Related papers: Quasi-Species and Aggregate Dynamics
In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
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…
Many important real-world networks manifest "small-world" properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is "preferential attachment", where nodes…
We consider a stochastic model for evolution of group-structured populations in which interactions between group members correspond to the Prisoner's Dilemma or the Hawk-Dove game. Selection operates at two organization levels: individuals…
The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since…
We study the large population limit of a multi-strategy discrete-time Moran process in the weak selection regime. We show that the replicator dynamics is interpreted as the large-population limit of the Moran process. This result is…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
Deterministic evolutionary theory robustly predicts that populations displaying altruistic behaviours will be driven to extinction by mutant cheats that absorb common benefits but do not themselves contribute. Here we show that when…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal.…
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
While generic competitive systems exhibit mixtures of hierarchy and cycles, real-world systems are predominantly hierarchical. We demonstrate and extend a mechanism for hierarchy; systems with similar agents approach perfect hierarchy in…
Traditionally, frequency dependent evolutionary dynamics is described by deterministic replicator dynamics assuming implicitly infinite population sizes. Only recently have stochastic processes been introduced to study evolutionary dynamics…
The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population…