Research
Current research projects include the following:
The role of adaptive substitution in genome evolution
It is still unclear how much of genome evolution is driven by Darwinian natural selection, and how much by non-adaptive processes, such as genetic drift.
When natural selection drives an allele to fixation in a population, it can leave a “signature” in the genomes of that population, and these signatures can be used to quantify the contribution of natural selection. However, such methods are controversial (lots of non-selective process can leave similar signatures). In addition, genome-wide average estimates from single species, tell us little about why natural selection was acting in that lineage, or why the population was able to respond.
In a series of collaborative projects, we are improving these tests for selection, and using them to address particular hypothesis about the selective pressures faced by wild populations. By comparing results from many different lineages, we can search for general patterns in adaptive molecular evolution. Ongoing work is investigating adaptation in the HIV-1 virus, the bacterial genus Rickettsia, the flies Drosophila melanogaster and Aedes aegypti, and the yeast Schizosaccharomyces pombe.
Many of the collaborations will involve members of Cambridge Evolutionary Genetics.
Interpreting genomic regions of enhanced differentiation
Genomic scans of sub-divided populations often reveal isolated regions of the genome that differ substantially between subpopulations. This pattern might be explained in many different ways. For example, differentiated regions might be involved in adaptation to local environmental conditions, or carry alleles that are intrinsically incompatible (i.e., reduce fitness in the genetic background of the alternative subpopulation), or might reflect the transient effects of a beneficial mutation “sweeping” between the subpopulations.
If we could reliably distinguish between these alternative hypotheses we could ask a range of important questions, including: How much of the genome is involved in adaptation to local conditions? How frequently do adaptive substitutions pass between subpopulations? etc. etc.
In collaboration with Nicolas Bierne, Denis Roze and others, we are aiming to provide tools for interpreting genomic data of this kind.
Life history evolution and mitochondrial genomes
The speed of molecular evolution can vary widely between different lineages, and some of this variation seems to be predictable from aspects of a species’ biology. Understanding this predictable rate variation can give us important clues as to why molecular evolution occurs.
Current research, in collaboration with Rob Lanfear, is focussing on animal mitochondrial genomes, whose gross properties seem to relate strongly to the longevity of the species. These results support longstanding, but controversial theories that damage to mitochondrial DNA is somehow linked to ageing.
There are also implications of this research for the use of genetic markers, e.g., for the building molecular phylogenies. Work in collaboration with Andrew Rambaut and Marc Suchard has been developing Bayesian phylogenetic methods that exploit additional information from life history traits – improving our ability to reconstruct adaptive radiations.
