Evolution in the light of fitness landscape theory

By formalizing the relationship between genotype or phenotype and fitness, fitness landscapes harbor information on molecular and evolutionary constraints. The shape of the fitness landscape determines the potential for adaptation and speciation, as well as our ability to predict evolution. Consequently, fitness landscape theory has been invoked across the natural sciences and across multiple levels of biological organization. We review here the existing literature on fitness landscape theory by describing the main types of fitness landscape models, and highlight how these are increasingly integrated into an applicable statistical framework for the study of evolution. Specifically, we demonstrate how the interpretation of experimental studies with respect to fitness landscape models enables a direct link between evolution, molecular biology, and systems biology. By formalizing the relationship between genotype or phenotype and fitness, fitness landscapes harbor information on molecular and evolutionary constraints. The shape of the fitness landscape determines the potential for adaptation and speciation, as well as our ability to predict evolution. Consequently, fitness landscape theory has been invoked across the natural sciences and across multiple levels of biological organization. We review here the existing literature on fitness landscape theory by describing the main types of fitness landscape models, and highlight how these are increasingly integrated into an applicable statistical framework for the study of evolution. Specifically, we demonstrate how the interpretation of experimental studies with respect to fitness landscape models enables a direct link between evolution, molecular biology, and systems biology. The set of elements (e.g., genes) necessary for the realization of a biological or ecological function, and the various relationships (e.g., activation, inhibition) that exist between the elements of the set. Genetic background-specific (fitness) effect of a mutation. The hypothetical population size of a Wright–Fisher population (panmictic and of constant size) that best reproduces the observed population genetics statistics. The ability of a biological system (a population, individual, network, or molecule) to have or produce variants that can be acted upon by selection. A measure of the reproductive or replicative success of a biological entity (from molecules to individuals). Usually, fitness-related phenotypes (e.g., growth rate) are used as proxies for fitness. Random change in allele frequencies over time in a population of finite size. The genetic constitution of an organism. A map from (usually) discrete genotypes to fitness. Genotypes tend to represent nucleotide, amino acid, or gene differences. A position in the genome of an individual. Depending on the focus of the study, a locus can correspond to a single nucleotide or amino acid position, several base pairs of DNA sequence, or a gene. A heritable change in the genetic sequence of an individual. A property of a mutation which harbors no fitness effect for an individual, such that its frequency in the population depends only on extraneous factors, such as genetic drift. A mutation is conditionally neutral if its neutrality is genetic-background or environment-dependent. Mathematical model that describes a genotype–fitness landscape with different degrees of epistasis. This model is defined by the parameters N, the number of loci in the landscape, and K, the degree of epistasis between loci. A set or subset of observable traits of an individual that stems from the interactions between genotype and environment. A map from (usually) continuous phenotypes to fitness. In a multidimensional phenotype space, each dimension is composed by a different one-dimensional trait. The property of a gene to affect more than one independent phenotypic trait. A model describing a genotype–fitness landscape that is composed of an additive component and an epistasic component. Ruggedness is then tuned by changing the relative proportions of the two components.