Stanford Advisors

All Publications

  • Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. Journal of molecular evolution Li, F., Tarkington, J., Sherlock, G. 2023


    The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of different cellular components affects a cell's ability to reproduce. Here, we describe an improved approach, implemented in Python, for estimating fitness in high throughput via pooled competition assays.

    View details for DOI 10.1007/s00239-023-10098-0

    View details for PubMedID 36877292

  • Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila. Evolution; international journal of organic evolution Tarkington, J., Zhang, H., Azevedo, R. B., Zufall, R. A. 2022


    Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional factors, such as genome architecture, that may also impact the amount of genetic variation in some populations, and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. To test the effect of genome architecture on the generation of genetic variation, and hence evolvability, we studied Tetrahymena thermophila, a ciliate with an unusual genome structure and mechanism of nuclear division, called amitosis, whereby homologous chromosomes are randomly distributed to daughter cells. Amitosis leads to genetic variation among the asexual descendants of a newly produced sexual progeny because different progeny cells will contain different combinations of parental alleles. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to their unmated parents and species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.

    View details for DOI 10.1093/evolut/qpac031

    View details for PubMedID 36622280

  • Experimental Evolution in Tetrahymena. Microorganisms Plum, K., Tarkington, J., Zufall, R. A. 2022; 10 (2)


    Experimental evolution has provided novel insight into a wide array of biological processes. Species in the genus Tetrahymena are proving to be a highly useful system for studying a range of questions using experimental evolution. Their unusual genomic architecture, diversity of life history traits, importance as both predator and prey, and amenability to laboratory culture allow them to be studied in a variety of contexts. In this paper, we review what we are learning from experimental evolution with Tetrahymena about mutation, adaptation, and eco-evolutionary dynamics. We predict that future experimental evolution studies using Tetrahyemena will continue to shed new light on these processes.

    View details for DOI 10.3390/microorganisms10020414

    View details for PubMedID 35208869

  • Temperature affects the repeatability of evolution in the microbial eukaryote Tetrahymena thermophila. Ecology and evolution Tarkington, J., Zufall, R. A. 2021; 11 (19): 13139-13152


    Evolutionary biologists have long sought to understand what factors affect the repeatability of adaptive outcomes. To better understand the role of temperature in determining the repeatability of adaptive trajectories, we evolved populations of different genotypes of the ciliate Tetrahymena thermophila at low and high temperatures and followed changes in growth rate over 6,500 generations. As expected, growth rate increased with a decelerating rate for all populations; however, there were differences in the patterns of evolution at the two temperatures. The growth rates of the different genotypes tended to converge as evolution proceeded at both temperatures, but this convergence was quicker and more pronounced at the higher temperature. Additionally, over the first 4,000 generations we found greater repeatability of evolution, in terms of change in growth rate, among replicates of the same genotype at the higher temperature. Finally, we found limited evidence of trade-offs in fitness between temperatures, and an asymmetry in the correlated responses, whereby evolution in a high temperature increases growth rate at the lower temperature significantly more than the reverse. These results demonstrate the importance of temperature in determining the repeatability of evolutionary trajectories for the eukaryotic microbe Tetrahymena thermophila and may provide clues to how temperature affects evolution more generally.

    View details for DOI 10.1002/ece3.8036

    View details for PubMedID 34646458

    View details for PubMedCentralID PMC8495795

  • Temperature affects the repeatability of evolution in the microbial eukaryote Tetrahymena thermophila ECOLOGY AND EVOLUTION Tarkington, J., Zufall, R. A. 2021

    View details for DOI 10.1002/ece3.8036

    View details for Web of Science ID 000687449700001