Modern ecology has re-emphasized the need for a quantitative understanding of the original 'survival of the fittest theme' based on analyzis of the intricate trade-offs between competing evolutionary strategies that characterize the evolution of life. This is key to the understanding of species coexistence and ecosystem diversity under the omnipresent constraint of limited resources. In this work we propose an agent based model replicating a community of interacting individuals, e.g. plants in a forest, where all are competing for the same finite amount of resources and each competitor is characterized by a specific growth-reproduction strategy. We show that such an evolution dynamics drives the system towards a stationary state characterized by an emergent optimal strategy, which in turn depends on the amount of available resources the ecosystem can rely on. We find that the share of resources used by individuals is power-law distributed with an exponent directly related to the optimal strategy. The model can be further generalized to devise optimal strategies in social and economical interacting systems dynamics.
The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key must lie in the creation of increased variability in offspring, causing enhanced response to selection. Rigorously quantifying the effects of assorted mechanisms which might lead to such increased variability, and establishing that these beneficial effects outweigh the immediate costs of sexual reproduction has, however, proved problematic. Here we introduce…
In human societies the probability of strategy adoption from a given person may be affected by the personal features. Now we investigate how an artificially imposed restricted ability to reproduce, overruling ones fitness, affects an evolutionary process. For this purpose we employ the evolutionary prisoner's dilemma game on different complex graphs. Reproduction restrictions can have a facilitative effect on the evolution of cooperation that sets in irrespective of particularities of the interaction network. Indeed, an appropriate fraction of less fertile individuals may lead to full supremac…
The process of `Evolutionary Diffusion', i.e. reproduction with local mutation but without selection in a biological population, resembles standard Diffusion in many ways. However, Evolutionary Diffusion allows the formation of local peaks with a characteristic width that undergo drift, even in the infinite population limit. We analytically calculate the mean peak width and the effective random walk step size, and obtain the distribution of the peak width which has a power law tail. We find that independent local mutations act as a diffusion of interacting particles with increased stepsize.
We present an agent-based model inspired by the Evolutionary Minority Game (EMG), albeit strongly adapted to the case of competition for limited resources in ecology. The agents in this game become able, after some time, to predict the a priori best option as a result of an evolution-driven learning process. We show that a self-segregated social structure can emerge from this process, i.e., extreme learning strategies are always favoured while intermediate learning strategies tend to die out. This result may contribute to understanding some levels of organization and cooperative behaviour in e…
The paper discusses a connection between asymmetric reproduction -- that is reproduction in a parent-child relationship where the parent does not mutate during reproduction --, the fact that all non-viral lifeforms bear genes of their reproduction machinery and how this could relate to evolutionary mechanisms behind aging. In a highly simplified model of the evolution process rules are derived under which aging is an important factor of the adaption in the evolution process and what groups of life-forms necessarily have to age and where exceptions from that rule are possible.
