Related papers: Effect of Mutation and Recombination on the Genoty…
Complex spatial structure, with partially isolated subpopulations, and environment heterogeneity, such as gradients in nutrients, oxygen, and drugs, both shape the evolution of natural populations. We investigate the impact of environment…
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…
We return to the geometry optimization problem of Lennard-Jones clusters to analyze the performance dependence of "cut and splice" genetic algorithms (GAs) on the employed population size. We generally find that admixing twinning mutation…
In addition to natural selection, adaptive evolution requires genetic variation to proceed. Yet the G-matrix may have limited 'genetic degrees of freedom', with certain combinations of trait values unavailable to evolution. Such limitations…
We consider the effect of network structure on the evolution of a population. Models of this kind typically consider a population of fixed size and distribution. Here we consider eco-evolutionary dynamics where population size and…
The dynamics of recombination in genetics leads to an interesting nonlinear differential equation, which has a natural generalization to a measure valued version. The latter can be solved explicitly under rather general circumstances. It…
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…
Optimal Mixing (OM) is a variation operator that integrates local search with genetic recombination. EAs with OM are capable of state-of-the-art optimization in discrete spaces, offering significant advantages over classic…
Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic…
A parametrically modulated oscillator has two opposite-phase vibrational states at half the modulation frequency. An extra force at the vibration frequency breaks the symmetry of the states. The effect can be extremely strong due to the…
In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient…
Intermediate feature representations represent the backbone for the expressivity and adaptability of deep neural networks. However, their geometric structure remains poorly understood. In this submission, we provide indirect insights into…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
Geographic structure can affect patterns of genetic differentiation and speciation rates. In this article, we investigate the dynamics of genetic distances in a geographically structured metapopulation. We model the metapopulation as a…
According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the…
Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of…
This work discusses single-objective constrained genetic algorithm with floating-point, integer, binary and permutation representation. Floating-point genetic algorithm tuning with use of test functions is done and leads to a…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…