Bridging developmental systems theory and evolutionary psychology using dynamic optimization.

Science.gov (United States)

Frankenhuis, Willem E; Panchanathan, Karthik; Clark Barrett, H

2013-07-01

Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic optimization integrates developmental systems theorists' focus on dynamics and contingency with the 'design stance' of evolutionary psychology. It provides a theoretical framework as well as a set of tools for exploring the properties of developmental systems that natural selection might favor, given particular evolutionary ecologies. We also discuss limitations of the approach. © 2013 Blackwell Publishing Ltd.

Evolutionary dynamics of complex communications networks

CERN Document Server

Karyotis, Vasileios; Papavassiliou, Symeon

2013-01-01

Until recently, most network design techniques employed a bottom-up approach with lower protocol layer mechanisms affecting the development of higher ones. This approach, however, has not yielded fascinating results in the case of wireless distributed networks. Addressing the emerging aspects of modern network analysis and design, Evolutionary Dynamics of Complex Communications Networks introduces and develops a top-bottom approach where elements of the higher layer can be exploited in modifying the lowest physical topology-closing the network design loop in an evolutionary fashion similar to

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs

Science.gov (United States)

Stollmeier, Frank; Nagler, Jan

2018-02-01

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair," meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the prisoner's dilemma, and an unexpected selection reversal in the hawk-dove game.

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

Energy Technology Data Exchange (ETDEWEB)

Maljkovic-berry, Irina [Los Alamos National Laboratory; Athreya, Gayathri [Los Alamos National Laboratory; Daniels, Marcus [Los Alamos National Laboratory; Bruno, William [Los Alamos National Laboratory; Korber, Bette [Los Alamos National Laboratory; Kuiken, Carla [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory

2009-01-01

Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.

Evolutionary dynamics of mammalian karyotypes

Directory of Open Access Journals (Sweden)

Carlo Alberto Redi

2012-12-01

Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

Science.gov (United States)

Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

2017-07-01

Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary dynamics on infinite strategy spaces

OpenAIRE

Oechssler, Jörg; Riedel, Frank

1998-01-01

The study of evolutionary dynamics was so far mainly restricted to finite strategy spaces. In this paper we show that this unsatisfying restriction is unnecessary. We specify a simple condition under which the continuous time replicator dynamics are well defined for the case of infinite strategy spaces. Furthermore, we provide new conditions for the stability of rest points and show that even strict equilibria may be unstable. Finally, we apply this general theory to a number of applications ...

Population and evolutionary dynamics in spatially structured seasonally varying environments.

Science.gov (United States)

Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

2018-03-25

Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

Evolutionary dynamics of a smoothed war of attrition game.

Science.gov (United States)

Iyer, Swami; Killingback, Timothy

2016-05-07

In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary game dynamics in a growing structured population

Energy Technology Data Exchange (ETDEWEB)

Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza (Spain); Traulsen, Arne [Emmy-Noether Group for Evolutionary Dynamics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen (Germany)], E-mail: traulsen@evolbio.mpg.de

2009-08-15

We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

Evolutionary game dynamics in a growing structured population

International Nuclear Information System (INIS)

Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

2009-01-01

We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

Evolutionary dynamics of cooperation in neutral populations

Science.gov (United States)

Szolnoki, Attila; Perc, Matjaž

2018-01-01

Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

Evolutionary dynamics on graphs: Efficient method for weak selection

Science.gov (United States)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Spatial effect on stochastic dynamics of bistable evolutionary games

International Nuclear Information System (INIS)

So, Kohaku H Z; Ohtsuki, Hisashi; Kato, Takeo

2014-01-01

We consider the lifetimes of metastable states in bistable evolutionary games (coordination games), and examine how they are affected by spatial structure. A semiclassical approximation based on a path integral method is applied to stochastic evolutionary game dynamics with and without spatial structure, and the lifetimes of the metastable states are evaluated. It is shown that the population dependence of the lifetimes is qualitatively different in these two models. Our result indicates that spatial structure can accelerate the transitions between metastable states. (paper)

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

Science.gov (United States)

Ma, Zhanshan (Sam)

In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Czech Academy of Sciences Publication Activity Database

Kejnovský, Eduard; Leitch, I.J.; Leitch, A.R.

2009-01-01

Roč. 24, č. 10 (2009), s. 572-582 ISSN 0169-5347 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : genomes * evolutionary dynamics * recombination Subject RIV: BO - Biophysics Impact factor: 11.564, year: 2009

Evolutionary dynamics of incubation periods.

Science.gov (United States)

Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H

2017-12-21

The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.

Evolutionary dynamics under interactive diversity

Science.gov (United States)

Su, Qi; Li, Aming; Wang, Long

2017-10-01

As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

2016-09-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. © 2016 American Society of Plant Biologists. All rights reserved.

Evolutionary dynamics of protein domain architecture in plants

Directory of Open Access Journals (Sweden)

Zhang Xue-Cheng

2012-01-01

Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

Passivity analysis of higher order evolutionary dynamics and population games

KAUST Repository

Mabrok, Mohamed; Shamma, Jeff S.

2017-01-01

Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population

The stability concept of evolutionary game theory a dynamic approach

CERN Document Server

1992-01-01

These Notes grew from my research in evolutionary biology, specifically on the theory of evolutionarily stable strategies (ESS theory), over the past ten years. Personally, evolutionary game theory has given me the opportunity to transfer my enthusiasm for abstract mathematics to more practical pursuits. I was fortunate to have entered this field in its infancy when many biologists recognized its potential but were not prepared to grant it general acceptance. This is no longer the case. ESS theory is now a rapidly expanding (in both applied and theoretical directions) force that no evolutionary biologist can afford to ignore. Perhaps, to continue the life-cycle metaphor, ESS theory is now in its late adolescence and displays much of the optimism and exuberance of this exciting age. There are dangers in writing a text about a theory at this stage of development. A comprehensive treatment would involve too many loose ends for the reader to appreciate the central message. On the other hand, the current central m...

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

2016-01-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

A Self-adaptive Dynamic Evaluation Model for Diabetes Mellitus, Based on Evolutionary Strategies

Directory of Open Access Journals (Sweden)

An-Jiang Lu

2016-03-01

Full Text Available In order to evaluate diabetes mellitus objectively and accurately, this paper builds a self-adaptive dynamic evaluation model for diabetes mellitus, based on evolutionary strategies. First of all, on the basis of a formalized description of the evolutionary process of diabetes syndromes, using a state transition function, it judges whether a disease is evolutionary, through an excitation parameter. It then, provides evidence for the rebuilding of the evaluation index system. After that, by abstracting and rebuilding the composition of evaluation indexes, it makes use of a heuristic algorithm to determine the composition of the evolved evaluation index set of diabetes mellitus, It then, calculates the weight of each index in the evolved evaluation index set of diabetes mellitus by building a dependency matrix and realizes the self-adaptive dynamic evaluation of diabetes mellitus under an evolutionary environment. Using this evaluation model, it is possible to, quantify all kinds of diagnoses and treatment experiences of diabetes and finally to adopt ideal diagnoses and treatment measures for different patients with diabetics.

A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

Science.gov (United States)

Lin, XuXun; Yuan, PengCheng

2018-01-01

In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

Science.gov (United States)

Turcotte, Martin M; Reznick, David N; Daniel Hare, J

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

A quantitative evolutionary theory of adaptive behavior dynamics.

Science.gov (United States)

McDowell, J J

2013-10-01

The idea that behavior is selected by its consequences in a process analogous to organic evolution has been discussed for over 100 years. A recently proposed theory instantiates this idea by means of a genetic algorithm that operates on a population of potential behaviors. Behaviors in the population are represented by numbers in decimal integer (phenotypic) and binary bit string (genotypic) forms. One behavior from the population is emitted at random each time tick, after which a new population of potential behaviors is constructed by recombining parent behavior bit strings. If the emitted behavior produced a benefit to the organism, then parents are chosen on the basis of their phenotypic similarity to the emitted behavior; otherwise, they are chosen at random. After parent behavior recombination, the population is subjected to a small amount of mutation by flipping random bits in the population's bit strings. The behavior generated by this process of selection, reproduction, and mutation reaches equilibrium states that conform to every empirically valid equation of matching theory, exactly and without systematic error. These equations are known to describe the behavior of many vertebrate species, including humans, in a variety of experimental, naturalistic, natural, and social environments. The evolutionary theory also generates instantaneous dynamics and patterns of preference change in constantly changing environments that are consistent with the dynamics of live-organism behavior. These findings support the assertion that the world of behavior we observe and measure is generated by evolutionary dynamics. PsycINFO Database Record (c) 2013 APA, all rights reserved

The Evolutionary Dynamics of Biofuel Value Chains

DEFF Research Database (Denmark)

Ponte, Stefano

2014-01-01

In this paper I propose to push the frontier of global value chain (GVC) governance analysis through the concept of ‘polarity’. Much of the existing GVC literature has focused on ‘unipolar’ value chains, where one group of ‘lead firms’ inhabiting a specific function in a chain plays a dominant role...... in governing it. Some scholars have explored the dynamics of governance in GVCs characterized as ‘bipolar’, where two sets of actors in different functional positions both drive the chain. I expand this direction further to suggest conceptualizing governance within a continuum between unipolarity...... and multipolarity. Empirically, I do so by examining the evolutionary dynamics of governance in biofuel value chains, with specific focus on the key regulatory and institutional features that facilitated their emergence and expansion. First, I examine the formation, evolution, and governance of three national/regional...

Attractive evolutionary equilibria

OpenAIRE

Roorda, Berend; Joosten, Reinoud

2011-01-01

We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary dynamics. For instance, each attractive evolutionarily stable strategy is an attractive evolutionarily stable equilibrium for certain barycentric ray-projection dynamics, and vice versa.

Evolutionary Design of Both Topologies and Parameters of a Hybrid Dynamical System

DEFF Research Database (Denmark)

Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

2012-01-01

This paper investigates the issue of evolutionary design of open-ended plants for hybrid dynamical systems--i.e. both their topologies and parameters. Hybrid bond graphs are used to represent dynamical systems involving both continuous and discrete system dynamics. Genetic programming, with some...... of hybrid dynamical systems that fulfill predefined design specifications. A comprehensive investigation of a case study of DC-DC converter design demonstrates the feasibility and effectiveness of the HBGGP approach. Important characteristics of the approach are also discussed, with some future research...

Unexpected Nongenetic Individual Heterogeneity and Trait Covariance in Daphnia and Its Consequences for Ecological and Evolutionary Dynamics.

Science.gov (United States)

Cressler, Clayton E; Bengtson, Stefan; Nelson, William A

2017-07-01

Individual differences in genetics, age, or environment can cause tremendous differences in individual life-history traits. This individual heterogeneity generates demographic heterogeneity at the population level, which is predicted to have a strong impact on both ecological and evolutionary dynamics. However, we know surprisingly little about the sources of individual heterogeneity for particular taxa or how different sources scale up to impact ecological and evolutionary dynamics. Here we experimentally study the individual heterogeneity that emerges from both genetic and nongenetic sources in a species of freshwater zooplankton across a large gradient of food quality. Despite the tight control of environment, we still find that the variation from nongenetic sources is greater than that from genetic sources over a wide range of food quality and that this variation has strong positive covariance between growth and reproduction. We evaluate the general consequences of genetic and nongenetic covariance for ecological and evolutionary dynamics theoretically and find that increasing nongenetic variation slows evolution independent of the correlation in heritable life-history traits but that the impact on ecological dynamics depends on both nongenetic and genetic covariance. Our results demonstrate that variation in the relative magnitude of nongenetic versus genetic sources of variation impacts the predicted ecological and evolutionary dynamics.

Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.

Directory of Open Access Journals (Sweden)

Guillaume Chevereau

Full Text Available The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the "morbidostat", a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations-an almost paradoxical behavior since this drug causes DNA damage and increases the mutation

Essays on nonlinear evolutionary game dynamics

NARCIS (Netherlands)

Ochea, M.I.

2010-01-01

Evolutionary game theory has been viewed as an evolutionary repair of rational actor game theory in the hope that a population of boundedly rational players may attain convergence to classic rational solutions, such as the Nash Equilibrium, via some learning or evolutionary process. In this thesis

Application of network methods for understanding evolutionary dynamics in discrete habitats.

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Greenbaum, Gili; Fefferman, Nina H

2017-06-01

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

Science.gov (United States)

Catania, Francesco; Lynch, Michael

2010-05-04

In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

Falsification of matching theory and confirmation of an evolutionary theory of behavior dynamics in a critical experiment.

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McDowell, J J; Calvin, Olivia L; Hackett, Ryan; Klapes, Bryan

2017-07-01

Two competing predictions of matching theory and an evolutionary theory of behavior dynamics, and one additional prediction of the evolutionary theory, were tested in a critical experiment in which human participants worked on concurrent schedules for money (Dallery et al., 2005). The three predictions concerned the descriptive adequacy of matching theory equations, and of equations describing emergent equilibria of the evolutionary theory. Tests of the predictions falsified matching theory and supported the evolutionary theory. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolutionary Game Dynamics in a Fitness-Dependent Wright-Fisher Process with Noise

International Nuclear Information System (INIS)

Quan Ji; Wang Xianjia

2011-01-01

Evolutionary game dynamics in finite size populations can be described by a fitness-dependent Wright-Fisher process. We consider symmetric 2x2 games in a well-mixed population. In our model, two parameters to describe the level of player's rationality and noise intensity in environment are introduced. In contrast with the fixation probability method that used in a noiseless case, the introducing of the noise intensity parameter makes the process an ergodic Markov process and based on the limit distribution of the process, we can analysis the evolutionary stable strategy (ESS) of the games. We illustrate the effects of the two parameters on the ESS of games using the Prisoner's dilemma games (PDG) and the snowdrift games (SG). We also compare the ESS of our model with that of the replicator dynamics in infinite size populations. The results are determined by simulation experiments. (general)

Pseudorandom numbers: evolutionary models in image processing, biology, and nonlinear dynamic systems

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Yaroslavsky, Leonid P.

1996-11-01

We show that one can treat pseudo-random generators, evolutionary models of texture images, iterative local adaptive filters for image restoration and enhancement and growth models in biology and material sciences in a unified way as special cases of dynamic systems with a nonlinear feedback.

Long range personalized cancer treatment strategies incorporating evolutionary dynamics.

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Yeang, Chen-Hsiang; Beckman, Robert A

2016-10-22

Current cancer precision medicine strategies match therapies to static consensus molecular properties of an individual's cancer, thus determining the next therapeutic maneuver. These strategies typically maintain a constant treatment while the cancer is not worsening. However, cancers feature complicated sub-clonal structure and dynamic evolution. We have recently shown, in a comprehensive simulation of two non-cross resistant therapies across a broad parameter space representing realistic tumors, that substantial improvement in cure rates and median survival can be obtained utilizing dynamic precision medicine strategies. These dynamic strategies explicitly consider intratumoral heterogeneity and evolutionary dynamics, including predicted future drug resistance states, and reevaluate optimal therapy every 45 days. However, the optimization is performed in single 45 day steps ("single-step optimization"). Herein we evaluate analogous strategies that think multiple therapeutic maneuvers ahead, considering potential outcomes at 5 steps ahead ("multi-step optimization") or 40 steps ahead ("adaptive long term optimization (ALTO)") when recommending the optimal therapy in each 45 day block, in simulations involving both 2 and 3 non-cross resistant therapies. We also evaluate an ALTO approach for situations where simultaneous combination therapy is not feasible ("Adaptive long term optimization: serial monotherapy only (ALTO-SMO)"). Simulations utilize populations of 764,000 and 1,700,000 virtual patients for 2 and 3 drug cases, respectively. Each virtual patient represents a unique clinical presentation including sizes of major and minor tumor subclones, growth rates, evolution rates, and drug sensitivities. While multi-step optimization and ALTO provide no significant average survival benefit, cure rates are significantly increased by ALTO. Furthermore, in the subset of individual virtual patients demonstrating clinically significant difference in outcome between

The co-evolutionary dynamics of directed network of spin market agents

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Horváth, Denis; Kuscsik, Zoltán; Gmitra, Martin

2006-09-01

The spin market model [S. Bornholdt, Int. J. Mod. Phys. C 12 (2001) 667] is generalized by employing co-evolutionary principles, where strategies of the interacting and competitive traders are represented by local and global couplings between the nodes of dynamic directed stochastic network. The co-evolutionary principles are applied in the frame of Bak-Sneppen self-organized dynamics [P. Bak, K. Sneppen, Phys. Rev. Lett. 71 (1993) 4083] that includes the processes of selection and extinction actuated by the local (node) fitness. The local fitness is related to orientation of spin agent with respect to the instant magnetization. The stationary regime is formed due to the interplay of self-organization and adaptivity effects. The fat tailed distributions of log-price returns are identified numerically. The non-trivial model consequence is the evidence of the long time market memory indicated by the power-law range of the autocorrelation function of volatility with exponent smaller than one. The simulations yield network topology with broad-scale node degree distribution characterized by the range of exponents 1.3social networks.

Ecological interactions drive evolutionary loss of traits.

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Ellers, Jacintha; Kiers, E Toby; Currie, Cameron R; McDonald, Bradon R; Visser, Bertanne

2012-10-01

Loss of traits can dramatically alter the fate of species. Evidence is rapidly accumulating that the prevalence of trait loss is grossly underestimated. New findings demonstrate that traits can be lost without affecting the external phenotype, provided the lost function is compensated for by species interactions. This is important because trait loss can tighten the ecological relationship between partners, affecting the maintenance of species interactions. Here, we develop a new perspective on so-called `compensated trait loss' and how this type of trait loss may affect the evolutionary dynamics between interacting organisms. We argue that: (1) the frequency of compensated trait loss is currently underestimated because it can go unnoticed as long as ecological interactions are maintained; (2) by analysing known cases of trait loss, specific factors promoting compensated trait loss can be identified and (3) genomic sequencing is a key way forwards in detecting compensated trait loss. We present a comprehensive literature survey showing that compensated trait loss is taxonomically widespread, can involve essential traits, and often occurs as replicated evolutionary events. Despite its hidden nature, compensated trait loss is important in directing evolutionary dynamics of ecological relationships and has the potential to change facultative ecological interactions into obligatory ones. © 2012 Blackwell Publishing Ltd/CNRS.

Biotic response to late Quaternary rapid climate switches in Santa Barbara Basin: Ecological and evolutionary implications

International Nuclear Information System (INIS)

Cannariato, K.G.; Kennett, J.P.; Behl, R.J.

1999-01-01

Benthic foraminiferal assemblages from Santa Barbara Basin exhibit major faunal and ecological switches associated with late Quaternary millennial- to decadal-scale global climate oscillations. Repeated turnovers of entire faunas occurred rapidly (<40--400 yr) without extinction or speciation in conjunction with Dansgaard-Oeschger shifts in thermohaline circulation, ventilation, and climate, confirming evolutionary model predictions of Roy et al. Consistent faunal successions of dysoxic taxa during successive interstadials reflect the extreme sensitivity and adaptation of the benthic ecosystem to the rapid environmental changes that marked the late Quaternary and possibly other transitional intervals in the history of the Earth's ocean-atmosphere-cryosphere system. These data support the hypothesis that broad segments of the biosphere are well adapted to rapid climate change

Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change†

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Xie, Gary; Keyhani, Nemat O.; Bonner; Jensen, Roy A.

2003-01-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

Ancient origin of the tryptophan operon and the dynamics of evolutionary change.

Science.gov (United States)

Xie, Gary; Keyhani, Nemat O; Bonner, Carol A; Jensen, Roy A

2003-09-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

Science.gov (United States)

Solé, Ricard V; Montoya, José M; Erwin, Douglas H

2002-01-01

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems. PMID:12079530

Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

Directory of Open Access Journals (Sweden)

Lynch Michael

2010-05-01

Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

Attractive evolutionary equilibria

NARCIS (Netherlands)

Joosten, Reinoud A.M.G.; Roorda, Berend

2011-01-01

We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary

Home and away- the evolutionary dynamics of homing endonucleases

Directory of Open Access Journals (Sweden)

Barzel Adi

2011-11-01

Full Text Available Abstract Background Homing endonucleases (HEases are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases have been the focus of extensive research due to their promising potential use in gene targeting procedures for the treatment of genetic diseases and for the genetic engineering of crop, animal models and cell lines. Results Using mathematical analysis and computational modeling, we present here a novel account for the evolution and population dynamics of HEase genes (HEGs. We describe HEGs as paradoxical selfish elements whose long-term persistence in a single population relies on low transmission rates and a positive correlation between transmission efficiency and toxicity. Conclusion Plausible conditions allow HEGs to sustain at high frequency through long evolutionary periods, with the endonuclease frequency being either at equilibrium or periodically oscillating. The predictions of our model may prove important not only for evolutionary theory but also for gene therapy and bio-engineering applications of HEases.

The evolutionary ecology of clonally propagated domesticated plants.

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McKey, Doyle; Elias, Marianne; Pujol, Benoît; Duputié, Anne

2010-04-01

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

Incorporating evolutionary principles into environmental management and policy

DEFF Research Database (Denmark)

Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

2011-01-01

As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

Learning and anticipation in online dynamic optimization with evolutionary algorithms: The stochastic case

NARCIS (Netherlands)

P.A.N. Bosman (Peter); J.A. La Poutré (Han); D. Thierens (Dirk)

2007-01-01

htmlabstractThe focus of this paper is on how to design evolutionary algorithms (EAs) for solving stochastic dynamic optimization problems online, i.e. as time goes by. For a proper design, the EA must not only be capable of tracking shifting optima, it must also take into account the future

Co-evolutionary dynamics of the human-environment system in the Heihe River basin in the past 2000years.

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Lu, Zhixiang; Wei, Yongping; Feng, Qi; Xie, Jiali; Xiao, Honglang; Cheng, Guodong

2018-09-01

There is limited quantitative understanding of interactions between human and environmental systems over the millennial scale. We aim to reveal the co-evolutionary dynamics of the human-environment system in a river basin by simulating the water use and net primary production (NPP) allocation for human and environmental systems over the last 2000years in Heihe River basin (HRB) in northwest China. We partition the catchment total evapotranspiration (ET) into ET for human and environmental systems with a social-hydrological framework and estimate the NPP for human and environmental systems using the Box-Lieth model, then classify the co-evolutionary processes of the human-environment system into distinct phases using the rate of changes of NPP over time, and discover the trade-offs or synergies relationships between them based on the elasticity of change of the NPP for humans to the change of NPP for environment. The co-evolutionary dynamics of human-environment system in the HRB can be divided into four periods, including: Phase I (Han Dynasty-Yuan Dynasty): predevelopment characterized by nearly no trade-offs between human and environment; Phase II (Yuan Dynasty-RC): slow agricultural development: characterized by a small human win due to small trade-offs between human and environment; Phase III (RC-2000): rapid agricultural development: characterized by a large human win due to large trade-offs between human and environment, and Phase IV (2000-2010): a rebalance characterized by large human wins with a small-environment win due to synergies, although these occurred very occasionally. This study provides a quantitative approach to describe the co-evolution of the human-environment system from the perspective of trade-offs and synergies in the millennial scale for the first time. The relationships between humans and environment changed from trade-off to synergy with the implementation of the water reallocation scheme in 2000. These findings improve the

Wolbachia age-sex-specific density in Aedes albopictus: a host evolutionary response to cytoplasmic incompatibility?

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Pablo Tortosa

2010-03-01

Full Text Available Wolbachia bacteria have invaded many arthropod species by inducing Cytoplasmic Incompatibility (CI. These symbionts represent fascinating objects of study for evolutionary biologists, but also powerful potential biocontrol agents. Here, we assess the density dynamics of Wolbachia infections in males and females of the mosquito Aedes albopitcus, an important vector of human pathogens, and interpret the results within an evolutionary framework.Wolbachia densities were measured in natural populations and in age controlled mosquitoes using quantitative PCR. We show that the density dynamics of the wAlbA Wolbachia strain infecting Aedes albopictus drastically differ between males and females, with a very rapid decay of infection in males only.Theory predicts that Wolbachia and its hosts should cooperate to improve the transmission of infection to offspring, because only infected eggs are protected from the effects of CI. However, incompatible matings effectively lower the fertility of infected males, so that selection acting on the host genome should tend to reduce the expression of CI in males, for example, by reducing infection density in males before sexual maturation. The rapid decay of one Wolbachia infection in Aedes albopictus males, but not in females, is consistent with this prediction. We suggest that the commonly observed reduction in CI intensity with male age reflects a similar evolutionary process. Our results also highlight the importance of monitoring infection density dynamics in both males and females to assess the efficiency of Wolbachia-based control strategies.

Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis

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Fujita, Hironori; Aoki, Seishiro; Kawaguchi, Masayoshi

2014-01-01

The stabilization of host–symbiont mutualism against the emergence of parasitic individuals is pivotal to the evolution of cooperation. One of the most famous symbioses occurs between legumes and their colonizing rhizobia, in which rhizobia extract nutrients (or benefits) from legume plants while supplying them with nitrogen resources produced by nitrogen fixation (or costs). Natural environments, however, are widely populated by ineffective rhizobia that extract benefits without paying costs and thus proliferate more efficiently than nitrogen-fixing cooperators. How and why this mutualism becomes stabilized and evolutionarily persists has been extensively discussed. To better understand the evolutionary dynamics of this symbiosis system, we construct a simple model based on the continuous snowdrift game with multiple interacting players. We investigate the model using adaptive dynamics and numerical simulations. We find that symbiotic evolution depends on the cost–benefit balance, and that cheaters widely emerge when the cost and benefit are similar in strength. In this scenario, the persistence of the symbiotic system is compatible with the presence of cheaters. This result suggests that the symbiotic relationship is robust to the emergence of cheaters, and may explain the prevalence of cheating rhizobia in nature. In addition, various stabilizing mechanisms, such as partner fidelity feedback, partner choice, and host sanction, can reinforce the symbiotic relationship by affecting the fitness of symbionts in various ways. This result suggests that the symbiotic relationship is cooperatively stabilized by various mechanisms. In addition, mixed nodule populations are thought to encourage cheater emergence, but our model predicts that, in certain situations, cheaters can disappear from such populations. These findings provide a theoretical basis of the evolutionary dynamics of legume–rhizobia symbioses, which is extendable to other single-host, multiple

Fast stochastic algorithm for simulating evolutionary population dynamics

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Tsimring, Lev; Hasty, Jeff; Mather, William

2012-02-01

Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

Organisational Factors of Rapid Growth of Slovenian Dynamic Enterprises

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Pšeničny Viljem

2013-01-01

Full Text Available The authors provide key findings on the internal and external environmental factors of growth that affect the rapid growth of dynamic enterprises in relation to individual key organisational factors or functions. The key organisational relationships in a growing enterprise are upgraded with previous research findings and identified key factors of rapid growth through qualitative and quantitative analysis based on the analysis of 4,511 dynamic Slovenian enterprises exhibiting growth potential. More than 250 descriptive attributes of a sample of firms from 2011 were also used for further qualitative analysis and verification of key growth factors. On the basis of the sample (the study was conducted with 131 Slovenian dynamic enterprises, the authors verify whether these factors are the same as the factors that were studied in previous researches. They also provide empirical findings on rapid growth factors in relation to individual organisational functions: administration - management - implementation (entrepreneur - manager - employees. Through factor analysis they look for the correlation strength between individual variables (attributes that best describe each factor of rapid growth and that relate to the aforementioned organisational functions in dynamic enterprises. The research findings on rapid growth factors offer companies the opportunity to consider these factors during the planning and implementation phases of their business, to choose appropriate instruments for the transition from a small fast growing firm to a professionally managed growing company, to stimulate growth and to choose an appropriate growth strategy and organisational factors in order to remain, or become, dynamic enterprises that can further contribute to the preservation, growth and development of the Slovenian economy

A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

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Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

2013-05-01

The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

OpenAIRE

Timothée Bonnet; Peter Wandeler; Glauco Camenisch; Erik Postma

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions: Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called ‘stasis paradox’ highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic enviro...

Mean-field approximations of fixation time distributions of evolutionary game dynamics on graphs

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Ying, Li-Min; Zhou, Jie; Tang, Ming; Guan, Shu-Guang; Zou, Yong

2018-02-01

The mean fixation time is often not accurate for describing the timescales of fixation probabilities of evolutionary games taking place on complex networks. We simulate the game dynamics on top of complex network topologies and approximate the fixation time distributions using a mean-field approach. We assume that there are two absorbing states. Numerically, we show that the mean fixation time is sufficient in characterizing the evolutionary timescales when network structures are close to the well-mixing condition. In contrast, the mean fixation time shows large inaccuracies when networks become sparse. The approximation accuracy is determined by the network structure, and hence by the suitability of the mean-field approach. The numerical results show good agreement with the theoretical predictions.

Evolutionary Dynamics of Collective Action in Structured Populations

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Santos, Marta Daniela de Almeida

The pervasiveness of cooperation in Nature is not easily explained. If evolution is characterized by competition and survival of the fittest, why should selfish individuals cooperate with each other? Evolutionary Game Theory (EGT) provides a suitable mathematical framework to study this problem, central to many areas of science. Conventionally, interactions between individuals are modeled in terms of one-shot, symmetric 2-Person Dilemmas of Cooperation, but many real-life situations involve decisions within groups with more than 2 individuals, which are best-dealt in the framework of N-Person games. In this Thesis, we investigate the evolutionary dynamics of two paradigmatic collective social dilemmas - the N-Person Prisoner's Dilemma (NPD) and the N-Person Snowdrift Game (NSG) on structured populations, modeled by networks with diverse topological properties. Cooperative strategies are just one example of the many traits that can be transmitted on social networks. Several recent studies based on empirical evidence from a medical database have suggested the existence of a 3 degrees of influence rule, according to which not only our "friends", but also our friends' friends, and our friends' friends' friends, have a non-trivial influence on our decisions. We investigate the degree of peer influence that emerges from the spread of cooperative strategies, opinions and diseases on populations with distinct underlying networks of contacts. Our results show that networks naturally entangle individuals into interactions of many-body nature and that for each network class considered different processes lead to identical degrees of influence. None

Analysis of Ant Colony Optimization and Population-Based Evolutionary Algorithms on Dynamic Problems

DEFF Research Database (Denmark)

Lissovoi, Andrei

the dynamic optimum for finite alphabets up to size μ, while MMAS is able to do so for any finite alphabet size. Parallel Evolutionary Algorithms on Maze. We prove that while a (1 + λ) EA is unable to track the optimum of the dynamic fitness function Maze for offspring population size up to λ = O(n1-ε......This thesis presents new running time analyses of nature-inspired algorithms on various dynamic problems. It aims to identify and analyse the features of algorithms and problem classes which allow efficient optimization to occur in the presence of dynamic behaviour. We consider the following...... settings: λ-MMAS on Dynamic Shortest Path Problems. We investigate how in-creasing the number of ants simulated per iteration may help an ACO algorithm to track optimum in a dynamic problem. It is shown that while a constant number of ants per-vertex is sufficient to track some oscillations, there also...

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

Science.gov (United States)

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Dynamic and photometric evolutionary models of tidal tails and ripples

International Nuclear Information System (INIS)

Wallin, J.F.

1989-01-01

An investigation into the causes of star formation in tidal tails has been conducted using a restricted three-body dynamical model in conjunction with a broad-band photometric evolutionary code. In these models, regions of compression form inside the disk and along the tidal tail and tidal bridge. The effects these density changes have on the colors of the tidal features are examined with a broad-band photometric evolutionary code. A spiral galaxy population is synthesized and the effects of modest changes in the star formation rate are explored. Limits on the density changes needed to make detectable changes in the colors are calculated using a Schmidt (1959) law. These models suggest that the blue colors and knotty features observed in the tidal features of some galaxies result from increased rates of star formation induced by tidally produced density increases. Limitations of this model are discussed along with photometric evolutionary models based on the density evolution in the tails. The Lynds and Toomre (1976) interpretation of ring galaxies as the natural result of a nearly head-on collision between a disk galaxy and a companion galaxy has become widely accepted. Similarly, Quinn's (1984) interpretation of the shells in elliptical galaxies as the aftermath of the cannibalization of a low-mass companion has been quite successful in accounting for the observations. Restricted three-body calculations of high inclination, low impact parameter encounters demonstrate that the shell-like ripples observed in a number of disk galaxies can also be produced as collisional artifacts from internal oscillations much as in ring galaxies

Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

Science.gov (United States)

Krasny, Darren P; Orin, David E

2004-08-01

Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

Effects of Gas Dynamics on Rapidly Collapsing Bubbles

OpenAIRE

Bauman, Spenser; Fomitchev-Zamilov, Max

2013-01-01

The dynamics of rapidly collapsing bubbles are of great interest due to the high degree of energy focusing that occurs withing the bubble. Molecular dynamics provides a way to model the interior of the bubble and couple the gas dynamics with the equations governing the bubble wall. While much theoretical work has been done to understand how a bubble will respond to an external force, the internal dynamics of the gas system are usually simplified greatly in such treatments. This paper shows ho...

