title: Visualizing fitness landscapes.
abstract: Fitness landscapes are a classical concept for thinking about the relationship between genotype and fitness. However, because the space of genotypes is typically high-dimensional, the structure of fitness landscapes can be difficult to understand and the heuristic approach of thinking about fitness landscapes as low-dimensional, continuous surfaces may be misleading. Here, I present a rigorous method for creating low-dimensional representations of fitness landscapes. The basic idea is to plot the genotypes in a manner that reflects the ease or difficulty of evolving from one genotype to another. Such a layout can be constructed using the eigenvectors of the transition matrix describing the evolution of a population on the fitness landscape when mutation is weak. In addition, the eigendecomposition of this transition matrix provides a new, high-level view of evolution on a fitness landscape. I demonstrate these techniques by visualizing the fitness landscape for selection for the amino acid serine and by visualizing a neutral network derived from the RNA secondary structure genotype-phenotype map.
authors.affiliation: Department of Biology, Duke University, Box 90338 Durham, North Carolina 27708, USA. david.mccandlish@duke.edu
authors.forename: David M
authors.initials: DM
authors.lastname: McCandlish
mesh_terms: D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D056084:Genetic Fitness; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D008957:Models, Genetic; D010641:Phenotype; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic; D012694:Serine / Q000235:genetics
chemical_list: D003062:Codon; D012694:Serine; D012313:RNA