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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…
Selective sweeps affect neutral genetic diversity through hitchhiking. While this effect is limited to the local genomic region of the sweep in panmictic populations, we find that in spatially-extended populations the combined effects of…
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…
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions.…
In human societies the probability of strategy adoption from a given person may be affected by the personal features. Now we investigate how an artificially imposed restricted ability to reproduce, overruling ones fitness, affects an…
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…
Formation and competition of associations are studied in a six-species ecological model where each species has two predators and two prey. Each site of a square lattice is occupied by an individual belonging to one of the six species. The…
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…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
We demonstrate diversification rather than optimisation for highly interacting organisms in a well mixed biological system by means of a simple model and reference to experiment, and find the cause to be the complex network of interactions…
Genetic Programming has been very successful in solving a large area of problems but its use as a machine learning algorithm has been limited so far. One of the reasons is the problem of overfitting which cannot be solved or suppresed as…
We study assortative mixing in networks, the tendency for vertices in networks to be connected to other vertices that are like (or unlike) them in some way. We consider mixing according to discrete characteristics such as language or race…
We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or…
We discuss general formation of complementary behaviors, functions and forms in biological species competing for resources. We call orthogonalization the related processes on macro and micro-level of a self-organized formation of…
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 study the limit of many small mutations of a model of population dynamics. The population is structured by phonological traits and is spatially inhomogeneous. The various sub-populations compete for the same nutrient which diffuses…
Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations…
We consider a random permutation drawn from the set of permutations of length $n$ that avoid some given set of patterns of length 3. We show that the number of occurrences of another pattern $\sigma$ has a limit distribution, after suitable…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…