Dynamics, morphogenesis and convergence of evolutionary quantum Prisoner's Dilemma games on networks

Science.gov (United States)

Yong, Xi

2016-01-01

The authors proposed a quantum Prisoner's Dilemma (PD) game as a natural extension of the classic PD game to resolve the dilemma. Here, we establish a new Nash equilibrium principle of the game, propose the notion of convergence and discover the convergence and phase-transition phenomena of the evolutionary games on networks. We investigate the many-body extension of the game or evolutionary games in networks. For homogeneous networks, we show that entanglement guarantees a quick convergence of super cooperation, that there is a phase transition from the convergence of defection to the convergence of super cooperation, and that the threshold for the phase transitions is principally determined by the Nash equilibrium principle of the game, with an accompanying perturbation by the variations of structures of networks. For heterogeneous networks, we show that the equilibrium frequencies of super-cooperators are divergent, that entanglement guarantees emergence of super-cooperation and that there is a phase transition of the emergence with the threshold determined by the Nash equilibrium principle, accompanied by a perturbation by the variations of structures of networks. Our results explore systematically, for the first time, the dynamics, morphogenesis and convergence of evolutionary games in interacting and competing systems. PMID:27118882

Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

Science.gov (United States)

Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

2012-01-01

Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics

Science.gov (United States)

Scott, Adam; King, Dawn; Bahar, Sonya

2013-03-01

An evolutionary model was recently introduced for sympatric, phenotypic evolution over a variable fitness landscape with assortative mating (Dees & Bahar 2010). Organisms in the model are described by coordinates in a two-dimensional phenotype space, born at random coordinates with limited variation from their parents as determined by a mutation parameter, mutability. The model has been extended to include both neutral evolution and asexual reproduction in Scott et al (submitted). It has been demonstrated that a second order, non-equilibrium phase transition occurs for the temporal dynamics as the mutability is varied, for both the original model and for neutral conditions. This transition likely belongs to the directed percolation universality class. In contrast, the spatial dynamics of the model shows characteristics of an ordinary percolation phase transition. Here, we characterize the phase transitions exhibited by this model by determining critical exponents for the relaxation times, characteristic lengths, and cluster (species) mass distributions. Missouri Research Board; J.S. McDonnell Foundation

Global analyses of evolutionary dynamics and exhaustive search for social norms that maintain cooperation by reputation.

Science.gov (United States)

Ohtsuki, Hisashi; Iwasa, Yoh

2007-02-07

Reputation formation is a key to understanding indirect reciprocity. In particular, the way to assign reputation to each individual, namely a norm that describes who is good and who is bad, greatly affects the possibility of sustained cooperation in the population. Previously, we have exhaustively studied reputation dynamics that are able to maintain a high level of cooperation at the ESS. However, this analysis examined the stability of monomorphic population and did not investigate polymorphic population where several strategies coexist. Here, we study the evolutionary dynamics of multiple behavioral strategies by replicator dynamics. We exhaustively study all 16 possible norms under which the reputation of a player in the next round is determined by the action of the self and the reputation of the opponent. For each norm, we explore evolutionary dynamics of three strategies: unconditional cooperators, unconditional defectors, and conditional cooperators. We find that only three norms, simple-standing, Kandori, and shunning, can make conditional cooperation evolutionarily stable, hence, realize sustained cooperation. The other 13 norms, including scoring, ultimately lead to the invasion by defectors. Also, we study the model in which private reputation errors exist to a small extent. In this case, we find the stable coexistence of unconditional and conditional cooperators under the three norms.

The puzzle of partial migration: Adaptive dynamics and evolutionary game theory perspectives.

Science.gov (United States)

De Leenheer, Patrick; Mohapatra, Anushaya; Ohms, Haley A; Lytle, David A; Cushing, J M

2017-01-07

We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

Science.gov (United States)

Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

2012-01-01

Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts.

Science.gov (United States)

Cerveau, Nicolas; Leclercq, Sébastien; Leroy, Elodie; Bouchon, Didier; Cordaux, Richard

2011-01-01

Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52-171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes.

Evolutionary biology of bacterial and fungal pathogens

National Research Council Canada - National Science Library

Baquero, F

2008-01-01

... and Evolutionary Dynamics of Pathogens * 21 Keith A. Crandall and Marcos Pérez-Losada II. Evolutionary Genetics of Microbial Pathogens 4. Environmental and Social Influences on Infectious Disea...

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Directory of Open Access Journals (Sweden)

David Lee Erickson

2014-11-01

Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

Expanding the eco-evolutionary context of herbicide resistance research.

Science.gov (United States)

Neve, Paul; Busi, Roberto; Renton, Michael; Vila-Aiub, Martin M

2014-09-01

The potential for human-driven evolution in economically and environmentally important organisms in medicine, agriculture and conservation management is now widely recognised. The evolution of herbicide resistance in weeds is a classic example of rapid adaptation in the face of human-mediated selection. Management strategies that aim to slow or prevent the evolution of herbicide resistance must be informed by an understanding of the ecological and evolutionary factors that drive selection in weed populations. Here, we argue for a greater focus on the ultimate causes of selection for resistance in herbicide resistance studies. The emerging fields of eco-evolutionary dynamics and applied evolutionary biology offer a means to achieve this goal and to consider herbicide resistance in a broader and sometimes novel context. Four relevant research questions are presented, which examine (i) the impact of herbicide dose on selection for resistance, (ii) plant fitness in herbicide resistance studies, (iii) the efficacy of herbicide rotations and mixtures and (iv) the impacts of gene flow on resistance evolution and spread. In all cases, fundamental ecology and evolution have the potential to offer new insights into herbicide resistance evolution and management. © 2014 Society of Chemical Industry.

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

Science.gov (United States)

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

Using Self-Adaptive Evolutionary Algorithms to Evolve Dynamism-Oriented Maps for a Real Time Strategy Game

OpenAIRE

Lara-Cabrera, Raúl; Cotta, Carlos; Fernández Leiva, Antonio J.

2013-01-01

This work presents a procedural content generation system that uses an evolutionary algorithm in order to generate interesting maps for a real-time strategy game, called Planet Wars. Interestingness is here captured by the dynamism of games (i.e., the extent to which they are action-packed). We consider two different approaches to measure the dynamism of the games resulting from these generated maps, one based on fluctuations in the resources controlled by either player and another one based ...

The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.

Directory of Open Access Journals (Sweden)

David Gresham

2008-12-01

Full Text Available The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes -- including point mutations, structural changes, and insertion variation -- that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for approximately 200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications to known features

Evolutionary Multiplayer Games

OpenAIRE

Gokhale, Chaitanya S.; Traulsen, Arne

2014-01-01

Evolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g.\\ increase less than linear wi...

How mutation alters the evolutionary dynamics of cooperation on networks

Science.gov (United States)

Ichinose, Genki; Satotani, Yoshiki; Sayama, Hiroki

2018-05-01

Cooperation is ubiquitous at every level of living organisms. It is known that spatial (network) structure is a viable mechanism for cooperation to evolve. A recently proposed numerical metric, average gradient of selection (AGoS), a useful tool for interpreting and visualizing evolutionary dynamics on networks, allows simulation results to be visualized on a one-dimensional phase space. However, stochastic mutation of strategies was not considered in the analysis of AGoS. Here we extend AGoS so that it can analyze the evolution of cooperation where mutation may alter strategies of individuals on networks. We show that our extended AGoS correctly visualizes the final states of cooperation with mutation in the individual-based simulations. Our analyses revealed that mutation always has a negative effect on the evolution of cooperation regardless of the payoff functions, fraction of cooperators, and network structures. Moreover, we found that scale-free networks are the most vulnerable to mutation and thus the dynamics of cooperation are altered from bistability to coexistence on those networks, undergoing an imperfect pitchfork bifurcation.

Innovation dynamics of Salvadoran agri-food industry from an evolutionary perspective

Energy Technology Data Exchange (ETDEWEB)

Peraza Castaneda, E.H.; Aleixandre Mendizábal, G.

2016-07-01

This paper presents a holistic approach to analyse the dynamics of innovation of a low-tech sector in a less developed economy, the agri-food industry in El Salvador, in the context of evolutionary economy. This requires using complementary quantitative and qualitative data and methodologies to better understand how Salvadoran agri-food industry innovation system works and how STI public policies can improve the performance of a key sector in terms of national socioeconomic development. The work already done shows a concentrated and vigorous sector with some upstream and downstream connections that innovate depending on firm size, age, R&D activities and use of industrial property rights. (Author)

Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

Science.gov (United States)

Burdon, J J; Thrall, P H; Ericson, L

2013-08-01

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Core principles of evolutionary medicine

Science.gov (United States)

Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

2018-01-01

Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

Evolutionary robotics

Indian Academy of Sciences (India)

In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to ...

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

Directory of Open Access Journals (Sweden)

Cécile Troupin

2016-12-01

Full Text Available The natural evolution of rabies virus (RABV provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Applications of Evolutionary Computation

NARCIS (Netherlands)

Mora, Antonio M.; Squillero, Giovanni; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Smith, Stephen L; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Mora, Antonio M.; Squillero, Giovanni; Jan, Mathieu; Matthias, M; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Esparcia-Alcazar, Anna I; Silva, Sara; Agapitos, Alexandros; Cotta, Carlos; De Falco, Ivanoe; Cioppa, Antonio Della; Diwold, Konrad; Ekart, Aniko; Tarantino, Ernesto; Vega, Francisco Fernandez De; Burelli, Paolo; Sim, Kevin; Cagnoni, Stefano; Simoes, Anabela; Merelo, J.J.; Urquhart, Neil; Haasdijk, Evert; Zhang, Mengjie; Squillero, Giovanni; Eiben, A E; Tettamanzi, Andrea G B; Glette, Kyrre; Rohlfshagen, Philipp; Schaefer, Robert; Caserta, Marco; Ramirez, Adriana; Voß, Stefan

2015-01-01

The application of genetic and evolutionary computation to problems in medicine has increased rapidly over the past five years, but there are specific issues and challenges that distinguish it from other real-world applications. Obtaining reliable and coherent patient data, establishing the clinical

On Reciprocal Causation in the Evolutionary Process.

Science.gov (United States)

Svensson, Erik I

2018-01-01

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach

Spatial evolutionary epidemiology of spreading epidemics.

Science.gov (United States)

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Stochastic win-stay-lose-shift strategy with dynamic aspirations in evolutionary social dilemmas

Science.gov (United States)

Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.

2016-09-01

In times of plenty expectations rise, just as in times of crisis they fall. This can be mathematically described as a win-stay-lose-shift strategy with dynamic aspiration levels, where individuals aspire to be as wealthy as their average neighbor. Here we investigate this model in the realm of evolutionary social dilemmas on the square lattice and scale-free networks. By using the master equation and Monte Carlo simulations, we find that cooperators coexist with defectors in the whole phase diagram, even at high temptations to defect. We study the microscopic mechanism that is responsible for the striking persistence of cooperative behavior and find that cooperation spreads through second-order neighbors, rather than by means of network reciprocity that dominates in imitation-based models. For the square lattice the master equation can be solved analytically in the large temperature limit of the Fermi function, while for other cases the resulting differential equations must be solved numerically. Either way, we find good qualitative agreement with the Monte Carlo simulation results. Our analysis also reveals that the evolutionary outcomes are to a large degree independent of the network topology, including the number of neighbors that are considered for payoff determination on lattices, which further corroborates the local character of the microscopic dynamics. Unlike large-scale spatial patterns that typically emerge due to network reciprocity, here local checkerboard-like patterns remain virtually unaffected by differences in the macroscopic properties of the interaction network.

Electricity demand and spot price forecasting using evolutionary computation combined with chaotic nonlinear dynamic model

International Nuclear Information System (INIS)

Unsihuay-Vila, C.; Zambroni de Souza, A.C.; Marangon-Lima, J.W.; Balestrassi, P.P.

2010-01-01

This paper proposes a new hybrid approach based on nonlinear chaotic dynamics and evolutionary strategy to forecast electricity loads and prices. The main idea is to develop a new training or identification stage in a nonlinear chaotic dynamic based predictor. In the training stage five optimal parameters for a chaotic based predictor are searched through an optimization model based on evolutionary strategy. The objective function of the optimization model is the mismatch minimization between the multi-step-ahead forecasting of predictor and observed data such as it is done in identification problems. The first contribution of this paper is that the proposed approach is capable of capturing the complex dynamic of demand and price time series considered resulting in a more accuracy forecasting. The second contribution is that the proposed approach run on-line manner, i.e. the optimal set of parameters and prediction is executed automatically which can be used to prediction in real-time, it is an advantage in comparison with other models, where the choice of their input parameters are carried out off-line, following qualitative/experience-based recipes. A case study of load and price forecasting is presented using data from New England, Alberta, and Spain. A comparison with other methods such as autoregressive integrated moving average (ARIMA) and artificial neural network (ANN) is shown. The results show that the proposed approach provides a more accurate and effective forecasting than ARIMA and ANN methods. (author)

Evolutionary dynamics of adult stem cells: Comparison of random and immortal strand segregation mechanisms

OpenAIRE

Tannenbaum, Emmanuel; Sherley, James L.; Shakhnovich, Eugene I.

2004-01-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) Random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell. (2) ``Immortal DNA strand'' co-segregation, for which the stem cell reta...

A system dynamics model based on evolutionary game theory for green supply chain management diffusion among Chinese manufacturers

DEFF Research Database (Denmark)

Tian, Yihui; Govindan, Kannan; Zhu, Qinghua

2014-01-01

In this study, a system dynamics (SD) model is developed to guide the subsidy policies to promote the diffusion of green supply chain management (GSCM) in China. The relationships of stakeholders such as government, enterprises and consumers are analyzed through evolutionary game theory. Finally...

Multivariate dynamic linear models for estimating the effect of experimental interventions in an evolutionary operations setup in dairy herds

DEFF Research Database (Denmark)

Stygar, Anna Helena; Krogh, Mogens Agerbo; Kristensen, Troels

2017-01-01

Evolutionary operations is a method to exploit the association of often small changes in process variables, planned during systematic experimentation and occurring during the normal production flow, to production characteristics to find a way to alter the production process to be more efficient....... The objective of this study was to construct a tool to assess the intervention effect on milk production in an evolutionary operations setup. The method used for this purpose was a dynamic linear model (DLM) with Kalman filtering. The DLM consisted of parameters describing milk yield in a herd, individual cows...... bulk tank records. The presented model proved to be a flexible and dynamic tool, and it was successfully applied for systematic experimentation in dairy herds. The model can serve as a decision support tool for on-farm process optimization exploiting planned changes in process variables...

Evolutionary dynamics of bacteria in a human host environment

DEFF Research Database (Denmark)

Yang, Lei; Jelsbak, Lars; Marvig, Rasmus Lykke

2011-01-01

Laboratory evolution experiments have led to important findings relating organism adaptation and genomic evolution. However, continuous monitoring of long-term evolution has been lacking for natural systems, limiting our understanding of these processes in situ. Here we characterize the evolution...... long-term in vitro evolution experiments. The evolved phenotype of the infecting bacteria further suggests that the opportunistic pathogen has transitioned to become a primary pathogen for cystic fibrosis patients.......Laboratory evolution experiments have led to important findings relating organism adaptation and genomic evolution. However, continuous monitoring of long-term evolution has been lacking for natural systems, limiting our understanding of these processes in situ. Here we characterize...... the evolutionary dynamics of a lineage of a clinically important opportunistic bacterial pathogen, Pseudomonas aeruginosa, as it adapts to the airways of several individual cystic fibrosis patients over 200,000 bacterial generations, and provide estimates of mutation rates of bacteria in a natural environment...

A New Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Complex Networks

Directory of Open Access Journals (Sweden)

Guoqiang Chen

2013-01-01

Full Text Available Community detection in dynamic networks is an important research topic and has received an enormous amount of attention in recent years. Modularity is selected as a measure to quantify the quality of the community partition in previous detection methods. But, the modularity has been exposed to resolution limits. In this paper, we propose a novel multiobjective evolutionary algorithm for dynamic networks community detection based on the framework of nondominated sorting genetic algorithm. Modularity density which can address the limitations of modularity function is adopted to measure the snapshot cost, and normalized mutual information is selected to measure temporal cost, respectively. The characteristics knowledge of the problem is used in designing the genetic operators. Furthermore, a local search operator was designed, which can improve the effectiveness and efficiency of community detection. Experimental studies based on synthetic datasets show that the proposed algorithm can obtain better performance than the compared algorithms.

Towards a mechanistic foundation of evolutionary theory.

Science.gov (United States)

Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

2017-02-15

Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review

KAUST Repository

Kim, Kiyeon

2016-01-13

Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.

Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review

KAUST Repository

Kim, Kiyeon; Omori, Ryosuke; Ueno, Keisuke; Iida, Sayaka; Ito, Kimihito

2016-01-01

Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.

Integrated evolutionary computation neural network quality controller for automated systems

Energy Technology Data Exchange (ETDEWEB)

Patro, S.; Kolarik, W.J. [Texas Tech Univ., Lubbock, TX (United States). Dept. of Industrial Engineering

1999-06-01

With increasing competition in the global market, more and more stringent quality standards and specifications are being demands at lower costs. Manufacturing applications of computing power are becoming more common. The application of neural networks to identification and control of dynamic processes has been discussed. The limitations of using neural networks for control purposes has been pointed out and a different technique, evolutionary computation, has been discussed. The results of identifying and controlling an unstable, dynamic process using evolutionary computation methods has been presented. A framework for an integrated system, using both neural networks and evolutionary computation, has been proposed to identify the process and then control the product quality, in a dynamic, multivariable system, in real-time.

Evolutionary principles and their practical application.

Science.gov (United States)

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-03-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

Stability properties of nonlinear dynamical systems and evolutionary stable states

Energy Technology Data Exchange (ETDEWEB)

Gleria, Iram, E-mail: iram@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL (Brazil); Brenig, Leon [Faculté des Sciences, Université Libre de Bruxelles, 1050 Brussels (Belgium); Rocha Filho, Tarcísio M.; Figueiredo, Annibal [Instituto de Física and International Center for Condensed Matter Physics, Universidade de Brasília, 70919-970 Brasília-DF (Brazil)

2017-03-18

Highlights: • We address the problem of equilibrium stability in a general class of non-linear systems. • We link Evolutionary Stable States (ESS) to stable fixed points of square quasi-polynomial (QP) systems. • We show that an interior ES point may be related to stable interior fixed points of QP systems. - Abstract: In this paper we address the problem of stability in a general class of non-linear systems. We establish a link between the concepts of asymptotic stable interior fixed points of square Quasi-Polynomial systems and evolutionary stable states, a property of some payoff matrices arising from evolutionary games.

Looking for the optimal rate of recombination for evolutionary dynamics

Science.gov (United States)

Saakian, David B.

2018-01-01

We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.

Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

Science.gov (United States)

Liao, David; Tlsty, Thea D

2014-08-06

Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

Evolutionary Dynamics of Collective Behavior Selection and Drift: Flocking, Collapse, and Oscillation.

Science.gov (United States)

Tan, Shaolin; Wang, Yaonan; Chen, Yao; Wang, Zhen

2016-06-14

Behavioral choice is ubiquitous across a wide range of interactive decision-making processes and a myriad of scientific disciplines. With regard to this issue, one entitative problem is actually to understand how collective social behaviors form and evolve among populations when they face a variety of conflict alternatives. In this paper, a selection-drift dynamic model is formulated to characterize the behavior imitation and exploration processes in social populations. Based on the proposed framework, several typical behavior evolution patterns, including behavioral flocking, collapse, and oscillation, are reproduced with different kinds of behavior networks. Interestingly, for the selection-drift dynamics on homogeneous symmetric behavior networks, we unveil the phase transition from behavioral flocking to collapse and derive the bifurcation diagram of the evolutionary stable behaviors in social behavior evolution. While via analyzing the survival conditions of the best behavior on heterogeneous symmetric behavior networks, we propose a selection-drift mechanism to guarantee consensus at the optimal behavior. Moreover, when the selection-drift dynamics on asymmetric behavior networks is simulated, it is shown that breaking the symmetry in behavior networks can induce various behavioral oscillations. These obtained results may shed new insights into understanding, detecting, and further controlling how social norm and cultural trends evolve.

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

Science.gov (United States)

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

Science.gov (United States)

Gorter, Florien A; Aarts, Mark G M; Zwaan, Bas J; de Visser, J Arjan G M

2018-01-01

The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change. Copyright © 2018 by the Genetics Society of America.

Heterogeneous update mechanisms in evolutionary games: Mixing innovative and imitative dynamics

Science.gov (United States)

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows the introduction of elements of novelty, while the latter is responsible for the motion of a system in its phase space. Often, these processes are strongly related, since an innovation can trigger the evolution, and the latter can provide the optimal conditions for the emergence of innovations. Both processes can be studied by using the framework of evolutionary game theory, where evolution constitutes an intrinsic mechanism. At the same time, the concept of innovation requires an opportune mathematical representation. Notably, innovation can be modeled as a strategy, or it can constitute the underlying mechanism that allows agents to change strategy. Here, we analyze the second case, investigating the behavior of a heterogeneous population, composed of imitative and innovative agents. Imitative agents change strategy only by imitating that of their neighbors, whereas innovative ones change strategy without the need for a copying source. The proposed model is analyzed by means of analytical calculations and numerical simulations in different topologies. Remarkably, results indicate that the mixing of mechanisms can be detrimental to cooperation near phase transitions. In those regions, the spatial reciprocity from imitative mechanisms is destroyed by innovative agents, leading to the downfall of cooperation. Our investigation sheds some light on the complex dynamics emerging from the heterogeneity of strategy revision methods, highlighting the role of innovation in evolutionary games.

Rapid solidification and dynamic compaction of Ni-base superalloy powders

Science.gov (United States)

Field, R. D.; Hales, S. J.; Powers, W. O.; Fraser, H. L.

1984-01-01

A Ni-base superalloy containing 13Al-9Mo-2Ta (in at. percent) has been characterized in both the rapidly solidified condition and after dynamic compaction. Dynamically compacted specimens were examined in the as-compacted condition and observations related to current theories of interparticle bonding. In addition, the recrystallization behavior of the compacted material at relatively low temperature (about 0.5-0.75 Tm) was investigated.

'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics: An R Package to Follow Accumulation of Within-Host Mutation in Pathogens.

Directory of Open Access Journals (Sweden)

Colin J Worby

Full Text Available Genome sequencing is an increasingly common component of infectious disease outbreak investigations. However, the relationship between pathogen transmission and observed genetic data is complex, and dependent on several uncertain factors. As such, simulation of pathogen dynamics is an important tool for interpreting observed genomic data in an infectious disease outbreak setting, in order to test hypotheses and to explore the range of outcomes consistent with a given set of parameters. We introduce 'seedy', an R package for the simulation of evolutionary and epidemiological dynamics (http://cran.r-project.org/web/packages/seedy/. Our software implements stochastic models for the accumulation of mutations within hosts, as well as individual-level disease transmission. By allowing variables such as the transmission bottleneck size, within-host effective population size and population mixing rates to be specified by the user, our package offers a flexible framework to investigate evolutionary dynamics during disease outbreaks. Furthermore, our software provides theoretical pairwise genetic distance distributions to provide a likelihood of person-to-person transmission based on genomic observations, and using this framework, implements transmission route assessment for genomic data collected during an outbreak. Our open source software provides an accessible platform for users to explore pathogen evolution and outbreak dynamics via simulation, and offers tools to assess observed genomic data in this context.

Evolutionary disarmament in interspecific competition.

Science.gov (United States)

Kisdi, E; Geritz, S A

2001-12-22

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

More rapid climate change promotes evolutionary rescue through selection for increased dispersal distance.

Science.gov (United States)

Boeye, Jeroen; Travis, Justin M J; Stoks, Robby; Bonte, Dries

2013-02-01

Species can either adapt to new conditions induced by climate change or shift their range in an attempt to track optimal environmental conditions. During current range shifts, species are simultaneously confronted with a second major anthropogenic disturbance, landscape fragmentation. Using individual-based models with a shifting climate window, we examine the effect of different rates of climate change on the evolution of dispersal distances through changes in the genetically determined dispersal kernel. Our results demonstrate that the rate of climate change is positively correlated to the evolved dispersal distances although too fast climate change causes the population to crash. When faced with realistic rates of climate change, greater dispersal distances evolve than those required for the population to keep track of the climate, thereby maximizing population size. Importantly, the greater dispersal distances that evolve when climate change is more rapid, induce evolutionary rescue by facilitating the population in crossing large gaps in the landscape. This could ensure population persistence in case of range shifting in fragmented landscapes. Furthermore, we highlight problems in using invasion speed as a proxy for potential range shifting abilities under climate change.

Genome-wide detection of selection and other evolutionary forces

DEFF Research Database (Denmark)

Xu, Zhuofei; Zhou, Rui

2015-01-01

As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed...... to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome...

Mean-Potential Law in Evolutionary Games

Science.gov (United States)

Nałecz-Jawecki, Paweł; Miekisz, Jacek

2018-01-01

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics.

Directory of Open Access Journals (Sweden)

Matthew T Aliota

2018-03-01

Full Text Available Defining the complex dynamics of Zika virus (ZIKV infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a "synthetic swarm" whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcodes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 67 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.

Evolutionary rate variation and RNA secondary structure prediction

DEFF Research Database (Denmark)

Knudsen, B.; Andersen, E.S.; Damgaard, C.

2004-01-01

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Science.gov (United States)

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

Neotropical fish-fruit interactions: eco-evolutionary dynamics and conservation.

Science.gov (United States)

Correa, Sandra Bibiana; Costa-Pereira, Raul; Fleming, Theodore; Goulding, Michael; Anderson, Jill T

2015-11-01

Frugivorous fish play a prominent role in seed dispersal and reproductive dynamics of plant communities in riparian and floodplain habitats of tropical regions worldwide. In Neotropical wetlands, many plant species have fleshy fruits and synchronize their fruiting with the flood season, when fruit-eating fish forage in forest and savannahs for periods of up to 7 months. We conducted a comprehensive analysis to examine the evolutionary origin of fish-fruit interactions, describe fruit traits associated with seed dispersal and seed predation, and assess the influence of fish size on the effectiveness of seed dispersal by fish (ichthyochory). To date, 62 studies have documented 566 species of fruits and seeds from 82 plant families in the diets of 69 Neotropical fish species. Fish interactions with flowering plants are likely to be as old as 70 million years in the Neotropics, pre-dating most modern bird-fruit and mammal-fruit interactions, and contributing to long-distance seed dispersal and possibly the radiation of early angiosperms. Ichthyochory occurs across the angiosperm phylogeny, and is more frequent among advanced eudicots. Numerous fish species are capable of dispersing small seeds, but only a limited number of species can disperse large seeds. The size of dispersed seeds and the probability of seed dispersal both increase with fish size. Large-bodied species are the most effective seed dispersal agents and remain the primary target of fishing activities in the Neotropics. Thus, conservation efforts should focus on these species to ensure continuity of plant recruitment dynamics and maintenance of plant diversity in riparian and floodplain ecosystems. © 2015 Cambridge Philosophical Society.

Dynamical role of Ekman pumping in rapidly rotating convection

Science.gov (United States)

Stellmach, Stephan; Julien, Keith; Cheng, Jonathan; Aurnou, Jonathan

2015-04-01

The exact nature of the mechanical boundary conditions (i.e. no-slip versus stress-free) is usually considered to be of secondary importance in the rapidly rotating parameter regime characterizing planetary cores. While they have considerable influence for the Ekman numbers achievable in today's global simulations, for planetary values both the viscous Ekman layers and the associated secondary flows are generally expected to become negligibly small. In fact, usually the main purpose of using stress-free boundary conditions in numerical dynamo simulations is to suppress unrealistically large friction and pumping effects. In this study, we investigate the influence of the mechanical boundary conditions on core convection systematically. By restricting ourselves to the idealized case of rapidly rotating Rayleigh-Bénard convection, we are able to combine results from direct numerical simulations (DNS), laboratory experiments and asymptotic theory into a coherent picture. Contrary to the general expectation, we show that the dynamical effects of Ekman pumping increase with decreasing Ekman number over the investigated parameter range. While stress-free DNS results converge to the asymptotic predictions, both no-slip simulations and laboratory experiments consistently reveal increasingly large deviations from the existing asymptotic theory based on dynamically passive Ekman layers. The implications of these results for core dynamics are discussed briefly.

Core principles of evolutionary medicine: A Delphi study.

Science.gov (United States)

Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

2018-01-01

Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

Insights into the Impact of CD8+ Immune Modulation on Human Immunodeficiency Virus Evolutionary Dynamics in Distinct Anatomical Compartments by Using Simian Immunodeficiency Virus-Infected Macaque Models of AIDS Progression.

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Rife Magalis, Brittany; Nolan, David J; Autissier, Patrick; Burdo, Tricia H; Williams, Kenneth C; Salemi, Marco

2017-12-01

A thorough understanding of the role of human immunodeficiency virus (HIV) intrahost evolution in AIDS pathogenesis has been limited by the need for longitudinally sampled viral sequences from the vast target space within the host, which are often difficult to obtain from human subjects. CD8 + lymphocyte-depleted macaques infected with simian immunodeficiency virus (SIV) provide an increasingly utilized model of pathogenesis due to clinical manifestations similar to those for HIV-1 infection and AIDS progression, as well as a characteristic rapid disease onset. Comparison of this model with SIV-infected non-CD8 + lymphocyte-depleted macaques also provides a unique opportunity to investigate the role of CD8 + cells in viral evolution and population dynamics throughout the duration of infection. Using several different phylogenetic methods, we analyzed viral gp120 sequences obtained from extensive longitudinal sampling of multiple tissues and enriched leukocyte populations from SIVmac251-infected macaques with or without CD8 + lymphocyte depletion. SIV evolutionary and selection patterns in non-CD8 + lymphocyte-depleted animals were characterized by sequential population turnover and continual viral adaptation, a scenario readily comparable to intrahost evolutionary patterns during human HIV infection in the absence of antiretroviral therapy. Alternatively, animals that were depleted of CD8 + lymphocytes exhibited greater variation in population dynamics among tissues and cell populations over the course of infection. Our findings highlight the major role for CD8 + lymphocytes in prolonging disease progression through continual control of SIV subpopulations from various anatomical compartments and the potential for greater independent viral evolutionary behavior among these compartments in response to immune modulation. IMPORTANCE Although developments in combined antiretroviral therapy (cART) strategies have successfully prolonged the time to AIDS onset in HIV-1

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

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Matos Margarida

2009-06-01

Full Text Available Abstract Here we present a correction to our article "Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura". We have recently detected an error concerning the application of the Ln RH formula – a test to detect positive selection – to our microsatellite data. Here we provide the corrected data and discuss its implications for our overall findings. The corrections presented here have produced some changes relative to our previous results, namely in a locus (dsub14 that presents indications of being affected by positive selection. In general, our populations present less consistent indications of positive selection for this particular locus in both periods studied – between generations 3 and 14 and between generation 14 and 40 of laboratory adaptation. Despite this, the main findings of our study regarding the possibility of positive selection acting on that particular microsatellite still hold. As previously concluded in our article, further studies should be performed on this specific microsatellite locus (and neighboring areas to elucidate in greater detail the evolutionary forces acting on this specific region of the O chromosome of Drosophila subobscura.

Evolutionary game dynamics of controlled and automatic decision-making.

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Toupo, Danielle F P; Strogatz, Steven H; Cohen, Jonathan D; Rand, David G

2015-07-01

We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.

Evolutionary game dynamics of controlled and automatic decision-making

Science.gov (United States)

Toupo, Danielle F. P.; Strogatz, Steven H.; Cohen, Jonathan D.; Rand, David G.

2015-07-01

We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.

Proteomics in evolutionary ecology.

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Baer, B; Millar, A H

2016-03-01

Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

Emergence of structured communities through evolutionary dynamics.

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Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Competition-colonization trade-offs, competitive uncertainty, and the evolutionary assembly of species.

Directory of Open Access Journals (Sweden)

Pradeep Pillai

Full Text Available We utilize a standard competition-colonization metapopulation model in order to study the evolutionary assembly of species. Based on earlier work showing how models assuming strict competitive hierarchies will likely lead to runaway evolution and self-extinction for all species, we adopt a continuous competition function that allows for levels of uncertainty in the outcome of competition. We then, by extending the standard patch-dynamic metapopulation model in order to include evolutionary dynamics, allow for the coevolution of species into stable communities composed of species with distinct limiting similarities. Runaway evolution towards stochastic extinction then becomes a limiting case controlled by the level of competitive uncertainty. We demonstrate how intermediate competitive uncertainty maximizes the equilibrium species richness as well as maximizes the adaptive radiation and self-assembly of species under adaptive dynamics with mutations of non-negligible size. By reconciling competition-colonization tradeoff theory with co-evolutionary dynamics, our results reveal the importance of intermediate levels of competitive uncertainty for the evolutionary assembly of species.

