sherlock lab



The Sherlock Lab - Experimental Evolution in Microbial Systems

The Sherlock lab uses experimental approaches to understand the evolutionary process, specifically interested in i) what's the rate of beneficial mutation, ii) what is the distribution of fitness effects of beneficial mutations, iii) what are the identities of beneficial mutations (and are they gain or loss of function, are they recessive, dominant or overdominant, are the genic or regulatory?) and iv) how do each of these change as a function of genotype, ploidy and environment. We are also interested in how mutations that are beneficial in one environment fare in others, to explore the trade-offs that inevitably occur when fitness increases in a specific environment, and we are interested in exploring at what level experimental evolution can be deterministic, and at what level it is stochastic. We typically use short-term continuous (chemostat) and serial batch culture experiments in conjunction with lineage tracking and high throughput sequencing to understand the adaptive changes that occur in yeast in response to selective pressures as they evolve in vitro.


Selected Recent Publications


  1. Chen, V.K.*, Johnson, M.*, Herissant, L.*, Humphrey, P.*, Yuan, D., Li, Y., Agarwala, A., Hoelscher, S.B. Petrov, D.A., Desai, M.M., Sherlock, G. Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. bioRxiv 10.1101/2023.02.28.530341. Elife 12:e92899.
    PubMed
  2. Hays, M.*, Schwartz, K.*, Schmidtke, D.T., Aggeli, D., and Sherlock, G. (2023). Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by transposons and microhomology-mediated recombination. PLoS Genet. 19(5):e1010747.
    PubMed
  3. Aggeli, D.*, Li, Y.*, Sherlock, G. (2021). Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun. 12(1), 5193.
    PubMed
  4. Boyer, S., Herissant, L., Sherlock, G. (2021). Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment. PloS Genetics 17(1), e1009314.
    PubMed
  5. Li, Y., Petrov, D.A.^, Sherlock, G.^ (2019). Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation. Nat Ecol Evol. 3, 1539-1551.
    PubMed
  6. Blundell, J.R., Schwartz, K., Francois, D., Fisher, D.S., Sherlock, G., Levy, S.F. (2019). The dynamics of adaptive genetic diversity during the early stages of clonal evolution. Nat Ecol Evol. 3(2)293-301.
    PubMed


Land Acknowledgement
We recognize that Stanford sits on the ancestral land of the Muwekma Ohlone Tribe. This land was and continues to be of great importance to the Ohlone people. Consistent with our values of community and inclusion, we have a responsibility to acknowledge, honor and make visible the university's relationship to Native peoples.