Figure 1.
Fitness averaged over all points at a particular distance from the peak for folding landscapes, additive landscapes with the same three levels of multiplicative noise used in Fig. 6 and the sesquiterpene synthase landscape.
Table 1.
Summary of the quantitative landscape characteristics.
Figure 2.
Deviation from additivity, monotonic paths and suboptimal peak suppression in folding and experimental landscapes.
(A) Deviation from additivity for the folding landscapes (larger symbols), their scrambled versions (smaller symbols) and the two experimental landscapes. Error bars show one standard deviation within the ensemble of permuted landscapes. (B) Fraction of monotonic paths to the main peak in folding, scrambled and experimental landscapes. (C) The number of peaks is vastly greater in scrambled landscapes than in folding or experimental landscapes (with the exception of the sesquiterpene synthase landscape).
Figure 3.
The Z-scores of different characteristics of the original folding and experimental landscapes measured with respect to the ensembles of their randomly permuted counterparts.
Figure 4.
Correlations between different quantitative characteristics of the folding landscapes.
Each panel quotes the Spearman rank correlation coefficient between the particular pair of characteristics.
Figure 5.
Mean path divergence as a function of selection pressure, which is a product of and
, for a folding landscape with 5936 nodes and 65 peaks.
Solid lines are labeled by the Hamming distance between the pairs of starting and ending points of the trajectory bundles over which the path divergence is averaged.
Figure 6.
The dependence of the path divergence (top row) and the monotonic path fraction (bottom row) on the measures of landscape roughness.
The dots of different color correspond to noisy additive landscapes with differing amounts of multiplicative noise: low (red), two intermediate levels (green smaller than blue), and high (magenta). Yellow circles represent the folding landscapes, the cyan squares–the -lactamase landscape, and the red triangles–the sesquiterpene synthase landscape.
Figure 7.
Mean path divergence in folding and experimental landscapes (larger symbols) landscapes, as well as their scrambled versions (smaller symbols) as a function of Hamming distance from the main peak.