Sherlock Lab Research: Evolution, using Yeast as a Model System

We have various interests (see publications for a more comprehensive idea as to our research interests), but the lab's main focus is on the process of evolution. We are interested in defining and understanding evolutionary phenomena, both at the level of population dynamics, as well as at the molecular level. We are interested in the following questions: What is the rate of adaptive mutation? What is the distribution of fitness effects for adaptive mutations? What are the identities of adaptive mutations? Does the spectrum of adaptive mutations differ between haploids and diploids? Do mutations that provide an adaptive advantage under one condition provide an advantage under another? Or a disadvantage (antagonistic pleiotropy). What is the underlying nature of clonal interference? We are also interested in how the answers to these questions can change as a function of genotype and environment. To answer these questions, we use experimental evolution, and the budding yeast, S. cerevisiae, as a model organism.

Our initial experiments in this area were using yeast grown in continuous culture in a chemostat, with glucose as the limiting nutrient. Under these conditions, we expected beneficial mutations to be selected, and to increase in frequency. The fundamental question we sought to answer in these early experiments was how pervasive is clonal interference. To investigate this, we marked 3 otherwise identical subpopulations with green, red and yellow fluorescent proteins, and then followed the sizes of the subpopulations. We expected, based on the landmark Paquin and Adams paper in 1983, that we would observe clear adaptive sweeps. Instead, we saw pervasive clonal interference (Kao and Sherlock, 2008).


We followed this study by comprehensively identifying the mutations in 5 selected clones from the above population (M1 through M5), and showed that mutations that increased glucose transport and signaling through the Ras pathway were beneficial. Remarkably, we found that when two of the beneficial mutations that increased glucose transport were combined (loss of function mutations in MTH1 and amplification of the HXT6/7 locus) that the fitness of the double mutant was less than not only both single mutants, but less even than wild-type (Kvitek and Sherlock, 2011). This is a clear case of reciprocal sign epistasis, where mutations are mutually exclusive.

It was however clear to us, that while we had comprehensively analyzed 5 clones, that it was likely that we had only scratched the surface of the complexity of the population dynamics, as well as the spectrum of beneficial mutations. To address this, we performed high coverage population sequencing with overlapping forward and reverse reads for error correction. This allowed us to identify alleles in the population at frequencies as low as 1%. Genotyping individuals from the populations for the alleles abover 10% allowed us to determine the dynamics of the evolutions as they progressed, revealing a much richer picture than was possible just using 3 colors (Kvitek and Sherlock, 2013). One of the three populations that we sequenced is shown below: References

• Kao, K.C. and Sherlock, G. (2008). Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nature Genetics 40, 1499 - 1504.
  
• Kvitek, D.J. and Sherlock, G. (2011). Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape. PLoS Genetics 7(4): e1002056.
  
• Kvitek, D.J., Sherlock, G. (2013). Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment. PLoS Genetics 9(11): e1003972.