A predator-2 prey fast-slow dynamical system for rapid predator evolution

DEFF Research Database (Denmark)

Piltz, Sofia Helena; Veerman, Frits; Maini, Philip K.

2017-01-01

We consider adaptive change of diet of a predator population that switches its feeding between two prey populations. We develop a novel 1 fast-3 slow dynamical system to describe the dynamics of the three populations amidst continuous but rapid evolution of the predator's diet choice. The two ext...

CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba.

Science.gov (United States)

Kouri, Vivian; Khouri, Ricardo; Alemán, Yoan; Abrahantes, Yeissel; Vercauteren, Jurgen; Pineda-Peña, Andrea-Clemencia; Theys, Kristof; Megens, Sarah; Moutschen, Michel; Pfeifer, Nico; Van Weyenbergh, Johan; Pérez, Ana B; Pérez, Jorge; Pérez, Lissette; Van Laethem, Kristel; Vandamme, Anne-Mieke

2015-03-01

Clinicians reported an increasing trend of rapid progression (RP) (AIDS within 3 years of infection) in Cuba. Recently infected patients were prospectively sampled, 52 RP at AIDS diagnosis (AIDS-RP) and 21 without AIDS in the same time frame (non-AIDS). 22 patients were sampled at AIDS diagnosis (chronic-AIDS) retrospectively assessed as > 3 years infected. Clinical, demographic, virological, epidemiological and immunological data were collected. Pol and env sequences were used for subtyping, transmission cluster analysis, and prediction of resistance, co-receptor use and evolutionary fitness. Host, immunological and viral predictors of RP were explored through data mining. Subtyping revealed 26 subtype B strains, 6 C, 6 CRF18_cpx, 9 CRF19_cpx, 29 BG-recombinants and other subtypes/URFs. All patients infected with CRF19 belonged to the AIDS-RP group. Data mining identified CRF19, oral candidiasis and RANTES levels as the strongest predictors of AIDS-RP. CRF19 was more frequently predicted to use the CXCR4 co-receptor, had higher fitness scores in the protease region, and patients had higher viral load at diagnosis. CRF19 is a recombinant of subtype D (C-part of Gag, PR, RT and nef), subtype A (N-part of Gag, Integrase, Env) and subtype G (Vif, Vpr, Vpu and C-part of Env). Since subtypes D and A have been associated with respectively faster and slower disease progression, our findings might indicate a fit PR driving high viral load, which in combination with co-infections may boost RANTES levels and thus CXCR4 use, potentially explaining the fast progression. We propose that CRF19 is evolutionary very fit and causing rapid progression to AIDS in many newly infected patients in Cuba.

Improving the Adaptability of Simulated Evolutionary Swarm Robots in Dynamically Changing Environments

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Yao, Yao; Marchal, Kathleen; Van de Peer, Yves

2014-01-01

One of the important challenges in the field of evolutionary robotics is the development of systems that can adapt to a changing environment. However, the ability to adapt to unknown and fluctuating environments is not straightforward. Here, we explore the adaptive potential of simulated swarm robots that contain a genomic encoding of a bio-inspired gene regulatory network (GRN). An artificial genome is combined with a flexible agent-based system, representing the activated part of the regulatory network that transduces environmental cues into phenotypic behaviour. Using an artificial life simulation framework that mimics a dynamically changing environment, we show that separating the static from the conditionally active part of the network contributes to a better adaptive behaviour. Furthermore, in contrast with most hitherto developed ANN-based systems that need to re-optimize their complete controller network from scratch each time they are subjected to novel conditions, our system uses its genome to store GRNs whose performance was optimized under a particular environmental condition for a sufficiently long time. When subjected to a new environment, the previous condition-specific GRN might become inactivated, but remains present. This ability to store ‘good behaviour’ and to disconnect it from the novel rewiring that is essential under a new condition allows faster re-adaptation if any of the previously observed environmental conditions is reencountered. As we show here, applying these evolutionary-based principles leads to accelerated and improved adaptive evolution in a non-stable environment. PMID:24599485

Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments.

Directory of Open Access Journals (Sweden)

Yao Yao

Full Text Available One of the important challenges in the field of evolutionary robotics is the development of systems that can adapt to a changing environment. However, the ability to adapt to unknown and fluctuating environments is not straightforward. Here, we explore the adaptive potential of simulated swarm robots that contain a genomic encoding of a bio-inspired gene regulatory network (GRN. An artificial genome is combined with a flexible agent-based system, representing the activated part of the regulatory network that transduces environmental cues into phenotypic behaviour. Using an artificial life simulation framework that mimics a dynamically changing environment, we show that separating the static from the conditionally active part of the network contributes to a better adaptive behaviour. Furthermore, in contrast with most hitherto developed ANN-based systems that need to re-optimize their complete controller network from scratch each time they are subjected to novel conditions, our system uses its genome to store GRNs whose performance was optimized under a particular environmental condition for a sufficiently long time. When subjected to a new environment, the previous condition-specific GRN might become inactivated, but remains present. This ability to store 'good behaviour' and to disconnect it from the novel rewiring that is essential under a new condition allows faster re-adaptation if any of the previously observed environmental conditions is reencountered. As we show here, applying these evolutionary-based principles leads to accelerated and improved adaptive evolution in a non-stable environment.

Evolutionary games on graphs

Science.gov (United States)

Szabó, György; Fáth, Gábor

2007-07-01

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

Bridging the gap between Schumpeterian competition and evolutionary game theory

DEFF Research Database (Denmark)

Andersen, Esben Sloth

This paper suggests that the analysis of Schumpeterian competition within the Nelson-Winter model should be complemented with evolutionary game theory. This model and its limitations for density-dependent Schumpeterian strategies are presented in terms of the equations of evolutionary dynamics. F...

Modeling evolutionary games in populations with demographic structure

DEFF Research Database (Denmark)

Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

2015-01-01

interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

An evolutionary algorithm technique for intelligence, surveillance, and reconnaissance plan optimization

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Langton, John T.; Caroli, Joseph A.; Rosenberg, Brad

2008-04-01

To support an Effects Based Approach to Operations (EBAO), Intelligence, Surveillance, and Reconnaissance (ISR) planners must optimize collection plans within an evolving battlespace. A need exists for a decision support tool that allows ISR planners to rapidly generate and rehearse high-performing ISR plans that balance multiple objectives and constraints to address dynamic collection requirements for assessment. To meet this need we have designed an evolutionary algorithm (EA)-based "Integrated ISR Plan Analysis and Rehearsal System" (I2PARS) to support Effects-based Assessment (EBA). I2PARS supports ISR mission planning and dynamic replanning to coordinate assets and optimize their routes, allocation and tasking. It uses an evolutionary algorithm to address the large parametric space of route-finding problems which is sometimes discontinuous in the ISR domain because of conflicting objectives such as minimizing asset utilization yet maximizing ISR coverage. EAs are uniquely suited for generating solutions in dynamic environments and also allow user feedback. They are therefore ideal for "streaming optimization" and dynamic replanning of ISR mission plans. I2PARS uses the Non-dominated Sorting Genetic Algorithm (NSGA-II) to automatically generate a diverse set of high performing collection plans given multiple objectives, constraints, and assets. Intended end users of I2PARS include ISR planners in the Combined Air Operations Centers and Joint Intelligence Centers. Here we show the feasibility of applying the NSGA-II algorithm and EAs in general to the ISR planning domain. Unique genetic representations and operators for optimization within the ISR domain are presented along with multi-objective optimization criteria for ISR planning. Promising results of the I2PARS architecture design, early software prototype, and limited domain testing of the new algorithm are discussed. We also present plans for future research and development, as well as technology

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

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Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A.; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe

2014-01-01

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells

Evolutionary public health: introducing the concept.

Science.gov (United States)

Wells, Jonathan C K; Nesse, Randolph M; Sear, Rebecca; Johnstone, Rufus A; Stearns, Stephen C

2017-07-29

The emerging discipline of evolutionary medicine is breaking new ground in understanding why people become ill. However, the value of evolutionary analyses of human physiology and behaviour is only beginning to be recognised in the field of public health. Core principles come from life history theory, which analyses the allocation of finite amounts of energy between four competing functions-maintenance, growth, reproduction, and defence. A central tenet of evolutionary theory is that organisms are selected to allocate energy and time to maximise reproductive success, rather than health or longevity. Ecological interactions that influence mortality risk, nutrient availability, and pathogen burden shape energy allocation strategies throughout the life course, thereby affecting diverse health outcomes. Public health interventions could improve their own effectiveness by incorporating an evolutionary perspective. In particular, evolutionary approaches offer new opportunities to address the complex challenges of global health, in which populations are differentially exposed to the metabolic consequences of poverty, high fertility, infectious diseases, and rapid changes in nutrition and lifestyle. The effect of specific interventions is predicted to depend on broader factors shaping life expectancy. Among the important tools in this approach are mathematical models, which can explore probable benefits and limitations of interventions in silico, before their implementation in human populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Random and non-random mating populations: Evolutionary dynamics in meiotic drive.

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Sarkar, Bijan

2016-01-01

Game theoretic tools are utilized to analyze a one-locus continuous selection model of sex-specific meiotic drive by considering nonequivalence of the viabilities of reciprocal heterozygotes that might be noticed at an imprinted locus. The model draws attention to the role of viability selections of different types to examine the stable nature of polymorphic equilibrium. A bridge between population genetics and evolutionary game theory has been built up by applying the concept of the Fundamental Theorem of Natural Selection. In addition to pointing out the influences of male and female segregation ratios on selection, configuration structure reveals some noted results, e.g., Hardy-Weinberg frequencies hold in replicator dynamics, occurrence of faster evolution at the maximized variance fitness, existence of mixed Evolutionarily Stable Strategy (ESS) in asymmetric games, the tending evolution to follow not only a 1:1 sex ratio but also a 1:1 different alleles ratio at particular gene locus. Through construction of replicator dynamics in the group selection framework, our selection model introduces a redefining bases of game theory to incorporate non-random mating where a mating parameter associated with population structure is dependent on the social structure. Also, the model exposes the fact that the number of polymorphic equilibria will depend on the algebraic expression of population structure. Copyright © 2015 Elsevier Inc. All rights reserved.

Evolutionary game theory and organizational ecology: The case of resource-partitioning theory

OpenAIRE

ZHOU, Chaohong; VAN WITTELOOSTUIJN, Arjen

2009-01-01

Abstract: In this paper, we construct a mathematical model that applies tools from evolutionary game theory to issues in organizational ecology. Evolutionary game theory shares the key feature of mathematical rigor with the industrial organization tradition, but is similar to organizational ecology by emphasizing evolutionary dynamics. Evolutionary game theory may well be a complementary modeling tool for the analytical study of organizational ecology issues, next to formal logic, standard ga...

Strengths and Weaknesses of McNamara's Evolutionary Psychological Model of Dreaming

Directory of Open Access Journals (Sweden)

Sandra Olliges

2010-10-01

Full Text Available This article includes a brief overview of McNamara's (2004 evolutionary model of dreaming. The strengths and weaknesses of this model are then evaluated in terms of its consonance with measurable neurological and biological properties of dreaming, its fit within the tenets of evolutionary theories of dreams, and its alignment with evolutionary concepts of cooperation and spirituality. McNamara's model focuses primarily on dreaming that occurs during rapid eye movement (REM sleep; therefore this article also focuses on REM dreaming.

Evolutionary pulsational mode dynamics in nonthermal turbulent viscous astrofluids

Science.gov (United States)

Karmakar, Pralay Kumar; Dutta, Pranamika

2017-11-01

The pulsational mode of gravitational collapse in a partially ionized self-gravitating inhomogeneous viscous nonthermal nonextensive astrofluid in the presence of turbulence pressure is illustratively analyzed. The constitutive thermal species, lighter electrons and ions, are thermostatistically treated with the nonthermal κ-distribution laws. The inertial species, such as identical heavier neutral and charged dust microspheres, are modelled in the turbulent fluid framework. All the possible linear processes responsible for dust-dust collisions are accounted. The Larson logatropic equations of state relating the dust thermal (linear) and turbulence (nonlinear) pressures with dust densities are included. A regular linear normal perturbation analysis (local) over the complex astrocloud ensues in a generalized quartic dispersion relation with unique nature of plasma-dependent multi-parametric coefficients. A numerical standpoint is provided to showcase the basic mode features in a judicious astronomical paradigm. It is shown that both the kinematic viscosity of the dust fluids and nonthermality parameter (kappa, the power-law tail index) of the thermal species act as stabilizing (damping) agent against the gravity; and so forth. The underlying evolutionary microphysics is explored. The significance of redistributing astrofluid material via waveinduced accretion in dynamic nonhomologic structureless cloud collapse leading to hierarchical astrostructure formation is actualized.

Individual-based modeling of ecological and evolutionary processes

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DeAngelis, Donald L.; Mooij, Wolf M.

2005-01-01

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

Fixation times in evolutionary games under weak selection

International Nuclear Information System (INIS)

Altrock, Philipp M; Traulsen, Arne

2009-01-01

In evolutionary game dynamics, reproductive success increases with the performance in an evolutionary game. If strategy A performs better than strategy B, strategy A will spread in the population. Under stochastic dynamics, a single mutant will sooner or later take over the entire population or go extinct. We analyze the mean exit times (or average fixation times) associated with this process. We show analytically that these times depend on the payoff matrix of the game in an amazingly simple way under weak selection, i.e. strong stochasticity: the payoff difference Δπ is a linear function of the number of A individuals i, Δπ=u i+v. The unconditional mean exit time depends only on the constant term v. Given that a single A mutant takes over the population, the corresponding conditional mean exit time depends only on the density dependent term u. We demonstrate this finding for two commonly applied microscopic evolutionary processes.

Evolutionary Games with Randomly Changing Payoff Matrices

Science.gov (United States)

Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun

2015-06-01

Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

KAUST Repository

Jackson, Andrew P.

2014-05-05

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

KAUST Repository

Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

2014-01-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction

Science.gov (United States)

Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

2014-01-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. PMID:24799432

Quantifying evolutionary dynamics from variant-frequency time series

Science.gov (United States)

Khatri, Bhavin S.

2016-09-01

From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Evolutionary constrained optimization

CERN Document Server

Deb, Kalyanmoy

2015-01-01

This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

Evolutionary dynamics of mating-type loci of Mycosphaerella spp. occurring on banana.

Science.gov (United States)

Arzanlou, Mahdi; Crous, Pedro W; Zwiers, Lute-Harm

2010-01-01

The devastating Sigatoka disease complex of banana is primarily caused by three closely related heterothallic fungi belonging to the genus Mycosphaerella: M. fijiensis, M. musicola, and M. eumusae. Previous phylogenetic work showing common ancestry led us to analyze the mating-type loci of these Mycosphaerella species occurring on banana. We reasoned that this might provide better insight into the evolutionary history of these species. PCR and chromosome-walking approaches were used to clone the mating-type loci of M. musicola and M. eumusae. Sequences were compared to the published mating-type loci of M. fijiensis and other Mycosphaerella spp., and a novel organization of the MAT loci was found. The mating-type loci of the examined Mycosphaerella species are expanded, containing two additional Mycosphaerella-specific genes in a unique genomic organization. The proteins encoded by these novel genes show a higher interspecies than intraspecies homology. Moreover, M. fijiensis, M. musicola, and M. eumusae contain two additional mating-type-like loci, containing parts of both MAT1-1-1 and MAT1-2-1. The data indicate that M. fijiensis, M. musicola, and M. eumusae share an ancestor in which a fusion event occurred between MAT1-1-1 and MAT1-2-1 sequences and in which additional genes became incorporated into the idiomorph. The new genes incorporated have since then evolved independently in the MAT1-1 and MAT1-2 loci. Thus, these data are an example of the evolutionary dynamics of fungal MAT loci in general and show the great flexibility of the MAT loci of Mycosphaerella species in particular.

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

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Skippington, Elizabeth; Ragan, Mark A.

2012-01-01

Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli–Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli–Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks. PMID:22223756

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

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Pinky Langat

2017-12-01

Full Text Available The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

Science.gov (United States)

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

Evolutionary dynamics of hepatitis C virus NS3 protease domain during and following treatment with narlaprevir, a potent NS3 protease inhibitor

NARCIS (Netherlands)

de Bruijne, J.; Thomas, X. V.; Rebers, S. P.; Weegink, C. J.; Treitel, M. A.; Hughes, E.; Bergmann, J. F.; de Knegt, R. J.; Janssen, H. L. A.; Reesink, H. W.; Molenkamp, R.; Schinkel, J.

2013-01-01

Narlaprevir, a hepatitis C virus (HCV) NS3/4A serine protease inhibitor, has demonstrated robust antiviral activity in a placebo-controlled phase 1 study. To study evolutionary dynamics of resistant variants, the NS3 protease sequence was clonally analysed in thirty-two HCV genotype 1-infected

Despotism, democracy, and the evolutionary dynamics of leadership and followership.

Science.gov (United States)

Van Vugt, Mark

2009-01-01

Responds to comments made by George B. Graen and Stephen J. Guastello on the current author's article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. In the original article my co-authors and I proposed a new way of thinking about leadership, informed by evolutionary (neo-Darwinian) theory. In the first commentary, Graen noted that we ignored a number of recently developed psychological theories of leadership that take into account the leader-follower relationship, most notably LMX theory. LMX theory asserts that leadership effectiveness and team performance are affected by the quality of working relationships between superior and subordinates. Because the original article primarily dealt with questions about the origins of leadership--the phylogenetic and evolutionary causes--we had to be concise in our review of proximate psychological theories of leadership. In the second commentary, Guastello concurred with the importance of an evolutionary game analysis for studying leadership but disagreed with certain details of our analysis. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Infrastructure system restoration planning using evolutionary algorithms

Science.gov (United States)

Corns, Steven; Long, Suzanna K.; Shoberg, Thomas G.

2016-01-01

This paper presents an evolutionary algorithm to address restoration issues for supply chain interdependent critical infrastructure. Rapid restoration of infrastructure after a large-scale disaster is necessary to sustaining a nation's economy and security, but such long-term restoration has not been investigated as thoroughly as initial rescue and recovery efforts. A model of the Greater Saint Louis Missouri area was created and a disaster scenario simulated. An evolutionary algorithm is used to determine the order in which the bridges should be repaired based on indirect costs. Solutions were evaluated based on the reduction of indirect costs and the restoration of transportation capacity. When compared to a greedy algorithm, the evolutionary algorithm solution reduced indirect costs by approximately 12.4% by restoring automotive travel routes for workers and re-establishing the flow of commodities across the three rivers in the Saint Louis area.

Cooperative Evolutionary Game and Applications in Construction Supplier Tendency

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Qianqian Shi

2018-01-01

Full Text Available Major construction projects have a great influence on the national economy and society, wherein cooperative relationship between construction suppliers plays an increasingly significant role in the overall supply chain system. However, the relationships between suppliers are noncontractual, multistage, dynamic, and complicated. To gain a deeper insight into the suppliers’ cooperative relationships, an evolutionary game model is developed to explore the cooperation tendency of multisuppliers. A replicator dynamic system is further formulated to investigate the evolutionary stable strategies of multisuppliers. Then, fourteen “when-then” type scenarios are concluded and classified into six different evolutionary tracks. Meanwhile, the critical influencing factors are identified. The results show that the suppliers’ production capacity, owner-supplier contract, and the owner’s incentive mechanism influence the cooperation tendency of suppliers directly. The managerial implications contribute to insightful references for a more stable cooperative relationship between the owner and suppliers.

Differential Dynamic Evolutionary Model of Emergency Financial Service Supply Chain in Natural Disaster Risk Management

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Shujian Ma

2016-01-01

Full Text Available A government-market-public partnership (GMPP could be a feasible arrangement for providing insurance coverage for natural disaster. Firstly, we put forward GMPP management mode. Secondly, the emergency financial service supply chain for natural disaster risk is built from the view of supply chain. Finally, the objective of this paper is to obtain insights into the cooperative and competitive relationship in GMPP system. We establish the cooperative and competitive differential dynamic evolutionary models and prove the existence of equilibrium solutions in order to solve the coordination problems. In conclusion, the equilibrium solutions can be achieved among the insurers, the operating governments, and the public.

A Dynamic Neighborhood Learning-Based Gravitational Search Algorithm.

Science.gov (United States)

Zhang, Aizhu; Sun, Genyun; Ren, Jinchang; Li, Xiaodong; Wang, Zhenjie; Jia, Xiuping

2018-01-01

Balancing exploration and exploitation according to evolutionary states is crucial to meta-heuristic search (M-HS) algorithms. Owing to its simplicity in theory and effectiveness in global optimization, gravitational search algorithm (GSA) has attracted increasing attention in recent years. However, the tradeoff between exploration and exploitation in GSA is achieved mainly by adjusting the size of an archive, named , which stores those superior agents after fitness sorting in each iteration. Since the global property of remains unchanged in the whole evolutionary process, GSA emphasizes exploitation over exploration and suffers from rapid loss of diversity and premature convergence. To address these problems, in this paper, we propose a dynamic neighborhood learning (DNL) strategy to replace the model and thereby present a DNL-based GSA (DNLGSA). The method incorporates the local and global neighborhood topologies for enhancing the exploration and obtaining adaptive balance between exploration and exploitation. The local neighborhoods are dynamically formed based on evolutionary states. To delineate the evolutionary states, two convergence criteria named limit value and population diversity, are introduced. Moreover, a mutation operator is designed for escaping from the local optima on the basis of evolutionary states. The proposed algorithm was evaluated on 27 benchmark problems with different characteristic and various difficulties. The results reveal that DNLGSA exhibits competitive performances when compared with a variety of state-of-the-art M-HS algorithms. Moreover, the incorporation of local neighborhood topology reduces the numbers of calculations of gravitational force and thus alleviates the high computational cost of GSA.

Evolutionary dynamics of fluctuating populations with strong mutualism

Science.gov (United States)

Chotibut, Thiparat; Nelson, David

2013-03-01

Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.

Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs

NARCIS (Netherlands)

Wang, Xiaofang; Wei, Zhong; Li, Mei; Wang, Xueqi; Shan, Anqi; Mei, Xinlan; Jousset, Alexandre; Shen, Qirong; Xu, Yangchun; Friman, Ville Petri

2017-01-01

Parasites and competitors are important for regulating pathogen densities and subsequent disease dynamics. It is, however, unclear to what extent this is driven by ecological and evolutionary processes. Here, we used experimental evolution to study the eco-evolutionary feedbacks among Ralstonia

Co-Evolution of Opinion and Strategy in Persuasion Dynamics:. AN Evolutionary Game Theoretical Approach

Science.gov (United States)

Ding, Fei; Liu, Yun; Li, Yong

In this paper, a new model of opinion formation within the framework of evolutionary game theory is presented. The model simulates strategic situations when people are in opinion discussion. Heterogeneous agents adjust their behaviors to the environment during discussions, and their interacting strategies evolve together with opinions. In the proposed game, we take into account payoff discount to join a discussion, and the situation that people might drop out of an unpromising game. Analytical and emulational results show that evolution of opinion and strategy always tend to converge, with utility threshold, memory length, and decision uncertainty parameters influencing the convergence time. The model displays different dynamical regimes when we set differently the rule when people are at a loss in strategy.

Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau.

Science.gov (United States)

Zhao, Zhe; Li, Shuqiang

2017-11-01

Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic

Evolutionary competition between boundedly rational behavioral rules in oligopoly games

International Nuclear Information System (INIS)

Cerboni Baiardi, Lorenzo; Lamantia, Fabio; Radi, Davide

2015-01-01

In this paper, we propose an evolutionary model of oligopoly competition where agents can select between different behavioral rules to make decisions on productions. We formalize the model as a general class of evolutionary oligopoly games and then we consider an example with two specific rules, namely Local Monopolistic Approximation and Gradient dynamics. We provide several results on the global dynamic properties of the model, showing that in some cases the attractor of the system may belong to an invariant plane where only one behavioral rule is adopted (monomorphic state). The attractors on the invariant planes can be either strong attractors or weak attractors. However, we also explain why the system can be in a state of Evolutionary Stable Heterogeneity, where it is more profitable for the agents to employ both heuristics in the long term (polymorphic state).

Insect herbivores drive real-time ecological and evolutionary change in plant populations.

Science.gov (United States)

Agrawal, Anurag A; Hastings, Amy P; Johnson, Marc T J; Maron, John L; Salminen, Juha-Pekka

2012-10-05

Insect herbivores are hypothesized to be major factors affecting the ecology and evolution of plants. We tested this prediction by suppressing insects in replicated field populations of a native plant, Oenothera biennis, which reduced seed predation, altered interspecific competitive dynamics, and resulted in rapid evolutionary divergence. Comparative genotyping and phenotyping of nearly 12,000 O. biennis individuals revealed that in plots protected from insects, resistance to herbivores declined through time owing to changes in flowering time and lower defensive ellagitannins in fruits, whereas plant competitive ability increased. This independent real-time evolution of plant resistance and competitive ability in the field resulted from the relaxation of direct selective effects of insects on plant defense and through indirect effects due to reduced herbivory on plant competitors.

Local Dynamics of a Laser with Rapidly Oscillating Parameters

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E. V. Grigorieva

2013-01-01

Full Text Available The dynamics of class B lasers with the incoherent optical feedback formed by quickly vibrating external mirrors is viewed. The problem of the stability of equilibrium in a model system with rapidly oscillating coefficients is studied. The averaged system with the distributed delay is received. It is determined that in the presence of fast delay oscillation the limit of instability of a balance state moves towards significantly greater values of the feedback coefficient. The dependence of the shift with increasing the amplitude modulation has a band structure, so the rapid oscillations of delay can stabilize or destabilize the equilibrium. Normal forms which show changes of the sign of Lyapunov quantityalong border are constructed. They describe characteristics of periodic and quasiperiodic modes close to the balance state.

Rapid evolutionary change of common bean (Phaseolus vulgaris L plastome, and the genomic diversification of legume chloroplasts

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Dávila Guillermo

2007-07-01

Full Text Available Abstract Background Fabaceae (legumes is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes for these crops is limited. Results We sequenced the complete genome of the common bean (Phaseolus vulgaris cv. Negro Jamapa chloroplast. The plastome of P. vulgaris is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, rpl33 and rps16. A distinct inversion occurred at the junction points of trnH-GUG/rpl14 and rps19/rps8, as in adzuki bean 1. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, P. vulgaris plastome had higher evolutionary rates of change on both genomic and gene levels than G. max, which could be the consequence of pressure from both mutation and natural selection. Conclusion Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The P. vulgaris plastome is a rapidly evolving genome.

An evolutionary explanation of the value premium puzzle

OpenAIRE

Hens, Thorsten; Lensberg, Terje; Schenk-Hoppé, Klaus Reiner; Wöhrmann, Peter

2011-01-01

As early as 1934 Graham and Dodd conjectured that excess returns from value investment originate from a tendency of stock prices to converge towards a fundamental value. This paper confirms their insights within the evolutionary finance model of Evstigneev et al. (Econ Theory 27:449–468, (Evstigneev et al. 2006)). Our empirical results show the predictive power of the evolutionary benchmark valuation for the relative market capitalization and its dynamics in the sample of firms listed in the ...

Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

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Jiaqin Shi

Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

Science.gov (United States)

Shi, Jiaqin; Huang, Shunmou; Fu, Donghui; Yu, Jinyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2013-01-01

Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

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Timothée Bonnet

2017-01-01

Full Text Available In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative genetic models are able to provide us with an understanding of the causes and consequences of

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

Science.gov (United States)

Wandeler, Peter; Camenisch, Glauco

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

Neurogenomics and the role of a large mutational target on rapid behavioral change.

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Stanley, Craig E; Kulathinal, Rob J

2016-11-08

Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast

Rapid Assessment of Small Changes to Major Gun and Projectile Dynamic Parameters

National Research Council Canada - National Science Library

Erline, Thomas

1997-01-01

The U.S. Navy's 5-in 54-cal. (5"/54) gun system Mark (Mk) 45 was subjected to first-order dynamic analysis tools that allowed rapid assessment of ballistic dispersion of a typical naval high explosive projectile...

Robustness of cooperation in the evolutionary prisoner's dilemma on complex networks

International Nuclear Information System (INIS)

Poncela, J; Gomez-Gardenes, J; FlorIa, L M; Moreno, Y

2007-01-01

Recent studies on the evolutionary dynamics of the prisoner's dilemma game in scale-free networks have demonstrated that the heterogeneity of the network interconnections enhances the evolutionary success of cooperation. In this paper we address the issue of how the characterization of the asymptotic states of the evolutionary dynamics depends on the initial concentration of cooperators. We find that the measure and the connectedness properties of the set of nodes where cooperation reaches fixation is largely independent of initial conditions, in contrast with the behaviour of both the set of nodes where defection is fixed, and the fluctuating nodes. We also check for the robustness of these results when varying the degree heterogeneity along a one-parametric family of networks interpolating between the class of Erdos-Renyi graphs and the Barabasi-Albert networks

Remotely Sensed Predictions and In Situ Observations of Lower Congo River Dynamics in Support of Fish Evolutionary Biology

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Gardiner, N.; Bjerklie, D. M.

2011-12-01

Ongoing research into the evolution of fishes in the lower Congo River suggests a close tie between diversity and hydraulic complexity of flow in the channel. For example, fish populations on each side of the rapids at the head of the lower Congo are within 1.5 km of one another, a distance normally allowing for interbreeding in river systems of comparable size, yet these fish populations show about 5% divergence in their mitochondrial DNA signatures. The proximal reason for this divergence is hydraulic complexity: the speed and turbulence of water moving through the thalweg is a barrier to dispersal for these fishes. Further examination of fish diversity suggests additional correlations of evolutionary divergence of fish clades in association with geomorphic and hydraulic features such as deep pools, extensive systems of rapids, alternating sections of fast and slow current, and recurring whirlpools. Due to prohibitive travel costs, limited field time, and the large geographic domain (approximately 400 river km) of the study area, we undertook a nested set of remote sensing analyses to extract habitat features, geomorphic descriptors, and hydraulic parameters including channel forming velocity, depth, channel roughness, slope, and shear stress. Each of these estimated parameters is mapped for each 1 km segment of the river from the rapids described above to below Inga Falls, a massive cataract where several endemic fish species have been identified. To validate remote sensing estimates, we collected depth and velocity data within the river using gps-enabled sonar measurements from a kayak and Doppler profiling from a motor-driven dugout canoe. Observations corroborate remote sensing estimates of geomorphic parameters. Remote sensing-based estimates of channel-forming velocity and depth were less than the observed maximum channel depth but correlated well with channel properties within 1 km reach segments. This correspondence is notable. The empirical models used

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

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Jackson, Andrew P; Otto, Thomas D; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B; Moussa, Ehab; Nair, Mridul; Reid, Adam J; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A; Weir, William; Wastling, Jonathan M; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R; Pain, Arnab

2014-06-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5' ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Langley's CSI evolutionary model: Phase O

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Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.

1991-01-01

A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.

Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

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Andrea Sottoriva

2011-05-01

Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

Dynamic Power Dispatch Considering Electric Vehicles and Wind Power Using Decomposition Based Multi-Objective Evolutionary Algorithm

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Boyang Qu

2017-12-01

Full Text Available The intermittency of wind power and the large-scale integration of electric vehicles (EVs bring new challenges to the reliability and economy of power system dispatching. In this paper, a novel multi-objective dynamic economic emission dispatch (DEED model is proposed considering the EVs and uncertainties of wind power. The total fuel cost and pollutant emission are considered as the optimization objectives, and the vehicle to grid (V2G power and the conventional generator output power are set as the decision variables. The stochastic wind power is derived by Weibull probability distribution function. Under the premise of meeting the system energy and user’s travel demand, the charging and discharging behavior of the EVs are dynamically managed. Moreover, we propose a two-step dynamic constraint processing strategy for decision variables based on penalty function, and, on this basis, the Multi-Objective Evolutionary Algorithm Based on Decomposition (MOEA/D algorithm is improved. The proposed model and approach are verified by the 10-generator system. The results demonstrate that the proposed DEED model and the improved MOEA/D algorithm are effective and reasonable.

Random Evolutionary Dynamics Driven by Fitness and House-of-Cards Mutations: Sampling Formulae

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Huillet, Thierry E.

