Topological properties of phylogenetic trees in evolutionary models

The extent to which evolutionary processes affect the shape of phylogenetic trees is an important open question. Analyses of small trees seem to detect non-trivial asymmetries which are usually ascribed to the presence of correlations in speciation rates. Many models used to construct phylogenetic trees have an algorithmic nature and are rarely biologically grounded. In this article, we analyze the topological properties of phylogenetic trees generated by different evolutionary models (populations of RNA sequences and a simple model with inheritance and mutation) and compare them with the trees produced by known uncorrelated models as the backward coalescent, paying special attention to large trees. Our results demonstrate that evolutionary parameters as mutation rate or selection pressure have a weak influence on the scaling behavior of the trees, while the size of phylogenies strongly affects measured scaling exponents. Within statistical errors, the topological properties of phylogenies generated by evolutionary models are compatible with those measured in balanced, uncorrelated trees.     

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.     

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     

Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.     

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.     

Dynamical role of the degree of intraspecific cooperation: A simple model for prebiotic replicators and ecosystems

We present a simple mean field model to analyze the dynamics of competition between two populations of replicators in terms of the degree of intraspecific cooperation (i.e., autocatalysis) in one of these populations. The first population can only replicate with Malthusian kinetics while the second one can reproduce with Malthusian or autocatalytic replication or with a combination of both reproducing strategies. The model consists of two coupled, nonlinear, autonomous ordinary differential equations. We investigate analytically and numerically the phase plane dynamics and the bifurcation scenarios of this ecologically coupled system, focusing on the outcome of competition for several degrees of intraspecific cooperation, σ, in the second population of replicators. We demonstrate that the dynamics of both populations can not be governed by a limit cycle, and also that once cooperation is considered, the topology of phase space does not allow for coexistence. Even for low values of the degree of intraspecific cooperation, for large enough autocatalytic replication rates, the second population of replicators is able to outcompete the first one, having a wide basin of attraction in state space. We characterize the same power law dependence between the outcompetition extinction times, τ, and the degree of intraspecific cooperation for both populations, given by τ∼c_iσ⁻¹. Our results suggest that, under some kinetic conditions, the appearance of autocatalysis might be favorable in a population of replicators growing with Malthusian kinetics competing with another population also reproducing exponentially.     

Cooperation and charity in spatial public goods game under different strategy update rules

Human cooperation can be influenced by other human behaviors and recent years have witnessed the flourishing of studying the coevolution of cooperation and punishment, yet the common behavior of charity is seldom considered in game-theoretical models. In this article, we investigate the coevolution of altruistic cooperation and egalitarian charity in spatial public goods game, by considering charity as the behavior of reducing inter-individual payoff differences. Our model is that, in each generation of the evolution, individuals play games first and accumulate payoff benefits, and then each egalitarian makes a charity donation by payoff transfer in its neighborhood. To study the individual-level evolutionary dynamics, we adopt different strategy update rules and investigate their effects on charity and cooperation. These rules can be classified into two global rules: random selection rule in which individuals randomly update strategies, and threshold selection rule where only those with payoffs below a threshold update strategies. Simulation results show that random selection enhances the cooperation level, while threshold selection lowers the threshold of the multiplication factor to maintain cooperation. When charity is considered, it is incapable in promoting cooperation under random selection, whereas it promotes cooperation under threshold selection. Interestingly, the evolution of charity strongly depends on the dispersion of payoff acquisitions of the population, which agrees with previous results. Our work may shed light on understanding human egalitarianism.     

Modelling Moran Process with Network Dynamics for the Evolution of Cooperation

We introduce a simple model based on the Moran process with network dynamics. Using pair approximation, the cooperation frequencies at equilibrium states are deduced for general interactions. Three usual social dilemmas are discussed in the framework of our model. It is found that they all have a phase transition at the same value of cost-to-benefit ratio. For the prisoner＇s dilemma game, notably it is exactly the simple rule reported in the literature [Nature 441 （2006） 502]. In our model, the simple rule results from the parent-offspring link. Thus the basic mechanism for cooperation enhancement in network reciprocity is in line with the Hamilton rule of kin selection. Our simulations verify the analysis obtained from pair approximation.     

Age-based model for weighted network with general assortative mixing

In this paper, we propose an evolutionary model for weighted networks by introducing an age-based mutual selection mechanism. Our model generates power-law distributions of degree, weight, and strength, which are confirmed by analytical predictions and are consistent with real observations. The investigation of the relationship between clustering and the connectivity of nodes suggests hierarchical organization in the weighted networks. Furthermore, both assortative and disassortative properties can be naturally obtained by tuning a parameter α, which controls the strength of age-based preferential attachments. Since the age information of nodes is easier to acquire than the degree and strength of nodes, and almost all empirically observed structural and weighted properties can be reproduced by the simple evolutionary regulation, our model may reveal some underlying mechanisms that are key for the evolution of weighted complex networks.     

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.     

