Related papers: Dynamics of genetic code evolution: The emergence …
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…
Genetic programming and artificial life systems commonly employ tag-matching schemes to determine interactions between model components. However, the implications of criteria used to determine affinity between tags with respect to…
Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to…
We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…
Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a…
Dimension reduction is the process of embedding high-dimensional data into a lower dimensional space to facilitate its analysis. In the Euclidean setting, one fundamental technique for dimension reduction is to apply a random linear map to…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that…
Exploiting the mathematical curiosity of intransitive dice, we present a simple theoretical model for co-evolution that captures scales ranging from the genome of the individual to the system-wide emergence of species diversity. We study a…
We consider a Moran-type model of cultural evolution, which describes how traits emerge, are transmitted, and get lost in populations. Our analysis focuses on the underlying cultural genealogies; they were first described by Aguilar and…
The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the…
Theoretical studies on evolutionary algorithms have developed vigorously in recent years. Many such algorithms have theoretical guarantees in both running time and approximation ratio. Some approximation mechanism seems to be inherently…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Since genetic algorithm was proposed by John Holland (Holland J. H., 1975) in the early 1970s, the study of evolutionary algorithm has emerged as a popular research field (Civicioglu & Besdok, 2013). Researchers from various scientific and…
In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random genetic drift, is encoded in gene-frequency trajectories. We determine…
Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…