Replicators with Hebb interactions

We do an analytical study of the statistical properties of an ecosystem composed of species that are coupled via pairwise interactions that are given by the Hebb rule and have deterministic self-interactions u. In the model each species is characterized by an infinite set of p = αN traits. As one of our main results, we observe that the ecosystem becomes less cooperative as the complexity of species (number of traits) is increased. Received 23 September 2002 Published online 4 February 2003 RID="a" ID="a"e-mail: viviane@if.sc.usp.br     

Survival and extinction in cyclic and neutral three-species systems

We study the ABC model ( A + B↦2B, B + C↦2C, C + A↦2A), and its counterpart: the three-component neutral drift model ( A + B↦2A or 2B, B + C↦2B or 2C, C + A↦2C or 2A.) In the former case, the mean-field approximation exhibits cyclic behaviour with an amplitude determined by the initial condition. When stochastic phenomena are taken into account the amplitude of oscillations will drift and eventually one and then two of the three species will become extinct. The second model remains stationary for all initial conditions in the mean-field approximation, and drifts when stochastic phenomena are considered. We analyzed the distribution of first extinction times of both models by simulations of the master equation, and from the point of view of the Fokker-Planck equation. Survival probability vs. time plots suggest an exponential decay. For the neutral model the extinction rate is inversely proportional to the system size, while the cyclic model exhibits anomalous behaviour for small system sizes. In the large system size limit the extinction times for both models will be the same. This result is compatible with the smallest eigenvalue obtained from the numerical solution of the Fokker-Planck equation. We also studied the behaviour of the probability distribution. The exponential decay is found to be robust against certain changes, such as the three reactions having different rates. Received 14 August 2002 and Received in final form 14 February 2003 / Published online: 1 April 2003 RID="a" ID="a"e-mail: ita@physics.ubc.ca     

Mathematical glimpse on the Y chromosome degeneration

The Y chromosomes are genetically degenerate and do not recombine with their matching partners X. Non-recombination of XY pairs has been pointed out as the key factor for the degeneration of the Y chromosome. The aim here is to show that there is a mathematical asymmetry in sex chromosomes which leads to the degeneration of Y chromosomes even in the absence of XX and XY recombination. A model for sex-chromosome evolution in a stationary regime is proposed. The consequences of their asymmetry are analyzed and lead us to a couple of conclusions. First, Y chromosome degeneration shows up more often than X chromosome degeneration. Second, if nature prohibits female mortalities from beeing exactly , then Y chromosome degeneration is inevitable.     

The effect of spatial structure in adaptive evolution

We study the dynamics of adaptation in a spatially structured population. The model assumes local competition for replication, where each organism interacts only with its nearest neighbors and is inspired by experimental methods that can be used to study the process of adaptive evolution in microbes. In such experiments microbial populations are grown on petri dishes and allowed to adapt by serial passage. We compare the rate of adaptation in a structured population where the structure is maintained intact to those where movement of individuals can occur. We observe that the rate of adaptive evolution is higher and the mean effect of fixed beneficial mutations is lower in intact structures than in structures with mixing.     

Epidemics in small world networks

For many infectious diseases, a small-world network on an underlying regular lattice is a suitable simplified model for the contact structure of the host population. It is well known that the contact network, described in this setting by a single parameter, the small-world parameter p, plays an important role both in the short term and in the long term dynamics of epidemic spread. We have studied the effect of the network structure on models of immune for life diseases and found that in addition to the reduction of the effective transmission rate, through the screening of infectives, spatial correlations may strongly enhance the stochastic fluctuations. As a consequence, time series of unforced Susceptible-Exposed-Infected-Recovered (SEIR) models provide patterns of recurrent epidemics with realistic amplitudes, suggesting that these models together with complex networks of contacts are the key ingredients to describe the prevaccination dynamical patterns of diseases such as measles and pertussis. We have also studied the role of the host contact strucuture in pathogen antigenic variation, through its effect on the final outcome of an invasion by a viral strain of a population where a very similar virus is endemic. Similar viral strains are modelled by the same infection and reinfection parameters, and by a given degree of cross immunity that represents the antigenic distance between the competing strains. We have found, somewhat surprisingly, that clustering on the network decreases the potential to sustain pathogen diversity.     

Fixation of advantageous mutations in an off-equilibrium population

We investigate the evolution of asexual populations subject to a large supply of deleterious mutations such that Muller's ratchet operates. In this regime, the accumulation of deleterious mutations takes place continuously with the resulting loss of the least-loaded class of individuals. In the current work, we study the effect of the supply of beneficial mutations on the ratchet's speed. We also examine how the rate of substitution of favorable mutations as well as the mean selective effect of favorable mutations that reach fixation is compared to those assuming a population at equilibrium. We observe that under Muller's ratchet, the rate of fixation of advantageous mutations is higher than that predicted for an equilibrium population. The difference between the rate supposing an equilibrium regime and that for the non-equilibrium case becomes larger as we increase the rate of deleterious mutations. On the other hand, the mean selective effect of beneficial mutations that reach fixation is smaller than the expected value for the equilibrium situation.     