2017-07-01

We first revisit the multi-allelic mutation-fitness balance problem, especially when mutations obey a house of cards condition, where the discrete-time deterministic evolutionary dynamics of the allelic frequencies derives from a Shahshahani potential. We then consider multi-allelic Wright-Fisher stochastic models whose deviation to neutrality is from the Shahshahani mutation/selection potential. We next focus on the weak selection, weak mutation cases and, making use of a Gamma calculus, we compute the normalizing partition functions of the invariant probability densities appearing in their Wright-Fisher diffusive approximations. Using these results, generalized Ewens sampling formulae (ESF) from the equilibrium distributions are derived. We start treating the ESF in the mixed mutation/selection potential case and then we restrict ourselves to the ESF in the simpler house-of-cards mutations only situation. We also address some issues concerning sampling problems from infinitely-many alleles weak limits.

Origin and evolutionary dynamics of Hepatitis B virus (HBV) genotype E in Madagascar.

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Lo Presti, Alessandra; Andriamandimby, Soa Fy; Lai, Alessia; Angeletti, Silvia; Cella, Eleonora; Mottini, Giovanni; Guarino, Michele Pier Luca; Balotta, Claudia; Galli, Massimo; Heraud, Jean-Michel; Zehender, Gianguglielmo; Ciccozzi, Massimo

2017-02-01

Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

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Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

Selfish genetic elements, genetic conflict, and evolutionary innovation.

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Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Achieving sustainable plant disease management through evolutionary principles.

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Zhan, Jiasui; Thrall, Peter H; Burdon, Jeremy J

2014-09-01

Plants and their pathogens are engaged in continuous evolutionary battles and sustainable disease management requires novel systems to create environments conducive for short-term and long-term disease control. In this opinion article, we argue that knowledge of the fundamental factors that drive host-pathogen coevolution in wild systems can provide new insights into disease development in agriculture. Such evolutionary principles can be used to guide the formulation of sustainable disease management strategies which can minimize disease epidemics while simultaneously reducing pressure on pathogens to evolve increased infectivity and aggressiveness. To ensure agricultural sustainability, disease management programs that reflect the dynamism of pathogen population structure are essential and evolutionary biologists should play an increasing role in their design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolutionary Trails of Plant Group II Pyridoxal Phosphate-Dependent Decarboxylase Genes.

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Kumar, Rahul

2016-01-01

Type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) enzymes play important metabolic roles during nitrogen metabolism. Recent evolutionary profiling of these genes revealed a sharp expansion of histidine decarboxylase genes in the members of Solanaceae family. In spite of the high sequence homology shared by PLP_deC orthologs, these enzymes display remarkable differences in their substrate specificities. Currently, limited information is available on the gene repertoires and substrate specificities of PLP_deCs which renders their precise annotation challenging and offers technical challenges in the immediate identification and biochemical characterization of their full gene complements in plants. Herein, we explored their evolutionary trails in a comprehensive manner by taking advantage of high-throughput data accessibility and computational approaches. We discussed the premise that has enabled an improved reconstruction of their evolutionary lineage and evaluated the factors offering constraints in their rapid functional characterization, till date. We envisage that the synthesized information herein would act as a catalyst for the rapid exploration of their biochemical specificity and physiological roles in more plant species.

The four cornerstones of Evolutionary Toxicology.

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Bickham, John W

2011-05-01

Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © Springer Science+Business Media, LLC 2011

A method for rapid similarity analysis of RNA secondary structures

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Liu Na

2006-11-01

Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

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Cruz Luisa Ana B

2012-12-01

Full Text Available Abstract Background Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial temperature responses and adaptation, we studied glycolytic pathway kinetics in Saccharomyces cerevisiae during temperature changes. Results Saccharomyces cerevisiae was grown under different temperature regimes and glucose availability conditions. These included glucose-excess batch cultures at different temperatures and glucose-limited chemostat cultures, subjected to fast linear temperature shifts and circadian sinoidal temperature cycles. An observed temperature-independent relation between intracellular levels of glycolytic metabolites and residual glucose concentration for all experimental conditions revealed that it is the substrate availability rather than temperature that determines intracellular metabolite profiles. This observation corresponded with predictions generated in silico with a kinetic model of yeast glycolysis, when the catalytic capacities of all glycolytic enzymes were set to share the same normalized temperature dependency. Conclusions From an evolutionary perspective, such similar temperature dependencies allow cells to adapt more rapidly to temperature changes, because they result in minimal perturbations of intracellular metabolite levels, thus circumventing the need for extensive modification of enzyme levels.

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents.

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Gilbert, Scott F; Bosch, Thomas C G; Ledón-Rettig, Cristina

2015-10-01

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons.

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Mensi, Skander; Hagens, Olivier; Gerstner, Wulfram; Pozzorini, Christian

2016-02-01

The way in which single neurons transform input into output spike trains has fundamental consequences for network coding. Theories and modeling studies based on standard Integrate-and-Fire models implicitly assume that, in response to increasingly strong inputs, neurons modify their coding strategy by progressively reducing their selective sensitivity to rapid input fluctuations. Combining mathematical modeling with in vitro experiments, we demonstrate that, in L5 pyramidal neurons, the firing threshold dynamics adaptively adjust the effective timescale of somatic integration in order to preserve sensitivity to rapid signals over a broad range of input statistics. For that, a new Generalized Integrate-and-Fire model featuring nonlinear firing threshold dynamics and conductance-based adaptation is introduced that outperforms state-of-the-art neuron models in predicting the spiking activity of neurons responding to a variety of in vivo-like fluctuating currents. Our model allows for efficient parameter extraction and can be analytically mapped to a Generalized Linear Model in which both the input filter--describing somatic integration--and the spike-history filter--accounting for spike-frequency adaptation--dynamically adapt to the input statistics, as experimentally observed. Overall, our results provide new insights on the computational role of different biophysical processes known to underlie adaptive coding in single neurons and support previous theoretical findings indicating that the nonlinear dynamics of the firing threshold due to Na+-channel inactivation regulate the sensitivity to rapid input fluctuations.

EVOLUTIONARY APPROACH TO DETERMINATION OF STRUCTURE OF TAX SYSTEM

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Nathalie V. Yurchenkova

2013-01-01

Full Text Available Capacity of national tax systems isn’t fully revealed across all countries. Problems with tax administration, tax avoidance, leaving from the taxation of corporations and the leading financial organizations in the offshore confirm adaptation hypothesis stating that taxpayers adapt for changes in times quicker and more qualitatively than the state institutes. The leading role in formation of an evolutionary paradigm of the taxation belongs now to tools of evolutionary dynamics at social level.

Evolutionary change in physiological phenotypes along the human lineage.

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Vining, Alexander Q; Nunn, Charles L

2016-01-01

Research in evolutionary medicine provides many examples of how evolution has shaped human susceptibility to disease. Traits undergoing rapid evolutionary change may result in associated costs or reduce the energy available to other traits. We hypothesize that humans have experienced more such changes than other primates as a result of major evolutionary change along the human lineage. We investigated 41 physiological traits across 50 primate species to identify traits that have undergone marked evolutionary change along the human lineage. We analysed the data using two Bayesian phylogenetic comparative methods. One approach models trait covariation in non-human primates and predicts human phenotypes to identify whether humans are evolutionary outliers. The other approach models adaptive shifts under an Ornstein-Uhlenbeck model of evolution to assess whether inferred shifts are more common on the human branch than on other primate lineages. We identified four traits with strong evidence for an evolutionary increase on the human lineage (amylase, haematocrit, phosphorus and monocytes) and one trait with strong evidence for decrease (neutrophilic bands). Humans exhibited more cases of distinct evolutionary change than other primates. Human physiology has undergone increased evolutionary change compared to other primates. Long distance running may have contributed to increases in haematocrit and mean corpuscular haemoglobin concentration, while dietary changes are likely related to increases in amylase. In accordance with the pathogen load hypothesis, human monocyte levels were increased, but many other immune-related measures were not. Determining the mechanisms underlying conspicuous evolutionary change in these traits may provide new insights into human disease. The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

Evolutionary Dynamics of Mating-Type Loci of Mycosphaerella spp. Occurring on Banana▿ †

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Arzanlou, Mahdi; Crous, Pedro W.; Zwiers, Lute-Harm

2010-01-01

The devastating Sigatoka disease complex of banana is primarily caused by three closely related heterothallic fungi belonging to the genus Mycosphaerella: M. fijiensis, M. musicola, and M. eumusae. Previous phylogenetic work showing common ancestry led us to analyze the mating-type loci of these Mycosphaerella species occurring on banana. We reasoned that this might provide better insight into the evolutionary history of these species. PCR and chromosome-walking approaches were used to clone the mating-type loci of M. musicola and M. eumusae. Sequences were compared to the published mating-type loci of M. fijiensis and other Mycosphaerella spp., and a novel organization of the MAT loci was found. The mating-type loci of the examined Mycosphaerella species are expanded, containing two additional Mycosphaerella-specific genes in a unique genomic organization. The proteins encoded by these novel genes show a higher interspecies than intraspecies homology. Moreover, M. fijiensis, M. musicola, and M. eumusae contain two additional mating-type-like loci, containing parts of both MAT1-1-1 and MAT1-2-1. The data indicate that M. fijiensis, M. musicola, and M. eumusae share an ancestor in which a fusion event occurred between MAT1-1-1 and MAT1-2-1 sequences and in which additional genes became incorporated into the idiomorph. The new genes incorporated have since then evolved independently in the MAT1-1 and MAT1-2 loci. Thus, these data are an example of the evolutionary dynamics of fungal MAT loci in general and show the great flexibility of the MAT loci of Mycosphaerella species in particular. PMID:19915079

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.

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Gilpin, William; Feldman, Marcus W

2017-07-01

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.

Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

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Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

2017-12-12

Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.

Rapid freezing of water under dynamic compression

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Myint, Philip C.; Belof, Jonathan L.

2018-06-01

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid–ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

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Podder Soumita

2012-01-01

Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

An evolutionary cosmology for scientists--and the modern world in general.

Science.gov (United States)

Charlton, Bruce G

2007-01-01

I believe that people will not feel comfortable and positive about the contemporary world until we can endorse and believe an evolutionary cosmology which is appropriate to modern conditions. A cosmology is a mythical account of the universe as it presents itself to the human mind; it needs to be poetic, symbolic, inspiring of a sense of awe and mystery. Furthermore, a complete cosmology should include the three levels of macro-, meso- and micro-cosm, in order to understand the nature of the universe, human society, and the individual's relation to them. Traditional cosmologies described an eternal underlying structure to ultimate reality--a static ideal state towards which the world ought to gravitate. However, modern life is characterized by rapid growth, novelty, destruction and fluidity of all kinds of structures, a feature which traditional static cosmologies interpret negatively and pessimistically. A modern cosmology therefore needs to be focused on underlying dynamic process instead of structure and stasis. Biologists are better placed than many to appreciate a cosmology based on evolutionary change; because this is the mainstream understanding of adaptation and diversity in the natural world. The same dynamic, neophiliac and open-ended process of 'creative destruction' can be seen at work in science, economics, and modern spirituality. But a modern cosmology will only be experienced as both deep and spontaneous when it takes the form of a mythic account that is first encountered and assimilated during childhood. Since myths arise as a consequence of human creativity; there is a vital future mythogenic role for artists in the realm of ideas, images and stories: people such as mystics, poets and philosophers--including, I hope and expect, creatively inspired scientists.

Reduced larval feeding rate is a strong evolutionary correlate of ...

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 85; Issue 3. Reduced larval feeding rate is a strong evolutionary correlate of rapid development in Drosophila melanogaster. M. Rajamani N. Raghavendra ... Keywords. life-history evolution; development time; larval feeding rate; competition; tradeoffs; Drosophila melanogaster.

Evolutionary Sound Synthesis Controlled by Gestural Data

Directory of Open Access Journals (Sweden)

Jose Fornari

2011-05-01

Full Text Available This article focuses on the interdisciplinary research involving Computer Music and Generative Visual Art. We describe the implementation of two interactive artistic systems based on principles of Gestural Data (WILSON, 2002 retrieval and self-organization (MORONI, 2003, to control an Evolutionary Sound Synthesis method (ESSynth. The first implementation uses, as gestural data, image mapping of handmade drawings. The second one uses gestural data from dynamic body movements of dance. The resulting computer output is generated by an interactive system implemented in Pure Data (PD. This system uses principles of Evolutionary Computation (EC, which yields the generation of a synthetic adaptive population of sound objects. Considering that music could be seen as “organized sound” the contribution of our study is to develop a system that aims to generate "self-organized sound" – a method that uses evolutionary computation to bridge between gesture, sound and music.

Diabetes and Obesity—An Evolutionary Perspective

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Sylvia Kirchengast

2017-01-01

Full Text Available Obesity and type II diabetes belong to the most serious public health challenges of the 21st century. Initially both diseases were typical of affluent societies. Currently both conditions however are increasingly found in low and middle income countries. In future obesity and diabetes are expected to reach epidemic proportions and affect developing countries to a greater extent than developed ones. A globalization of obesity and diabetes is observable. Recently prevalence rates increased, especially in Asia, the Near and Middle East, the Western Pacific region and even in Sub-Saharan Africa. Evolutionary Anthropology tries to understand the evolutionary mechanisms promoting rising obesity and diabetes type II rates. Homo sapiens evolved in an environment quite different from our recent one. Profound changes in physical activity patterns and nutritional habits during the last 10,000 years and increasingly during the last 200 years increased the risk of obesity and diabetes type II. Consequently our recent environment is called “obesogenic”. This mismatch has been recently observable among societies experiencing rapid cultural changes characterized by Westernization and modernization. This review focuses on obesity and type II diabetes from the viewpoint of evolutionary anthropology.

Genome landscape and evolutionary plasticity of chromosomes in malaria mosquitoes.

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Ai Xia

2010-05-01

Full Text Available Nonrandom distribution of rearrangements is a common feature of eukaryotic chromosomes that is not well understood in terms of genome organization and evolution. In the major African malaria vector Anopheles gambiae, polymorphic inversions are highly nonuniformly distributed among five chromosomal arms and are associated with epidemiologically important adaptations. However, it is not clear whether the genomic content of the chromosomal arms is associated with inversion polymorphism and fixation rates.To better understand the evolutionary dynamics of chromosomal inversions, we created a physical map for an Asian malaria mosquito, Anopheles stephensi, and compared it with the genome of An. gambiae. We also developed and deployed novel Bayesian statistical models to analyze genome landscapes in individual chromosomal arms An. gambiae. Here, we demonstrate that, despite the paucity of inversion polymorphisms on the X chromosome, this chromosome has the fastest rate of inversion fixation and the highest density of transposable elements, simple DNA repeats, and GC content. The highly polymorphic and rapidly evolving autosomal 2R arm had overrepresentation of genes involved in cellular response to stress supporting the role of natural selection in maintaining adaptive polymorphic inversions. In addition, the 2R arm had the highest density of regions involved in segmental duplications that clustered in the breakpoint-rich zone of the arm. In contrast, the slower evolving 2L, 3R, and 3L, arms were enriched with matrix-attachment regions that potentially contribute to chromosome stability in the cell nucleus.These results highlight fundamental differences in evolutionary dynamics of the sex chromosome and autosomes and revealed the strong association between characteristics of the genome landscape and rates of chromosomal evolution. We conclude that a unique combination of various classes of genes and repetitive DNA in each arm, rather than a single type

The faith dynamic in creationism and evolutionary theory

OpenAIRE

Jackson, Edgar Basil

2012-01-01

This study attempts to examine evolutionary theory and creationism objectively without engaging in an apology for or a criticism of either. It compares the presuppositions and assumptions of both systems, and examines the role of faith in religion and in the scientific theory of evolution. After discussing the nature of the scientific method and the development of the theory of evolution, the study explores the dichotomy of faith and reason, the ways in which these operate in theories of int...

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

Science.gov (United States)

Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

2016-05-01

Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary dynamics of populations with conflicting interactions: Classification and analytical treatment considering asymmetry and power

Science.gov (United States)

Helbing, Dirk; Johansson, Anders

2010-01-01

Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination or cooperation of interacting entities will occur, be it spins, particles, bacteria, animals, or humans. Here, we analyze the case, where the entities are heterogeneous, particularly the case of two populations with conflicting interactions and two possible states. For such systems, explicit mathematical formulas will be determined for the stationary solutions and the associated eigenvalues, which determine their stability. In this way, four different types of system dynamics can be classified and the various kinds of phase transitions between them will be discussed. While these results are interesting from a physics point of view, they are also relevant for social, economic, and biological systems, as they allow one to understand conditions for (1) the breakdown of cooperation, (2) the coexistence of different behaviors (“subcultures”), (3) the evolution of commonly shared behaviors (“norms”), and (4) the occurrence of polarization or conflict. We point out that norms have a similar function in social systems that forces have in physics.

An Evolutionary Framework for Understanding the Origin of Eukaryotes

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Neil W. Blackstone

2016-04-01

Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Evolutionary modeling-based approach for model errors correction

Directory of Open Access Journals (Sweden)

S. Q. Wan

2012-08-01

Full Text Available The inverse problem of using the information of historical data to estimate model errors is one of the science frontier research topics. In this study, we investigate such a problem using the classic Lorenz (1963 equation as a prediction model and the Lorenz equation with a periodic evolutionary function as an accurate representation of reality to generate "observational data."

On the basis of the intelligent features of evolutionary modeling (EM, including self-organization, self-adaptive and self-learning, the dynamic information contained in the historical data can be identified and extracted by computer automatically. Thereby, a new approach is proposed to estimate model errors based on EM in the present paper. Numerical tests demonstrate the ability of the new approach to correct model structural errors. In fact, it can actualize the combination of the statistics and dynamics to certain extent.

Exponential Expansion in Evolutionary Economics

DEFF Research Database (Denmark)

Frederiksen, Peter; Jagtfelt, Tue

2013-01-01

This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...

Hidden long evolutionary memory in a model biochemical network

Science.gov (United States)

Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2018-04-01

We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

Science.gov (United States)

Vlachostergios, Panagiotis J; Faltas, Bishoy M

2018-05-02

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

Evolutionary stability concepts in a stochastic environment

Science.gov (United States)

Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi

2017-09-01

Over the past 30 years, evolutionary game theory and the concept of an evolutionarily stable strategy have been not only extensively developed and successfully applied to explain the evolution of animal behaviors, but also widely used in economics and social sciences. Nonetheless, the stochastic dynamical properties of evolutionary games in randomly fluctuating environments are still unclear. In this study, we investigate conditions for stochastic local stability of fixation states and constant interior equilibria in a two-phenotype model with random payoffs following pairwise interactions. Based on this model, we develop the concepts of stochastic evolutionary stability (SES) and stochastic convergence stability (SCS). We show that the condition for a pure strategy to be SES and SCS is more stringent than in a constant environment, while the condition for a constant mixed strategy to be SES is less stringent than the condition to be SCS, which is less stringent than the condition in a constant environment.

Suppression of chaos at slow variables by rapidly mixing fast dynamics

Science.gov (United States)

Abramov, R.

2012-04-01

One of the key questions about chaotic multiscale systems is how the fast dynamics affects chaos at the slow variables, and, therefore, impacts uncertainty and predictability of the slow dynamics. Here we demonstrate that the linear slow-fast coupling with the total energy conservation property promotes the suppression of chaos at the slow variables through the rapid mixing at the fast variables, both theoretically and through numerical simulations. A suitable mathematical framework is developed, connecting the slow dynamics on the tangent subspaces to the infinite-time linear response of the mean state to a constant external forcing at the fast variables. Additionally, it is shown that the uncoupled dynamics for the slow variables may remain chaotic while the complete multiscale system loses chaos and becomes completely predictable at the slow variables through increasing chaos and turbulence at the fast variables. This result contradicts the common sense intuition, where, naturally, one would think that coupling a slow weakly chaotic system with another much faster and much stronger mixing system would result in general increase of chaos at the slow variables.

A Distributed Dynamic Super Peer Selection Method Based on Evolutionary Game for Heterogeneous P2P Streaming Systems

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Jing Chen

2013-01-01

Full Text Available Due to high efficiency and good scalability, hierarchical hybrid P2P architecture has drawn more and more attention in P2P streaming research and application fields recently. The problem about super peer selection, which is the key problem in hybrid heterogeneous P2P architecture, is becoming highly challenging because super peers must be selected from a huge and dynamically changing network. A distributed super peer selection (SPS algorithm for hybrid heterogeneous P2P streaming system based on evolutionary game is proposed in this paper. The super peer selection procedure is modeled based on evolutionary game framework firstly, and its evolutionarily stable strategies are analyzed. Then a distributed Q-learning algorithm (ESS-SPS according to the mixed strategies by analysis is proposed for the peers to converge to the ESSs based on its own payoff history. Compared to the traditional randomly super peer selection scheme, experiments results show that the proposed ESS-SPS algorithm achieves better performance in terms of social welfare and average upload rate of super peers and keeps the upload capacity of the P2P streaming system increasing steadily with the number of peers increasing.

Evolutionary programming for goal-driven dynamic planning

Science.gov (United States)

Vaccaro, James M.; Guest, Clark C.; Ross, David O.

2002-03-01

one step closer to solving more difficult real-world AI problems. Using a hybrid approach that includes adaptation via evolutionary computation for the intelligent planning of a Risk player's turn provides better dynamic intelligent planning than more uniform approaches.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

OpenAIRE

Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V

2007-01-01

Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...

Dynamic Ising model: reconstruction of evolutionary trees

International Nuclear Information System (INIS)

De Oliveira, P M C

2013-01-01

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N − 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed. (paper)

Evolutionary Nephrology.

Science.gov (United States)

Chevalier, Robert L

2017-05-01

Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

Evolutionary Nephrology

Directory of Open Access Journals (Sweden)

Robert L. Chevalier

2017-05-01

Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

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Yuki Furuse

2016-11-01

Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

A rapid loss of stripes: the evolutionary history of the extinct quagga

OpenAIRE

Leonard, Jennifer A; Rohland, Nadin; Glaberman, Scott; Fleischer, Robert C; Caccone, Adalgisa; Hofreiter, Michael

2005-01-01

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature 312, 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated...

Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.

Science.gov (United States)

Prisilla, A; Prathiviraj, R; Chellapandi, P

2017-04-01

Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.

Evolutionary games under incompetence.

Science.gov (United States)

Kleshnina, Maria; Filar, Jerzy A; Ejov, Vladimir; McKerral, Jody C

2018-02-26

The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here, we investigate this process by combining the idea of incompetence with evolutionary game theory. In the sense of evolution, incompetence and training can be interpreted as a special learning process. With focus on the social side of the problem, we analyze the influence of incompetence on behavior of species. We introduce an incompetence parameter into a learning function in a single-population game and analyze its effect on the outcome of the replicator dynamics. Incompetence can change the outcome of the game and its dynamics, indicating its significance within what are inherently imperfect natural systems.

Synergistic Coherence of Bifurcation Evolutionary Processes of Mergers and Acquisitions of Enterprises

Directory of Open Access Journals (Sweden)

Ivanchenko Hennadii F.

2016-08-01

Full Text Available The aim of the article is developing information tools for the economic and mathematical modeling of the dynamics of evolutionary processes concerning trophic relationships of populations of enterprises, which allowed to conduct the phase and bifurcation analysis of possible dynamic regimes of the populations’ evolution, determine the mechanisms of influence of the external environment and the internal structure of the system, identify patterns and limits of stability of M&A processes. In the work the main provisions of the evolutionary concept concerning development of the population of enterprises as an economic system are analyzed, the provisions of the evolutionary concept of population systems’ development are considered, the basis of evolutionary modeling methods allowing to analyze the functioning of populations of enterprises in terms of individual strategies of each enterprise’s behavior is studied. The basic principles of synergy of the life cycle evolution for populations of enterprises are determined. An evolutionary approach to the evaluation of a synergistic effect of M & A is proposed. The evolutionary modeling of the scenario for self-organization of populations of dairy industry enterprises through a combination of statistical and expert data is applied. There also created a model of the population of firms reflecting behavioral and resource and technological characteristics of the studied in the work real population of industrial enterprises, which form the input flows of matter, energy and information to the dairy industry, which allows to combine the reflection of main possible options in terms of the external conditions of the population functioning and its internal structure.

Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

Science.gov (United States)

Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

2017-10-01

Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

Stochastic Dynamics through Hierarchically Embedded Markov Chains.

Science.gov (United States)

Vasconcelos, Vítor V; Santos, Fernando P; Santos, Francisco C; Pacheco, Jorge M

2017-02-03

Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects-such as mutations in evolutionary dynamics and a random exploration of choices in social systems-including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

Science.gov (United States)

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The extended evolutionary synthesis: its structure, assumptions and predictions

Science.gov (United States)

Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

2015-01-01

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

Evolutionary molecular medicine.

Science.gov (United States)

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.

Science.gov (United States)

Tannenbaum, Emmanuel; Sherley, James L; Shakhnovich, Eugene I

2005-04-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell and (2) "immortal DNA strand" co-segregation, for which the stem cell retains the daughter chromosomes with the oldest parent strands. Immortal strand co-segregation is a mechanism, originally proposed by [Cairns Nature (London) 255, 197 (1975)], by which stem cells preserve the integrity of their genomes. For random segregation, we develop an ordered strand pair formulation of the dynamics, analogous to the ordered strand pair formalism developed for quasispecies dynamics involving semiconservative replication with imperfect lesion repair (in this context, lesion repair is taken to mean repair of postreplication base-pair mismatches). Interestingly, a similar formulation is possible with immortal strand co-segregation, despite the fact that this segregation mechanism is age dependent. From our model we are able to mathematically show that, when lesion repair is imperfect, then immortal strand co-segregation leads to better preservation of the stem cell lineage than random chromosome segregation. Furthermore, our model allows us to estimate the optimal lesion repair efficiency for preserving an adult stem cell population for a given period of time. For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands.

An Extensible Component-Based Multi-Objective Evolutionary Algorithm Framework

DEFF Research Database (Denmark)

Sørensen, Jan Corfixen; Jørgensen, Bo Nørregaard

2017-01-01

The ability to easily modify the problem definition is currently missing in Multi-Objective Evolutionary Algorithms (MOEA). Existing MOEA frameworks do not support dynamic addition and extension of the problem formulation. The existing frameworks require a re-specification of the problem definition...

Rapid cable tension estimation using dynamic and mechanical properties

Science.gov (United States)

Martínez-Castro, Rosana E.; Jang, Shinae; Christenson, Richard E.

2016-04-01

Main tension elements are critical to the overall stability of cable-supported bridges. A dependable and rapid determination of cable tension is desired to assess the state of a cable-supported bridge and evaluate its operability. A portable smart sensor setup is presented to reduce post-processing time and deployment complexity while reliably determining cable tension using dynamic characteristics extracted from spectral analysis. A self-recording accelerometer is coupled with a single-board microcomputer that communicates wirelessly with a remote host computer. The portable smart sensing device is designed such that additional algorithms, sensors and controlling devices for various monitoring applications can be installed and operated for additional structural assessment. The tension-estimating algorithms are based on taut string theory and expand to consider bending stiffness. The successful combination of cable properties allows the use of a cable's dynamic behavior to determine tension force. The tension-estimating algorithms are experimentally validated on a through-arch steel bridge subject to ambient vibration induced by passing traffic. The tension estimation is determined in well agreement with previously determined tension values for the structure.

A network growth model based on the evolutionary ultimatum game

International Nuclear Information System (INIS)

Deng, L L; Zhou, G G; Cai, J H; Wang, C; Tang, W S

2012-01-01

In this paper, we provide a network growth model with incorporation into the ultimatum game dynamics. The network grows on the basis of the payoff-oriented preferential attachment mechanism, where a new node is added into the network and attached preferentially to nodes with higher payoffs. The interplay between the network growth and the game dynamics gives rise to quite interesting dynamical behaviors. Simulation results show the emergence of altruistic behaviors in the ultimatum game, which is affected by the growing network structure. Compared with the static counterpart case, the levels of altruistic behaviors are promoted. The corresponding strategy distributions and wealth distributions are also presented to further demonstrate the strategy evolutionary dynamics. Subsequently, we turn to the topological properties of the evolved network, by virtue of some statistics. The most studied characteristic path length and the clustering coefficient of the network are shown to indicate their small-world effect. Then the degree distributions are analyzed to clarify the interplay of structure and evolutionary dynamics. In particular, the difference between our growth network and the static counterpart is revealed. To explain clearly the evolved networks, the rich-club ordering and the assortative mixing coefficient are exploited to reveal the degree correlation. (paper)

Evolutionary diversity and turn-over of sex determination in teleost fishes.

Science.gov (United States)

Mank, J E; Avise, J C

2009-01-01

Sex determination, due to the obvious association with reproduction and Darwinian fitness, has been traditionally assumed to be a relatively conserved trait. However, research on teleost fishes has shown that this need not be the case, as these animals display a remarkable diversity in the ways that they determine sex. These different mechanisms, which include constitutive genetic mechanisms on sex chromosomes, polygenic constitutive mechanisms, environmental influences, hermaphroditism, and unisexuality have each originated numerous independent times in the teleosts. The evolutionary lability of sex determination, and the corresponding rapid rate of turn-over among different modes, makes the teleost clade an excellent model with which to test theories regarding the evolution of sex determining adaptations. Much of the plasticity in sex determination likely results from the dynamic teleost genome, and recent advances in fish genetics and genomics have revealed the role of gene and genome duplication in fostering emergence and turn-over of sex determining mechanisms. 2009 S. Karger AG, Basel.

On the Existence of Evolutionary Learning Equilibriums

Directory of Open Access Journals (Sweden)

Masudul Alam Choudhury

2011-12-01

Full Text Available The usual kinds of Fixed-Point Theorems formalized on the existence of competitive equilibrium that explain much of economic theory at the core of economics can operate only on bounded and closed sets with convex mappings. But these conditions are hardly true of the real world of economic and financial complexities and perturbations. The category of learning sets explained by continuous fields of interactive, integrative and evolutionary behaviour caused by dynamic preferences at the individual and institutional and social levels cannot maintain the assumption of closed, bounded and convex sets. Thus learning sets and multi-system inter-temporal relations explained by pervasive complementarities and  participation between variables and entities, and evolution by learning, have evolutionary equilibriums. Such a study requires a new methodological approach. This paper formalizes such a methodology for evolutionary equilibriums in learning spaces. It briefly points out the universality of learning equilibriums in all mathematical structures. For a particular case though, the inter-systemic interdependence between sustainable development and ethics and economics in the specific understanding of learning domain is pointed out.

When Reputation Enforces Evolutionary Cooperation in Unreliable MANETs.

Science.gov (United States)

Tang, Changbing; Li, Ang; Li, Xiang

2015-10-01

In self-organized mobile ad hoc networks (MANETs), network functions rely on cooperation of self-interested nodes, where a challenge is to enforce their mutual cooperation. In this paper, we study cooperative packet forwarding in a one-hop unreliable channel which results from loss of packets and noisy observation of transmissions. We propose an indirect reciprocity framework based on evolutionary game theory, and enforce cooperation of packet forwarding strategies in both structured and unstructured MANETs. Furthermore, we analyze the evolutionary dynamics of cooperative strategies and derive the threshold of benefit-to-cost ratio to guarantee the convergence of cooperation. The numerical simulations verify that the proposed evolutionary game theoretic solution enforces cooperation when the benefit-to-cost ratio of the altruistic exceeds the critical condition. In addition, the network throughput performance of our proposed strategy in structured MANETs is measured, which is in close agreement with that of the full cooperative strategy.

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

NARCIS (Netherlands)

A.F. van Belkum (Alex); M. Struelens; A. de Visser (Arjan); H.A. Verbrugh (Henri); M. Tibayrench

2001-01-01

textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and

Eco-evolutionary feedback and the invasion of cooperation in prisoner's dilemma games.

Directory of Open Access Journals (Sweden)

Feng Zhang

Full Text Available Unveiling the origin and forms of cooperation in nature poses profound challenges in evolutionary ecology. The prisoner's dilemma game is an important metaphor for studying the evolution of cooperation. We here classified potential mechanisms for cooperation evolution into schemes of frequency- and density-dependent selection, and focused on the density-dependent selection in the ecological prisoner's dilemma games. We found that, although assortative encounter is still the necessary condition in ecological games for cooperation evolution, a harsh environment, indicated by a high mortality, can foster the invasion of cooperation. The Hamilton rule provides a fundamental condition for the evolution of cooperation by ensuring an enhanced relatedness between players in low-density populations. Incorporating ecological dynamics into evolutionary games opens up a much wider window for the evolution of cooperation, and exhibits a variety of complex behaviors of dynamics, such as limit and heteroclinic cycles. An alternative evolutionary, or rather succession, sequence was proposed that cooperation first appears in harsh environments, followed by the invasion of defection, which leads to a common catastrophe. The rise of cooperation (and altruism, thus, could be much easier in the density-dependent ecological games than in the classic frequency-dependent evolutionary games.

