arXiv subjects

José A. Cuesta

Publications and source records attributed to José A. Cuesta.

At least 37 records · Page 2Linked to original sources

arXiv2018

On the networked architecture of genotype spaces and its critical effects on molecular evolution

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at the macroevolutionary, ecological, and molecular level. Actually, when the complex architecture of genotype spaces is taken into account, the evolutionary dynamics of molecular populations becomes intrinsically non-uniform, sharing deep qualitative and quantitative similarities with slowly driven physical systems: non-linear responses analogous to critical transitions, sudden state changes, or hysteresis, among others. Furthermore, the phenotypic plasticity inherent to genotypes transforms classical fitness landscapes into multiscapes where adaptation in response to an environmental change may be very fast. The quantitative nature of adaptive molecular processes is deeply dependent on a networks-of-networks multilayered structure of the map from genotype to function that we begin to unveil.

q-bio.PE↗

arXiv2017

Plankton: the paradox and the power law

Two basic features of assemblages of unicellular plankton: (1) their high biodiversity and (2) the power-law structure of their abundance, can be explained by an allometric scaling of cell growth and mortality with respect to cell size. To show this, we describe a numerical study of a size-structured, multispecies, population-dynamic model; the model has a single resource, supporting an arbitrary number of phytoplankton and zooplankton species. If the number of plankton species is large enough, the death rate of prey and cell growth rate of predators have approximate allometric scalings with cell size. Together, these scalings give rise to an equilibrium distribution of abundance near the power law, on which many species can coexist. Scalings of this kind cannot be achieved if the number of species is small. This suggests that the conjunction of species-richness and power-law structures in plankton communities is more than a coincidence. Although the exact allometric scalings used here should not be expected in practice, exclusion of species should be relatively slow if they lie close to the power law. Thus the forces needed to achieve coexistence could be effective, even if they are relatively weak.

q-bio.PE↗

arXiv2017

Enumerating secondary structures and structural moieties for circular RNAs

A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenotype. Here, we count the secondary structures of circular RNAs of length $n$ and calculate the asymptotic distributions of different structural moieties, such as stems or hairpin loops, by means of symbolic combinatorics. Circular RNAs differ in essential ways from their linear counterparts. From the mathematical viewpoint, the enumeration of the corresponding secondary structures demands the use of combinatorial techniques additional to those used for linear RNAs. The asymptotic number of secondary structures for circular RNAs grows as $a^nn^{-5/2}$, with a depending on particular constraints applied to the secondary structure. The abundance of any structural moiety is normally distributed in the limit $n\to\infty$, with a mean and a variance that increase linearly with $n$.

q-bio.PE↗

arXiv2016

Sheldon Spectrum and the Plankton Paradox: Two Sides of the Same Coin. A trait-based plankton size-spectrum model

The Sheldon spectrum describes a remarkable regularity in aquatic ecosystems: the biomass density as a function of logarithmic body mass is approximately constant over many orders of magnitude. While size-spectrum models have explained this phenomenon for assemblages of multicellular organisms, this paper introduces a species-resolved size-spectrum model to explain the phenomenon in unicellular plankton. A Sheldon spectrum spanning the cell-size range of unicellular plankton necessarily consists of a large number of coexisting species covering a wide range of characteristic sizes. The coexistence of many phytoplankton species feeding on a small number of resources is known as the Paradox of the Plankton. Our model resolves the paradox by showing that coexistence is facilitated by the allometric scaling of four physiological rates. Two of the allometries have empirical support, the remaining two emerge from predator-prey interactions exactly when the abundances follow a Sheldon spectrum. Our plankton model is a scale-invariant trait-based size-spectrum model: it describes the abundance of phyto- and zooplankton cells as a function of both size and species trait (the maximal size before cell division). It incorporates growth due to resource consumption and predation on smaller cells, death due to predation, and a flexible cell division process. We give analytic solutions at steady state for both the within-species size distributions and the relative abundances across species.

q-bio.PE↗

arXiv2015

General approach for dealing with dynamical systems with spatiotemporal periodicities

Dynamical systems often contain oscillatory forces or depend on periodic potentials. Time or space periodicity is reflected in the properties of these systems through a dependence on the parameters of their periodic terms. In this paper we provide a general theoretical framework for dealing with these kinds of systems, regardless of whether they are classical or quantum, stochastic or deterministic, dissipative or nondissipative, linear or nonlinear, etc. In particular, we are able to show that simple symmetry considerations determine, to a large extent, how their properties depend functionally on some of the parameters of the periodic terms. For the sake of illustration, we apply this formalism to find the functional dependence of the expectation value of the momentum of a Bose-Einstein condensate, described by the Gross-Pitaewskii equation, when it is exposed to a sawtooth potential whose amplitude is periodically modulated in time. We show that, by using this formalism, a small set of measurements is enough to obtain the functional form for a wide range of parameters. This can be very helpful when characterizing experimentally the response of systems for which performing measurements is costly or difficult.

