Research Group Microbial Molecular Evolution
The research in the Microbial Molecular Evolution group combines laboratory experiments, computational methods and mathematical modeling to study the evolution of bacteria, viruses and selfish genetic elements. The research in the group focuses on three main topics: (1) the predictability and dynamics of evolution during early adaptation to a new environment; (2) the ecology and evolution of REPIN populations in bacterial genomes; and (3) the functional significance of the REPIN-RAYT system for bacteria.
Predictability of evolution during early adaptation
We are currently studying the adaptation of phage φX174 to infecting an E. coli population. By studying a large number of replicate populations we are hoping to (1) determine the detailed dynamics of novel mutations sweeping through the population, (2) infer the mutational effect distribution of novel mutations, and (3) be able to predict at different time points of the experiment what mutation will eventually dominate the population.
The ecology of REPIN populations
We have recently demonstrated that short repetitive sequences in bacterial genomes (REPINs) can be modeled as evolving populations (http://biorxiv.org/content/early/2017/03/24/119743). Different to most other natural populations, an entire REPIN population evolves in a single bacterial genome. Hence by sequencing a bacterial genome we can attain a snap shot of the exact composition of a REPIN population. Similar to other natural populations, REPIN populations interact with their environment. We will study interactions such as competition and cooperation between populations, population decline and population growth. Our first study will focus on tracking the evolution of a single REPIN population through a number of P. fluorescens genomes and explore the alternative evolutionary paths this population has taken as the different P. fluorescens strains have diverged over time.
The functional significance of the REPIN-RAYT system for bacteria
As described above REPINs are short repetitive sequences in bacteria. RAYTs are the transposases that replicate REPINs (http://www.tandfonline.com/doi/full/10.4161/mge.18610 and http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002132). Unlike selfish insertion sequences there is only a single RAYT that replicates one type of REPIN in a bacterial genome. RAYTs do not replicate themselves and are not horizontally transferred between bacteria. This means RAYTs have a function that is beneficial for the host bacterium, otherwise the gene would be easily lost over evolutionary time. Instead we find RAYTs in about 23% of all fully sequenced bacterial species (http://biorxiv.org/content/early/2017/03/23/119735).
We will perform a range of laboratory experiments to identify the functional significance of RAYTs.