Stochastic evolutionary dynamics in minimum-effort coordination games

Science.gov (United States)

Li, Kun; Cong, Rui; Wang, Long

2016-08-01

The minimum-effort coordination game draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classical game theory. Here, we combine evolutionary game theory and coalescence theory to investigate this game in finite populations. Both analytic results and individual-based simulations show that effort costs play a key role in the evolution of contribution levels, which is in good agreement with those observed experimentally. Besides well-mixed populations, set structured populations have also been taken into consideration. Therein we find that large number of sets and moderate migration rate greatly promote effort levels, especially for high effort costs.

An evolutionary perspective on anti-tumor immunity

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David John Klinke

2013-01-01

Full Text Available The challenges associated with demonstrating a durable response using molecular targeted therapies in cancer has sparked a renewed interest in viewing cancer from an evolutionary perspective. Evolutionary processes have three common traits: heterogeneity, dynamics, and a selective fitness landscape. Mutagens randomly alter the genome of host cells creating a population of cells that contain different somatic mutations. This genomic rearrangement perturbs cellular homeostasis through changing how cells interact with their tissue microenvironment. To counterbalance the ability of mutated cells to outcompete for limited resources, control structures are encoded within the cell and within the organ system, such as innate and adaptive immunity, to restore cellular homeostasis. These control structures shape the selective fitness landscape and determine whether a cell that harbors particular somatic mutations is retained or eliminated from a cell population. While next-generation sequencing has revealed the complexity and heterogeneity of oncogenic transformation, understanding the dynamics of oncogenesis and how cancer cells alter the selective fitness landscape remain unclear. In this technology review, we will summarize how recent advances in technology have impacted our understanding of these three attributes of cancer as an evolutionary process. In particular, we will focus on how advances in genome sequencing have enabled quantifying cellular heterogeneity, advances in computational power have enabled explicit testing of postulated intra- and intercellular control structures against the available data using simulation, and advances in proteomics have enabled identifying novel mechanisms of cellular cross-talk that cancer cells use to alter the fitness landscape.

Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae and its diploid relatives.

Directory of Open Access Journals (Sweden)

Xing Fan

Full Text Available The level and pattern of nucleotide variation in duplicate gene provide important information on the evolutionary history of polyploids and divergent process between homoeologous loci within lineages. Kengyilia is a group of allohexaploid species with the StYP genomic constitutions in the wheat tribe. To investigate the evolutionary dynamics of the Pgk1 gene in Kengyilia and its diploid relatives, three copies of Pgk1 homoeologues were isolated from all sampled hexaploid Kengyilia species and analyzed with the Pgk1 sequences from 47 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1 Kengyilia species from the Central Asia and the Qinghai-Tibetan plateau have independent origins with geographically differentiated P genome donors and diverged levels of nucleotide diversity at Pgk1 locus; (2 a relatively long-time sweep event has allowed the Pgk1 gene within Agropyron to adapt to cold climate triggered by the recent uplifts of the Qinghai-Tibetan Plateau; (3 sweep event and population expansion might result in the difference in the d(N/d(S value of the Pgk1 gene in allopatric Agropyron populations, and this difference may be genetically transmitted to Kengyilia lineages via independent polyploidization events; (4 an 83 bp MITE element insertion has shaped the Pgk1 loci in the P genome lineage with different geographical regions; (5 the St and P genomes in Kengyilia were donated by Pseudoroegneria and Agropyron, respectively, and the Y genome is closely related to the Xp genome of Peridictyon sanctum. The interplay of evolutionary forces involving diverged natural selection, population expansion, and transposable events in geographically differentiated P genome donors could attribute to geographical differentiation of Kengyilia species via independent origins.

A multilevel evolutionary framework for sustainability analysis

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Timothy M. Waring

2015-06-01

Full Text Available Sustainability theory can help achieve desirable social-ecological states by generalizing lessons across contexts and improving the design of sustainability interventions. To accomplish these goals, we argue that theory in sustainability science must (1 explain the emergence and persistence of social-ecological states, (2 account for endogenous cultural change, (3 incorporate cooperation dynamics, and (4 address the complexities of multilevel social-ecological interactions. We suggest that cultural evolutionary theory broadly, and cultural multilevel selection in particular, can improve on these fronts. We outline a multilevel evolutionary framework for describing social-ecological change and detail how multilevel cooperative dynamics can determine outcomes in environmental dilemmas. We show how this framework complements existing sustainability frameworks with a description of the emergence and persistence of sustainable institutions and behavior, a means to generalize causal patterns across social-ecological contexts, and a heuristic for designing and evaluating effective sustainability interventions. We support these assertions with case examples from developed and developing countries in which we track cooperative change at multiple levels of social organization as they impact social-ecological outcomes. Finally, we make suggestions for further theoretical development, empirical testing, and application.

Large fluctuations and fixation in evolutionary games

International Nuclear Information System (INIS)

Assaf, Michael; Mobilia, Mauro

2010-01-01

We study large fluctuations in evolutionary games belonging to the coordination and anti-coordination classes. The dynamics of these games, modeling cooperation dilemmas, is characterized by a coexistence fixed point separating two absorbing states. We are particularly interested in the problem of fixation that refers to the possibility that a few mutants take over the entire population. Here, the fixation phenomenon is induced by large fluctuations and is investigated by a semiclassical WKB (Wentzel–Kramers–Brillouin) theory generalized to treat stochastic systems possessing multiple absorbing states. Importantly, this method allows us to analyze the combined influence of selection and random fluctuations on the evolutionary dynamics beyond the weak selection limit often considered in previous works. We accurately compute, including pre-exponential factors, the probability distribution function in the long-lived coexistence state and the mean fixation time necessary for a few mutants to take over the entire population in anti-coordination games, and also the fixation probability in the coordination class. Our analytical results compare excellently with extensive numerical simulations. Furthermore, we demonstrate that our treatment is superior to the Fokker–Planck approximation when the selection intensity is finite

Late-time dynamics of rapidly rotating black holes

International Nuclear Information System (INIS)

Glampedakis, K.; Andersson, N.

2001-01-01

We study the late-time behaviour of a dynamically perturbed rapidly rotating black hole. Considering an extreme Kerr black hole, we show that the large number of virtually undamped quasinormal modes (that exist for nonzero values of the azimuthal eigenvalue m) combine in such a way that the field (as observed at infinity) oscillates with an amplitude that decays as 1/t at late times. For a near extreme black hole, these modes, collectively, give rise to an exponentially decaying field which, however, is considerably 'long-lived'. Our analytic results are verified using numerical time-evolutions of the Teukolsky equation. Moreover, we argue that the physical mechanism behind the observed behaviour is the presence of a 'superradiance resonance cavity' immediately outside the black hole. We present this new feature in detail, and discuss whether it may be relevant for astrophysical black holes. (author)

The evolutionary status of symbiotic stars

International Nuclear Information System (INIS)

Rudak, B.

1982-01-01

The evolutionary relations between symbiotic stars and cataclysmic variables are presented. The symbiotic stars are assumed to be long period detached binaries containing a carbon-oxygen degenerate primary and a red giant losing its mass through a spherically symmetric wind. Such systems can be obtained in Case C evolution, provided a common envelope during a rapid mass transfer phase was not formed. The same way recurrent novae containing a red giant as a secondary component may be produced. The factors influencing the differences between symbiotic stars and nova-type stars are discussed. (Auth.)

Evolutionary thinking

Science.gov (United States)

Hunt, Tam

2014-01-01

Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

Evolutionary relationships between miRNA genes and their activity.

Science.gov (United States)

Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue

2012-12-22

The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.

Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

Science.gov (United States)

Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

2016-06-01

Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

Investigating intertemporal choice through experimental evolutionary robotics.

Science.gov (United States)

Paglieri, Fabio; Parisi, Domenico; Patacchiola, Massimiliano; Petrosino, Giancarlo

2015-06-01

In intertemporal choices, subjects face a trade-off between value and delay: achieving the most valuable outcome requires a longer time, whereas the immediately available option is objectively poorer. Intertemporal choices are ubiquitous, and comparative studies reveal commonalities and differences across species: all species devalue future rewards as a function of delay (delay aversion), yet there is a lot of inter-specific variance in how rapidly such devaluation occurs. These differences are often interpreted in terms of ecological rationality, as depending on environmental factors (e.g., feeding ecology) and the physiological and morphological constraints of different species (e.g., metabolic rate). Evolutionary hypotheses, however, are hard to verify in vivo, since it is difficult to observe precisely enough real environments, not to mention ancestral ones. In this paper, we discuss the viability of an approach based on evolutionary robotics: in Study 1, we evolve robots without a metabolism in five different ecologies; in Study 2, we evolve metabolic robots (i.e., robots that consume energy over time) in three different ecologies. The intertemporal choices of the robots are analyzed both in their ecology and under laboratory conditions. Results confirm the generality of delay aversion and the usefulness of studying intertemporal choice through experimental evolutionary robotics. Copyright © 2015 Elsevier B.V. All rights reserved.

Evolutionary perspectives into placental biology and disease

Directory of Open Access Journals (Sweden)

Edward B. Chuong

2013-12-01

Full Text Available In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal–fetal conflict shapes both basic placental and reproductive biology – in all species – will provide key insights into diseases of pregnancy.

An Evolutionary Game Theory Model of Spontaneous Brain Functioning.

Science.gov (United States)

Madeo, Dario; Talarico, Agostino; Pascual-Leone, Alvaro; Mocenni, Chiara; Santarnecchi, Emiliano

2017-11-22

Our brain is a complex system of interconnected regions spontaneously organized into distinct networks. The integration of information between and within these networks is a continuous process that can be observed even when the brain is at rest, i.e. not engaged in any particular task. Moreover, such spontaneous dynamics show predictive value over individual cognitive profile and constitute a potential marker in neurological and psychiatric conditions, making its understanding of fundamental importance in modern neuroscience. Here we present a theoretical and mathematical model based on an extension of evolutionary game theory on networks (EGN), able to capture brain's interregional dynamics by balancing emulative and non-emulative attitudes among brain regions. This results in the net behavior of nodes composing resting-state networks identified using functional magnetic resonance imaging (fMRI), determining their moment-to-moment level of activation and inhibition as expressed by positive and negative shifts in BOLD fMRI signal. By spontaneously generating low-frequency oscillatory behaviors, the EGN model is able to mimic functional connectivity dynamics, approximate fMRI time series on the basis of initial subset of available data, as well as simulate the impact of network lesions and provide evidence of compensation mechanisms across networks. Results suggest evolutionary game theory on networks as a new potential framework for the understanding of human brain network dynamics.

Evolutionary considerations in the development of chronic pelvic pain.

Science.gov (United States)

Jarrell, John; Arendt-Nielsen, Lars

2016-08-01

Chronic pelvic pain is common among women of reproductive age and is associated with significant morbidity and comorbidities. In this Viewpoint, we explore the evolutionary cause of pelvic pain and summarize evidence that supports a menstruation-related evolutionary cause of chronic visceral pelvic pain: (1) lifetime menstruation has increased; (2) severe dysmenorrhea is common in the chronic pelvic pain population, particularly among those with pain sensitization; and (3) a potential biological mechanism can be identified. Thus, chronic pelvic pain may arise from the mismatch between the slow pace of biological evolution in our bodies and the relatively rapid pace of cultural changes that have resulted in increased menstrual frequency due to earlier menarche, later mortality, and lower fecundity. One possible mechanism that explains the development of persistent pain from repeated episodes of intermittent pain is hyperalgesic priming, a physiological process defined as a long-lasting latent hyperresponsiveness of nociceptors to inflammatory mediators after an inflammatory or neuropathic insult. The repetitive severely painful menstrual episodes may play such a role. From an evolutionary perspective the relatively rapid increase in lifetime menstruation experience in contemporary society may contribute to a mismatch between lifetime menstruation and the physiological pain processes, leading to a maladaptive state of chronic visceral pelvic pain. Our current physiology does not conform to current human needs. Copyright © 2016 Elsevier Inc. All rights reserved.

Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants.

Science.gov (United States)

Barton, Ian S; Fuqua, Clay; Platt, Thomas G

2018-01-01

Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens. We focus on several features common among facultative pathogens, such as the physiological remodelling required to colonize hosts from environmental reservoirs and the consequences of competition with host and non-host associated microbiota. In addition, we discuss how the life history of facultative pathogens likely often results in ecological tradeoffs associated with performance in disease and non-disease environments. These pathogens may therefore have different competitive dynamics in disease and non-disease environments and are subject to shifting selective pressures that can result in pathoadaptation or the within-host spread of avirulent phenotypes. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of behavioral response and vaccination policy on epidemic spreading--an approach based on evolutionary-game dynamics.

Science.gov (United States)

Zhang, Hai-Feng; Wu, Zhi-Xi; Tang, Ming; Lai, Ying-Cheng

2014-07-11

How effective are governmental incentives to achieve widespread vaccination coverage so as to prevent epidemic outbreak? The answer largely depends on the complex interplay among the type of incentive, individual behavioral responses, and the intrinsic epidemic dynamics. By incorporating evolutionary games into epidemic dynamics, we investigate the effects of two types of incentives strategies: partial-subsidy policy in which certain fraction of the cost of vaccination is offset, and free-subsidy policy in which donees are randomly selected and vaccinated at no cost. Through mean-field analysis and computations, we find that, under the partial-subsidy policy, the vaccination coverage depends monotonically on the sensitivity of individuals to payoff difference, but the dependence is non-monotonous for the free-subsidy policy. Due to the role models of the donees for relatively irrational individuals and the unchanged strategies of the donees for rational individuals, the free-subsidy policy can in general lead to higher vaccination coverage. Our findings indicate that any disease-control policy should be exercised with extreme care: its success depends on the complex interplay among the intrinsic mathematical rules of epidemic spreading, governmental policies, and behavioral responses of individuals.

[Landscape pattern gradient dynamics and desakota features in rapid urbanization area: a case study in Panyu of Guangzhou].

Science.gov (United States)

Yu, Long-Sheng; Fu, Yi-Fu; Yu, Huai-Yi; Li, Zhi-Qin

2011-01-01

In order to understand the landscape pattern gradient dynamics and desakota features in rapid urbanization area, this paper took the rapidly urbanizing Panyu District of Guangzhou City as a case, and analyzed its land use and land cover data, based on four Landsat TM images from 1990 to 2008. With the combination of gradient analysis and landscape pattern analysis, and by using the landscape indices in both class and landscape scales, the spatial dynamics and desakota feature of this rapidly urbanizing district were quantified. In the study district, there was a significant change in the landscape pattern, and a typical desakota feature presented along buffer gradient zones. Urban landscape increased and expanded annually, accompanied with serious fragmentation of agricultural landscape. The indices patch density, contagion, and landscape diversity, etc., changed regularly in the urbanization gradient, and the peak of landscape indices appeared in the gradient zone of 4-6 km away from the urban center. The landscape patterns at time series also reflected the differences among the dynamics in different gradient zones. The landscape pattern in desakota region was characterized by complex patch shape, high landscape diversity and fragmentation, and remarkable landscape dynamics. The peaks of landscape indices spread from the urban center to border areas, and desakota region was expanding gradually. The general trend of spatiotemporal dynamics in desakota region and its driving forces were discussed, which could be benefit to the regional land use policy-making and sustainable development planning.

Evolutionary Stable Strategy

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General Article Volume 21 Issue 9 September 2016 pp 803- ... Keywords. Evolutionary game theory, evolutionary stable state, conflict, cooperation, biological games.

Pleiades rapid rotators - evidence for an evolutionary sequence

International Nuclear Information System (INIS)

Butler, R.P.; Marcy, G.W.; Cohen, R.D.; Duncan, D.K.; California Univ., La Jolla; Space Telescope Science Institute, Baltimore, MD)

1987-01-01

Four rapidly rotating early-K dwarfs in the Pleiades are shown to contain an order of magnitude more Li than four slow rotators of the same spectral type, as would be expected if they were systematically younger. This supports the idea that late-type stars first arrive on the main sequence with V(rot) greater than about 100 km/s, that they spin down to V(rot) less than about 10 km/s in 10 to the 7th to 10 to the 8th yr, and that the Pleiades lower main sequence shows such an age spread. 14 references

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

Science.gov (United States)

Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang

2015-01-01

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism. PMID:25691981

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

NARCIS (Netherlands)

Belkum, van A.; Struelens, M.; Visser, de J.A.G.M.; Verburgh, H.; Tibayrenc., M.

2001-01-01

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

Science.gov (United States)

Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Marine Dispersal Scales Are Congruent over Evolutionary and Ecological Time

KAUST Repository

Pinsky, Malin L.

2016-12-15

The degree to which offspring remain near their parents or disperse widely is critical for understanding population dynamics, evolution, and biogeography, and for designing conservation actions. In the ocean, most estimates suggesting short-distance dispersal are based on direct ecological observations of dispersing individuals, while indirect evolutionary estimates often suggest substantially greater homogeneity among populations. Reconciling these two approaches and their seemingly competing perspectives on dispersal has been a major challenge. Here we show for the first time that evolutionary and ecological measures of larval dispersal can closely agree by using both to estimate the distribution of dispersal distances. In orange clownfish (Amphiprion percula) populations in Kimbe Bay, Papua New Guinea, we found that evolutionary dispersal kernels were 17 km (95% confidence interval: 12–24 km) wide, while an exhaustive set of direct larval dispersal observations suggested kernel widths of 27 km (19–36 km) or 19 km (15–27 km) across two years. The similarity between these two approaches suggests that ecological and evolutionary dispersal kernels can be equivalent, and that the apparent disagreement between direct and indirect measurements can be overcome. Our results suggest that carefully applied evolutionary methods, which are often less expensive, can be broadly relevant for understanding ecological dispersal across the tree of life.

Using RapidEye and MODIS Data Fusion to Monitor Vegetation Dynamics in Semi-Arid Rangelands in South Africa

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Andreas Tewes

2015-05-01

Full Text Available Image time series of high temporal and spatial resolution capture land surface dynamics of heterogeneous landscapes. We applied the ESTARFM (Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model algorithm to multi-spectral images covering two semi-arid heterogeneous rangeland study sites located in South Africa. MODIS 250 m resolution and RapidEye 5 m resolution images were fused to produce synthetic RapidEye images, from June 2011 to July 2012. We evaluated the performance of the algorithm by comparing predicted surface reflectance values to real RapidEye images. Our results show that ESTARFM predictions are accurate, with a coefficient of determination for the red band 0.80 < R2 < 0.92, and for the near-infrared band 0.83 < R2 < 0.93, a mean relative bias between 6% and 12% for the red band and 4% to 9% in the near-infrared band. Heterogeneous vegetation at sub-MODIS resolution is captured adequately: A comparison of NDVI time series derived from RapidEye and ESTARFM data shows that the characteristic phenological dynamics of different vegetation types are reproduced well. We conclude that the ESTARFM algorithm allows us to produce synthetic remote sensing images at high spatial combined with high temporal resolution and so provides valuable information on vegetation dynamics in semi-arid, heterogeneous rangeland landscapes.

EVOLUTIONARY THEORY AND THE MARKET COMPETITION

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SIRGHI Nicoleta

2014-12-01

Full Text Available Evolutionary theory study of processes that transform economy for firms, institutions, industries, employment, production, trade and growth within, through the actions of diverse agents from experience and interactions, using evolutionary methodology. Evolutionary theory analyses the unleashing of a process of technological and institutional innovation by generating and testing a diversity of ideas which discover and accumulate more survival value for the costs incurred than competing alternatives.This paper presents study the behavior of the firms on the market used the evolutionary theory.The paper is to present in full the developments that have led to the re-assessment of theories of firms starting from the criticism on Coase's theory based on the lack of testable hypotheses and on non-operative definition of transaction costs. In the literature in the field studies on firms were allotted a secondary place for a long period of time, to date the new theories of the firm hold a dominant place in the firms’ economic analysis. In an article, published in 1937, Ronald H. Coase identified the main sources of the cost of using the market mechanism. The firms theory represent a issue intensively studied in the literature in the field, regarding the survival, competitiveness and innovation of firm on the market. The research of Nelson and Winter, “An Evolutionary Theory of Economic Change” (1982 is the starting point for a modern literature in the field which considers the approach of the theory of the firm from an evolutionary perspective. Nelson and Winter have shown that the “orthodox” theory, is objectionable primarily by the fact that the hypothesis regarding profit maximization has a normative character and is not valid in any situation. Nelson and Winter reconsidered their microeconomic analysis showing that excessive attention should not be paid to market equilibrium but rather to dynamic processes resulting from irreversible

Multiparty Evolutionary Game Model in Coal Mine Safety Management and Its Application

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Rongwu Lu

2018-01-01

Full Text Available Coal mine safety management involves many interested parties and there are complex relationships between them. According to game theory, a multiparty evolutionary game model is established to analyze the selection of strategies. Then, a simplified three-party model is taken as an example to carry out detailed analysis and solution. Based on stability theory of dynamics system and phase diagram analysis, this article studies replicator dynamics of the evolutionary model to make an optimization analysis of the behaviors of those interested parties and the adjustment mechanism of safety management policies and decisions. The results show how the charge of supervision of government department and inspection of coal mine enterprise impact the efficiency of safety management and the effect of constraint measures and incentive and other measures in safety management.

The ecological and evolutionary implications of merging different types of networks

NARCIS (Netherlands)

Fontaine, C.; Guimaraes, P.R.; Kéfi, S.; Loeuille, N.; Memmott, J.; Putten, van der W.H.; Veen, F.J.; Thébault, E.

2011-01-01

Interactions among species drive the ecological and evolutionary processes in ecological communities. These interactions are effectively key components of biodiversity. Studies that use a network approach to study the structure and dynamics of communities of interacting species have revealed many

Network evolution driven by dynamics applied to graph coloring

International Nuclear Information System (INIS)

Wu Jian-She; Li Li-Guang; Yu Xin; Jiao Li-Cheng; Wang Xiao-Hua

2013-01-01

An evolutionary network driven by dynamics is studied and applied to the graph coloring problem. From an initial structure, both the topology and the coupling weights evolve according to the dynamics. On the other hand, the dynamics of the network are determined by the topology and the coupling weights, so an interesting structure-dynamics co-evolutionary scheme appears. By providing two evolutionary strategies, a network described by the complement of a graph will evolve into several clusters of nodes according to their dynamics. The nodes in each cluster can be assigned the same color and nodes in different clusters assigned different colors. In this way, a co-evolution phenomenon is applied to the graph coloring problem. The proposed scheme is tested on several benchmark graphs for graph coloring

Evolutionary Algorithm for Optimal Vaccination Scheme

International Nuclear Information System (INIS)

Parousis-Orthodoxou, K J; Vlachos, D S

2014-01-01

The following work uses the dynamic capabilities of an evolutionary algorithm in order to obtain an optimal immunization strategy in a user specified network. The produced algorithm uses a basic genetic algorithm with crossover and mutation techniques, in order to locate certain nodes in the inputted network. These nodes will be immunized in an SIR epidemic spreading process, and the performance of each immunization scheme, will be evaluated by the level of containment that provides for the spreading of the disease

Game equilibrium models I evolution and game dynamics

CERN Document Server

1991-01-01

There are two main approaches towards the phenotypic analysis of frequency dependent natural selection. First, there is the approach of evolutionary game theory, which was introduced in 1973 by John Maynard Smith and George R. Price. In this theory, the dynamical process of natural selection is not modeled explicitly. Instead, the selective forces acting within a population are represented by a fitness function, which is then analysed according to the concept of an evolutionarily stable strategy or ESS. Later on, the static approach of evolutionary game theory has been complemented by a dynamic stability analysis of the replicator equations. Introduced by Peter D. Taylor and Leo B. Jonker in 1978, these equations specify a class of dynamical systems, which provide a simple dynamic description of a selection process. Usually, the investigation of the replicator dynamics centers around a stability analysis of their stationary solutions. Although evolutionary stability and dynamic stability both intend to charac...

Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes

Energy Technology Data Exchange (ETDEWEB)

Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou, E-mail: eatonch@gmail.com

2014-10-01

Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast β-relaxation is followed by a much slower α-relaxation. There is a little change in the structural properties in the β-relaxation region, while major configuration rearrangements occurred in the α-relaxation range and the crystallization process was completed at the end of α-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.

The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics.

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Goswami, Anjali; Binder, Wendy J; Meachen, Julie; O'Keefe, F Robin

2015-04-21

Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change.

Evaluation of Induced Settlements of Piled Rafts in the Coupled Static-Dynamic Loads Using Neural Networks and Evolutionary Polynomial Regression

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Ali Ghorbani

2017-01-01

Full Text Available Coupled Piled Raft Foundations (CPRFs are broadly applied to share heavy loads of superstructures between piles and rafts and reduce total and differential settlements. Settlements induced by static/coupled static-dynamic loads are one of the main concerns of engineers in designing CPRFs. Evaluation of induced settlements of CPRFs has been commonly carried out using three-dimensional finite element/finite difference modeling or through expensive real-scale/prototype model tests. Since the analyses, especially in the case of coupled static-dynamic loads, are not simply conducted, this paper presents two practical methods to gain the values of settlement. First, different nonlinear finite difference models under different static and coupled static-dynamic loads are developed to calculate exerted settlements. Analyses are performed with respect to different axial loads and pile’s configurations, numbers, lengths, diameters, and spacing for both loading cases. Based on the results of well-validated three-dimensional finite difference modeling, artificial neural networks and evolutionary polynomial regressions are then applied and introduced as capable methods to accurately present both static and coupled static-dynamic settlements. Also, using a sensitivity analysis based on Cosine Amplitude Method, axial load is introduced as the most influential parameter, while the ratio l/d is reported as the least effective parameter on the settlements of CPRFs.

Exploring social influence on evolutionary prisoner’s dilemma games in networks

Science.gov (United States)

Zong, Hengshan; Jia, Guozhu; Cheng, Yang

2015-11-01

Though numerous studies demonstrate the importance of social influence in deciding individual decision-making process in networks, little has been done to explore its impact on players’ behavioral patterns in evolutionary prisoner’s dilemma games (PDGs). This study investigates how social influenced strategy updating rules may affect the final equilibrium of game dynamics. The results show that weak social influence usually inhibits cooperation, while strong social influence has a mediating effect. The impacts of network structure and the existence of rebels in social influence scenarios are also tested. The paper provides a comprehensive interpretation on social influence effects on evolutionary PDGs in networks.

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India.

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Lewnard, Joseph A; Townsend, Jeffrey P

2016-12-20

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference.

Recent advances in evolutionary multi-objective optimization

CERN Document Server

Datta, Rituparna; Gupta, Abhishek

2017-01-01

This book covers the most recent advances in the field of evolutionary multiobjective optimization. With the aim of drawing the attention of up-andcoming scientists towards exciting prospects at the forefront of computational intelligence, the authors have made an effort to ensure that the ideas conveyed herein are accessible to the widest audience. The book begins with a summary of the basic concepts in multi-objective optimization. This is followed by brief discussions on various algorithms that have been proposed over the years for solving such problems, ranging from classical (mathematical) approaches to sophisticated evolutionary ones that are capable of seamlessly tackling practical challenges such as non-convexity, multi-modality, the presence of multiple constraints, etc. Thereafter, some of the key emerging aspects that are likely to shape future research directions in the field are presented. These include:< optimization in dynamic environments, multi-objective bilevel programming, handling high ...

Research on Information Sharing Mechanism of Network Organization Based on Evolutionary Game

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Wang, Lin; Liu, Gaozhi

2018-02-01

This article first elaborates the concept and effect of network organization, and the ability to share information is analyzed, secondly introduces the evolutionary game theory, network organization for information sharing all kinds of limitations, establishes the evolutionary game model, analyzes the dynamic evolution of network organization of information sharing, through reasoning and evolution. The network information sharing by the initial state and two sides of the game payoff matrix of excess profits and information is the information sharing of cost and risk sharing are the influence of network organization node information sharing decision.

Multi types DG expansion dynamic planning in distribution system under stochastic conditions using Covariance Matrix Adaptation Evolutionary Strategy and Monte-Carlo simulation

International Nuclear Information System (INIS)

Sadeghi, Mahmood; Kalantar, Mohsen

2014-01-01

Highlights: • Defining a DG dynamic planning problem. • Applying a new evolutionary algorithm called “CMAES” in planning process. • Considering electricity price and fuel price variation stochastic conditions. • Scenario generation and reduction with MCS and backward reduction programs. • Considering approximately all of the costs of the distribution system. - Abstract: This paper presents a dynamic DG planning problem considering uncertainties related to the intermittent nature of the DG technologies such as wind turbines and solar units in addition to the stochastic economic conditions. The stochastic economic situation includes the uncertainties related to the fuel and electricity price of each year. The Monte Carlo simulation is used to generate the possible scenarios of uncertain situations and the produced scenarios are reduced through backward reduction program. The aim of this paper is to maximize the revenue of the distribution system through the benefit cost analysis alongside the encouraging and punishment functions. In order to close to reality, the different growth rates for the planning period are selected. In this paper the Covariance Matrix Adaptation Evolutionary Strategy is introduced and is used to find the best planning scheme of the DG units. The different DG types are considered in the planning problem. The main assumption of this paper is that the DISCO is the owner of the distribution system and the DG units. The proposed method is tested on a 9 bus test distribution system and the results are compared with the known genetic algorithm and PSO methods to show the applicability of the CMAES method in this problem

Multifrequency Excitation Method for Rapid and Accurate Dynamic Test of Micromachined Gyroscope Chips

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Yan Deng

2014-10-01

Full Text Available A novel multifrequency excitation (MFE method is proposed to realize rapid and accurate dynamic testing of micromachined gyroscope chips. Compared with the traditional sweep-frequency excitation (SFE method, the computational time for testing one chip under four modes at a 1-Hz frequency resolution and 600-Hz bandwidth was dramatically reduced from 10 min to 6 s. A multifrequency signal with an equal amplitude and initial linear-phase-difference distribution was generated to ensure test repeatability and accuracy. The current test system based on LabVIEW using the SFE method was modified to use the MFE method without any hardware changes. The experimental results verified that the MFE method can be an ideal solution for large-scale dynamic testing of gyroscope chips and gyroscopes.

The Hawaiian cave planthoppers (Homoptera: Fulgoroidea: Cixiidae - A model for rapid subterranean speciation?

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Hannelore Hoch

1997-01-01

Full Text Available After the successful colonization of a single ancestral species in the Hawaiian Islands, planthoppers of the cixiid genus Oliarus underwent intensive adaptive radiation resulting in 80 described endemic species. Oliarus habitats range from montaneous rain forests to dry coastal biotopes and subterranean environments. At least 7 independant evolutionary lines represented by different species have adapted to lava tubes on Molokai (1, Maui (3, and Hawaii Island (3. Behavioral and morphological studies on one of these evolutionary lines on Hawaii Island, the blind, flight- and pigmentless Oliarus polyphentus have provided evidence for reproductive isolation between allopatric populations which may in fact be separate species. Significant differences in song parameters were observed even between populations from neighbouring lava tubes, although the planthoppers are capable of underground migration through the voids and cracks of the mesocavernous rock system which is extant in young basalt: after a little more than 20 years, lava tubes within the Mauna Ulu 1974 flow had been colonized by O. ‘polyphenius” individuals, most probably originating from a near-by forestkipuka. Amazingly, this species complex is found on the youngest of the Hawaiian Islands, with probably less than 0.5 m.y., which suggests rapid speciation processes. Field observations have led to the development of a hypothesis to match underground speciation with the dynamics of vegetational succession on the surface of active volcanoes. Planthopper range partitioning and geographic separation of populations by young lava flows, founder events and small population size may be important factors involved in rapid divergence.

Evidence Combination From an Evolutionary Game Theory Perspective.

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Deng, Xinyang; Han, Deqiang; Dezert, Jean; Deng, Yong; Shyr, Yu

2016-09-01

Dempster-Shafer evidence theory is a primary methodology for multisource information fusion because it is good at dealing with uncertain information. This theory provides a Dempster's rule of combination to synthesize multiple evidences from various information sources. However, in some cases, counter-intuitive results may be obtained based on that combination rule. Numerous new or improved methods have been proposed to suppress these counter-intuitive results based on perspectives, such as minimizing the information loss or deviation. Inspired by evolutionary game theory, this paper considers a biological and evolutionary perspective to study the combination of evidences. An evolutionary combination rule (ECR) is proposed to help find the most biologically supported proposition in a multievidence system. Within the proposed ECR, we develop a Jaccard matrix game to formalize the interaction between propositions in evidences, and utilize the replicator dynamics to mimick the evolution of propositions. Experimental results show that the proposed ECR can effectively suppress the counter-intuitive behaviors appeared in typical paradoxes of evidence theory, compared with many existing methods. Properties of the ECR, such as solution's stability and convergence, have been mathematically proved as well.

Extrapolating Weak Selection in Evolutionary Games

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Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

2013-01-01

In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

Polymorphic Evolutionary Games.

Science.gov (United States)

Fishman, Michael A

2016-06-07

In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

Remembering the evolutionary Freud.