The concept of fitness as a measure for a species's success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations, influence a species' prosperity and thereby its fitness. Interestingly, we find that not only larger growth rates but also reduced sensitivities to environmental changes substantially increase the fitness. Thereby, depending on the noise level of the environment, it might be an evolutionary successful strategy to minimize this sensitivity rather than to optimi…
A trademark of eusocial insect species is reproductive division of labor, in which workers forego their own reproduction while the queen produces almost all offspring. The presence of the queen is key for maintaining social harmony, but the specific role of the queen in the evolution of eusociality remains unclear. A long-discussed scenario is that a queen either behaviorally or chemically sterilizes her workers. However, the demographic and ecological conditions that enable such manipulation are unknown. Accordingly, we propose a simple model of evolutionary dynamics that is based on haplodip…
A proper understanding of the links between varying gene expression levels and complex trait adaptation is still lacking, despite recent advances in sequencing techniques leading to new insights on their importance in some evolutionary processes. This calls for extensions of the continuum-of-alleles framework first introduced by Kimura (1965) that bypass the classical Gaussian approximation. Here, we propose a novel mathematical framework to study the evolutionary dynamics of quantitative alleles for sexually reproducing populations under natural selection and competition through an integro-di…
Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show…
We investigate by means of a simple theoretical model the emergence of prime numbers as life cycles, as those seen for some species of cicadas. The cicadas, more precisely, the Magicicadas spend most of their lives below the ground and then emerge and die in a short period of time. The Magicicadas display an uncommon behavior: their emergence is synchronized and these periods are usually prime numbers. In the current work, we develop a spatially extended model at which preys and predators coexist and can change their evolutionary dynamics through the occurrence of mutations. We verified that p…
The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models were limited to asexual reproduction with inherited information coming from a single parent with no recombination. We present a general extension to sexual reproduction and an analytical solution for a particular but important case, the infinitesimal model of quantitative genetics which assumes traits to be normally distributed. We study with this model the co…
Empirical evidence suggesting that living systems might operate in the vicinity of critical points, at the borderline between order and disorder, has proliferated in recent years, with examples ranging from spontaneous brain activity to flock dynamics. However, a well-founded theory for understanding how and why interacting living systems could dynamically tune themselves to be poised in the vicinity of a critical point is lacking. Here we employ tools from statistical mechanics and information theory to show that complex adaptive or evolutionary systems can be much more efficient in coping wi…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these models revolve around speciation, dispersal, and extinction, but they usually neglect trophic structure. Here, we propose and study a spatially extended evolutionary food web model that allows us to study large spatial systems with several trophic layers. Our computer simulations show that the model gives rise simultaneously to several biodiversity patterns …
Cooperation and competition between pathogens can alter the amount of individuals affected by a co-infection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a co-evolutionary model where the simultaneous spreading is described by a two-pathogen susceptible-infected-recovered model in an either synergistic or competitive manner. At the end of each epidemic season, the pathogens species reproduce according to their fitness that, in turn, depends on the payoff accumulated during the spreading season in a hawk-and-dove game. This co-evolutionary model …
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and interactions of proteins encoded in their genomes. Simulating evolution of populations, we found that fitness increases in punctuated steps via epistatic events, leading to formation of stable and functionally interacting proteins. At low mutation rates, species - populations of organisms with identical genotypes - form, while at higher mutation rates, species ar…
Social insect colonies can be seen as a distinct form of biological organization because they function as superorganisms. Understanding how natural selection acts on the emergence and maintenance of these colonies remains a major question in evolutionary biology and ecology. Here, we explore this by using multi-type branching processes to calculate the basic reproductive ratios and the extinction probabilities for solitary versus eusocial reproductive strategies. In order to derive precise mathematical results, we use a simple haploid, asexual model. In general, we show that eusocial reproduct…
The 2014 epidemic of the Ebola virus is governed by a genetically diverse viral population. In the early Sierra Leone outbreak, a recent study has identified new mutations that generate genetically distinct sequence clades. Here we find evidence that major Sierra Leone clades have systematic differences in growth rate and reproduction number. If this growth heterogeneity remains stable, it will generate major shifts in clade frequencies and influence the overall epidemic dynamics on time scales within the current outbreak. Our method is based on simple summary statistics of clade growth, which…
This paper develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. We consider two forms of genome organization. In one case, we assume that the genome consists of two multi-gene chromosomes, while in the second case we assume that each gene defines a separate chromosome. If the organism has $ l $ homologous pairs that lack a functional copy of the given gene, then the fitness of the organism is $ κ_l $. The $ κ_l $ are assumed to be monotonically decreasing, so that $ κ_0 = 1 > κ_1 > κ_2 > ... >…
We present an individual based model of evolutionary ecology. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and the macro-evolutionary mode of the dynamics are emergent properties. The macro-dynamics exhibit intermittent two mode switching with a gradually decreasing extinction rate. The generated ecologies become gradually better adapted as well as more complex in a collective sense. The form of the species abundance curve compares well with observed functional forms. …
Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecologic…
A cell-molecular based evolutionary model of tumor development driven by a stochastic Moran birth-death process is developed, where each cell carries molecular information represented by a four-digit binary string, used to differentiate cells into 16 molecular types. The binary string value determines cell fitness, with lower fit cells (e.g. 0000) defined as healthy phenotypes, and higher fit cells (e.g. 1111) defined as malignant phenotypes. At each step of the birth-death process, the two phenotypic sub-populations compete in a prisoner's dilemma evolutionary game with healthy cells (coopera…
Our wellbeing depends as much on our personal success, as it does on the success of our society. The realization of this fact makes cooperation a very much needed trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remain elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. R…
The Penna bit-string model successfully encompasses many phenomena of population evolution, including inheritance, mutation, evolution and ageing. If we consider social interactions among individuals in the Penna model, the population will form a complex network. In this paper, we first modify the Verhulst factor to control only the birth rate, and introduce activity-based preferential reproduction of offspring in the Penna model. The social interactions among individuals are generated by both inheritance and activity-based preferential increase. Then we study the properties of the complex net…
Open-ended evolutionary dynamics remains an elusive goal for artificial evolutionary systems. Many ideas exist in the biological literature beyond the basic Darwinian requirements of variation, differential reproduction and inheritance. I argue that these ideas can be seen as aspects of five fundamental requirements for open-ended evolution: (1) robustly reproductive individuals, (2) a medium allowing the possible existence of a practically unlimited diversity of individuals and interactions, (3) individuals capable of producing more complex offspring, (4) mutational pathways to other viable i…
Several physical mechanisms have been proposed to explain allostery in proteins. They differ by the number of internal states that they assume a protein to occupy, leaving open the question of what controls the emergence of these distinct physical forms of allostery. Here, we analyze a simplified model of protein allostery under a range of physical and evolutionary constraints. We find that two archetypal mechanisms can emerge through evolution: a single-state mechanism where ligand binding induces a displacement along a soft normal mode or a multi-state mechanism where ligand binding induces …
In this paper, we inspect well-known population genetics and social dynamics models. In these models, interacting individuals, while participating in a self-organizing process, give rise to the emergence of complex behaviors and patterns. While one main focus in population genetics is on the adaptive behavior of a population, social dynamics is more often concerned with the splitting of a connected array of individuals into a state of global polarization, that is, the emergence of speciation. Applying computational and mathematical tools we show that the way the mechanisms of selection, intera…
Understanding the emergence and sustainability of cooperation is a fundamental problem in evolutionary biology and is frequently studied by the framework of evolutionary game theory. A very powerful mechanism to promote cooperation is network reciprocity, where the interaction patterns and opportunities for strategy spread of agents are constrained to limited sets of permanent interactions partners. Cooperation survives because it is possible for close-knit communities of cooperation to be shielded from invasion by defectors. Here we show that parameter ranges in which cooperation can survive …
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from non-life to "life," where the life phase is d…
In the evolutionary Prisoner's Dilemma (PD) game, agents play with each other and update their strategies in every generation according to some microscopic dynamical rule. In its spatial version, agents do not play with every other but, instead, interact only with their neighbors, thus mimicking the existing of a social or contact network that defines who interacts with whom. In this work, we explore evolutionary, spatial PD systems consisting of two types of agents, each with a certain update (reproduction, learning) rule. We investigate two different scenarios: in the first case, update rule…
In this work we study the process of mutant invasion on an example of a consumer-resource system with annual character of the behavior. Namely, individuals are active during seasons of fixed length separated by winter periods. All individuals die at the end of the season and the size of the next generation is determined by the number of offspring produced during the past season. The rate at which the consumers produce immature offspring depends on their internal energy which can be increased by feeding. The reproduction of the resource simply occurs at a constant rate. At the beginning, we con…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and minimizing its associated free energy, we find the structural properties which emerge as the selective pressure is increased and identify a phase transition from a random topology to a "segregated core" structure, where a smaller and more densely connected subset of the nodes is responsible for most of the regulation in the network. This segregated structure i…
We consider a particular instance of the lift of controlled systems recently proposed in the theory of irreversible thermodynamics and show that it leads to a variational principle for an optimal control in the sense of Pontryagin. Then we focus on two important applications: in thermodynamics and in evolutionary biology. In the thermodynamic context, we show that this principle provides a dynamical implementation of the Second Law, which stabilizes the equilibrium manifold of a system. In the evolutionary context, we discuss several interesting features: it provides a robust scheme for the co…
We consider a simple mathematical model of gradual Darwinian evolution in continuous time and continuous trait space, due to intraspecific competition for common resource in an asexually reproducing population in constant environment, while far from evolutionary stable equilibrium. The model admits exact analytical solution. In particular, Gaussian distribution of the trait emerges from generic initial conditions.
