Related papers: Is modularity the reason why recombination is so u…
The interaction networks of biological systems are known to take on several non-random structural properties, some of which are believed to positively influence system robustness. Researchers are only starting to understand how these…
The spatial heterogeneity of cities -- the uneven distribution of population and activities -- is fundamental to urban dynamics and related to critical issues such as infrastructure overload, housing affordability, and social inequality.…
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…
Resource are often not uniformly distributed within a population. Spatial variations of concentration of a resource, change the fitness of competing strategies locally. The notion of fitness varying with respect to both genotype and…
Modularity is widely used to effectively measure the strength of the disjoint community structure found by community detection algorithms. Although several overlapping extensions of modularity were proposed to measure the quality of…
Why sex evolved and it prevails in nature remains one of the great puzzles of evolution. Most biologists would explain that it promotes genetic variability, however this explanation suffers from several difficulties. What advantages might…
This paper develops a simplified set of models describing asexual and sexual replication in unicel- lular diploid organisms. The models assume organisms whose genomes consist of two chromosomes, where each chromosome is assumed to be…
This paper develops a simplified model for sexual replication within the quasispecies formalism. We assume that the genomes of the replicating organisms are two-chromosomed and diploid, and that the fitness is determined by the number of…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger…
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?…
We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The…
A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
Boolean networks have been widely used to explore aspects of gene regulation, traditionally with a single network. A modified form of the model to explore the effects of increasing the number of gene states has also recently been…
Is there an advantage to heterogeneity in a population where individuals grow and divide by fission? This is a broad question, to which there is no easy universal answer. This article aims to provide a quantitative answer in the specific…
Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome…
Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for…
In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a…