Instabilities in population dynamics

Biologists have long known that the smaller the population, the more susceptible it is to extinction from various causes. Biologists define minimum viable population size (MVP), which is the critical population size, below which the population has a very small chance to survive. There are several theoretical models for predicting the probability that a small population will become extinct. But these models either embody unrealistic assumptions or lead to currently unresolved mathematical problems. In other popular models of population dynamics, like the logistic model, MVP does not exist. In this paper we find the existence of such a critical concentration in a simple model of evolution. We solve this model by a mean field theory and show, in one and two dimensions, the existence of the critical adaptation and concentration below which a population dies out. We also show that, like in the logistic model, above the critical value a population reaches its carrying capacity. Moreover, in the two-dimensional case we find - the so common in biological models - periodic solutions and their biffurcations. Received 15 February 2000     

Model of evolution with sexual and non-sexual reproduction

Using a previously introduced model (Refs. [9, 10]) of biological evolution, we study the role of the reproduction pattern on the fate of an evolving population. Each individual is under the selectional pressure from the environment and random harmful mutations. The habitat (“climate") is changing periodically. Evolution of populations following three reproduction patterns are compared - an asexual one (without recombination) and two with recombination - asexual (meiotic parthenogenesis) and sexual. We show, via Monte-Carlo simulations, that sexual reproduction leads to a better adaptation to the environment, slightly better survival rates for the individuals and higher probability that the population will not become extinct in difficult external conditions. The benefits of sexual reproduction are enhanced by higher birth rates and lower mutation rates. In the case of low birth rates and high mutation rates there is a small preference for the meiotic parthenogenesis. Received 9 August 1999     

Time evolution of non-lethal infectious diseases: a semi-continuous approach

A model describing the dynamics related to the spreading of non-lethal infectious diseases in a fixed-size population is proposed. The model consists of a non-linear delay-differential equation describing the time evolution of the increment in the number of infectious individuals and depends upon a limited number of parameters. Predictions are in good qualitative agreement with data on influenza, which is taken to be a representative type of non-lethal infectious disease.     

Recognition games

In this work we propose an evolution model based on the competition between individuals belonging to populations of neural networks, obeying the Hopfield dynamics. The selection rule adopted relies on generalization and natural classification abilities. The results obtained through computer simulation show that these populations self-organize and evolve towards equilibrium states in the region of transition between ordered and disordered phases. Received 28 October 1998 and Received in final form 2 December 1998     

Noise-controlled slow–fast oscillations in predator–prey models with the Beddington functional response

The influence of environmental fluctuations (modeled as a multiplicative dichotomous noise) on predator–prey interaction is studied using a metapopulation model with N prey-subpopulations. Investigating the role that predator interference plays in the dynamics of such trophic systems, the Beddington functional response is considered. In case the growth rates of prey and predator are widely different, we obtain analytic results by a dynamical mean-field approximation. In some regions of the system parameters, variations of noise amplitude or correlation time can cause transitions of the mean field from a globally stable equilibrium to the stable limit cycle as well as in the opposite direction. The conditions for the occurrence of such a phenomenon are found and illustrated by phase diagrams. Implications of the results on the colored-noise-induced extinction of a predator population are also discussed.     

Simple models of proteins with repulsive non-native contacts

The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies may lead to folding at T=0 for some unusual two-dimensional sequences and to reduction in complexity of disconnectivity graphs for local energy minima. Received 10 May 1999 and Received in final form 13 October 1999     

A model based on <Emphasis Type="Italic">TTC</Emphasis> to describe how drivers controltheir vehicles

We have used the Penna ageing model to analyze how the differences in evolution of sex chromosomes depend on the strategy of reproduction. In panmictic populations, when females (XX) can freely choose the male partner (XY) for reproduction from the whole population, the Y chromosome accumulates defects and eventually the only information it brings is a male sex determination. As a result of shrinking Y chromosome the male genomes de facto loose one copy of the X chromosome information and, as a result, males are characterized by higher mortality, observed also in the human populations. If it is assumed in the model that the presence of the male is indispensable at least during the pregnancy of his female partner and he cannot be seduced by another female at least during the one reproduction cycle-the Y chromosome preserves its content, does not shrink and the lifespan of females and males is the same. Thus, Y chromosome shrinks not because of existing in one copy, without the possibility of recombination, but because it stays under weaker selection pressure; in panmictic populations without the necessity of being faithful, a considerable fraction of males is dispensable and they can be eliminated from the population without reducing its reproduction potential.     

Model of population evolution with and without eugenics

We propose, and solve via Monte-Carlo simulation, a model describing evolution of population subject to harmful mutations. The habitat changes periodically. The evolution of two, initially identical, populations is compared. One without any external ingerence and the second in which we eliminate all individuals which are ill-fitted to the changed environment (eugenics). We show that although in the short run the individuals in the latter are better adapted and live longer, after some more changes of the environment, the populations with eugenics become extinct, while the others live on. Received 8 April 1999     

Boerdijk-Coxeter helix and biological helices

Helices and dense packing of spherical objects are two closely related problems. For instance, the Boerdijk-Coxeter helix, which is obtained as a linear packing of regular tetrahedra, is a very efficient solution to some close-packing problems. The shapes of biological helices result from various kinds of interaction forces, including steric repulsion. Thus, the search for a maximum density can lead to structures related to the Boerdijk-Coxeter helix. Examples are presented for the -helix structure in proteins and for the structure of the protein collagen, but there are other examples of helical packings at different scales in biology. Models based on packing efficiency related to the Boerdijk-Coxeter helix, explain, mainly from topological arguments, why the number of amino acids per turn is close to 3.6 in -helices and 2.7 in collagen. Received 26 November 1998 and Received in final form 12 April 1999