Physics of evolution: Selection without fitness

Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish. Survival probabilities and proliferation rates are typically associated with the ‘fitness’ of particular variations. In this paper we argue that the notion of fitness is an a posteriori concept, in the sense that one can assign higher fitness to species that survive but one can generally not derive or predict fitness per se. Proliferation rates can be measured, whereas fitness landscapes, i.e. the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. In this spirit, here we propose a random matrix model of evolution where selection mechanisms are encoded in interaction matrices of species, thereby extending the previous work of ours by a control parameter describing suppressors in the system. We are able to recover some key facts of evolution dynamics endogenously, such as punctuated equilibrium, i.e. the existence of intrinsic large extinction events, and, at the same time, periods of dramatic diversification, as known e.g. from the fossil record. Further, we comment on two fundamental technical problems of a ‘physics of evolution’, the non-closedness of its phase space and the problem of co-evolving boundary conditions, apparent in all systems subject to evolution.     

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.     

Risk of population extinction from periodic and abrupt changes of environment

A simulation model of a population having internal (genetic) structure is presented. The population is subject to selection pressure coming from the environment which is the same in the whole system but changes in time. Reproduction has a sexual character with recombination and mutation. Two cases are considered — oscillatory changes of the environment and abrupt ones (catastrophes). We show how the survival chance of a population depends on the maximum allowed size of the population, the length of the genotypes characterizing individuals, selection pressure and the characteristics of the “climate” changes, either their period of oscillations or the scale of the abrupt shift.     

Evolution of a population of random Boolean networks

We investigate the evolution of populations of random Boolean networks under selection for robustness of the dynamics with respect to the perturbation of the state of a node. The fitness landscape contains a huge plateau of maximum fitness that spans the entire network space. When selection is so strong that it dominates over drift, the evolutionary process is accompanied by a slow increase in the mean connectivity and a slow decrease in the mean fitness. Populations evolved with higher mutation rates show a higher robustness under mutations. This means that even though all the evolved populations exist close to the plateau of maximum fitness, they end up in different regions of network space.     

Evolutionary Prisoner's Dilemma Game Based on Pursuing Higher Average Payoff

We investigate the prisoner＇s dilemma game based on a new rule： players will change their current strategies to opposite strategies with some probability if their neighbours＇ average payoffs are higher than theirs. Compared with the cases on regular lattices （RL） and Newman-Watts small world network （NW）, cooperation can be best enhanced on the scale-free Barabasi-Albert network （BA）. It is found that cooperators are dispersive on RL network, which is different from previously reported results that cooperators will form large clusters to resist the invasion of defectors. Cooperative behaviours on the BA network are discussed in detail. It is found that large-degree individuals have lower cooperation level and gain higher average payoffs than that of small-degree individuals. In addition, we find that small-degree individuals more frequently change strategies than do large- degree individuals.     

Evolution of the linguistic diversity on correlated landscapes

We have recently investigated the evolution of linguistic diversity by means of a simple spatial model that considers selective geographic colonization, linguistic anomalous diffusion and mutation. In the model, regions of the lattice are characterized by the amount of resources available to populations which are going to colonize the region. In that approach, the resources were ascribed in a randomly and uncorrelated way. Here, we extend the previous model and introduce a degree of correlation for the resource landscape. A change of the qualitative scenario is observed for high correlation, where the increase of the linguistic diversity on area is faster than for low correlated landscapes. For low correlated landscapes, the dependence of diversity on area shows two scaling regimes, while we observe the rising of another scaling region for high correlated landscapes.     

Structurally constrained protein evolution: results from a lattice simulation

We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We use a cubic lattice model of the protein structure and test the neutrality conditions by extensive Monte Carlo simulations. We observe that sequence space is traversed by neutral networks, i.e. sets of sequences with the same fold connected by point mutations. Typical pairs of sequences on a neutral network are nearly as different as randomly chosen sequences. The fraction of neutral neighbors has strong sequence to sequence variations, which influence the rate of neutral evolution. In this paper we study the thermodynamic stability of different protein sequences. We relate the high variability of the fraction of neutral mutations to the complex energy landscape within a neutral network, arguing that valleys in this landscape are associated to high values of the neutral mutation rate. We find that when a point mutation produces a sequence with a new ground state, this is likely to have a low stability. Thus we tentatively conjecture that neutral networks of different structures are typically well separated in sequence space. This result indicates that changing significantly a protein structure through a biologically acceptable chain of point mutations is a rare, although possible, event. Received 8 July 1999     

Network structure of cross-correlations among the world market indices

We report the results of an investigation of the properties of the networks formed by the cross-correlations of the daily and weekly index changes of 143 stock market indices from 59 different countries. Analysis of the asset graphs, minimum spanning trees (MST) and planar maximally filtered graphs (PMFG) of the afermentioned networks confirms that globalization has been increasing in recent years. North American and European markets are observed to be much more strongly connected among themselves compared to the integration with the other geographical regions. Surprisingly, the integration of East Asian markets among themselves as well as to the Western markets is found to be rather weak. MST and PMFG of both daily and weekly return correlations indicates that the clustering of the indices is mostly geographical. The French fsbf250 index is found to be most important node of the MST and PMFG based on several graph centrality measures.     

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.