Predictability of evolutionary trajectories in fitness landscapes

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.Comment: 14 pages, 7 figure

Incremental embodied chaotic exploration of self-organized motor behaviors with proprioceptor adaptation

This paper presents a general and fully dynamic embodied artificial neural system, which incrementally explores and learns motor behaviors through an integrated combination of chaotic search and reflex learning. The former uses adaptive bifurcation to exploit the intrinsic chaotic dynamics arising from neuro-body-environment interactions, while the latter is based around proprioceptor adaptation. The overall iterative search process formed from this combination is shown to have a close relationship to evolutionary methods. The architecture developed here allows realtime goal-directed exploration and learning of the possible motor patterns (e.g., for locomotion) of embodied systems of arbitrary morphology. Examples of its successful application to a simple biomechanical model, a simulated swimming robot, and a simulated quadruped robot are given. The tractability of the biomechanical systems allows detailed analysis of the overall dynamics of the search process. This analysis sheds light on the strong parallels with evolutionary search

Statistical Laws Governing Fluctuations in Word Use from Word Birth to Word Death

We analyze the dynamic properties of 10^7 words recorded in English, Spanish and Hebrew over the period 1800--2008 in order to gain insight into the coevolution of language and culture. We report language independent patterns useful as benchmarks for theoretical models of language evolution. A significantly decreasing (increasing) trend in the birth (death) rate of words indicates a recent shift in the selection laws governing word use. For new words, we observe a peak in the growth-rate fluctuations around 40 years after introduction, consistent with the typical entry time into standard dictionaries and the human generational timescale. Pronounced changes in the dynamics of language during periods of war shows that word correlations, occurring across time and between words, are largely influenced by coevolutionary social, technological, and political factors. We quantify cultural memory by analyzing the long-term correlations in the use of individual words using detrended fluctuation analysis.Comment: Version 1: 31 pages, 17 figures, 3 tables. Version 2 is streamlined, eliminates substantial material and incorporates referee comments: 19 pages, 14 figures, 3 table

Virus Replication as a Phenotypic Version of Polynucleotide Evolution

In this paper we revisit and adapt to viral evolution an approach based on the theory of branching process advanced by Demetrius, Schuster and Sigmund ("Polynucleotide evolution and branching processes", Bull. Math. Biol. 46 (1985) 239-262), in their study of polynucleotide evolution. By taking into account beneficial effects we obtain a non-trivial multivariate generalization of their single-type branching process model. Perturbative techniques allows us to obtain analytical asymptotic expressions for the main global parameters of the model which lead to the following rigorous results: (i) a new criterion for "no sure extinction", (ii) a generalization and proof, for this particular class of models, of the lethal mutagenesis criterion proposed by Bull, Sanju\'an and Wilke ("Theory of lethal mutagenesis for viruses", J. Virology 18 (2007) 2930-2939), (iii) a new proposal for the notion of relaxation time with a quantitative prescription for its evaluation, (iv) the quantitative description of the evolution of the expected values in in four distinct "stages": extinction threshold, lethal mutagenesis, stationary "equilibrium" and transient. Finally, based on these quantitative results we are able to draw some qualitative conclusions.Comment: 23 pages, 1 figure, 2 tables. arXiv admin note: substantial text overlap with arXiv:1110.336

Evolvability signatures of generative encodings: beyond standard performance benchmarks

Evolutionary robotics is a promising approach to autonomously synthesize machines with abilities that resemble those of animals, but the field suffers from a lack of strong foundations. In particular, evolutionary systems are currently assessed solely by the fitness score their evolved artifacts can achieve for a specific task, whereas such fitness-based comparisons provide limited insights about how the same system would evaluate on different tasks, and its adaptive capabilities to respond to changes in fitness (e.g., from damages to the machine, or in new situations). To counter these limitations, we introduce the concept of "evolvability signatures", which picture the post-mutation statistical distribution of both behavior diversity (how different are the robot behaviors after a mutation?) and fitness values (how different is the fitness after a mutation?). We tested the relevance of this concept by evolving controllers for hexapod robot locomotion using five different genotype-to-phenotype mappings (direct encoding, generative encoding of open-loop and closed-loop central pattern generators, generative encoding of neural networks, and single-unit pattern generators (SUPG)). We observed a predictive relationship between the evolvability signature of each encoding and the number of generations required by hexapods to adapt from incurred damages. Our study also reveals that, across the five investigated encodings, the SUPG scheme achieved the best evolvability signature, and was always foremost in recovering an effective gait following robot damages. Overall, our evolvability signatures neatly complement existing task-performance benchmarks, and pave the way for stronger foundations for research in evolutionary robotics.Comment: 24 pages with 12 figures in the main text, and 4 supplementary figures. Accepted at Information Sciences journal (in press). Supplemental videos are available online at, see http://goo.gl/uyY1R