Related papers: Selection for Fitness vs. Selection for Robustness…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
In this paper, we investigate a two-species Lotka-Volterra competition patch model in a Y-shaped river network, where the two species are assumed to be identical except for their random and directed movements. We show that competition…
Co-evolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this co-adaptive model, besides the classical error catastrophe for high virus mutation rates, a…
Using methods of statistical physics, we present rigorous theoretical calculations of Eigen's quasispecies theory with the truncated fitness landscape which dramatically limits the available sequence space of a reproducing quasispecies.…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Understanding the interplay of different traits in a co-infection system with multiple strains has many applications in ecology and epidemiology. Because of high dimensionality and complex feedbacks between traits manifested in infection…
We investigate the relationship between the nested organization of mutualistic systems and their robustness against the extinction of species. We establish that a nested pattern of contacts is the best possible one as far as robustness is…
We investigate extinction dynamics in the paradigmatic model of two competing species A and B that reproduce (A-->2A, B-->2B), self-regulate by annihilation (2A-->0, 2B-->0), and compete (A+B-->A, A+B-->B). For a finite system that is in…
Quasispecies theory provides the conceptual and theoretical bases for describing the dynamics of biological information of replicators subject to large mutation rates. This theory, initially conceived within the framework of prebiotic…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
This paper extends Eigen's quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Quasispecies theory predicts that there is a critical mutation probability above which a viral population will go extinct. Above this threshold the virus loses the ability to replicate the best adapted genotype, leading to a population…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
We are interested in the long time behavior of a two-type density-dependent biological population conditioned to non-extinction, in both cases of competition or weak cooperation between the two species. This population is described by a…
In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and…
Many mathematical models of evolution assume that all individuals experience the same environment. Here, we study the Moran process in heterogeneous environments. The population is of finite size with two competing types, which are exposed…
There is empirical evidence from a range of disciplines that as the connectivity of a network increases, we observe an increase in the average fitness of the system. But at the same time, there is an increase in the proportion of…
The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of species that are disconnected from the rest of the network when extinctions occur…
Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to…