Related papers: Quasispecies dynamics with network constraints
We describe a simple model of evolution which incorporates the branching and extinction of species lines, and also includes abiotic influences. A first principles approach is taken in which the probability for speciation and extinction are…
The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the…
Highly-diverse ecosystems exhibit a broad distribution of population sizes and species turnover, where species at high and low abundances are exchanged over time. We show that these two features generically emerge in the fluctuating phase…
A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated…
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…
The notions of bounded-size and quasibounded-size decompositions with bounded treedepth base classes are central to the structural theory of graph sparsity introduced by two of the authors years ago, and provide a characterization of both…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
All possible phenotypes are not equally accessible to evolving populations. In fact, only phenotypes of large size, i.e. those resulting from many different genotypes, are found in populations of sequences, presumably because they are…
Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections…
We show that, under certain assumptions, the fitness of almost all quasi-species becomes independent of mutational probabilities and the initial frequency distributions of the sequences in high dimensional sequence spaces. This result is…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
We consider a multi-species community modelled as a complex network of populations, where the links are given by a random asymmetric matrix J, with fraction 1-C of zero entries, where C reflects the over-all connectivity of the system. The…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
The quasispecies model introduced by Eigen in 1971 has close connections with the isometry group of the space of binary sequences relative to the Hamming distance metric. Generalizing this observation we introduce an abstract quasispecies…
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…
We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length $L$. The population evolves in a maximally rugged fitness landscape with a large number of local optima.…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Evolutionary dynamics have been traditionally studied in the context of homogeneous populations, mainly described my the Moran process. Recently, this approach has been generalized in \cite{LHN} by arranging individuals on the nodes of a…
We consider the quasispecies description of a population evolving in both the "master sequence" landscape (where a single sequence is evolutionarily preferred over all others) and the REM landscape (where the fitness of different sequences…