Better explicating the strengths and shortcomings of these models will help refine projections and improve transparency in the years ahead.
Image credit: Witsawat.S.
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Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan (received for review June 30, 2005)
Article Figures & SI
Figures
- Fig. 1.
Cross-species energy transition probabilities
for neutral evolution (blue) and for evolution under time-independent selection in the fitness landscape of Fig. 3a (red). Curves are shown for fixed initial energy E
1 = 8 and various evolutionary distances t. The third curve in each family belongs to the distance between aligned loci of E. coli and S. typhimurium. Typical loci evolve toward weaker binding under neutrality but maintain their binding energy under selection. - Fig. 2.
Functional phylogenies for two species at evolutionary distances t 1 and t 2, counted from their last common ancestor at time ta = 0. Branch segments with neutral evolution are shown in blue with evolution under selection in red. (a) Neutral evolution of nonfunctional loci, described by the energy pair distribution
. (b) Evolution of functional loci under time-independent selection, described by the distribution Qt
. (c) Evolution under time-dependent selection generating a functional locus in species 1 and a nonfunctional locus in species 2, described by the distribution . This mode involves either a gain of function between ancestor and 1 or a loss of function between ancestor and 2. The switching event at time t′ is denoted by a green arrow. The corresponding mode where the roles of the two species are interchanged is described by the distribution . - Fig. 3.
Energy statistics and fitness landscape for CRP-binding loci in E. coli.(a) Count histogram with energy bins of width 0.1 (black), expected background counts (blue), and excess counts above background (red), with a 30-fold zoom into the region E < 14. The color bar indicates the probability of functionalityρ Q (E), ranging from 1 (red) to 0 (blue). (b) Decomposition of the counts (log-scale, left y axis) according to the single-species hidden Markov model: background distribution (1 - λ)P 0(E) (blue), distribution λQ(E) of functional loci (red), and total distribution W(E) (orange). The resulting fitness landscape ΔF(E) according to Eq. 6 is also shown in orange (thick curve, right y axis).
- Fig. 4.
Binding energy pairs and functional histories for aligned loci in E. coli and S. typhimurium.(a) Dot plot of counts (E 1, E 2), including verified binding sites (light blue). The background color shading indicates the likelihood of functional histories, varying between blue (conserved neutrality), red (conserved function), and green (functional switching). Isoprobability lines
(α = 0, Q, 0s, s0) are dotted. (b) Energy pair density obtained from the counts (filled contours), compared with the distribution W
t
(E
1, E
2) (contour lines, W
t
= 10-7, 10-6, 10-5, 10-4).
Data supplements
Mustonen and Lässig et al. 10.1073/pnas.0505537102.
Supporting Information
Files in this Data Supplement:
Supporting Text
Supporting Figure 5
Supporting Figure 6
Supporting Figure 7
Supporting Figure 5Fig. 5. Detection error trade-off for CRP binding site prediction. Expected rates of false positives vs. false negatives for a single-species search with position weight scoring in E. coli (1), a two-species search including S. typhimurium (2), and a three-species search including also Y. pseudotuberculosis (3). The diamonds indicate the points rQ= 0.30, used as lower cutoff in our prediction lists.
Supporting Figure 6Fig. 6. Dot plot of energies for three species comparisons. E1, E2, and E3 refer to E. coli, S. typhimurium, and Y. pseudotuberculosis, respectively.
Supporting Figure 7Fig. 7. Functional phylogenies for three species. Example of the Rt00s(E1,E2,E3) ensemble. Green arrows denote the switching point. Blue lines mark the neutral evolution of nonfunctional loci (Gt0) and red evolution under selection (Gts).
Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
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