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Young, Allan

2006-03-01

Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

Cosmic Evolutionary Philosophy and a Dialectical Approach to Technological Singularity

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Cadell Last

2018-04-01

Full Text Available The anticipated next stage of human organization is often described by futurists as a global technological singularity. This next stage of complex organization is hypothesized to be actualized by scientific-technic knowledge networks. However, the general consequences of this process for the meaning of human existence are unknown. Here, it is argued that cosmic evolutionary philosophy is a useful worldview for grounding an understanding of the potential nature of this futures event. In the cosmic evolutionary philosophy, reality is conceptualized locally as a universal dynamic of emergent evolving relations. This universal dynamic is structured by a singular astrophysical origin and an organizational progress from sub-atomic particles to global civilization mediated by qualitative phase transitions. From this theoretical ground, we attempt to understand the next stage of universal dynamics in terms of the motion of general ideation attempting to actualize higher unity. In this way, we approach technological singularity dialectically as an event caused by ideational transformations and mediated by an emergent intersubjective objectivity. From these speculations, a historically-engaged perspective on the nature of human consciousness is articulated where the truth of reality as an emergent unity depends on the collective action of a multiplicity of human observers.

Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

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O'Malley, Maureen A

2012-01-01

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

Science.gov (United States)

Shackelford, Todd K; Liddle, James R

2014-05-01

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

THE THEORY OF THE FIRM AND THE EVOLUTIONARY GAMES

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Sirghi Nicoleta

2013-07-01

Full Text Available The neoclassical theory of the firm deals with the pattern of perfect competition, within which the perfect information available to economic agents provides instant allocation of production factors and access to economic goods. The Austrian School (C. Menger, L. von Mises, Hayek, etc. supported the idea of minimal state intervention on the markets, bringing important conceptual developments on the theory of the firm. Hirschleifer (1982 put forward the model of social and institutional functioning, arguing that the game theory is able to predict the outcome of the collective behavior and the human characteristics necessary for building the respective institutions.The evolutionary theory provides the firm and the entrepreneur the recognition of the functions of innovation, of generating and exploiting information and of organizing and coordinating production. The evolutionary perspective of the firm assumes the existence of a body of knowledge that is acquired through and builds up the organizational memory, subsequently found in routines, all choices being made based on these routines (Nelson and Winter, 2002. The evolution of the firm is considered to be similar to natural selection, but unlike the classic market selection, the evolutionists suggest the existence of a plurality of selection media. The present research is structured as follows: a brief introduction into the theories of the firm, the second part of the paper analyzes the theories of the firm from an institutional, neo-institutional and evolutionary perspective. In the third part of the paper the evolutionary games are described and analyzed from the evolutionary perspective of the firm. The last part of the paper represents a study of the “hawk-dove” game dynamic replicator. The final conclusions of the paper show that the evolutionary theory brings valuable contributions to the foundation of explanations regarding economic phenomena, indicating new directions for advanced

Aspiration dynamics of multi-player games in finite populations.

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Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

Evolution of man in the light of molecular genetics: a review. Part I. Our evolutionary history and genomics.

Science.gov (United States)

Portin, Petter

2007-07-01

The discovery in the mid 1970s of efficient methods of DNA sequencing and their subsequent development into more and more rapid procedures followed by sequencing the genomes of many species, including man in 2001, revolutionised the whole of biology. Remarkably, new light could be cast on the evolutionary relations of different species, and the tempo and mode of evolution within a given species, notably man, could quantitatively be illuminated including ongoing evolution possibly involving also the size of the brains. This review is a short summary of the results of the molecular genetic investigations of human evolution including the time and place of the formation of our species, our evolutionary relation to the closest living species relatives as well as extinct forms of the genus Homo. The nature and amount of genetic polymorphism in man is also considered with special emphasis on the causes of this variation, and the role of natural selection in human evolution. A consensus about the mosaic nature of our genome and the rather dynamic structure of our ancestral population is gradually emerging. The modern gene pool has most likely been contributed to several different ancestral demes either before or after the emergence of the anatomically modern human phenotype in the extent that even the nature of the evolutionary lineage leading to the anatomically modern man as a distinct biological species is disputable. Regulation of the function of genes, as well as the evolution of brains will be dealt with in the second part of this review.

[Evolutionary medicine].

Science.gov (United States)

Wjst, M

2013-12-01

Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

Applying evolutionary anthropology.

Science.gov (United States)

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

Applying Evolutionary Anthropology

Science.gov (United States)

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

Dosimetric comparison of RapidArc with fixed gantry dynamic IMRT for loco-regionally advanced nasopharyngeal carcinoma

International Nuclear Information System (INIS)

Wu Hao; Han Shukui; Sun Yan; Jiang Fan

2010-01-01

Objective: To compare the dosimetric difference of RapidArc and fixed gantry angle dynamic IMRT (dIMRT) for loco-regionally advanced nasopharyngeal carcinoma. Methods: Ten previously treated patients with loco-regionally advanced nasopharyngeal carcinoma were replanned with RapidArc and dIMRT, respectively. The prescription dose was GTV 70 Gy/33 f and PTV 60 Gy/33 f. All plans met the requirement: 95% of PTV was covered by 60 Gy. Dose-volume histogram data, isodose distribution, monitor units, and treatment time were compared. Results: Dose distribution has no significant difference between the two techniques. RapidArc reduced the dose of the brainstem, mandible, and other normal tissues compared with dIMRT. Mean monitor units were 589.5 and 1381.0 for RapidArc and dIMRT (reduced by 57% relatively). Mean treatment time was 2.33 min and 7.82 min for RapidArc and dIMRT (reduced by 70% relatively). Conclusions: Compared with dIMRT, RapidArc achieves equal target coverage and OAR sparing while using fewer monitor units and less time during radiotherapy for patient with loco-regionally advanced nasopharyngeal carcinoma. (authors)

A study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast.

Science.gov (United States)

Hagman, Arne; Piškur, Jure

2015-01-01

Baker's yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anaerobic and aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125-150 million years ago in the Saccharomyces lineage. The "invention" of overflow metabolism was the first step in the evolution of aerobic fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The "invention" of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to "starve" competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently "invented" as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that were semi-anaerobic.

A study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast.

Directory of Open Access Journals (Sweden)

Arne Hagman

Full Text Available Baker's yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anaerobic and aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125-150 million years ago in the Saccharomyces lineage. The "invention" of overflow metabolism was the first step in the evolution of aerobic fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The "invention" of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to "starve" competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently "invented" as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that

Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells.

Directory of Open Access Journals (Sweden)

Mandy Y M Lo

Full Text Available Single cell imaging studies suggest that transcription is not continuous and occurs as discrete pulses of gene activity. To study mechanisms by which retroviral transgenes can transcribe to high levels, we used the MS2 system to visualize transcriptional dynamics of high expressing proviral integration sites in embryonic stem (ES cells. We established two ES cell lines each bearing a single copy, self-inactivating retroviral vector with a strong ubiquitous human EF1α gene promoter directing expression of mRFP fused to an MS2-stem-loop array. Transfection of MS2-EGFP generated EGFP focal dots bound to the mRFP-MS2 stem loop mRNA. These transcription foci colocalized with the transgene integration site detected by immunoFISH. Live tracking of single cells for 20 minutes detected EGFP focal dots that displayed frequent and rapid fluctuations in transcription over periods as short as 25 seconds. Similarly rapid fluctuations were detected from focal doublet signals that colocalized with replicated proviral integration sites by immunoFISH, consistent with transcriptional pulses from sister chromatids. We concluded that retroviral transgenes experience rapid transcriptional pulses in clonal ES cell lines that exhibit high level expression. These events are directed by a constitutive housekeeping gene promoter and may provide precedence for rapid transcriptional pulsing at endogenous genes in mammalian stem cells.

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes.

Science.gov (United States)

Mank, Judith E

2012-01-01

Although sex chromosomes have been the focus of a great deal of scientific scrutiny, most interest has centred on understanding the evolution and relative importance of X and Z chromosomes. By contrast, the sex-limited W and Y chromosomes have received far less attention, both because of their generally degenerate nature and the difficulty in studying non-recombining and often highly heterochromatic genomic regions. However, recent theory and empirical evidence suggest that the W and Y chromosomes play a far more important role in sex-specific fitness traits than would be expected based on their size alone, and this importance may explain the persistence of some Y and W chromosomes in the face of powerful degradative forces. In addition to their role in fertility and fecundity, the sex-limited nature of these genomic regions results in unique evolutionary forces acting on Y and W chromosomes, implicating them as potentially major contributors to sexual selection and speciation. Recent empirical studies have borne out these predictions and revealed that some W and Y chromosomes play a vital role in key sex-specific evolutionary processes.

Synthesizing mixed H2/H-infinity dynamic controller using evolutionary algorithms

DEFF Research Database (Denmark)

Pedersen, Gerulf; Langballe, A.S.; Wisniewski, Rafal

2001-01-01

This paper covers the design of an Evolutionary Algorithm (EA), which should be able to synthesize a mixed H2/H-infinity. It will be shown how a system can be expressed as Matrix Inequalities (MI) and these will then be used in the design of the EA. The main objective is to examine whether a mixed...... H2/H-infinity controller is feasible, and if so, how the optimal mixed controller might befound....

Evolutionary Expectations

DEFF Research Database (Denmark)

Nash, Ulrik William

2014-01-01

, they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...

Evolutionary Awareness

Directory of Open Access Journals (Sweden)

Gregory Gorelik

2014-10-01

Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

Evolutionary autonomous agents and the nature of apraxia

Directory of Open Access Journals (Sweden)

Jin Frank

2005-01-01

Full Text Available Abstract Background Evolutionary autonomous agents are robots or robot simulations whose controller is a dynamical neural network and whose evolution occurs autonomously under the guidance of a fitness function without the detailed or explicit direction of an external programmer. They are embodied agents with a simple neural network controller and as such they provide the optimal forum by which sensorimotor interactions in a specified environment can be studied without the computational assumptions inherent in standard neuroscience. Methods Evolutionary autonomous agents were evolved that were able to perform identical movements under two different contexts, one which represented an automatic movement and one which had a symbolic context. In an attempt to model the automatic-voluntary dissociation frequently seen in ideomotor apraxia, lesions were introduced into the neural network controllers resulting in a behavioral dissociation with loss of the ability to perform the movement which had a symbolic context and preservation of the simpler, automatic movement. Results Analysis of the changes in the hierarchical organization of the networks in the apractic EAAs demonstrated consistent changes in the network dynamics across all agents with loss of longer duration time scales in the network dynamics. Conclusion The concepts of determinate motor programs and perceptual representations that are implicit in the present day understanding of ideomotor apraxia are assumptions inherent in the computational understanding of brain function. The strength of the present study using EAAs to model one aspect of ideomotor apraxia is the absence of these assumptions and a grounding of all sensorimotor interactions in an embodied, autonomous agent. The consistency of the hierarchical changes in the network dynamics across all apractic agents demonstrates that this technique is tenable and will be a valuable adjunct to a computational formalism in the understanding

Identification and evolutionary dynamics of cacta DNA transposons in brassica

International Nuclear Information System (INIS)

Nouroz, F.; Noreen, S.; Harrison, J.S.H.

2017-01-01

Transposable elements are the major drivers of genome evolution and plasticity. Due to their transposition mode, they are classified into two major classes as Retrotransposons and DNA transposons. The En/Spm or CACTA elements are diverse group of DNA transposons proliferating in plant genomes. Various bioinformatics and molecular approaches were used for identification and distribution of CACTA transposons in Brassica genome. A combination of dot plot analysis and BLASTN searches yielded 35 autonomous and 7 non-autonomous CACTA elements in Brassica. The elements ranged in sizes from 1.2 kb non-autonomous elements to 11kb autonomous elements, terminated by 3 bp Target Site Duplication (TSD) and ~15 bp conserved Terminal Inverted Repeat (TIR) motifs (5'-CACTACAAGAAAACA-3'), with heterogeneous internal regions. The transposase (TNP) was identified from autonomous CACTA elements, while other protein domains from Brassica and other plants CACTA revealed similar organizations with minor differences. Both transposases (TNPD, TNPA) are present in most CACTA, while a few CACTA harboured an additional ATHILA ORF1-like domain. The PCR analysis amplified the CACTA transposases from 40 Brassica accessions (A, B, and C-genome) suggesting their distribution among various Brassica crops. A detailed characterization and evolutionary analysis of the identified CACTA elements allowed some to be placed in genome-specific groups, while most of them (Brassica-Arabidopsis elements) have followed the same evolutionary line. The distribution of CACTA in Brassica concluded that 3 bp TSDs generating CACTA transposons contributed significantly to genome size and evolution of Brassica genome. (author)

A rapid loss of stripes: the evolutionary history of the extinct quagga.

Science.gov (United States)

Leonard, Jennifer A; Rohland, Nadin; Glaberman, Scott; Fleischer, Robert C; Caccone, Adalgisa; Hofreiter, Michael

2005-09-22

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature312, 282-284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

Evolutionary programming as a platform for in silico metabolic engineering

DEFF Research Database (Denmark)

Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen

2005-01-01

, and it is therefore interesting to develop new faster algorithms. Results In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters...... of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span several different pathways and may be necessary for solving challenging metabolic engineering problems....

Fixation Probabilities of Evolutionary Graphs Based on the Positions of New Appearing Mutants

Directory of Open Access Journals (Sweden)

Pei-ai Zhang

2014-01-01

Full Text Available Evolutionary graph theory is a nice measure to implement evolutionary dynamics on spatial structures of populations. To calculate the fixation probability is usually regarded as a Markov chain process, which is affected by the number of the individuals, the fitness of the mutant, the game strategy, and the structure of the population. However the position of the new mutant is important to its fixation probability. Here the position of the new mutant is laid emphasis on. The method is put forward to calculate the fixation probability of an evolutionary graph (EG of single level. Then for a class of bilevel EGs, their fixation probabilities are calculated and some propositions are discussed. The conclusion is obtained showing that the bilevel EG is more stable than the corresponding one-rooted EG.

USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

Science.gov (United States)

Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

Science.gov (United States)

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

Effects of dynamic operating conditions on nitrification in biological rapid sand filters for drinking water treatment

DEFF Research Database (Denmark)

Lee, Carson Odell; Boe-Hansen, Rasmus; Musovic, Sanin

2014-01-01

Biological rapid sand filters are often used to remove ammonium from groundwater for drinking water supply. They often operate under dynamic substrate and hydraulic loading conditions, which can lead to increased levels of ammonium and nitrite in the effluent. To determine the maximum nitrification...... operating conditions. The ammonium removal rate of the filter was determined by the ammonium loading rate, but was independent of both the flow and influent ammonium concentration individually. Ammonia-oxidizing bacteria and archaea were almost equally abundant in the filter. Both ammonium removal...... rates and safe operating windows of rapid sand filters, a pilot scale rapid sand filter was used to test short-term increased ammonium loads, set by varying either influent ammonium concentrations or hydraulic loading rates. Ammonium and iron (flock) removal were consistent between the pilot...

The AquaDEB project (phase I): Analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using Dynamic Energy Budgets

OpenAIRE

Alunno-bruscia, Marianne; Van Der Veer, Henk W.; Kooijman, Sebastiaan A.l.m.

2009-01-01

The European Research Project AquaDEB (2007–2011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main sci...

Variants of Evolutionary Algorithms for Real-World Applications

CERN Document Server

Weise, Thomas; Michalewicz, Zbigniew

2012-01-01

Evolutionary Algorithms (EAs) are population-based, stochastic search algorithms that mimic natural evolution. Due to their ability to find excellent solutions for conventionally hard and dynamic problems within acceptable time, EAs have attracted interest from many researchers and practitioners in recent years. This book “Variants of Evolutionary Algorithms for Real-World Applications” aims to promote the practitioner’s view on EAs by providing a comprehensive discussion of how EAs can be adapted to the requirements of various applications in the real-world domains. It comprises 14 chapters, including an introductory chapter re-visiting the fundamental question of what an EA is and other chapters addressing a range of real-world problems such as production process planning, inventory system and supply chain network optimisation, task-based jobs assignment, planning for CNC-based work piece construction, mechanical/ship design tasks that involve runtime-intense simulations, data mining for the predictio...

Biophysics of protein evolution and evolutionary protein biophysics

Science.gov (United States)

Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

Rapidity gap survival in central exclusive diffraction: Dynamical mechanisms and uncertainties

International Nuclear Information System (INIS)

Strikman, Mark; Weiss, Christian

2009-01-01

We summarize our understanding of the dynamical mechanisms governing rapidity gap survival in central exclusive diffraction, pp -> p + H + p (H = high-mass system), and discuss the uncertainties in present estimates of the survival probability. The main suppression of diffractive scattering is due to inelastic soft spectator interactions at small pp impact parameters and can be described in a mean-field approximation (independent hard and soft interactions). Moderate extra suppression results from fluctuations of the partonic configurations of the colliding protons. At LHC energies absorptive interactions of hard spectator partons associated with the gg -> H process reach the black-disk regime and cause substantial additional suppression, pushing the survival probability below 0.01.

Dinosaurs reveal the geographical signature of an evolutionary radiation.

Science.gov (United States)

O'Donovan, Ciara; Meade, Andrew; Venditti, Chris

2018-03-01

Dinosaurs dominated terrestrial ecosystems across the globe for over 100 million years and provide a classic example of an evolutionary radiation. However, little is known about how these animals radiated geographically to become globally distributed. Here, we use a biogeographical model to reconstruct the dinosaurs' ancestral locations, revealing the spatial mechanisms that underpinned this 170-million-year-long radiation. We find that dinosaurs spread rapidly initially, followed by a significant continuous and gradual reduction in their speed of movement towards the Cretaceous/Tertiary boundary (66 million years ago). This suggests that the predominant mode of dinosaur speciation changed through time with speciation originally largely driven by geographical isolation-when dinosaurs speciated more, they moved further. This was gradually replaced by increasing levels of sympatric speciation (species taking advantage of ecological opportunities within their existing environment) as terrestrial space became a limiting factor. Our results uncover the geographical signature of an evolutionary radiation.

A rapid and robust gradient measurement technique using dynamic single-point imaging.

Science.gov (United States)

Jang, Hyungseok; McMillan, Alan B

2017-09-01

We propose a new gradient measurement technique based on dynamic single-point imaging (SPI), which allows simple, rapid, and robust measurement of k-space trajectory. To enable gradient measurement, we utilize the variable field-of-view (FOV) property of dynamic SPI, which is dependent on gradient shape. First, one-dimensional (1D) dynamic SPI data are acquired from a targeted gradient axis, and then relative FOV scaling factors between 1D images or k-spaces at varying encoding times are found. These relative scaling factors are the relative k-space position that can be used for image reconstruction. The gradient measurement technique also can be used to estimate the gradient impulse response function for reproducible gradient estimation as a linear time invariant system. The proposed measurement technique was used to improve reconstructed image quality in 3D ultrashort echo, 2D spiral, and multi-echo bipolar gradient-echo imaging. In multi-echo bipolar gradient-echo imaging, measurement of the k-space trajectory allowed the use of a ramp-sampled trajectory for improved acquisition speed (approximately 30%) and more accurate quantitative fat and water separation in a phantom. The proposed dynamic SPI-based method allows fast k-space trajectory measurement with a simple implementation and no additional hardware for improved image quality. Magn Reson Med 78:950-962, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Statistical mechanics of spatial evolutionary games

International Nuclear Information System (INIS)

Miekisz, Jacek

2004-01-01

We discuss the long-run behaviour of stochastic dynamics of many interacting players in spatial evolutionary games. In particular, we investigate the effect of the number of players and the noise level on the stochastic stability of Nash equilibria. We discuss similarities and differences between systems of interacting players maximizing their individual payoffs and particles minimizing their interaction energy. We use concepts and techniques of statistical mechanics to study game-theoretic models. In order to obtain results in the case of the so-called potential games, we analyse the thermodynamic limit of the appropriate models of interacting particles

An evolutionary-game model of tumour-cell interactions: possible relevance to gene therapy

DEFF Research Database (Denmark)

Bach, L.A.; Bentzen, S.M.; Alsner, Jan

2001-01-01

Evolutionary games have been applied as simple mathematical models of populations where interactions between individuals control the dynamics. Recently, it has been proposed to use this type of model to describe the evolution of tumour cell populations with interactions between cells. We extent...

Open Issues in Evolutionary Robotics.

Science.gov (United States)

Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

2016-01-01

One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

Packets Distributing Evolutionary Algorithm Based on PSO for Ad Hoc Network

Science.gov (United States)

Xu, Xiao-Feng

2018-03-01

Wireless communication network has such features as limited bandwidth, changeful channel and dynamic topology, etc. Ad hoc network has lots of difficulties in accessing control, bandwidth distribution, resource assign and congestion control. Therefore, a wireless packets distributing Evolutionary algorithm based on PSO (DPSO)for Ad Hoc Network is proposed. Firstly, parameters impact on performance of network are analyzed and researched to obtain network performance effective function. Secondly, the improved PSO Evolutionary Algorithm is used to solve the optimization problem from local to global in the process of network packets distributing. The simulation results show that the algorithm can ensure fairness and timeliness of network transmission, as well as improve ad hoc network resource integrated utilization efficiency.

Evolutionary potential games on lattices

Energy Technology Data Exchange (ETDEWEB)

Szabó, György, E-mail: szabo@mfa.kfki.hu; Borsos, István, E-mail: borsos@mfa.kfki.hu

2016-04-05

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

Evolutionary potential games on lattices

International Nuclear Information System (INIS)

Szabó, György; Borsos, István

2016-01-01

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

Evolutionary potential games on lattices

Science.gov (United States)

Szabó, György; Borsos, István

2016-04-01

Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by adding non-potential components representing games of cyclic dominance.

Rapid sampling of stochastic displacements in Brownian dynamics simulations with stresslet constraints

Science.gov (United States)

Fiore, Andrew M.; Swan, James W.

2018-01-01

Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material are a significant computational challenge. Here, we present a new method for Brownian dynamics simulations of suspended colloidal scale particles such as colloids, polymers, surfactants, and proteins subject to a particular and important class of hydrodynamic constraints. The total computational cost of the algorithm is practically linear with the number of particles modeled and can be further optimized when the characteristic mass fractal dimension of the suspended particles is known. Specifically, we consider the so-called "stresslet" constraint for which suspended particles resist local deformation. This acts to produce a symmetric force dipole in the fluid and imparts rigidity to the particles. The presented method is an extension of the recently reported positively split formulation for Ewald summation of the Rotne-Prager-Yamakawa mobility tensor to higher order terms in the hydrodynamic scattering series accounting for force dipoles [A. M. Fiore et al., J. Chem. Phys. 146(12), 124116 (2017)]. The hydrodynamic mobility tensor, which is proportional to the covariance of particle Brownian displacements, is constructed as an Ewald sum in a novel way which guarantees that the real-space and wave-space contributions to the sum are independently symmetric and positive-definite for all possible particle configurations. This property of the Ewald sum is leveraged to rapidly sample the Brownian displacements from a superposition of statistically independent processes with the wave-space and real-space contributions as respective covariances. The cost of computing the Brownian displacements in this way is comparable to the cost of computing the deterministic displacements. The addition of a stresslet constraint to the over-damped particle

Evolutionary equations with applications in natural sciences

CERN Document Server

Mokhtar-Kharroubi, Mustapha

2015-01-01

With the unifying theme of abstract evolutionary equations, both linear and nonlinear, in a complex environment, the book presents a multidisciplinary blend of topics, spanning the fields of theoretical and applied functional analysis, partial differential equations, probability theory and numerical analysis applied to various models coming from theoretical physics, biology, engineering and complexity theory. The unique features of the book are: the first simultaneous presentation of two complementary approaches to fragmentation and coagulation problems, by weak compactness methods and by using semigroup techniques, comprehensive exposition of probabilistic methods of analysis of long term dynamics of dynamical systems, semigroup analysis of biological problems and cutting edge pattern formation theory. The book will appeal to postgraduate students and researchers specializing in applications of mathematics to problems arising in natural sciences and engineering.

Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems.

Science.gov (United States)

Rogalski, Mary A; Gowler, Camden D; Shaw, Clara L; Hufbauer, Ruth A; Duffy, Meghan A

2017-01-19

Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches. Very dense host populations resulting from urbanization and agriculture can drive the evolution of more virulent parasites and, in some cases, more resistant host populations. Human activities that reduce host genetic diversity or impose abiotic stress can impair the ability of hosts to adapt to disease threats. Further, evolutionary responses of hosts and parasites can thwart disease management and biocontrol efforts. Finally, in rare cases, humans influence evolution by eradicating an infectious disease. If we hope to fully understand the factors driving disease emergence and potentially control these epidemics we must consider the widespread influence of humans on host and parasite evolutionary trajectories.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Optimizing a reconfigurable material via evolutionary computation

Science.gov (United States)

Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.

2015-08-01

Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

Insight into the Physical and Dynamical Processes that Control Rapid Increases in Total Flash Rate

Science.gov (United States)

Schultz, Christopher J.; Carey, Lawrence D.; Schultz, Elise V.; Blakeslee, Richard J.; Goodman, Steven J.

2015-01-01

Rapid increases in total lightning (also termed "lightning jumps") have been observed for many decades. Lightning jumps have been well correlated to severe and hazardous weather occurrence. The main focus of lightning jump work has been on the development of lightning algorithms to be used in real-time assessment of storm intensity. However, in these studies it is typically assumed that the updraft "increases" without direct measurements of the vertical motion, or specification of which updraft characteristic actually increases (e.g., average speed, maximum speed, or convective updraft volume). Therefore, an end-to-end physical and dynamical basis for coupling rapid increases in total flash rate to increases in updraft speed and volume must be understood in order to ultimately relate lightning occurrence to severe storm metrics. Herein, we use polarimetric, multi-Doppler, and lightning mapping array measurements to provide physical context as to why rapid increases in total lightning are closely tied to severe and hazardous weather.

Phylogenetic and evolutionary analyses of dengue viruses isolated in Jakarta, Indonesia.

Science.gov (United States)

Lestari, C S Whinie; Yohan, Benediktus; Yunita, Anisa; Meutiawati, Febrina; Hayati, Rahma Fitri; Trimarsanto, Hidayat; Sasmono, R Tedjo

2017-12-01

Dengue has affected Indonesia for the last five decades and become a major health problem in many cities in the country. Jakarta, the capital of Indonesia, reports dengue cases annually, with several outbreaks documented. To gain information on the dynamic and evolutionary history of dengue virus (DENV) in Jakarta, we conducted phylogenetic and evolutionary analyses of DENV isolated in 2009. Three hundred thirty-three dengue-suspected patients were recruited. Our data revealed that dengue predominantly affected young adults, and the majority of cases were due to secondary infection. A total of 171 virus isolates were successfully serotyped. All four DENV serotypes were circulating in the city, and DENV-1 was the predominant serotype. The DENV genotyping of 17 isolates revealed the presence of Genotypes I and IV in DENV-1, while DENV-2 isolates were grouped into the Cosmopolitan genotype. The grouping of isolates into Genotype I and II was seen for DENV-3 and DENV-4, respectively. Evolutionary analysis revealed the relatedness of Jakarta isolates with other isolates from other cities in Indonesia and isolates from imported cases in other countries. We revealed the endemicity of DENV and the role of Jakarta as the potential source of imported dengue cases in other countries. Our study provides genetic information regarding DENV from Jakarta, which will be useful for upstream applications, such as the study of DENV epidemiology and evolution and transmission dynamics.

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

Science.gov (United States)

Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

2014-03-20

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

Evolutionary modelling of transitions to sustainable development

International Nuclear Information System (INIS)

Safarzynska, K.

2010-01-01

This thesis has examined how evolutionary economics can contribute to modelling the micromechanisms that underlie transitions towards sustainable development. In general, transitions are fundamental or structural system changes. They involve, or even require, escaping lock-in of dominant, environmentally unsustainable technologies, introducing major technical or social innovations, and changing prevailing social practices and structures. Due to the complexity of socioeconomic interactions, it is not always possible to identify, and thus target with appropriate policy instruments, causes of specific unsustainable patterns of behaviour. Formal modelling exercises can help improve our understanding of the interaction of various transition mechanisms which are otherwise difficult to grasp intuitively. They allow exploring effects of policy interventions in complex systems. However, existing models of transitions focus on social phenomena and seldom address economic problems. As opposed, mainstream (neoclassical) economic models of technological change do not account for social interactions, and changing heterogeneity of users and their perspectives - even though all of these can influence the direction of innovations and patterns of socio-technological development. Evolutionary economics offers an approach that goes beyond neoclassical economics - in the sense of employing more realistic assumptions regarding the behaviour and heterogeneity of consumers, firms and investors. It can complement current transition models by providing them with a better understanding of associated economic dynamics. In this thesis, formal models were proposed to illustrate the usefulness of a range of evolutionary-economic techniques for modelling transitions. Modelling exercises aimed to explain the core properties of socio-economic systems, such as lock-in, path-dependence, coevolution, group selection and recombinant innovation. The studies collected in this dissertation illustrate that

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes

Science.gov (United States)

2012-01-01

Although sex chromosomes have been the focus of a great deal of scientific scrutiny, most interest has centred on understanding the evolution and relative importance of X and Z chromosomes. By contrast, the sex-limited W and Y chromosomes have received far less attention, both because of their generally degenerate nature and the difficulty in studying non-recombining and often highly heterochromatic genomic regions. However, recent theory and empirical evidence suggest that the W and Y chromosomes play a far more important role in sex-specific fitness traits than would be expected based on their size alone, and this importance may explain the persistence of some Y and W chromosomes in the face of powerful degradative forces. In addition to their role in fertility and fecundity, the sex-limited nature of these genomic regions results in unique evolutionary forces acting on Y and W chromosomes, implicating them as potentially major contributors to sexual selection and speciation. Recent empirical studies have borne out these predictions and revealed that some W and Y chromosomes play a vital role in key sex-specific evolutionary processes. PMID:22038285

Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.

Science.gov (United States)

Mukherjee, Dola; Mukherjee, Ashutosh; Ghosh, Tapash Chandra

2015-11-10

Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Application of evolutionary games to modeling carcinogenesis.

Science.gov (United States)

Swierniak, Andrzej; Krzeslak, Michal

2013-06-01

We review a quite large volume of literature concerning mathematical modelling of processes related to carcinogenesis and the growth of cancer cell populations based on the theory of evolutionary games. This review, although partly idiosyncratic, covers such major areas of cancer-related phenomena as production of cytotoxins, avoidance of apoptosis, production of growth factors, motility and invasion, and intra- and extracellular signaling. We discuss the results of other authors and append to them some additional results of our own simulations dealing with the possible dynamics and/or spatial distribution of the processes discussed.

Characterization and evolutionary analysis of tributyltin-binding protein and pufferfish saxitoxin and tetrodotoxin-binding protein genes in toxic and nontoxic pufferfishes.

