Research ArticleEVOLUTIONARY BIOLOGY

The feedback between selection and demography shapes genomic diversity during coevolution

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Science Advances  02 Oct 2019:
Vol. 5, no. 10, eaax0530
DOI: 10.1126/sciadv.aax0530
  • Fig. 1 Ecological and evolutionary change of coevolving host and virus populations.

    The three columns correspond to three replicate experiments. (A) Population sizes of host (green, first vertical axis) and virus (orange, second vertical axis) were assessed daily (dots, total population size, log10 scale) and smoothed using cubic splines (lines). (B) Phenotypic evolution of resistance (green), i.e., the proportion of virus populations from all time points a host is resistant to, with circle size corresponding to the number of clones with the same phenotype and of infectivity (orange), i.e., the proportion of host individuals a virus population can infect. Dotted lines represent the maximum range per time point that was maintained at consecutive time points. Assays were done for 1320 comparisons of 10 host clones and one virus population collected from, respectively, 12 and 11 time points. (C) Fitness (growth rate per day in the presence of contemporary virus) of host individuals. (D) Binary visualization of the phenotypic interaction, with orange indicating a phenotypic match and green indicating a mismatch.

  • Fig. 2 Molecular evolution differs between host and virus populations.

    (A and B) Overall number of observed genetic changes of host (A) and virus (B) populations colored by the predicted severity of their effect on protein structure (phenotype). Intergenic regions cover 74 and 21% of the host and virus reference genomes, respectively. Bars correspond to the three replicate experiments.

  • Fig. 3 Adaptation and population expansion reciprocally influence each other.

    (A) Nucleotide diversity for the host populations was calculated per time point using derived allele frequencies of all loci that exhibited variation over the time course of the experiments. Lines are colored by replicate, with the black dashed line indicating the average. (B) Host allele frequency trajectories of all derived SNPs, with every line corresponding to an SNP. Distributions of VAFs match expectations under a neutral population expansion (Luria-Delbrück model) at the time points highlighted in gray. (C) Indicator variable reflecting if the distributions of VAFs in the host population matched the expectations of a neutral expansion phase (y axis) plotted against population growth in the 3 days leading up to the corresponding time point. Every dot reflects a time point and is colored by replicate, and the line corresponds to a generalized linear model fit with replicate as random effect.

  • Fig. 4 Repeatable selective sweeps match periods of population expansions in both populations.

    (A) Allele frequency trajectories of all derived SNPs are plotted for the host in gray (first vertical axis). Sweeps are evidential by a decrease in relative nucleotide diversity (second vertical axis), plotted in green. Light green highlight indicates the host sweeps identified. (B) Derived allele frequency trajectories for the virus. Gray lines reflect trajectories of mutations observed in one replicate only. Colored lines indicate trajectories of variants that were observed in more than one replicate, colored by the gene they occur in. Light orange highlight indicates the first virus sweep that occurs at the same time in all three replicates. (C) Population sizes of host (green) and virus (orange) were assessed daily (dots, total population size, log10 scale) and smoothed using cubic splines (lines). Light green and orange shadings indicate periods that match with sweeps as indicated in (A) and (B).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/10/eaax0530/DC1

    Fig. S1. Full infection matrix highlights coevolutionary phenotypic changes.

    Fig. S2. Resistance is costly.

    Fig. S3. Genetic diversity after selective sweeps matches expectations under neutrality.

    Fig. S4. Repeatable genomic change provides evidence for the action of natural selection.

    Fig. S5. Ecological change is less dynamic in the absence of species interactions.

    Table S1. Sequencing and filtering statistics indicate the reliability of the genomic datasets.

    Table S2. Observing mutations in multiple replicates independently is unlikely under neutrality.

    Table S3. Functional annotations of SNPs at high frequency in host populations after selective sweep at day 27.

    Table S4. Functional annotations of SNPs at high frequency in host populations after selective sweep at day 64.

    Data file S1. Population sizes (observed and smoothed values).

    Data file S2. Results of phenotypic assays.

    Data file S3. Filtered derived allele frequencies.

  • Supplementary Materials

    The PDF file includes:

    • Fig. S1. Full infection matrix highlights coevolutionary phenotypic changes.
    • Fig. S2. Resistance is costly.
    • Fig. S3. Genetic diversity after selective sweeps matches expectations under neutrality.
    • Fig. S4. Repeatable genomic change provides evidence for the action of natural selection.
    • Fig. S5. Ecological change is less dynamic in the absence of species interactions.
    • Table S1. Sequencing and filtering statistics indicate the reliability of the genomic datasets.
    • Table S2. Observing mutations in multiple replicates independently is unlikely under neutrality.
    • Table S3. Functional annotations of SNPs at high frequency in host populations after selective sweep at day 27.
    • Table S4. Functional annotations of SNPs at high frequency in host populations after selective sweep at day 64.
    • Legends for data files S1 to S3

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    Other Supplementary Material for this manuscript includes the following:

    • Data file S1 (.csv format). Population sizes (observed and smoothed values).
    • Data file S2 (.csv format). Results of phenotypic assays.
    • Data file S3 (.csv format). Filtered derived allele frequencies.

    Files in this Data Supplement:

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