1. Evolutionary Biology
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Rank orders and signed interactions in evolutionary biology

  1. Kristina Crona  Is a corresponding author
  1. American University, United States
Research Advance
Cite this article as: eLife 2020;9:e51004 doi: 10.7554/eLife.51004
3 figures, 2 tables and 1 additional file

Figures

The graphs illustrate (A) no sign epistasis, (B) sign epistasis, and (C) reciprocal sign epistasis.

The peaks are marked red. Under the assumption that 00 has minimal fitness, and that the genotypes are positioned as in the figure, the three types can be characterized as graphs with no arrows down, one arrow down, or two arrows down.

Each arrow points toward the genotype of higher fitness.

The undirected edges connect mutational neighbors and carry no information about fitness differences. The graph 2A is compatible with additive fitness. The other graphs are not compatible with additive fitness because at least one pair of parallel arrows point in different directions. The lower graphs indicate sign epistasis, as is clear from the short arrows. The right graphs indicate size two perturbations, as is clear from the long arrows.

The fitness landscapes are additive and each mutation 01 decreases fitness.

The graphs compare replacements 01,0011 and 000111. Because of measurement errors, some replacements appear to increase fitness. The graphs show the proportion of such cases.

Tables

Table 1
Rectangular perturbations for drug-exposed and drug-free malaria fitness landscapes.

The third line shows the total number of expressions checked. The prevalence of sign epistasis is similar for the landscapes, whereas the remaining perturbations differ by a factor of two.

Perturbation size123Size (1-3)
Drug-exposed5521581
Drug-free54399102
Expressions checked1127216200
Table 2
Order perturbations of size 1 and 2 for Methylobacterium extorquens.

The landscape has no sign epistasis. However, perturbations of size 2 reveal that the landscape is not additive.

Perturbation of size12
Number of perturbations03
Expressions checked11272

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files.

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