Related papers: Genomic mutation rates that neutralize adaptive ev…
Additive genetic variance in natural populations is commonly estimated using mixed models, in which the covariance of the genetic effects is modeled by a genetic similarity matrix derived from a dense set of markers. An important but…
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
This is an introductory review of deterministic mutation-selection models for asexual populations (i.e., quasispecies theory) and related topics. First, the basic concepts of fitness, mutations, and sequence space are introduced. Different…
The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here,…
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the…
Adaptation of asexual populations is driven by beneficial mutations and therefore the dynamics of this process, besides other factors, depend on the distribution of beneficial fitness effects. It is known that on uncorrelated fitness…
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with…
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes,…
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…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and…
In evolutionary games the fitness of individuals is not constant but depends on the relative abundance of the various strategies in the population. Here we study general games among n strategies in populations of large but finite size. We…
We study a mutation-selection model with a fluctuating environment. More precisely, individuals in a large population are assumed to have a modifier locus determining the mutation rate $u \in [0,\vartheta]$ at a second locus with types $v…
The interrelationships of the fundamental biological processes natural selection, mutation, and stochastic drift are quantified by the entropy rate of Moran processes with mutation, measuring the long-run variation of a Markov process. The…
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…
Muller's ratchet describes the irreversible accumulation of deleterious mutations in asexual populations. In well-mixed populations the speed of fitness decline is exponentially small in the population size, and any positive rate of…
The tendency of repeating past choices more often than expected from the history of outcomes has been repeatedly empirically observed in reinforcement learning experiments. It can be explained by at least two computational processes:…
We introduce a dynamical annealing schedule for population-based optimization algorithms with mutation. On the basis of a statistical mechanics formulation of the population dynamics, the mutation rate adapts to a value maximizing expected…