Science.gov (United States)

Hashiguchi, Y; Lee, J M; Shiraishi, M; Komatsu, S; Miki, S; Shimasaki, Y; Mochioka, N; Kusakabe, T; Oshima, Y

2015-05-01

Understanding the evolutionary mechanisms of toxin accumulation in pufferfishes has been long-standing problem in toxicology and evolutionary biology. Pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) is involved in the transport and accumulation of tetrodotoxin and is one of the most intriguing proteins related to the toxicity of pufferfishes. PSTBPs are fusion proteins consisting of two tandem repeated tributyltin-binding protein type 2 (TBT-bp2) domains. In this study, we examined the evolutionary dynamics of TBT-bp2 and PSTBP genes to understand the evolution of toxin accumulation in pufferfishes. Database searches and/or PCR-based cDNA cloning in nine pufferfish species (6 toxic and 3 nontoxic) revealed that all species possessed one or more TBT-bp2 genes, but PSTBP genes were found only in 5 toxic species belonging to genus Takifugu. These toxic Takifugu species possessed two or three copies of PSTBP genes. Phylogenetic analysis of TBT-bp2 and PSTBP genes suggested that PSTBPs evolved in the common ancestor of Takifugu species by repeated duplications and fusions of TBT-bp2 genes. In addition, a detailed comparison of Takifugu TBT-bp2 and PSTBP gene sequences detected a signature of positive selection under the pressure of gene conversion. The complicated evolutionary dynamics of TBT-bp2 and PSTBP genes may reflect the diversity of toxicity in pufferfishes. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Plant dynamics analyses of fast reactor concept: RAPID-A without any control rod

International Nuclear Information System (INIS)

Kambe, Mitsuru

1996-01-01

Plant dynamics analyses of a fast reactor concept RAPID-A without any control rod have been demonstrated in case of reactor startup and sudden change of the primary flow rate. RAIP-A concept involves Lithium Expansion Module (LEM) for inherent reactivity feedback, Lithium Injection Module (LIM) for inherent ultimate shutdown and Lithium Release Module (LRM) for automated reactor startup. LEM consists of Quick-LEM and Slow-LEM. Slow-LEM provides with moderate reactivity addition as decreasing temperature. Quick-LEM assures quick negative reactivity feedback as increasing temperature. Plant dynamics analyses revealed that reactor power is nearly proportional to the primary flow rate even if the flow rate increases suddenly. Fully automated reactor startup from the subcritical condition has been attempted by inserting reactivity at a constant rate by LRM. Allowable rate of reactivity addition has been obtained in respect to Quick-LEM reactivity worth. (author)

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

Science.gov (United States)

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

Science.gov (United States)

Chen, Bor-Sen; Yeh, Chin-Hsun

2017-12-01

We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

Science.gov (United States)

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective

Dynamics, Stability, and Evolutionary Patterns of Mesoscale Intrathermocline Vortices

Science.gov (United States)

2016-12-01

different manner from a dynamic eddy, which underscores inherent limitations of intrusion modeling in quiescent background states. Finally, it...of observed values. (3) A static eddy dissipates in a very different manner from a dynamic eddy, which underscores inherent limitations of...does not react to the environment in a physical manner . This establishes a need for future research on eddies to be modeled on a dynamically rotating

The numerical simulation study of the dynamic evolutionary processes in an earthquake cycle on the Longmen Shan Fault

Science.gov (United States)

Tao, Wei; Shen, Zheng-Kang; Zhang, Yong

2016-04-01

The Longmen Shan, located in the conjunction of the eastern margin the Tibet plateau and Sichuan basin, is a typical area for studying the deformation pattern of the Tibet plateau. Following the 2008 Mw 7.9 Wenchuan earthquake (WE) rupturing the Longmen Shan Fault (LSF), a great deal of observations and studies on geology, geophysics, and geodesy have been carried out for this region, with results published successively in recent years. Using the 2D viscoelastic finite element model, introducing the rate-state friction law to the fault, this thesis makes modeling of the earthquake recurrence process and the dynamic evolutionary processes in an earthquake cycle of 10 thousand years. By analyzing the displacement, velocity, stresses, strain energy and strain energy increment fields, this work obtains the following conclusions: (1) The maximum coseismic displacement on the fault is on the surface, and the damage on the hanging wall is much more serious than that on the foot wall of the fault. If the detachment layer is absent, the coseismic displacement would be smaller and the relative displacement between the hanging wall and foot wall would also be smaller. (2) In every stage of the earthquake cycle, the velocities (especially the vertical velocities) on the hanging wall of the fault are larger than that on the food wall, and the values and the distribution patterns of the velocity fields are similar. While in the locking stage prior to the earthquake, the velocities in crust and the relative velocities between hanging wall and foot wall decrease. For the model without the detachment layer, the velocities in crust in the post-seismic stage is much larger than those in other stages. (3) The maximum principle stress and the maximum shear stress concentrate around the joint of the fault and detachment layer, therefore the earthquake would nucleate and start here. (4) The strain density distribution patterns in stages of the earthquake cycle are similar. There are two

Online networks, social interaction and segregation: An evolutionary approach

OpenAIRE

Antoci, Angelo; Sabatini, Fabio

2018-01-01

There is growing evidence that face-to-face interaction is declining in many countries, exacerbating the phenomenon of social isolation. On the other hand, social interaction through online networking sites is steeply rising. To analyze these societal dynamics, we have built an evolutionary game model in which agents can choose between three strategies of social participation: 1) interaction via both online social networks and face-to-face encounters; 2) interaction by exclusive means of face...

Self-Organized Criticality and Mass Extinction in Evolutionary Algorithms

DEFF Research Database (Denmark)

Krink, Thiemo; Thomsen, Rene

2001-01-01

The gaps in the fossil record gave rise to the hypothesis that evolution proceeded in long periods of stasis, which alternated with occasional, rapid changes that yielded evolutionary progress. One mechanism that could cause these punctuated bursts is the re-colonbation of changing and deserted...... at a critical state between chaos and order, known as self-organized criticality (SOC). Based on this background, we used SOC to control the size of spatial extinction zones in a diffusion model. The SOC selection process was easy to implement and implied only negligible computational costs. Our results show...

Evolutionary games in the multiverse.

Science.gov (United States)

Gokhale, Chaitanya S; Traulsen, Arne

2010-03-23

Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may, in fact, take place between a number of individuals and not just between two. Here we address one-shot games with multiple players. As long as we have only two strategies, many results from two-player games can be generalized to multiple players. For games with multiple players and more than two strategies, we show that statements derived for pairwise interactions no longer hold. For two-player games with any number of strategies there can be at most one isolated internal equilibrium. For any number of players with any number of strategies , there can be at most isolated internal equilibria. Multiplayer games show a great dynamical complexity that cannot be captured based on pairwise interactions. Our results hold for any game and can easily be applied to specific cases, such as public goods games or multiplayer stag hunts.

Suppression of chaos at slow variables by rapidly mixing fast dynamics through linear energy-preserving coupling

Science.gov (United States)

Abramov, R. V.

2011-12-01

Chaotic multiscale dynamical systems are common in many areas of science, one of the examples being the interaction of the low-frequency dynamics in the atmosphere with the fast turbulent weather dynamics. One of the key questions about chaotic multiscale systems is how the fast dynamics affects chaos at the slow variables, and, therefore, impacts uncertainty and predictability of the slow dynamics. Here we demonstrate that the linear slow-fast coupling with the total energy conservation property promotes the suppression of chaos at the slow variables through the rapid mixing at the fast variables, both theoretically and through numerical simulations. A suitable mathematical framework is developed, connecting the slow dynamics on the tangent subspaces to the infinite-time linear response of the mean state to a constant external forcing at the fast variables. Additionally, it is shown that the uncoupled dynamics for the slow variables may remain chaotic while the complete multiscale system loses chaos and becomes completely predictable at the slow variables through increasing chaos and turbulence at the fast variables. This result contradicts the common sense intuition, where, naturally, one would think that coupling a slow weakly chaotic system with another much faster and much stronger chaotic system would result in general increase of chaos at the slow variables.

A new evolutionary solution method for dynamic expansion planning of DG-integrated primary distribution networks

International Nuclear Information System (INIS)

Ahmadigorji, Masoud; Amjady, Nima

2014-01-01

Highlights: • A new dynamic distribution network expansion planning model is presented. • A Binary Enhanced Particle Swarm Optimization (BEPSO) algorithm is proposed. • A Modified Differential Evolution (MDE) algorithm is proposed. • A new bi-level optimization approach composed of BEPSO and MDE is presented. • The effectiveness of the proposed optimization approach is extensively illustrated. - Abstract: Reconstruction in the power system and appearing of new technologies for generation capacity of electrical energy has led to significant innovation in Distribution Network Expansion Planning (DNEP). Distributed Generation (DG) includes the application of small/medium generation units located in power distribution networks and/or near the load centers. Appropriate utilization of DG can affect the various technical and operational indices of the distribution network such as the feeder loading, energy losses and voltage profile. In addition, application of DG in proper size is an essential tool to achieve the DG maximum potential benefits. In this paper, a time-based (dynamic) model for DNEP is proposed to determine the optimal size, location and installation year of DG in distribution system. Also, in this model, the Optimal Power Flow (OPF) is exerted to determine the optimal generation of DGs for every potential solution in order to minimize the investment and operation costs following the load growth in a specified planning period. Besides, the reinforcement requirements of existing distribution feeders are considered, simultaneously. The proposed optimization problem is solved by the combination of evolutionary methods of a new Binary Enhanced Particle Swarm Optimization (BEPSO) and Modified Differential Evolution (MDE) to find the optimal expansion strategy and solve OPF, respectively. The proposed planning approach is applied to two typical primary distribution networks and compared with several other methods. These comparisons illustrate the

Evolutionary Demography

DEFF Research Database (Denmark)

Levitis, Daniel

2015-01-01

of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness......Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...

Evolutionary dynamics of consumers' crowdfunding strategies based on replicator dynamics%基于复制动态的消费者众筹策略演化动态

Institute of Scientific and Technical Information of China (English)

王先甲; 何奇龙; 全吉

2017-01-01

Use large group repeated game-replicator dynamics research on consumer groups who are bounded rationality got through imitating and learning to update their strategies supporting or nonsupporting crowdfunding under two scenarios fairness and altruism contribution rule.Established two people mult-strategy evolutionary game dynamic equations.Through analyzing the change of different parameters how to influence on the evolutionary stable equilibrium and the basin of attraction of the system,considering the failure of crowdfunding bringing regrets this paper researched the effects of crowdfunding success from different factors.The study find that under the fair contribution mechanism and without regard to regrets,supporting is the dominant strategy.Considering the failure of crowdfunding bringing regrets and generating negative benefit to consumer,when the target is smaller,the higher of the product quality level,the bigger of consumer's preferences and group benefits,the more beneficial to the crowdfunding evolutionary success.But the increasing of issued shares brings consumer's free-riding behavior,thus it restrains the success of crowdfunding.Under the altruism behavior,the bigger of consumer's preferences and group benefits,the higher of product quality level,the more beneficial to the crowdfunding evolutionary success.When financing target is fixed and the issued shares is increased,free-rider behavior don't increase,instead the success probability of crowdfunding be enhanced.%采用大群体反复博弈-复制动态演化博弈,在公平贡献和利他主义两种情景下,建立了有限理性的消费者群体通过模仿学习不断调整支持众筹和不支持众筹两策略多人博弈的演化系统.通过对不�

RAPID DYNAMICAL CHAOS IN AN EXOPLANETARY SYSTEM

Energy Technology Data Exchange (ETDEWEB)

Deck, Katherine M.; Winn, Joshua N. [Department of Physics and Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Holman, Matthew J.; Carter, Joshua A.; Ragozzine, Darin [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Agol, Eric [Department of Astronomy, Box 351580, University of Washington, Seattle, WA 98195 (United States); Lissauer, Jack J. [NASA Ames Research Center, Moffet Field, CA 94035 (United States)

2012-08-10

We report on the long-term dynamical evolution of the two-planet Kepler-36 system, which consists of a super-Earth and a sub-Neptune in a tightly packed orbital configuration. The orbits of the planets, which we studied through numerical integrations of initial conditions that are consistent with observations of the system, are chaotic with a Lyapunov time of only {approx}10 years. The chaos is a consequence of a particular set of orbital resonances, with the inner planet orbiting 34 times for every 29 orbits of the outer planet. The rapidity of the chaos is due to the interaction of the 29:34 resonance with the nearby first-order 6:7 resonance, in contrast to the usual case in which secular terms in the Hamiltonian play a dominant role. Only one contiguous region of phase space, accounting for {approx}4.5% of the sample of initial conditions studied, corresponds to planetary orbits that do not show large-scale orbital instabilities on the timescale of our integrations ({approx}200 million years). Restricting the orbits to this long-lived region allows a refinement of estimates of the masses and radii of the planets. We find that the long-lived region consists of the initial conditions that satisfy the Hill stability criterion by the largest margin. Any successful theory for the formation of this system will need to account for why its current state is so close to unstable regions of phase space.

Does sex speed up evolutionary rate and increase biodiversity?

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Melián, Carlos J; Alonso, David; Allesina, Stefano; Condit, Richard S; Etienne, Rampal S

2012-01-01

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy.

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Jolly Chatterjee

Full Text Available Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the 'sativa leaf type' that we see today in domesticated species.

A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

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Shan Li

2014-01-01

Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

Top predators induce the evolutionary diversification of intermediate predator species.

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Zu, Jian; Yuan, Bo; Du, Jianqiang

2015-12-21

We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Designing synthetic networks in silico: a generalised evolutionary algorithm approach.

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Smith, Robert W; van Sluijs, Bob; Fleck, Christian

2017-12-02

Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rates that respond to pulses or produce stable oscillations. In this work we present a generalised in silico evolutionary algorithm that simultaneously finds network structures and reaction rates (genotypes) that can satisfy multiple defined objectives (phenotypes). The key step to our approach is to translate a schema/binary-based description of biological networks into systems of ordinary differential equations (ODEs). The ODEs can then be solved numerically to provide dynamic information about an evolved networks functionality. Initially we benchmark algorithm performance by finding optimal networks that can recapitulate concentration time-series data and perform parameter optimisation on oscillatory dynamics of the Repressilator. We go on to show the utility of our algorithm by finding new designs for robust synthetic oscillators, and by performing multi-objective optimisation to find a set of oscillators and feed-forward loops that are optimal at balancing different system properties. In sum, our results not only confirm and build on previous observations but we also provide new designs of synthetic oscillators for experimental construction. In this work we have presented and tested an evolutionary algorithm that can design a biological network to produce desired output. Given that previous designs of synthetic networks have been limited to subregions of network- and parameter-space, the use of our evolutionary optimisation algorithm will enable Synthetic Biologists to construct new systems with the potential to display a wider range of complex responses.

Long-term social dynamics drive loss of function in pathogenic bacteria

DEFF Research Database (Denmark)

Breum Andersen, Sandra; Marvig, Rasmus Lykke; Molin, Søren

2015-01-01

Laboratory experiments show that social interactions between bacterial cells can drive evolutionary change at the population level, but significant challenges limit attempts to assess the relevance of these findings to natural populations, where selection pressures are unknown. We have increasingly...... sophisticated methods for monitoring phenotypic and genotypic dynamics in bacteria causing infectious disease, but in contrast, we lack evidence-based adaptive explanations for those changes. Evolutionary change during infection is often interpreted as host adaptation, but this assumption neglects to consider...... social dynamics shown to drive evolutionary change in vitro. We provide evidence to show that long-term behavioral dynamics observed in a pathogen are driven by selection to outcompete neighboring conspecific cells through social interactions. We find that Pseudomonas aeruginosa bacteria, causing lung...

Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

OpenAIRE

van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

2001-01-01

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. ...

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

OpenAIRE

Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.

2001-01-01

textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiologi...

Evolutionary Dynamics of Tumor-Stroma Interactions in Multiple Myeloma.

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Javad Salimi Sartakhti

Full Text Available Cancer cells and stromal cells cooperate by exchanging diffusible factors that sustain tumor growth, a form of frequency-dependent selection that can be studied in the framework of evolutionary game theory. In the case of multiple myeloma, three types of cells (malignant plasma cells, osteoblasts and osteoclasts exchange growth factors with different effects, and tumor-stroma interactions have been analysed using a model of cooperation with pairwise interactions. Here we show that a model in which growth factors have autocrine and paracrine effects on multiple cells, a more realistic assumption for tumor-stroma interactions, leads to different results, with implications for disease progression and treatment. In particular, the model reveals that reducing the number of malignant plasma cells below a critical threshold can lead to their extinction and thus to restore a healthy balance between osteoclast and osteoblast, a result in line with current therapies against multiple myeloma.

Some Analytical Properties of the Model for Stochastic Evolutionary Games in Finite Populations with Non-uniform Interaction Rate

International Nuclear Information System (INIS)

Quan Ji; Wang Xianjia

2013-01-01

Traditional evolutionary games assume uniform interaction rate, which means that the rate at which individuals meet and interact is independent of their strategies. But in some systems, especially biological systems, the players interact with each other discriminately. Taylor and Nowak (2006) were the first to establish the corresponding non-uniform interaction rate model by allowing the interaction rates to depend on strategies. Their model is based on replicator dynamics which assumes an infinite size population. But in reality, the number of individuals in the population is always finite, and there will be some random interference in the individuals' strategy selection process. Therefore, it is more practical to establish the corresponding stochastic evolutionary model in finite populations. In fact, the analysis of evolutionary games in a finite size population is more difficult. Just as Taylor and Nowak said in the outlook section of their paper, ''The analysis of non-uniform interaction rates should be extended to stochastic game dynamics of finite populations''. In this paper, we are exactly doing this work. We extend Taylor and Nowak's model from infinite to finite case, especially focusing on the infiuence of non-uniform connection characteristics on the evolutionary stable state of the system. We model the strategy evolutionary process of the population by a continuous ergodic Markov process. Based on the limit distribution of the process, we can give the evolutionary stable state of the system. We make a complete classification of the symmetric 2 × 2 games. For each case game, the corresponding limit distribution of the Markov-based process is given when noise intensity is small enough. In contrast with most literatures in evolutionary games using the simulation method, all our results obtained are analytical. Especially, in the dominant-case game, coexistence of the two strategies may become evolutionary stable states in our model. This result can be

Between Pleasure and Contentment: Evolutionary Dynamics of Some Possible Parameters of Happiness

OpenAIRE

Gao, Yue; Edelman, Shimon

2016-01-01

We offer and test a simple operationalization of hedonic and eudaimonic well-being ("happiness") as mediating variables that link outcomes to motivation. In six evolutionary agent-based simulation experiments, we compared the relative performance of agents endowed with different combinations of happiness-related traits (parameter values), under four types of environmental conditions. We found (i) that the effects of attaching more weight to longer-term than to momentary happiness and of exten...

Synthesizing multi-objective H2/H-infinity dynamic controller using evolutionary algorithms

DEFF Research Database (Denmark)

Pedersen, Gerulf; Langballe, A.S.; Wisniewski, Rafal

This paper covers the design of an Evolutionary Algorithm (EA), which should be able to synthesize a mixed H2/H-infinity. It will be shown how a system can be expressed as Matrix Inequalities (MI) and these will then be used in the design of the EA. The main objective is to examine whether a mixed...... H2/H-infinity controller is feasible, and if so, how the optimal mixed controller might befound....

Of Hissing Snakes and Angry Voices: Human Infants Are Differentially Responsive to Evolutionary Fear-Relevant Sounds

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Erlich, Nicole; Lipp, Ottmar V.; Slaughter, Virginia

2013-01-01

Adult humans demonstrate differential processing of stimuli that were recurrent threats to safety and survival throughout evolutionary history. Recent studies suggest that differential processing of evolutionarily ancient threats occurs in human infants, leading to the proposal of an inborn mechanism for rapid identification of, and response to,…

Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids.

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Breitkopf, Hendrik; Onstein, Renske E; Cafasso, Donata; Schlüter, Philipp M; Cozzolino, Salvatore

2015-07-01

Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

The Price Equation, Gradient Dynamics, and Continuous Trait Game Theory.

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Lehtonen, Jussi

2018-01-01

A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts. Using Taylor polynomials and the Price equation, I derive a dynamic measure of evolutionary change, a condition for singular points, the convergence stability criterion, and an alternative interpretation of evolutionary stability. Furthermore, by applying the Price equation to a multivariable Taylor polynomial, the direct fitness approach to kin selection emerges. Finally, I compare these results to the mean gradient equation of quantitative genetics and the canonical equation of adaptive dynamics.

Combining environment-driven adaptation and task-driven optimisation in evolutionary robotics.

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Haasdijk, Evert; Bredeche, Nicolas; Eiben, A E

2014-01-01

Embodied evolutionary robotics is a sub-field of evolutionary robotics that employs evolutionary algorithms on the robotic hardware itself, during the operational period, i.e., in an on-line fashion. This enables robotic systems that continuously adapt, and are therefore capable of (re-)adjusting themselves to previously unknown or dynamically changing conditions autonomously, without human oversight. This paper addresses one of the major challenges that such systems face, viz. that the robots must satisfy two sets of requirements. Firstly, they must continue to operate reliably in their environment (viability), and secondly they must competently perform user-specified tasks (usefulness). The solution we propose exploits the fact that evolutionary methods have two basic selection mechanisms-survivor selection and parent selection. This allows evolution to tackle the two sets of requirements separately: survivor selection is driven by the environment and parent selection is based on task-performance. This idea is elaborated in the Multi-Objective aNd open-Ended Evolution (monee) framework, which we experimentally validate. Experiments with robotic swarms of 100 simulated e-pucks show that monee does indeed promote task-driven behaviour without compromising environmental adaptation. We also investigate an extension of the parent selection process with a 'market mechanism' that can ensure equitable distribution of effort over multiple tasks, a particularly pressing issue if the environment promotes specialisation in single tasks.

Combining environment-driven adaptation and task-driven optimisation in evolutionary robotics.

Directory of Open Access Journals (Sweden)

Evert Haasdijk

Full Text Available Embodied evolutionary robotics is a sub-field of evolutionary robotics that employs evolutionary algorithms on the robotic hardware itself, during the operational period, i.e., in an on-line fashion. This enables robotic systems that continuously adapt, and are therefore capable of (re-adjusting themselves to previously unknown or dynamically changing conditions autonomously, without human oversight. This paper addresses one of the major challenges that such systems face, viz. that the robots must satisfy two sets of requirements. Firstly, they must continue to operate reliably in their environment (viability, and secondly they must competently perform user-specified tasks (usefulness. The solution we propose exploits the fact that evolutionary methods have two basic selection mechanisms-survivor selection and parent selection. This allows evolution to tackle the two sets of requirements separately: survivor selection is driven by the environment and parent selection is based on task-performance. This idea is elaborated in the Multi-Objective aNd open-Ended Evolution (monee framework, which we experimentally validate. Experiments with robotic swarms of 100 simulated e-pucks show that monee does indeed promote task-driven behaviour without compromising environmental adaptation. We also investigate an extension of the parent selection process with a 'market mechanism' that can ensure equitable distribution of effort over multiple tasks, a particularly pressing issue if the environment promotes specialisation in single tasks.

Sequential interactions-in which one player plays first and another responds-promote cooperation in evolutionary-dynamical simulations of single-shot Prisoner's Dilemma and Snowdrift games.

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Laird, Robert A

2018-05-21

Cooperation is a central topic in evolutionary biology because (a) it is difficult to reconcile why individuals would act in a way that benefits others if such action is costly to themselves, and (b) it underpins many of the 'major transitions of evolution', making it essential for explaining the origins of successively higher levels of biological organization. Within evolutionary game theory, the Prisoner's Dilemma and Snowdrift games are the main theoretical constructs used to study the evolution of cooperation in dyadic interactions. In single-shot versions of these games, wherein individuals play each other only once, players typically act simultaneously rather than sequentially. Allowing one player to respond to the actions of its co-player-in the absence of any possibility of the responder being rewarded for cooperation or punished for defection, as in simultaneous or sequential iterated games-may seem to invite more incentive for exploitation and retaliation in single-shot games, compared to when interactions occur simultaneously, thereby reducing the likelihood that cooperative strategies can thrive. To the contrary, I use lattice-based, evolutionary-dynamical simulation models of single-shot games to demonstrate that under many conditions, sequential interactions have the potential to enhance unilaterally or mutually cooperative outcomes and increase the average payoff of populations, relative to simultaneous interactions-benefits that are especially prevalent in a spatially explicit context. This surprising result is attributable to the presence of conditional strategies that emerge in sequential games that can't occur in the corresponding simultaneous versions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Shining evolutionary light on human sleep and sleep disorders.

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Nunn, Charles L; Samson, David R; Krystal, Andrew D

2016-01-01

Sleep is essential to cognitive function and health in humans, yet the ultimate reasons for sleep-i.e. 'why' sleep evolved-remain mysterious. We integrate findings from human sleep studies, the ethnographic record, and the ecology and evolution of mammalian sleep to better understand sleep along the human lineage and in the modern world. Compared to other primates, sleep in great apes has undergone substantial evolutionary change, with all great apes building a sleeping platform or 'nest'. Further evolutionary change characterizes human sleep, with humans having the shortest sleep duration, yet the highest proportion of rapid eye movement sleep among primates. These changes likely reflect that our ancestors experienced fitness benefits from being active for a greater portion of the 24-h cycle than other primates, potentially related to advantages arising from learning, socializing and defending against predators and hostile conspecifics. Perspectives from evolutionary medicine have implications for understanding sleep disorders; we consider these perspectives in the context of insomnia, narcolepsy, seasonal affective disorder, circadian rhythm disorders and sleep apnea. We also identify how human sleep today differs from sleep through most of human evolution, and the implications of these changes for global health and health disparities. More generally, our review highlights the importance of phylogenetic comparisons in understanding human health, including well-known links between sleep, cognitive performance and health in humans. © The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals.

Science.gov (United States)

Sunagar, Kartik; Moran, Yehu

2015-10-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a 'two-speed' mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species-the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia-the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals.

Directory of Open Access Journals (Sweden)

Kartik Sunagar

2015-10-01

Full Text Available Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes. By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a 'two-speed' mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion in the evolutionary history of the species-the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia-the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

Science.gov (United States)

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Adaptive Topographies and Equilibrium Selection in an Evolutionary Game

Science.gov (United States)

Osinga, Hinke M.; Marshall, James A. R.

2015-01-01

It has long been known in the field of population genetics that adaptive topographies, in which population equilibria maximise mean population fitness for a trait regardless of its genetic bases, do not exist. Whether one chooses to model selection acting on a single locus or multiple loci does matter. In evolutionary game theory, analysis of a simple and general game involving distinct roles for the two players has shown that whether strategies are modelled using a single ‘locus’ or one ‘locus’ for each role, the stable population equilibria are unchanged and correspond to the fitness-maximising evolutionary stable strategies of the game. This is curious given the aforementioned population genetical results on the importance of the genetic bases of traits. Here we present a dynamical systems analysis of the game with roles detailing how, while the stable equilibria in this game are unchanged by the number of ‘loci’ modelled, equilibrium selection may differ under the two modelling approaches. PMID:25706762

Statistical physics and computational methods for evolutionary game theory

CERN Document Server

Javarone, Marco Alberto

2018-01-01

This book presents an introduction to Evolutionary Game Theory (EGT) which is an emerging field in the area of complex systems attracting the attention of researchers from disparate scientific communities. EGT allows one to represent and study several complex phenomena, such as the emergence of cooperation in social systems, the role of conformity in shaping the equilibrium of a population, and the dynamics in biological and ecological systems. Since EGT models belong to the area of complex systems, statistical physics constitutes a fundamental ingredient for investigating their behavior. At the same time, the complexity of some EGT models, such as those realized by means of agent-based methods, often require the implementation of numerical simulations. Therefore, beyond providing an introduction to EGT, this book gives a brief overview of the main statistical physics tools (such as phase transitions and the Ising model) and computational strategies for simulating evolutionary games (such as Monte Carlo algor...

A single-rate context-dependent learning process underlies rapid adaptation to familiar object dynamics.

Science.gov (United States)

Ingram, James N; Howard, Ian S; Flanagan, J Randall; Wolpert, Daniel M

2011-09-01

Motor learning has been extensively studied using dynamic (force-field) perturbations. These induce movement errors that result in adaptive changes to the motor commands. Several state-space models have been developed to explain how trial-by-trial errors drive the progressive adaptation observed in such studies. These models have been applied to adaptation involving novel dynamics, which typically occurs over tens to hundreds of trials, and which appears to be mediated by a dual-rate adaptation process. In contrast, when manipulating objects with familiar dynamics, subjects adapt rapidly within a few trials. Here, we apply state-space models to familiar dynamics, asking whether adaptation is mediated by a single-rate or dual-rate process. Previously, we reported a task in which subjects rotate an object with known dynamics. By presenting the object at different visual orientations, adaptation was shown to be context-specific, with limited generalization to novel orientations. Here we show that a multiple-context state-space model, with a generalization function tuned to visual object orientation, can reproduce the time-course of adaptation and de-adaptation as well as the observed context-dependent behavior. In contrast to the dual-rate process associated with novel dynamics, we show that a single-rate process mediates adaptation to familiar object dynamics. The model predicts that during exposure to the object across multiple orientations, there will be a degree of independence for adaptation and de-adaptation within each context, and that the states associated with all contexts will slowly de-adapt during exposure in one particular context. We confirm these predictions in two new experiments. Results of the current study thus highlight similarities and differences in the processes engaged during exposure to novel versus familiar dynamics. In both cases, adaptation is mediated by multiple context-specific representations. In the case of familiar object dynamics

A single-rate context-dependent learning process underlies rapid adaptation to familiar object dynamics.

Directory of Open Access Journals (Sweden)

James N Ingram

2011-09-01

Full Text Available Motor learning has been extensively studied using dynamic (force-field perturbations. These induce movement errors that result in adaptive changes to the motor commands. Several state-space models have been developed to explain how trial-by-trial errors drive the progressive adaptation observed in such studies. These models have been applied to adaptation involving novel dynamics, which typically occurs over tens to hundreds of trials, and which appears to be mediated by a dual-rate adaptation process. In contrast, when manipulating objects with familiar dynamics, subjects adapt rapidly within a few trials. Here, we apply state-space models to familiar dynamics, asking whether adaptation is mediated by a single-rate or dual-rate process. Previously, we reported a task in which subjects rotate an object with known dynamics. By presenting the object at different visual orientations, adaptation was shown to be context-specific, with limited generalization to novel orientations. Here we show that a multiple-context state-space model, with a generalization function tuned to visual object orientation, can reproduce the time-course of adaptation and de-adaptation as well as the observed context-dependent behavior. In contrast to the dual-rate process associated with novel dynamics, we show that a single-rate process mediates adaptation to familiar object dynamics. The model predicts that during exposure to the object across multiple orientations, there will be a degree of independence for adaptation and de-adaptation within each context, and that the states associated with all contexts will slowly de-adapt during exposure in one particular context. We confirm these predictions in two new experiments. Results of the current study thus highlight similarities and differences in the processes engaged during exposure to novel versus familiar dynamics. In both cases, adaptation is mediated by multiple context-specific representations. In the case of familiar

The AquaDEB project (phase I): Analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using Dynamic Energy Budgets

Science.gov (United States)

Alunno-Bruscia, Marianne; van der Veer, Henk W.; Kooijman, Sebastiaan A. L. M.

2009-08-01

The European Research Project AquaDEB (2007-2011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main scientific objectives in AquaDEB are i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability of natural or human origin, and ii) to evaluate the related consequences at different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). At mid-term life, the AquaDEB collaboration has already yielded interesting results by quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) with a single mathematical framework. It has also allowed to federate scientists with different backgrounds, e.g. mathematics, microbiology, ecology, chemistry, and working in different fields, e.g. aquaculture, fisheries, ecology, agronomy, ecotoxicology, climate change. For the two coming years, the focus of the AquaDEB collaboration will be in priority: (i) to compare energetic and physiological strategies among species through the DEB parameter values and to identify the factors responsible for any differences in bioenergetics and physiology; and to compare dynamic (DEB) versus static (SEB) energy models to study the physiological performance of aquatic species; (ii) to consider different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) to scale up the models for a few species from

Cyclic dominance in evolutionary games: a review

Science.gov (United States)

Szolnoki, Attila; Mobilia, Mauro; Jiang, Luo-Luo; Szczesny, Bartosz; Rucklidge, Alastair M.; Perc, Matjaž

2014-01-01

Rock is wrapped by paper, paper is cut by scissors and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator–prey interactions, the mating strategy of side-blotched lizards, the overgrowth of marine sessile organisms and competition in microbial populations. Cyclical interactions also emerge spontaneously in evolutionary games entailing volunteering, reward, punishment, and in fact are common when the competing strategies are three or more, regardless of the particularities of the game. Here, we review recent advances on the rock–paper–scissors (RPS) and related evolutionary games, focusing, in particular, on pattern formation, the impact of mobility and the spontaneous emergence of cyclic dominance. We also review mean-field and zero-dimensional RPS models and the application of the complex Ginzburg–Landau equation, and we highlight the importance and usefulness of statistical physics for the successful study of large-scale ecological systems. Directions for future research, related, for example, to dynamical effects of coevolutionary rules and invasion reversals owing to multi-point interactions, are also outlined. PMID:25232048

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

Science.gov (United States)

McPherson, Andrew W; Chan, Fong Chun; Shah, Sohrab P

2018-02-01

The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones. In this review, we provide a brief overview of the concepts involved in predicting evolutionary histories, and provide a workflow based on bulk and targeted-genome sequencing. We then describe the application of this workflow to time series data obtained for transformed and progressed follicular lymphomas (FL), and contrast the observed evolutionary dynamics between these two subtypes. We next describe results from a spatial sampling study of high-grade serous (HGS) ovarian cancer, propose mechanisms of disease spread based on the observed clonal mixtures, and provide examples of diversification through subclonal acquisition of driver mutations and convergent evolution. Finally, we state implications of the techniques discussed in this review as a necessary but insufficient step on the path to predictive modelling of disease dynamics. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Stochastic evolutionary voluntary public goods game with punishment in a Quasi-birth-and-death process.

