The structure of genotype-phenotype maps makes fitness landscapes navigable
Nature Ecology and Evolution Springer Nature 6:11 (2022) 1742-1752
Abstract:
Fitness landscapes are often described in terms of 'peaks' and 'valleys', indicating an intuitive low-dimensional landscape of the kind encountered in everyday experience. The space of genotypes, however, is extremely high dimensional, which results in counter-intuitive structural properties of genotype-phenotype maps. Here we show that these properties, such as the presence of pervasive neutral networks, make fitness landscapes navigable. For three biologically realistic genotype-phenotype map models-RNA secondary structure, protein tertiary structure and protein complexes-we find that, even under random fitness assignment, fitness maxima can be reached from almost any other phenotype without passing through fitness valleys. This in turn indicates that true fitness valleys are very rare. By considering evolutionary simulations between pairs of real examples of functional RNA sequences, we show that accessible paths are also likely to be used under evolutionary dynamics. Our findings have broad implications for the prediction of natural evolutionary outcomes and for directed evolution.Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection.
Proceedings of the National Academy of Sciences of the United States of America 119:28 (2022) e2205299119
Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
Chapter in Frontiers of Nanoscience, Elsevier 21 (2022) 195-210
Abstract:
This chapter will provide an overview of how characterising free energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The landscapes for these complex systems are accessible through the use of accurate coarse-grained descriptions of DNA. Particular foci will be the landscapes associated with DNA self-assembly and mechanical deformation, where the latter can arise from either externally imposed forces or internal stresses.The long and winding road to understanding organismal construction: reply to comments on "From genotypes to organisms: state-of-the-art and perspectives of a cornerstone in evolutionary dynamics"
Physics of Life Reviews Elsevier 42 (2022) 19-24
Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution
Proceedings of the National Academy of Sciences of the United States of America National Academy of Sciences 119:11 (2022) e2113883119