Grupo Interdisciplinar de Sistemas Complejos (GISC)http://hdl.handle.net/10016/58602015-02-28T15:57:02Z2015-02-28T15:57:02ZEvolution on neutral networks accelerates the ticking rate of the molecular clockManrubia, SusannaCuesta, José A.http://hdl.handle.net/10016/200812015-02-27T12:02:27Z2014-11-12T00:00:00ZEvolution on neutral networks accelerates the ticking rate of the molecular clock
Manrubia, Susanna; Cuesta, José A.
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as they transform its genotype into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into genotype networks (GN). These networks are known to be heterogeneous and assortative. As these features condition the probability that mutations keep the phenotype unchanged---hence becoming blind to natural selection---it follows that the topology of the GN will influence the evolutionary dynamics of the population. In this letter we analyze this effect by studying the dynamics of random walks (RW) on assortative networks with arbitrary topology. We find that the probability that a RW leaves the network is smaller the longer the time spent in it---i.e., the process is not Markovian. From the biological viewpoint, this "phenotypic entrapment" entails an acceleration in the fixation of neutral mutations, thus implying a non-uniform increase in the ticking rate of the molecular clock with the age of branches in phylogenetic trees. We also show that this effect is stronger the larger the fitness of the current phenotype relative to that of neighboring phenotypes.
2014-11-12T00:00:00ZThe Joker effect: cooperation driven by destructive agentsArenas, AlexCamacho, JuanCuesta, José A.Requejo, Rubén J.http://hdl.handle.net/10016/200712015-02-27T12:03:39Z2011-06-21T00:00:00ZThe Joker effect: cooperation driven by destructive agents
Arenas, Alex; Camacho, Juan; Cuesta, José A.; Requejo, Rubén J.
Understanding the emergence of cooperation is a central issue in evolutionary game theory. The hardest setup for the attainment of cooperation in a population of individuals is the Public Goods game in which cooperative agents generate a common good at their own expenses, while defectors "free-ride" this good. Eventually this causes the exhaustion of the good, a situation which is bad for everybody. Previous results have shown that introducing reputation, allowing for volunteer participation, punishing defectors, rewarding cooperators or structuring agents, can enhance cooperation. Here we present a model which shows how the introduction of rare, malicious agents &- that we term jokers &- performing just destructive actions on the other agents induce bursts of cooperation. The appearance of jokers promotes a rock-paper-scissors dynamics, where jokers outbeat defectors and cooperators outperform jokers, which are subsequently invaded by defectors. Thus, paradoxically, the existence of destructive agents acting indiscriminately promotes cooperation.
2011-06-21T00:00:00ZHuge Progeny Production during the Transient of a Quasispecies Model of Viral Infection, Reproduction and MutationCuesta, José A.http://hdl.handle.net/10016/191812014-07-25T08:46:34Z2011-10-01T00:00:00ZHuge Progeny Production during the Transient of a Quasispecies Model of Viral Infection, Reproduction and Mutation
Cuesta, José A.
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When the mutation rate is sufficiently high, the master type no longer survives and gets replaced by a wide range of mutant types, thus destroying the quasi-species. It is the so-called "error catastrophe". But natural selection acts on phenotypes, not genotypes, and huge amounts of genotypes yield the same phenotype. An important consequence of this is the appearance of beneficial mutations which increase the fitness of mutants. A model has been recently proposed to describe quasi-species in the presence of beneficial mutations. This model lacks the error catastrophe of Eigen's model and predicts a steady state in which the viral population grows exponentially. Extinction can only occur if the infectivity of the quasi-species is so low that this exponential is negative. In this work I investigate the transient of this model when infection is started from a small amount of low fitness virions. I prove that, beyond an initial regime where viral population decreases (and can go extinct), the growth of the population is super-exponential. Hence this population quickly becomes so huge that selection due to lack of host cells to be infected begins to act before the steady state is reached. This result suggests that viral infection may widespread before the virus has developed its optimal form.
2011-10-01T00:00:00ZRatchet effect on a relativistic particle driven by external forcesQuintero, Niurka R.Álvarez Nodarse, RenatoCuesta, José A.http://hdl.handle.net/10016/191522014-12-04T11:22:56Z2011-10-21T00:00:00ZRatchet effect on a relativistic particle driven by external forces
Quintero, Niurka R.; Álvarez Nodarse, Renato; Cuesta, José A.
We study the ratchet effect of a damped relativistic particle driven by both asymmetric temporal bi-harmonic and time-periodic piecewise constant forces. This system can be formally solved for any external force, providing the ratchet velocity as a nonlinear functional of the driving force. This allows us to explicitly illustrate the functional Taylor expansion formalism recently proposed for this kind of systems. The Taylor expansion reveals particularly useful to obtain the shape of the current when the force is periodic, piecewise constant.We also illustrate the somewhat counterintuitive effect that introducing damping may induce a ratchet effect.When the force is symmetric under time-reversal and the system is undamped, under symmetry principles no ratchet effect is possible. In this situation increasing damping generates a ratchet current which, upon increasing the damping coefficient eventually reaches a maximum and decreases toward zero. We argue that this effect is not specific of this example and should appear in any ratchet system with tunable damping driven by a time-reversible external force.
2011-10-21T00:00:00Z