Related papers: Polytopes, graphs and fitness landscapes
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
Due to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
A fitness landscape is a mapping from the space of genetic sequences, which is modeled here as a binary hypercube of dimension $L$, to the real numbers. We consider random models of fitness landscapes, where fitness values are assigned…
The replicator-mutator equation is a model for populations of individuals carrying different traits, with a fitness function mediating their ability to replicate, and a stochastic model for mutation. We derive analytical solutions for the…
The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as source of negative linkage disequilibrium and associated long-term sex advantage…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
The fitness landscape metaphor plays a central role on the modeling of optimizing principles in many research fields, ranging from evolutionary biology, where it was first introduced, to management research. Here we consider the ensemble of…
A microscopic agent dynamical model for diploid age-structured populations is used to study evolution of polymorphism and sympatric speciation. The underlying ecology is represented by a unimodal distribution of resources of some width.…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
Selection in a time-periodic environment is modeled via the continuous-time two-player replicator dynamics, which for symmetric pay-offs reduces to the Fisher equation of mathematical genetics. For a sufficiently rapid and cyclic…
Evolution depends on the fitness of organisms, the expected rate of reproducing. Directly getting offspring is the most basic form of fitness, but fitness can also be increased indirectly by helping genetically related individuals (such as…
A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…
The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary…
Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…
In order to analyze and extract different structural properties of distributions, one can introduce different coordinate systems over the manifold of distributions. In Evolutionary Computation, the Walsh bases and the Building Block Bases…
A model for the evolution of a finite population in a rugged fitness landscape is introduced and solved. The population is trapped in an evolutionary loop, alternating periods of stasis to periods in which it performs adaptive walks. The…
We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of quasispecies type equipped with a mesa shaped fitness landscape. We obtain…