Experimental Evolution
Experimental evolution is a powerful approach to study all aspects of the evolutionary process under controlled conditions. which allows for real-time observations of changing phenotypes and genotypes. Microbial experimental evolution is an ideal system because microbes have fast generation times, are easy to archive, and can be propagated with high-throughput techniques. Findings are largely applicable to understanding evolutionary processes that drive population diversity and adaptation across the tree of life.
Whole Genome Population Sequencing
We are leaders in evolve and resequence studies and prioritize speed of inquiry. We either use our own Illumina NextSeq550 for large sample sets or send samples to preferred providers that we advise. Since 2015, we have sequenced >20,000 bacterial clones and populations. A favorite phrase in our laboratory is “sequencing is cheap, analysis is expensive”, and it is in this analysis where we thrive. Whole population genome sequencing allows us to study dynamics of evolving populations.. When we combine this with single-cell barcoding, a technique we have developed, we will achieve fine-scale resolution of the demography and dynamics of populations over even smaller time scales and survey greater diversity.
Bioinformatics
We develop bioinformatic tools and tutorials to better analyze, visualize, and draw conclusions from big data generated when sequencing evolving populations. For instance, Lolipop is a tool developed to infer genotype linkage and to visualize allele frequency dynamics of a population over time. We also have developed many scripts that streamline the analysis of whole genome sequencing data.