cond-mat.stat-mech↗

arXiv2014

Evolution on neutral networks accelerates the ticking rate of the molecular clock

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 thegenotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NN). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NN with arbitrary topology we analyze the effect of assortativity, of NN (phenotype) fitness, and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive "phenotypic entrapment" entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.

q-bio.PE↗

arXiv2014

toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map

The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain evolutionary innovations. An exhaustive experimental characterization of the relationship between genotypes and phenotypes is at present out of reach. Therefore, several models mimicking that map have been proposed and investigated, leading to the identification of a number of general features: genotypes differ in their robustness to mutations, phenotypes are represented by a broadly varying number of genotypes, and simple point mutations seem to suffice to navigate the space of genotypes while maintaining a phenotype. However, most current models address only one level of the map (sequences and folded structures in RNA or proteins; networks of genes and their dynamical attractors; sets of chemical reactions and their ability to undergo molecular catalysis), such that many relevant questions cannot be addressed. Here we introduce toyLIFE, a multi-level model for the genotype-phenotype map based on simple genomes and interaction rules from which a complex behavior at upper levels emerges, remarkably plastic gene regulatory networks and metabolism. toyLIFE is a tool that permits the investigation of how different levels are coupled, in particular how and where do mutations affect phenotype or how the presence of certain metabolites determines the dynamics of toyLIFE gene regulatory networks. The possibilities of this model are not exhausted by the results presented in this contribution. It can be easily generalized to incorporate evolution through mutations that change genome length or through recombination, to consider gene duplication or deletion, and therefore to explore further properties of extended genotype-phenotype maps.

q-bio.PE↗

arXiv2014

Spreading of intolerance under economic stress: results from a model with reputation

When a population is engaged in successive prisoner's dilemmas, indirect reciprocity through reputation fosters cooperation through the emergence of moral and action rules. A simplified model has recently been proposed where individuals choose between helping or not others, and are judged good or bad for it by the rest of the population. The reputation so acquired will condition future actions. In this model, eight strategies (referred to as 'leading eight') enforce a high level of cooperation, generate high payoffs and are therefore resistant to invasions by other strategies. Here we show that, by assigning each individual one out of two labels that peers can distinguish (e.g., political ideas, religion, skin colour...) and allowing moral and action rules to depend on the label, intolerant behaviours can emerge within minorities under sufficient economic stress. We analyse the sets of conditions where this can happen and also discuss the circumstances under which tolerance can be restored. Our results agree with empirical observations that correlate intolerance and economic stress, and predict a correlation between the degree of tolerance of a population and its composition and ethical stance.

physics.soc-ph↗

arXiv2014

Time-shift invariance determines the functional shape of the current in dissipative rocking ratchets

Ratchets are devices able to rectify an otherwise oscillatory behavior by exploiting an asymmetry of the system. In rocking ratchets the asymmetry is induced through a proper choice of external forces and modulations of nonlinear symmetric potentials. The ratchet currents thus obtained in systems as different as semiconductors, Josephson junctions, optical lattices, or ferrofluids, show a set of universal features. A satisfactory explanation for them has challenged theorist for decades, and so far we still lack a general theory of this phenomenon. Here we provide such a theory by exploring ---through functional analysis--- the constraints that the simple assumption of time-shift invariance of the ratchet current imposes on its dependence on the external drivings. Because the derivation is based on so general a principle, the resulting expression is valid irrespective of the details and the nature of the physical systems to which it is applied, and of whether they are classical, quantum, or stochastic. The theory also explains deviations observed from universality under special conditions, and allows to make predictions of phenomena not yet observed in any experiment or simulation.

nlin.PS↗

arXiv2013

Comment on "Ratchet universality in the presence of thermal noise"

A recent paper [Phys. Rev. E 87, 062114 (2013)] presents numerical simulations on a system exhibiting directed ratchet transport of a driven overdamped Brownian particle subjected to a spatially periodic, symmetric potential. The authors claim that their simulations prove the existence of a universal waveform of the external force which optimally enhances directed transport, hence confirming the validity of a previous conjecture put forward by one of them in the limit of vanishing noise intensity. With minor corrections due to noise, the conjecture holds even in the presence of noise, according to the authors. On the basis of their results the authors claim that all previous theories, which predict a different optimal force waveform, are incorrect. In this comment we provide sufficient numerical evidence showing that there is no such universal force waveform and that the evidence obtained by the authors otherwise is due to a fortunate choice of the parameters. Our simulations also suggest that previous theories correctly predict the shape of the optimal waveform within their validity regime, namely when the forcing is weak. On the contrary, the aforementioned conjecture is shown to be wrong.

nlin.PS↗

arXiv2013

Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation

Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity are reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies, thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can resist the invasion of any other strategy. However, if actions are not always witnessed, cheaters (i.e., individuals with a probability of defecting regardless of the opponent's reputation) have a chance to defeat the stable strategies for some choices of the probabilities of cheating and of being witnessed. Remarkably, by analyzing this issue with adaptive dynamics we find that whether a honest population resists the invasion of cheaters is determined by a Hamilton-like rule---with the probability that the cheat is discovered playing the role of the relatedness parameter.

