Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements

  1. Bram van van Dijk  Is a corresponding author
  2. Paulien Hogeweg  Is a corresponding author
  3. Hilje M Doekes
  4. Nobuto Takeuchi
  1. Utrecht University, Netherlands
  2. University of Auckland, New Zealand

Abstract

Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study how HGT of slightly beneficial genes impacts growth rates of bacterial populations, and if bacteria collectives can evolve to take up DNA despite selfish elements. We find four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes — genes with small fitness benefits that are lost from the population without HGT — can be collectively retained by a community that engages in costly HGT. While this `gene-sharing' cannot evolve in well-mixed cultures, it does evolve in a spatial population like a biofilm. Despite enabling infection by harmful SGEs, the uptake of DNA is evolutionarily maintained by the hosts, explaining the coexistence of bacteria and SGEs.

Data availability

All data are either mathematical or computationally generated, and therefore easily reproduced. All scripts and programs to so do are publically available on GitHub (https://github.com/bramvandijk88/HGT_Genes_And_SGEs).For Figure 2 and 3 we used the analytical model. To (numerically) reproduce our results, use the Rscripts provided in the repository. For Figure 4, 5 and 6 we used the individual-based model. This was implemented in C, and can be run with simple command-line options (readme file found in the zip).

Article and author information

Author details

  1. Bram van van Dijk

    Theoretical Biology, Utrecht University, Utrecht, Netherlands
    For correspondence
    b.vandijk@uu.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6330-6934
  2. Paulien Hogeweg

    Biology, Utrecht University, Utrecht, Netherlands
    For correspondence
    p.hogeweg@uu.nl
    Competing interests
    The authors declare that no competing interests exist.
  3. Hilje M Doekes

    Theoretical Biology, Utrecht University, Utrecht, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6360-5176
  4. Nobuto Takeuchi

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.

Funding

Seventh Framework Programme (ICT-610427)

  • Bram van van Dijk

Seventh Framework Programme (ICT-610427)

  • Paulien Hogeweg

Human Frontier Science Program (RGY0072/2015)

  • Hilje M Doekes

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2020, van Dijk et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 5,012
    views
  • 378
    downloads
  • 32
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Bram van van Dijk
  2. Paulien Hogeweg
  3. Hilje M Doekes
  4. Nobuto Takeuchi
(2020)
Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements
eLife 9:e56801.
https://doi.org/10.7554/eLife.56801

Share this article

https://doi.org/10.7554/eLife.56801

Further reading

    1. Computational and Systems Biology
    2. Genetics and Genomics
    Daniel Hui, Scott Dudek ... Marylyn D Ritchie
    Research Article

    Apart from ancestry, personal or environmental covariates may contribute to differences in polygenic score (PGS) performance. We analyzed the effects of covariate stratification and interaction on body mass index (BMI) PGS (PGSBMI) across four cohorts of European (N = 491,111) and African (N = 21,612) ancestry. Stratifying on binary covariates and quintiles for continuous covariates, 18/62 covariates had significant and replicable R2 differences among strata. Covariates with the largest differences included age, sex, blood lipids, physical activity, and alcohol consumption, with R2 being nearly double between best- and worst-performing quintiles for certain covariates. Twenty-eight covariates had significant PGSBMI–covariate interaction effects, modifying PGSBMI effects by nearly 20% per standard deviation change. We observed overlap between covariates that had significant R2 differences among strata and interaction effects – across all covariates, their main effects on BMI were correlated with their maximum R2 differences and interaction effects (0.56 and 0.58, respectively), suggesting high-PGSBMI individuals have highest R2 and increase in PGS effect. Using quantile regression, we show the effect of PGSBMI increases as BMI itself increases, and that these differences in effects are directly related to differences in R2 when stratifying by different covariates. Given significant and replicable evidence for context-specific PGSBMI performance and effects, we investigated ways to increase model performance taking into account nonlinear effects. Machine learning models (neural networks) increased relative model R2 (mean 23%) across datasets. Finally, creating PGSBMI directly from GxAge genome-wide association studies effects increased relative R2 by 7.8%. These results demonstrate that certain covariates, especially those most associated with BMI, significantly affect both PGSBMI performance and effects across diverse cohorts and ancestries, and we provide avenues to improve model performance that consider these effects.

    1. Computational and Systems Biology
    2. Neuroscience
    Cesare V Parise, Marc O Ernst
    Research Article

    Audiovisual information reaches the brain via both sustained and transient input channels, representing signals’ intensity over time or changes thereof, respectively. To date, it is unclear to what extent transient and sustained input channels contribute to the combined percept obtained through multisensory integration. Based on the results of two novel psychophysical experiments, here we demonstrate the importance of the transient (instead of the sustained) channel for the integration of audiovisual signals. To account for the present results, we developed a biologically inspired, general-purpose model for multisensory integration, the multisensory correlation detectors, which combines correlated input from unimodal transient channels. Besides accounting for the results of our psychophysical experiments, this model could quantitatively replicate several recent findings in multisensory research, as tested against a large collection of published datasets. In particular, the model could simultaneously account for the perceived timing of audiovisual events, multisensory facilitation in detection tasks, causality judgments, and optimal integration. This study demonstrates that several phenomena in multisensory research that were previously considered unrelated, all stem from the integration of correlated input from unimodal transient channels.