Dataset: Model code for the EpiGen model used in Walworth et al. 2020 and example output

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.862458.1Version 1 (2021-10-12)Dataset Type:model results

Principal Investigator, Contact: Naomi M. Levine (University of Southern California)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)

Project: How does intensity and frequency of environmental variability affect phytoplankton growth? (Enviro variability and phytoplankton growth)

Abstract

Model code and example model output for the EpiGen model used in Walworth et al. 2020. The EpiGen model is an individual-based model of adaptation modified from Fisher’s model in which a simulated population moves between a “new” and “ancestral” environment following a step function with varying frequencies. This model calculates the rate of adaptation of the population where adaption proceeds through both fast variation, low transmission and slow variation, high transmission (HT) modifications....

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The EpiGen model is an individual-based model of adaptation modified from Fisher’s model in which a simulated population moves between a “new” and “ancestral” environment following a step function with varying frequencies. This model calculates the rate of adaptation of the population where adaption proceeds through both fast variation, low transmission and slow variation, high transmission (HT) modifications.

The model output is for the adaptation of a population of 1000 individuals to a fluctuating environment (50 generations selective pressure, 50 generations non-selective) over 15000 generations. Every row is a generation (time). Columns are different statistics characterizing the population of 1000 individuals.

  • Column 1 is generation #,
  • Column 2 is mean fitness at that time step,
  • Column 3 is mean # of HT modifications  at that time step,
  • Column 4 is mean number of LT modifications,
  • Column 5 is cumulative distance traveled towards optimum by HT modifications,
  • Column 6 is cum. distance traveled towards optimum by LT modifications,
  • Column 7 is standard dev of number of HT modifications,
  • Column 8 is standard dev of number of LT modifications,
  • Column 9 is mean distance traveled toward optimum by HT modifications,
  • Column 10 is sd of distance traveled toward optimum by HT modifications,
  • Column 11 is mean distance travelled toward optimum by LT modifications, and
  • Column 12 is sd of distance travelled toward optimum by LT modifications.

The model code is available in a .zip file: (see section data files). These files are also available in the following GitHub repository: https://github.com/BCODMO/EpiGen

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Related Publications

Results
Walworth, N. G., Zakem, E. J., Dunne, J. P., Collins, S., & Levine, N. M. (2020). Microbial evolutionary strategies in a dynamic ocean. Proceedings of the National Academy of Sciences, 117(11), 5943–5948. doi:10.1073/pnas.1919332117
Methods
Fisher, R.A. (1930). The Genetical Theory of Natural Selection. Clarendon Press, Oxford, UK, est. 272 pp.
Methods
Hartl, D. L., & Taubes, C. H. (1998). Genetica, 102/103, 525–533. doi:10.1023/a:1017071901530
Methods
Kronholm, I., & Collins, S. (2015). Epigenetic mutations can both help and hinder adaptive evolution. Molecular Ecology, 25(8), 1856–1868. doi:10.1111/mec.13296
Methods
Orr, H. A. (1998). The Population Genetics of Adaptation: The Distribution of Factors Fixed during Adaptive Evolution. Evolution, 52(4), 935. doi:10.2307/2411226

Levine, N. M. (2021) Model code for the EpiGen model used in Walworth et al. 2020 and example output. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.862458.1 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


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Funded by the U.S. National Science Foundation