physics.soc-ph↗

arXiv2012

Stability and robustness analysis of cooperation cycles driven by destructive agents in finite populations

The emergence and promotion of cooperation are two of the main issues in evolutionary game theory, as cooperation is amenable to exploitation by defectors, which take advantage of cooperative individuals at no cost, dooming them to extinction. It has been recently shown that the existence of purely destructive agents (termed jokers) acting on the common enterprises (public goods games) can induce stable limit cycles among cooperation, defection, and destruction when infinite populations are considered. These cycles allow for time lapses in which cooperators represent a relevant fraction of the population, providing a mechanism for the emergence of cooperative states in nature and human societies. Here we study analytically and through agent-based simulations the dynamics generated by jokers in finite populations for several selection rules. Cycles appear in all cases studied, thus showing that the joker dynamics generically yields a robust cyclic behavior not restricted to infinite populations. We also compute the average time in which the population consists mostly of just one strategy and compare the results with numerical simulations.

physics.soc-ph↗

arXiv2012

On the coexistence of cooperators, defectors and conditional cooperators in the multiplayer iterated Prisoner's Dilemma

Recent experimental evidence [Grujić et al., PLoS ONE 5, e13749 (2010)] on the spatial Prisoner's Dilemma suggests that players choosing to cooperate or not on the basis of their previous action and the actions of their neighbors coexist with steady defectors and cooperators. We here study the coexistence of these three strategies in the multiplayer iterated Prisoner's Dilemma by means of the replicator dynamics. We consider groups with n = 2, 3, 4 and 5 players and compute the payoffs to every type of player as the limit of a Markov chain where the transition probabilities between actions are found from the corresponding strategies. We show that for group sizes up to n = 4 there exists an interior point in which the three strategies coexist, the corresponding basin of attraction decreasing with increasing number of players, whereas we have not been able to locate such a point for n = 5. We analytically show that in the infinite n limit no interior points can arise. We conclude by discussing the implications of this theoretical approach on the behavior observed in experiments.

q-bio.PE↗

arXiv2011

Ratchet effect on a relativistic particle driven by external forces

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 non-linear 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.

nlin.PS↗

arXiv2011

The Joker effect: cooperation driven by destructive agents

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.

physics.soc-ph↗

arXiv2009

Evolutionary game theory: Temporal and spatial effects beyond replicator dynamics

Evolutionary game dynamics is one of the most fruitful frameworks for studying evolution in different disciplines, from Biology to Economics. Within this context, the approach of choice for many researchers is the so-called replicator equation, that describes mathematically the idea that those individuals performing better have more offspring and thus their frequency in the population grows. While very many interesting results have been obtained with this equation in the three decades elapsed since it was first proposed, it is important to realize the limits of its applicability. One particularly relevant issue in this respect is that of non-mean-field effects, that may arise from temporal fluctuations or from spatial correlations, both neglected in the replicator equation. This review discusses these temporal and spatial effects focusing on the non-trivial modifications they induce when compared to the outcome of replicator dynamics. Alongside this question, the hypothesis of linearity and its relation to the choice of the rule for strategy update is also analyzed. The discussion is presented in terms of the emergence of cooperation, as one of the current key problems in Biology and in other disciplines.

q-bio.PE↗

arXiv2009

Effect of spatial structure on the evolution of cooperation

Spatial structure is known to have an impact on the evolution of cooperation, and so it has been intensively studied during recent years. Previous work has shown the relevance of some features, such as the synchronicity of the updating, the clustering of the network or the influence of the update rule. This has been done, however, for concrete settings with particular games, networks and update rules, with the consequence that some contradictions have arisen and a general understanding of these topics is missing in the broader context of the space of 2x2 games. To address this issue, we have performed a systematic and exhaustive simulation in the different degrees of freedom of the problem. In some cases, we generalize previous knowledge to the broader context of our study and explain the apparent contradictions. In other cases, however, our conclusions refute what seems to be established opinions in the field, as for example the robustness of the effect of spatial structure against changes in the update rule, or offer new insights into the subject, e.g. the relation between the intensity of selection and the asymmetry between the effects on games with mixed equilibria.

q-bio.PE↗

arXiv2009

Imperfect Imitation Can Enhance Cooperation

The promotion of cooperation on spatial lattices is an important issue in evolutionary game theory. This effect clearly depends on the update rule: it diminishes with stochastic imitative rules whereas it increases with unconditional imitation. To study the transition between both regimes, we propose a new evolutionary rule, which stochastically combines unconditional imitation with another imitative rule. We find that, surprinsingly, in many social dilemmas this rule yields higher cooperative levels than any of the two original ones. This nontrivial effect occurs because the basic rules induce a separation of timescales in the microscopic processes at cluster interfaces. The result is robust in the space of 2x2 symmetric games, on regular lattices and on scale-free networks.

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