Host-Parasite Co-evolution and Optimal Mutation Rates for Semi-conservative Quasispecies

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 conservative hosts converge for realistic genome lengths, thus maintaining the admirable agreement between theory and experiment found previously for the conservative model and justifying the conservative approximation in some cases. We demonstrate that, while the optimal mutation rate for a conservative and semi-conservative parasite interacting with a given immune system is similar to that of a conservative parasite, the properties away from this optimum differ significantly. We suspect that this difference, coupled with the requirement that a parasite optimize survival in a range of viable hosts, may help explain why semi-conservative viruses are known to have significantly lower mutation rates than their conservative counterparts

Error threshold in the evolution of diploid organisms

The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully investigated. In particular, it is shown that dominance can protect the wild-type alleles from the error catastrophe. The analysis is restricted to a diploid analogue of the single-peaked landscape.Comment: 9 pages, 4 Postscript figures. Submitted to J. Phy. A: Mat. and Ge

A Population Genetic Approach to the Quasispecies Model

A population genetics formulation of Eigen's molecular quasispecies model is proposed and several simple replication landscapes are investigated analytically. Our results show a remarcable similarity to those obtained with the original kinetics formulation of the quasispecies model. However, due to the simplicity of our approach, the space of the parameters that define the model can be explored. In particular, for the simgle-sharp-peak landscape our analysis yelds some interesting predictions such as the existence of a maximum peak height and a mini- mum molecule length for the onset of the error threshold transition.Comment: 16 pages, 4 Postscript figures. Submited to Phy. Rev.

Equilibrium Distribution of Mutators in the Single Fitness Peak Model

This paper develops an analytically tractable model for determining the equilibrium distribution of mismatch repair deficient strains in unicellular populations. The approach is based on the single fitness peak (SFP) model, which has been used in Eigen's quasispecies equations in order to understand various aspects of evolutionary dynamics. As with the quasispecies model, our model for mutator-nonmutator equilibrium undergoes a phase transition in the limit of infinite sequence length. This "repair catastrophe" occurs at a critical repair error probability of $\epsilon_r = L_{via}/L$, where $L_{via}$ denotes the length of the genome controlling viability, while $L$ denotes the overall length of the genome. The repair catastrophe therefore occurs when the repair error probability exceeds the fraction of deleterious mutations. Our model also gives a quantitative estimate for the equilibrium fraction of mutators in {\it Escherichia coli}.Comment: 4 pages, 2 figures (included as separate PS files

Genetic Polymorphism in Evolving Population

We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping diversity in the gene pool under abrupt environmental changes. The model provides reasonable estimates for the proportions of polymorphic and heterozygous loci and for the mutation rate, as observed in nature

Anderson Localization, Non-linearity and Stable Genetic Diversity

In many models of genotypic evolution, the vector of genotype populations satisfies a system of linear ordinary differential equations. This system of equations models a competition between differential replication rates (fitness) and mutation. Mutation operates as a generalized diffusion process on genotype space. In the large time asymptotics, the replication term tends to produce a single dominant quasispecies, unless the mutation rate is too high, in which case the populations of different genotypes becomes de-localized. We introduce a more macroscopic picture of genotypic evolution wherein a random replication term in the linear model displays features analogous to Anderson localization. When coupled with non-linearities that limit the population of any given genotype, we obtain a model whose large time asymptotics display stable genotypic diversityComment: 25 pages, 8 Figure

Global Fits of the CKM Matrix

We report upon the present status of global fits to Cabibbo-Kobayashi-Maskawa matrix.Comment: 3 pages, 3 figures invited talk presented at EPS conference, Aachen July 17-2

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.Comment: 22 pages, 10 figure