difficult to study. We are developing new model systems and strategies to provide some of the first experimental tests of theories of adaptation. Projects on-going include:
- Characterizing the distribution of fitness effects among beneficial mutations
- Testing theory on the pleiotropic effects of beneficial mutations, especially those involved in antibiotic resistance
- The factors governing the length of adaptive walks (the sequential substitution of beneficial mutations by selection)
- Examining the role of no-cost antibiotic resistance mutations in chronic cystic fibrosis infections
- Genomics of adaptation
Ecological diversification and adaptive radiation
The history of life is punctuated by unusually spectacular periods of diversification called adaptive radiation. The factors that control the extent and rate of diversification during a radiation are poorly understood. We primarily use the soil bacterium, Pseudomonas fluorescens, to study adaptive radiation in the lab. Current work includes:
- The role of resource competition in governing the rate of diversification
- The importance of spatial structure and dispersal to the emergence and maintenance of diversity
- The effect of interspecific competition and competitive release on diversification
- The long-term dynamics and fate of diversity during adaptive radiation
- The role of predators and multi-trophic interactions in governing adaptive radiation
Interesting but tangentially related topics we are working on
The study of adaptation and diversification constitute the two main axes of research in my lab. We are not, however, limited to these topics. Anything that has to do with 'big-picture' questions in biology is fair game, provided that we can develop strong, direct experimental tests. Some of the questions we are investigating at the moment include:
- Bacteriocin evolution– Bacteriocins are compounds produced by bacteria that kill or inhibit distinct genotypes of the same species. We have been conducting selection experiments to see if it is possible to ramp-up bacteriocin production, and what sort of trade-offs result as a consequence. If killing effectiveness does evolve and is specific, it may be possible to use bacteriocins as custom-designed drugs to fight infection.
- The evolution of sex– Sexual reproduction dilutes a genome by half every time and is often energetically expensive and time consuming, so it is difficult to understand how a sexually reproducing lineage could evolve against an asexual one. One suggestion has been that sex brings 'good' genes together in the same genome. If sex happens preferentially in low fitness genotypes but not in high fitness genotypes (so-called fitness-associated sex) then this could be an intermediate step between asexual and obligately sexual reproduction. We have been studying fitness-associated sex in the filamentous fungus, Aspergillus nidulans.
- Microbial community evolution in traditional food products in Zambia– Many traditional, fermented food products in Zambia are made from starter cultures unique to a particular village. These cultures thus represent independently evolved communities of microbes, ones that are remarkably safe to eat because they resist invasion by pathogens. We are interested in the evolution of these communities and what makes them so resistant to invasion. Because there is very little migration of starter cultures from village to village, we effectively have a series of independent, co-evolved communities that have undergone parallel evolution. Work is just starting on this, so check back in a year's time or so and we will try to post some updates.
- Evolutionary medicine and antibiotic resistance– The widespread use of antibiotics leads inevitably to the emergence of resistant strains. When this happens, the typical response has been to stop using the drug, under the assumption that resistance is costly and so will decline in competition against antibiotic-sensitive strains. This does not always happen, however: even after the offending drug has been removed, resistance often persists at quite high levels–higher than would be expected if antibiotic resistance were very costly. We are investigating the reasons behind this for fluoroquinolone resistance in chronic Pseudomonas aeruginosa infections of cystic fibrosis patients.