We study general properties of the leading eigenvalue $\overline{w}(q)$ of Eigen's evolutionary matrices depending on the probability $q$ of faithful reproduction. This is a linear algebra problem that has various applications in theoretical biology, including such diverse fields as the origin of life, evolution of cancer progression, and virus evolution. We present the exact expressions for $\overline{w}(q),\overline{w}'(q),\overline{w}''(q)$ for $q=0,0.5,1$ and prove that the absolute minimum of $\overline{w}(q)$, which always exists, belongs to the interval $[0,0.5]$. For the specific case …
We define a novel quantitative strategy inspired by the ecological notion of nestedness to single out the scale at which innovation complexity emerges from the aggregation of specialized building blocks. Our analysis not only suggests that the innovation space can be interpreted as a natural system in which advantageous capabilities are selected by evolutionary pressure, but also that the emerging structure of capabilities is not independent of the scale of observation at which they are observed. Expanding on this insight allows us to understand whether the capabilities characterizing the inno…
Game theory research on the snowdrift game has showed that gradual evolution of the continuously varying level of cooperation in joint enterprises can demonstrate evolutionary merging as well as evolutionary branching. However, little is known about the consequences of changes in diversity at the cooperation level. In the present study I consider effects of costly rewards on the continuous snowdrift game. I show that not evolutionary merging but evolutionary branching can promote the emergence of pool reward, which can then enhance social welfare.
University of Washington（华盛顿大学）；University of Calgary（卡尔加里大学）
We consider the effects of social learning on the individual learning and genetic evolution of a colony of artificial agents capable of genetic, individual and social modes of adaptation. We confirm that there is strong selection pressure to acquire traits of individual learning and social learning when these are adaptive traits. We show that selection pressure for learning of either kind can supress selection pressure for reproduction or greater fitness. We show that social learning differs from individual learning in that it can support a second evolutionary system that is decoupled from the…
Since its emergence in 1968, influenza A (H3N2) has evolved extensively in genotype and antigenic phenotype. Antigenic evolution occurs in the context of a two-dimensional 'antigenic map', while genetic evolution shows a characteristic ladder-like genealogical tree. Here, we use a large-scale individual-based model to show that evolution in a Euclidean antigenic space provides a remarkable correspondence between model behavior and the epidemiological, antigenic, genealogical and geographic patterns observed in influenza virus. We find that evolution away from existing human immunity results in…
We study the evolutionary Prisoner's Dilemma on two social networks obtained from actual relational data. We find very different cooperation levels on each of them that can not be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifical…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur, and via which sequence of steps is it most likely to emerge? For growing populations, these questions can be formulated in a general framework of branching processes spreading through a graph from a root to a target vertex. Cells have a particular fitness value on each vertex and can transition along edges at specific rates. Vertices represents cell states, sa…
