Related papers: Inferring epistasis from genomic data with compara…
We derive an approximate relic neutrino asymmetry evolution equation that systematically incorporates repopulation processes from the full quantum kinetic equations (QKEs). It is shown that in the collision dominant epoch, the said equation…
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…
Recombination is introduced into Eigen's theory of quasispecies evolution. Comparing numerical simulations of the rate equations in the non-recombining and recombining cases show that recombination has a strong effect on the error threshold…
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
The class of epistatic fitness landscapes is much more diverse than the class of non-epistatic landscapes, and so it stands to reason that there exist dynamical phenomena that can only be realized in the presence of epistasis. Here, we…
We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage…
We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…
In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…
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…
We investigate the evolutionary dynamics of a finite population of RNA sequences adapting to a neutral fitness landscape. Despite the lack of differential fitness between viable sequences, we observe typical properties of adaptive…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
We present stochastic, finite-population formulations of the Crow-Kimura and Eigen models of quasispecies theory, for fitness functions that depend in an arbitrary way on the number of mutations from the wild type. We include back mutations…
We revisit the model by Wiser, Ribeck, and Lenski (Science \textbf{342} (2013), 1364--1367), which describes how the mean fitness increases over time due to beneficial mutations in Lenski's long-term evolution experiment. We develop the…
When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are…
For a one-locus haploid infinite population with discrete generations, the celebrated Kingman's model describes the evolution of fitness distributions under the competition of selection and mutation, with a constant mutation probability.…