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Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with…
The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…
We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
Differential diffusion is a source of instability in population dynamics systems when species diffuse with different rates. Predator-prey systems show this instability only under certain specific conditions, usually requiring Holling-type…
Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations…
Background. In a number of recent experiments with food-and-mouth disease virus, a deleterious mutant, was found to avoid extinction and remain in the population for long periods of time. This observation was called quasispecies memory. The…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
Meloidogyne root knot nematodes (RKN) can infect most of the world's agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of…
This paper investigates the long-term dynamics of a reaction-diffusion predator-prey system subject to random environmental fluctuations modeled by Markovian switching. The model is formulated as a hybrid system of partial differential…
The outcome of competition among species is influenced by the spatial distribution of species and effects such as demographic stochasticity, immigration fluxes, and the existence of preferred habitats. We introduce an individual-based model…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
We present a model that investigates preference evolution with endogenous matching. In the short run, individuals' subjective preferences influence partner selection and behavior in strategic interactions, which affect their material…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
Mutualists and pathogens, collectively called symbionts, are ubiquitous in plant communities. While some symbionts are highly host-specific, others associate with multiple hosts. The outcomes of multispecies host-symbiont interactions with…
Multi-strain pathogens such as Group A Streptococcus, Streptococcus pneumoniae, and Staphylococcus aureus cause millions of infections each year with a substantial health burden. Control of multi-strain pathogens can be complicated by the…
This paper introduces a speciation principle for neuroevolution where evolving networks are grouped into species based on the number of hidden neurons, which is indicative of the complexity of the search space. This speciation principle is…