Related papers: Accessibility percolation in random fitness landsc…

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…

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…

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…

In this paper we present a combinatorial optimisation view on the routing problem for connectionless packet networks by using the metaphor of a landscape. We examine the main properties of the routing landscapes as we define them and how…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…

Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts, and any other predictors of phenotype that are of interest. Second, describe fitness…

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 population is composed of individuals characterised by their genetic strings, phenotypes and ages. We discuss the influence of probabilities of survival of the individuals on the dynamics and phenotypic variability of the population. We…

We explore some aspects of the relationship between biological evolution processes and the mathematical theory of records. For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories…

The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper…

Current GP frameworks are highly effective on a range of real and simulated benchmarks. However, due to the high dimensionality of the genotypes for GP, the task of visualising the fitness landscape for GP search can be difficult. This…

We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which…

Species do not merely evolve, they also coevolve with other organisms. Coevolution is a major force driving interacting species to continuously evolve ex- ploring their fitness landscapes. Coevolution involves the coupling of species fit-…

The metaphor of holey adaptive landscapes provides a pictorial representation of the process of speciation as a consequence of genetic divergence. In this metaphor, biological populations diverge along connected clusters of well-fit…

We study biological evolution on a random fitness landscape where correlations are introduced through a linear fitness gradient of strength $c$. When selection is strong and mutations rare the dynamics is a directed uphill walk that…

Local search is widely used to solve combinatorial optimisation problems and to model biological evolution, but the performance of local search algorithms on different kinds of fitness landscapes is poorly understood. Here we consider how…

Many studies have analyzed how variability in reproductive success affects fitness. However, each study tends to focus on a particular problem, leaving unclear the overall structure of variability in populations. This fractured conceptual…

Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…