Related papers: Quasispecies and recombination
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…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…
We investigate the error threshold for the emergence of quasispecies in the Eigen model. By mapping to to an effective Hamiltonian ruled by the "imaginary-time" Schr\"odinger equation, a variational ansatz is proposed and applied to…
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…
We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring…
We study the question of existence of positive steady states of nonlinear evolution equations. We recast the steady state equation in the form of eigenvalue problems for a parametrised family of unbounded linear operators, which are…
Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here…
The quasispecies model of biological evolution for asexual organisms such as bacteria and viruses has attracted considerable attention of biological physicists. Many variants of the model have been proposed and subsequently solved using the…
We compared the properties of the error threshold transition in quasispecies evolution for three different topologies of the genome space. They are a) hypercube b) rugged landscape modelled by an ultrametric space, and c) holey landscape…
We find an advantage of recombination for a category of complex fitness landscapes. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks, and recombination can be a powerful mechanism for…
Identifying and quantifying the benefits of sex and recombination is a long standing problem in evolutionary theory. In particular, contradictory claims have been made about the existence of a benefit of recombination on high dimensional…
Migration between different habitats is ubiquitous among biological populations. In this Letter, we study a simple quasispecies model for evolution in two different habitats, with different fitness landscapes, coupled through one-way…
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…
Cancer is a complex disease and thus is complicated to model. However, simple models that describe the main processes involved in tumoral dynamics, e.g., competition and mutation, can give us clues about cancer behaviour, at least…
We present a hybrid algorithm between an evolution strategy and a quasi Newton method. The design is based on the Hessian Estimation Evolution Strategy, which iteratively estimates the inverse square root of the Hessian matrix of the…
The probability that an advantageous mutant rises to fixation in a viral quasispecies is investigated in the framework of multi-type branching processes. Whether fixation is possible depends on the overall growth rate of the quasispecies…
Co-evolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this co-adaptive model, besides the classical error catastrophe for high virus mutation rates, a…
We show that, under certain assumptions, the fitness of almost all quasi-species becomes independent of mutational probabilities and the initial frequency distributions of the sequences in high dimensional sequence spaces. This result is…
We use a path integral representation to solve the Eigen and Crow-Kimura molecular evolution models for the case of multiple fitness peaks with arbitrary fitness and degradation functions. In the general case, we find that the solution to…