Science.gov (United States)

Quan, Ji; Liu, Wei; Chu, Yuqing; Wang, Xianjia

2017-11-23

Traditional replication dynamic model and the corresponding concept of evolutionary stable strategy (ESS) only takes into account whether the system can return to the equilibrium after being subjected to a small disturbance. In the real world, due to continuous noise, the ESS of the system may not be stochastically stable. In this paper, a model of voluntary public goods game with punishment is studied in a stochastic situation. Unlike the existing model, we describe the evolutionary process of strategies in the population as a generalized quasi-birth-and-death process. And we investigate the stochastic stable equilibrium (SSE) instead. By numerical experiments, we get all possible SSEs of the system for any combination of parameters, and investigate the influence of parameters on the probabilities of the system to select different equilibriums. It is found that in the stochastic situation, the introduction of the punishment and non-participation strategies can change the evolutionary dynamics of the system and equilibrium of the game. There is a large range of parameters that the system selects the cooperative states as its SSE with a high probability. This result provides us an insight and control method for the evolution of cooperation in the public goods game in stochastic situations.

The dynamics of categorization: Unraveling rapid categorization.

Science.gov (United States)

Mack, Michael L; Palmeri, Thomas J

2015-06-01

We explore a puzzle of visual object categorization: Under normal viewing conditions, you spot something as a dog fastest, but at a glance, you spot it faster as an animal. During speeded category verification, a classic basic-level advantage is commonly observed (Rosch, Mervis, Gray, Johnson, & Boyes-Braem, 1976), with categorization as a dog faster than as an animal (superordinate) or Golden Retriever (subordinate). A different story emerges during ultra-rapid categorization with limited exposure duration (categorization faster than basic or subordinate categorization (Thorpe, Fize, & Marlot, 1996). These two widely cited findings paint contrary theoretical pictures about the time course of categorization, yet no previous study has investigated them together. We systematically examined two experimental factors that could explain the qualitative difference in categorization across the two paradigms: exposure duration and category trial context. Mapping out the time course of object categorization by manipulating exposure duration and the timing of a post-stimulus mask revealed that brief exposure durations favor superordinate-level categorization, but with more time a basic-level advantage emerges. However, these advantages were modulated by category trial context. With randomized target categories, the superordinate advantage was eliminated; and with only four repetitions of superordinate categorization within an otherwise randomized context, the basic-level advantage was eliminated. Contrary to theoretical accounts that dictate a fixed priority for certain levels of abstraction in visual processing and access to semantic knowledge, the dynamics of object categorization are flexible, depending jointly on the level of abstraction, time for perceptual encoding, and category context. (c) 2015 APA, all rights reserved).

Genetic and evolutionary analysis of the Drosophila larval neuromuscular junction

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Campbell, Megan

Although evolution of brains and behaviors is of fundamental biological importance, we lack comprehensive understanding of the general principles governing these processes or the specific mechanisms and molecules through which the evolutionary changes are effected. Because synapses are the basic structural and functional units of nervous systems, one way to address these problems is to dissect the genetic and molecular pathways responsible for morphological evolution of a defined synapse. I have undertaken such an analysis by examining morphology of the larval neuromuscular junction (NMJ) in wild caught D. melanogaster as well as in over 20 other species of Drosophila. Whereas variation in NMJ morphology within a species is limited, I discovered a surprisingly extensive variation among different species. Compared with evolution of other morphological traits, NMJ morphology appears to be evolving very rapidly. Moreover, my data indicate that natural selection rather than genetic drift is primarily responsible for evolution of NMJ morphology. To dissect underlying molecular mechanisms that may govern NMJ growth and evolutionary divergence, I focused on a naturally occurring variant in D. melanogaster that causes NMJ overgrowth. I discovered that the variant mapped to Mob2, a gene encoding a kinase adapter protein originally described in yeast as a member of the Mitotic Exit Network (MEN). I have subsequently examined mutations in the Drosophila orthologs of all the core components of the yeast MEN and found that all of them function as part of a common pathway that acts presynaptically to negatively regulate NMJ growth. As in the regulation of yeast cytokinesis, these components of the MEN appear to act ultimately by regulating actin dynamics during the process of bouton growth and division. These studies have thus led to the discovery of an entirely new role for the MEN---regulation of synaptic growth---that is separate from its function in cell division. This work

Algorithmic Mechanism Design of Evolutionary Computation.

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Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Does sex speed up evolutionary rate and increase biodiversity?

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Carlos J Melián

Full Text Available Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

Evolutionary Explanations of Eating Disorders

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Igor Kardum

2008-12-01

Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

The (1+λ) evolutionary algorithm with self-adjusting mutation rate

DEFF Research Database (Denmark)

Doerr, Benjamin; Witt, Carsten; Gießen, Christian

2017-01-01

We propose a new way to self-adjust the mutation rate in population-based evolutionary algorithms. Roughly speaking, it consists of creating half the offspring with a mutation rate that is twice the current mutation rate and the other half with half the current rate. The mutation rate is then upd......We propose a new way to self-adjust the mutation rate in population-based evolutionary algorithms. Roughly speaking, it consists of creating half the offspring with a mutation rate that is twice the current mutation rate and the other half with half the current rate. The mutation rate...... is then updated to the rate used in that subpopulation which contains the best offspring. We analyze how the (1 + A) evolutionary algorithm with this self-adjusting mutation rate optimizes the OneMax test function. We prove that this dynamic version of the (1 + A) EA finds the optimum in an expected optimization...... time (number of fitness evaluations) of O(nA/log A + n log n). This time is asymptotically smaller than the optimization time of the classic (1 + A) EA. Previous work shows that this performance is best-possible among all A-parallel mutation-based unbiased black-box algorithms. This result shows...

Ecological theatre and the evolutionary game: how environmental and demographic factors determine payoffs in evolutionary games.

Science.gov (United States)

Argasinski, K; Broom, M

2013-10-01

In the standard approach to evolutionary games and replicator dynamics, differences in fitness can be interpreted as an excess from the mean Malthusian growth rate in the population. In the underlying reasoning, related to an analysis of "costs" and "benefits", there is a silent assumption that fitness can be described in some type of units. However, in most cases these units of measure are not explicitly specified. Then the question arises: are these theories testable? How can we measure "benefit" or "cost"? A natural language, useful for describing and justifying comparisons of strategic "cost" versus "benefits", is the terminology of demography, because the basic events that shape the outcome of natural selection are births and deaths. In this paper, we present the consequences of an explicit analysis of births and deaths in an evolutionary game theoretic framework. We will investigate different types of mortality pressures, their combinations and the possibility of trade-offs between mortality and fertility. We will show that within this new approach it is possible to model how strictly ecological factors such as density dependence and additive background fitness, which seem neutral in classical theory, can affect the outcomes of the game. We consider the example of the Hawk-Dove game, and show that when reformulated in terms of our new approach new details and new biological predictions are produced.

The citation field of evolutionary economics

NARCIS (Netherlands)

Dolfsma, Wilfred; Leydesdorff, Loet

2010-01-01

Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal

Rapid evolution in insect pests: the importance of space and time in population genomics studies.

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Pélissié, Benjamin; Crossley, Michael S; Cohen, Zachary Paul; Schoville, Sean D

2018-04-01

Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

OpenAIRE

Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

2015-01-01

The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution e...

The Hitchhiker’s Guide to Adaptive Dynamics

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Jacob Johansson

2013-06-01

Full Text Available Adaptive dynamics is a mathematical framework for studying evolution. It extends evolutionary game theory to account for more realistic ecological dynamics and it can incorporate both frequency- and density-dependent selection. This is a practical guide to adaptive dynamics that aims to illustrate how the methodology can be applied to the study of specific systems. The theory is presented in detail for a single, monomorphic, asexually reproducing population. We explain the necessary terminology to understand the basic arguments in models based on adaptive dynamics, including invasion fitness, the selection gradient, pairwise invasibility plots (PIP, evolutionarily singular strategies, and the canonical equation. The presentation is supported with a worked-out example of evolution of arrival times in migratory birds. We show how the adaptive dynamics methodology can be extended to study evolution in polymorphic populations using trait evolution plots (TEPs. We give an overview of literature that generalises adaptive dynamics techniques to other scenarios, such as sexual, diploid populations, and spatially-structured populations. We conclude by discussing how adaptive dynamics relates to evolutionary game theory and how adaptive-dynamics techniques can be used in speciation research.

Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

Science.gov (United States)

Hunt, Tam

2014-12-01

Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

The evolutionary dynamics of major regulators for sexual development among Hymenoptera species

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Matthias eBiewer

2015-04-01

Full Text Available All hymenopteran species, such as bees, wasps and ants, are characterized by the common principle of haplodiploid sex determination in which haploid males arise from unfertilized eggs and females from fertilized eggs. The underlying molecular mechanism has been studied in detail in the western honey bee Apis mellifera, in which the gene complementary sex determiner (csd acts as primary signal of the sex determining pathway, initiating female development by csd-heterozygotes. Csd arose from gene duplication of the feminizer (fem gene, a transformer (tra ortholog, and mediates in conjunction with transformer2 (tra2 sex-specific splicing of fem. Comparative molecular analyses identified fem/tra and its downstream target doublesex (dsx as conserved unit within the sex determining pathway of holometabolous insects. In this study, we aim to examine evolutionary differences among these key regulators. Our main hypothesis is that sex determining key regulators in Hymenoptera species show signs of coevolution within single phylogenetic lineages. We take advantage of several newly sequenced genomes of bee species to test this hypothesis using bioinformatic approaches. We found evidences that duplications of fem are restricted to certain bee lineages and notable amino acid differences of tra2 between Apis and non-Apis species propose structural changes in Tra2 protein affecting co-regulatory function on target genes. These findings may help to gain deeper insights into the ancestral mode of hymenopteran sex determination and support the common view of the remarkable evolutionary flexibility in this regulatory pathway.

Where Evolutionary Psychology Meets Cognitive Neuroscience: A Précis to Evolutionary Cognitive Neuroscience1

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Austen L. Krill

2007-01-01

Full Text Available Cognitive neuroscience, the study of brain-behavior relationships, has long attempted to map the brain. The discipline is flourishing, with an increasing number of functional neuroimaging studies appearing in the scientific literature daily. Unlike biology and even psychology, the cognitive neurosciences have only recently begun to apply evolutionary meta-theory and methodological guidance. Approaching cognitive neuroscience from an evolutionary perspective allows scientists to apply biologically based theoretical guidance to their investigations and can be conducted in both humans and nonhuman animals. In fact, several investigations of this sort are underway in laboratories around the world. This paper and two new volumes (Platek, Keenan, and Shackelford [Eds.], 2007; Platek and Shackelford [Eds.], under contract represent the first formal attempts to document the burgeoning field of evolutionary cognitive neuroscience. Here, we briefly review the current state of the science of evolutionary cognitive neuroscience, the methods available to the evolutionary cognitive neuroscientist, and what we foresee as the future directions of the discipline.

A Novel Evolutionary Engineering Design Approach for Mixed-Domain Systems

DEFF Research Database (Denmark)

Fan, Zhun; Hu, J.; Seo, K.

2004-01-01

This paper presents an approach to engineering design of mixed-domain dynamic systems. The approach aims at system-level design and has two key features: first, it generates engineering designs that satisfy predefined specifications in an automatic manner; second, it can design systems belonging ...... often encountered in evolutionary computation, a HFC (Hierarchical Fair Competition) model is adopted in this work. Examples of an analog filter design and a MEM filter design illustrate the application of the approach....

Evolutionary design assistants for architecture

Directory of Open Access Journals (Sweden)

N. Onur Sönmez

2015-04-01

existing literature and the proposals and applications of the thesis; secondly, proposals for descriptive and prescriptive models, mappings, summary illustrations, task structures, decomposition schemes, and integratory frameworks; and finally, experimental applications of these proposals. This tripartite progression allows an evaluation of each proposal both conceptually and practically; thereby, enabling a progressive improvement of the understanding regarding the research question, while producing concrete outputs on the way. Besides theoretical and interpretative examinations, the thesis investigates its subject through a set of practical and speculative proposals, which function as both research instruments and the outputs of the study. The first main output of the study is the “design_proxy” approach (d_p, which is an integrated approach for draft making design assistants. It is an outcome of both theoretical examinations and experimental applications, and proposes an integration of, (1 flexible and relaxed task definitions and representations (instead of strict formalisms, (2 intuitive interfaces that make use of usual design media, (3 evaluation of solution proposals through their similarity to given examples, and (4 a dynamic evolutionary approach for solution generation. The design_proxy approach may be useful for AD researchers that aim at developing practical design assistants, as has been examined and demonstrated with the two applications, i.e., design_proxy.graphics and design_proxy.layout. The second main output, the “Interleaved Evolutionary Algorithm” (IEA, or Interleaved EA is a novel evolutionary algorithm proposed and used as the underlying generative mechanism of design_proxybased design assistants. The Interleaved EA is a dynamic, adaptive, and multi-objective EA, in which one of the objectives leads the evolution until its fitness progression stagnates; in the sense that the settings and fitness values of this objective is used for most

Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.

Science.gov (United States)

Newton, Matilda S; Arcus, Vickery L; Patrick, Wayne M

2015-06-06

The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The system-dynamic and evolutionary non-Euclidean approach and the 'Lobachevsky-Poincare programme' idea for its successive realization in high energy physics

International Nuclear Information System (INIS)

Bubelev, E.G.; Kuchin, I.A.

1998-01-01

The necessity of creating mesophysics is motivated on the basis of a general likeness of the description of many phenomena and processes in micro- and macroworld. For a general and detailed investigation of the former in modern high energy physics (HEP), the Absolute (arising from Minkovsky and irrespective of any reference system) universal approach is used. Its two conceptually new branches are non-linear system-dynamic and non-Euclidean evolutionary ones. They are complementary ones and completely adequate to an extreme complexity of directly unobservable HEP objects. Some primary problems of them are briefly made clear on the basis of synergetics principles and HEP's internal Lobachevsky-Euclidean geometry. They are noted as the primary content of the Lobachevsky-Poincare Programme (LPP) the idea of which has been proposed recently for their successive solution

Polyploidy can drive rapid adaptation in yeast

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Selmecki, Anna M.; Maruvka, Yosef E.; Richmond, Phillip A.; Guillet, Marie; Shoresh, Noam; Sorenson, Amber L.; de, Subhajyoti; Kishony, Roy; Michor, Franziska; Dowell, Robin; Pellman, David

2015-03-01

Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations. For example, in diverse cell types and organisms, immediately after a whole-genome duplication, newly formed polyploids missegregate chromosomes and undergo genetic instability. The instability following whole-genome duplications is thought to provide adaptive mutations in microorganisms and can promote tumorigenesis in mammalian cells. Polyploidy may also affect adaptation independently of beneficial mutations through ploidy-specific changes in cell physiology. Here we perform in vitro evolution experiments to test directly whether polyploidy can accelerate evolutionary adaptation. Compared with haploids and diploids, tetraploids undergo significantly faster adaptation. Mathematical modelling suggests that rapid adaptation of tetraploids is driven by higher rates of beneficial mutations with stronger fitness effects, which is supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provide large fitness gains. We identify several mutations whose beneficial effects are manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.

Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila.

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Caizzi, Ruggiero; Moschetti, Roberta; Piacentini, Lucia; Fanti, Laura; Marsano, Renè Massimiliano; Dimitri, Patrizio

2016-08-01

The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentric heterochromatin, yet little is known about the evolutionary processes through which this has occurred. By combining genome annotation analysis and high-resolution cytology, we have identified and mapped 53 orthologs of D. melanogaster heterochromatic genes in the genomes of two evolutionarily distant species, D. pseudoobscura and D. virilis. Our results show that the orthologs of the D. melanogaster heterochromatic genes are clustered at three main genomic regions in D. virilis and D. pseudoobscura. In D. virilis, the clusters lie in the middle of euchromatin, while those in D. pseudoobscura are located in the proximal portion of the chromosome arms. Some orthologs map to the corresponding Muller C element in D. pseudoobscura and D. virilis, while others localize on the Muller B element, suggesting that chromosomal rearrangements that have been instrumental in the fusion of two separate elements involved the progenitors of genes currently located in D. melanogaster heterochromatin. These results demonstrate an evolutionary repositioning of gene clusters from ancestral locations in euchromatin to the pericentromeric heterochromatin of descendent D. melanogaster chromosomes. Remarkably, in both D. virilis and D. pseudoobscura the gene clusters show a conserved association with the HP1a protein, one of the most highly evolutionarily conserved epigenetic marks. In light of these results, we suggest a new scenario whereby ancestral HP1-like proteins (and possibly other epigenetic marks) may have contributed to the evolutionary repositioning of gene clusters into heterochromatin.

The evolutionary and ecological consequences of animal social networks: emerging issues.

Science.gov (United States)

Kurvers, Ralf H J M; Krause, Jens; Croft, Darren P; Wilson, Alexander D M; Wolf, Max

2014-06-01

The first generation of research on animal social networks was primarily aimed at introducing the concept of social networks to the fields of animal behaviour and behavioural ecology. More recently, a diverse body of evidence has shown that social fine structure matters on a broader scale than initially expected, affecting many key ecological and evolutionary processes. Here, we review this development. We discuss the effects of social network structure on evolutionary dynamics (genetic drift, fixation probabilities, and frequency-dependent selection) and social evolution (cooperation and between-individual behavioural differences). We discuss how social network structure can affect important coevolutionary processes (host-pathogen interactions and mutualisms) and population stability. We also discuss the potentially important, but poorly studied, role of social network structure on dispersal and invasion. Throughout, we highlight important areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

Directory of Open Access Journals (Sweden)

Naoki Takata

Full Text Available EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Evolutionary plasticity of plasma membrane interaction in DREPP family proteins.

Science.gov (United States)

Vosolsobě, Stanislav; Petrášek, Jan; Schwarzerová, Kateřina

2017-05-01

The plant-specific DREPP protein family comprises proteins that were shown to regulate the actin and microtubular cytoskeleton in a calcium-dependent manner. Our phylogenetic analysis showed that DREPPs first appeared in ferns and that DREPPs have a rapid and plastic evolutionary history in plants. Arabidopsis DREPP paralogues called AtMDP25/PCaP1 and AtMAP18/PCaP2 are N-myristoylated, which has been reported as a key factor in plasma membrane localization. Here we show that N-myristoylation is neither conserved nor ancestral for the DREPP family. Instead, by using confocal microscopy and a new method for quantitative evaluation of protein membrane localization, we show that DREPPs rely on two mechanisms ensuring their plasma membrane localization. These include N-myristoylation and electrostatic interaction of a polybasic amino acid cluster. We propose that various plasma membrane association mechanisms resulting from the evolutionary plasticity of DREPPs are important for refining plasma membrane interaction of these signalling proteins under various conditions and in various cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Universal scaling for the dilemma strength in evolutionary games

Science.gov (United States)

Wang, Zhen; Kokubo, Satoshi; Jusup, Marko; Tanimoto, Jun

2015-09-01

Why would natural selection favor the prevalence of cooperation within the groups of selfish individuals? A fruitful framework to address this question is evolutionary game theory, the essence of which is captured in the so-called social dilemmas. Such dilemmas have sparked the development of a variety of mathematical approaches to assess the conditions under which cooperation evolves. Furthermore, borrowing from statistical physics and network science, the research of the evolutionary game dynamics has been enriched with phenomena such as pattern formation, equilibrium selection, and self-organization. Numerous advances in understanding the evolution of cooperative behavior over the last few decades have recently been distilled into five reciprocity mechanisms: direct reciprocity, indirect reciprocity, kin selection, group selection, and network reciprocity. However, when social viscosity is introduced into a population via any of the reciprocity mechanisms, the existing scaling parameters for the dilemma strength do not yield a unique answer as to how the evolutionary dynamics should unfold. Motivated by this problem, we review the developments that led to the present state of affairs, highlight the accompanying pitfalls, and propose new universal scaling parameters for the dilemma strength. We prove universality by showing that the conditions for an ESS and the expressions for the internal equilibriums in an infinite, well-mixed population subjected to any of the five reciprocity mechanisms depend only on the new scaling parameters. A similar result is shown to hold for the fixation probability of the different strategies in a finite, well-mixed population. Furthermore, by means of numerical simulations, the same scaling parameters are shown to be effective even if the evolution of cooperation is considered on the spatial networks (with the exception of highly heterogeneous setups). We close the discussion by suggesting promising directions for future research

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Directory of Open Access Journals (Sweden)

Sofie Van Holle

2017-05-01

Full Text Available Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica. The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST, hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

The role of non-genetic inheritance in evolutionary rescue: epigenetic buffering, heritable bet hedging and epigenetic traps.

Science.gov (United States)

O'Dea, Rose E; Noble, Daniel W A; Johnson, Sheri L; Hesselson, Daniel; Nakagawa, Shinichi

2016-01-01

Rapid environmental change is predicted to compromise population survival, and the resulting strong selective pressure can erode genetic variation, making evolutionary rescue unlikely. Non-genetic inheritance may provide a solution to this problem and help explain the current lack of fit between purely genetic evolutionary models and empirical data. We hypothesize that epigenetic modifications can facilitate evolutionary rescue through 'epigenetic buffering'. By facilitating the inheritance of novel phenotypic variants that are generated by environmental change-a strategy we call 'heritable bet hedging'-epigenetic modifications could maintain and increase the evolutionary potential of a population. This process may facilitate genetic adaptation by preserving existing genetic variation, releasing cryptic genetic variation and/or facilitating mutations in functional loci. Although we show that examples of non-genetic inheritance are often maladaptive in the short term, accounting for phenotypic variance and non-adaptive plasticity may reveal important evolutionary implications over longer time scales. We also discuss the possibility that maladaptive epigenetic responses may be due to 'epigenetic traps', whereby evolutionarily novel factors (e.g. endocrine disruptors) hack into the existing epigenetic machinery. We stress that more ecologically relevant work on transgenerational epigenetic inheritance is required. Researchers conducting studies on transgenerational environmental effects should report measures of phenotypic variance, so that the possibility of both bet hedging and heritable bet hedging can be assessed. Future empirical and theoretical work is required to assess the relative importance of genetic and epigenetic variation, and their interaction, for evolutionary rescue.

Dynamic Adaptive Neural Network Arrays: A Neuromorphic Architecture

Energy Technology Data Exchange (ETDEWEB)

Disney, Adam [University of Tennessee (UT); Reynolds, John [University of Tennessee (UT)

2015-01-01

Dynamic Adaptive Neural Network Array (DANNA) is a neuromorphic hardware implementation. It differs from most other neuromorphic projects in that it allows for programmability of structure, and it is trained or designed using evolutionary optimization. This paper describes the DANNA structure, how DANNA is trained using evolutionary optimization, and an application of DANNA to a very simple classification task.

Integrating genomics into evolutionary medicine.

Science.gov (United States)

Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

2014-12-01

The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

Practical advantages of evolutionary computation

Science.gov (United States)

Fogel, David B.

1997-10-01

Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.

Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.

Science.gov (United States)

Chi, Albert; Curi, Sebastian; Clayton, Kevin; Luciano, David; Klauber, Kameron; Alexander-Katz, Alfredo; D'hers, Sebastian; Elman, Noel M

2014-08-01

Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.

Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production.

Science.gov (United States)

Mans, Robert; Daran, Jean-Marc G; Pronk, Jack T

2018-04-01

Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci. Recent studies indicate that phenotypic trade-offs, which are often observed after evolution under constant conditions, can be mitigated by using dynamic cultivation regimes. Advances in research on synthetic regulatory circuits offer exciting possibilities to extend the applicability of evolutionary engineering to products of yeasts whose synthesis requires a net input of cellular energy. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America.

Science.gov (United States)

Campitelli, Brandon E; Stinchcombe, John R

2014-06-03

Disentangling the historical evolutionary processes that contribute to patterns of phenotypic and genetic variation is important for understanding contemporary patterns of both traits of interest and genetic diversity of a species. Ipomoea hederacea is a self-compatible species whose geographic origin is contested, and previous work suggests that although there are signals of adaptation (significant leaf shape and flowering time clines), no population structure or neutral genetic differentiation of I. hederacea populations was detected. Here, we use DNA sequence data to characterize patterns of genetic variation to establish a more detailed understanding of the current and historical processes that may have generated the patterns of genetic variation in this species. We resequenced ca. 5000 bp across 7 genes for 192 individuals taken from 24 populations in North America. Our results indicate that North American I. hederacea populations are ubiquitously genetically depauperate, and patterns of nucleotide diversity are consistent with population expansion. Contrary to previous findings, we discovered significant population subdivision and isolation-by-distance, but genetic structure was spatially discontinuous, potentially implicating long-distance dispersal. We further found significant genetic differentiation at sequenced loci but nearly fourfold stronger differentiation at the leaf shape locus, strengthening evidence that the leaf shape locus is under divergent selection. We propose that North American I. hederacea has experienced a recent founder event, and/or population dynamics are best described by a metapopulation model (high turnover and dispersal), leading to low genetic diversity and a patchy genetic distribution. Copyright © 2014 Campitelli and Stinchcombe.

Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

Directory of Open Access Journals (Sweden)

Jeffrey K Noel

2016-01-01

Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

Evolutionary optimization and game strategies for advanced multi-disciplinary design applications to aeronautics and UAV design

CERN Document Server

Periaux, Jacques; Lee, Dong Seop Chris

2015-01-01

Many complex aeronautical design problems can be formulated with efficient multi-objective evolutionary optimization methods and game strategies. This book describes the role of advanced innovative evolution tools in the solution, or the set of solutions of single or multi disciplinary optimization. These tools use the concept of multi-population, asynchronous parallelization and hierarchical topology which allows different models including precise, intermediate and approximate models with each node belonging to the different hierarchical layer handled by a different Evolutionary Algorithm. The efficiency of evolutionary algorithms for both single and multi-objective optimization problems are significantly improved by the coupling of EAs with games and in particular by a new dynamic methodology named “Hybridized Nash-Pareto games”. Multi objective Optimization techniques and robust design problems taking into account uncertainties are introduced and explained in detail. Several applications dealing with c...

Behavioural, ecological and evolutionary responses to extreme climatic events: challenges and directions.

Science.gov (United States)

van de Pol, Martijn; Jenouvrier, Stéphanie; Cornelissen, Johannes H C; Visser, Marcel E

2017-06-19

More extreme climatic events (ECEs) are among the most prominent consequences of climate change. Despite a long-standing recognition of the importance of ECEs by paleo-ecologists and macro-evolutionary biologists, ECEs have only recently received a strong interest in the wider ecological and evolutionary community. However, as with many rapidly expanding fields, it lacks structure and cohesiveness, which strongly limits scientific progress. Furthermore, due to the descriptive and anecdotal nature of many ECE studies it is still unclear what the most relevant questions and long-term consequences are of ECEs. To improve synthesis, we first discuss ways to define ECEs that facilitate comparison among studies. We then argue that biologists should adhere to more rigorous attribution and mechanistic methods to assess ECE impacts. Subsequently, we discuss conceptual and methodological links with climatology and disturbance-, tipping point- and paleo-ecology. These research fields have close linkages with ECE research, but differ in the identity and/or the relative severity of environmental factors. By summarizing the contributions to this theme issue we draw parallels between behavioural, ecological and evolutionary ECE studies, and suggest that an overarching challenge is that most empirical and theoretical evidence points towards responses being highly idiosyncratic, and thus predictability being low. Finally, we suggest a roadmap based on the proposition that an increased focus on the mechanisms behind the biological response function will be crucial for increased understanding and predictability of the impacts of ECE.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'. © 2017 The Author(s).

Evolutionary thinking in microeconomic models: prestige bias and market bubbles.

Directory of Open Access Journals (Sweden)

Adrian Viliami Bell

Full Text Available Evolutionary models broadly support a number of social learning strategies likely important in economic behavior. Using a simple model of price dynamics, I show how prestige bias, or copying of famed (and likely successful individuals, influences price equilibria and investor disposition in a way that exacerbates or creates market bubbles. I discuss how integrating the social learning and demographic forces important in cultural evolution with economic models provides a fruitful line of inquiry into real-world behavior.

Optimization of externalities using DTM measures: a Pareto optimal multi objective optimization using the evolutionary algorithm SPEA2+

NARCIS (Netherlands)

Wismans, Luc Johannes Josephus; van Berkum, Eric C.; Bliemer, Michiel; Allkim, T.P.; van Arem, Bart

2010-01-01

Multi objective optimization of externalities of traffic is performed solving a network design problem in which Dynamic Traffic Management measures are used. The resulting Pareto optimal set is determined by employing the SPEA2+ evolutionary algorithm.

Asymmetric Evolutionary Games

Science.gov (United States)

McAvoy, Alex; Hauert, Christoph

2015-01-01

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: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

On the Runtime of Randomized Local Search and Simple Evolutionary Algorithms for Dynamic Makespan Scheduling

DEFF Research Database (Denmark)

Neumann, Frank; Witt, Carsten

2015-01-01

combinatorial optimization problem, namely makespan scheduling. We study the model of a strong adversary which is allowed to change one job at regular intervals. Furthermore, we investigate the setting of random changes. Our results show that randomized local search and a simple evolutionary algorithm are very...

Dynamic Self-Assembly Induced Rapid Dissolution of Cellulose at Low Temperatures

International Nuclear Information System (INIS)

Cai, J.; Zhang, L.; Liu, S.; Liu, Y.; Xu, X.; Chen, X.; Chu, B.; Guo, X.; Xu, J.

2008-01-01

Cellulose can be dissolved in precooled (-12 C) 7 wt % NaOH-12 wt % urea aqueous solution within 2 min. This interesting process, to our knowledge, represents the most rapid dissolution of native cellulose. The results from 13C NMR, 15N NMR, 1H NMR, FT-IR, small-angle neutron scattering (SANS), transmission electron microscopy (TEM), and wide-angle X-ray diffraction (WAXD) suggested that NaOH 'hydrates' could be more easily attracted to cellulose chains through the formation of new hydrogen-bonded networks at low temperatures, while the urea hydrates could not be associated directly with cellulose. However, the urea hydrates could possibly be self-assembled at the surface of the NaOH hydrogen-bonded cellulose to form an inclusion complex (IC), leading to the dissolution of cellulose. Scattering experiments, including dynamic and static light scattering, indicated that most cellulose molecules, with limited amounts of aggregation, could exist as extended rigid chains in dilute solution. Further, the cellulose solution was relatively unstable and could be very sensitive to temperature, polymer concentration, and storage time, leading to additional aggregations. TEM images and WAXD provided experimental evidence on the formation of a wormlike cellulose IC being surrounded with urea. Therefore, we propose that the cellulose dissolution at -12 C could arise as a result of a fast dynamic self-assembly process among solvent small molecules (NaOH, urea, and water) and the cellulose macromolecules.

Industrial Applications of Evolutionary Algorithms

CERN Document Server

Sanchez, Ernesto; Tonda, Alberto

2012-01-01

This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

Selective evolutionary generation systems: Theory and applications

Science.gov (United States)

Menezes, Amor A.

This dissertation is devoted to the problem of behavior design, which is a generalization of the standard global optimization problem: instead of generating the optimizer, the generalization produces, on the space of candidate optimizers, a probability density function referred to as the behavior. The generalization depends on a parameter, the level of selectivity, such that as this parameter tends to infinity, the behavior becomes a delta function at the location of the global optimizer. The motivation for this generalization is that traditional off-line global optimization is non-resilient and non-opportunistic. That is, traditional global optimization is unresponsive to perturbations of the objective function. On-line optimization methods that are more resilient and opportunistic than their off-line counterparts typically consist of the computationally expensive sequential repetition of off-line techniques. A novel approach to inexpensive resilience and opportunism is to utilize the theory of Selective Evolutionary Generation Systems (SECS), which sequentially and probabilistically selects a candidate optimizer based on the ratio of the fitness values of two candidates and the level of selectivity. Using time-homogeneous, irreducible, ergodic Markov chains to model a sequence of local, and hence inexpensive, dynamic transitions, this dissertation proves that such transitions result in behavior that is called rational; such behavior is desirable because it can lead to both efficient search for an optimizer as well as resilient and opportunistic behavior. The dissertation also identifies system-theoretic properties of the proposed scheme, including equilibria, their stability and their optimality. Moreover, this dissertation demonstrates that the canonical genetic algorithm with fitness proportional selection and the (1+1) evolutionary strategy are particular cases of the scheme. Applications in three areas illustrate the versatility of the SECS theory: flight

Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

Science.gov (United States)

Delpech, Roger

2009-01-01

This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

Conceptual Barriers to Progress Within Evolutionary Biology.

Science.gov (United States)

Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

2009-08-01

In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

Evolutionary Statistical Procedures

CERN Document Server

Baragona, Roberto; Poli, Irene

2011-01-01

This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli

DEFF Research Database (Denmark)

McCloskey, Douglas; Xu, Julia; Schrübbers, Lars

2018-01-01

Fast metabolite quantification methods are required for high throughput screening of microbial strains obtained by combinatorial or evolutionary engineering approaches. In this study, a rapid RIP-LC-MS/MS (RapidRIP) method for high-throughput quantitative metabolomics was developed and validated...... to quantify the metabolome of seven industrial strains of E. coli revealing significant differences in glycolytic, pentose phosphate, TCA cycle, amino acid, and energy and cofactor metabolites were found. These differences translated to statistically and biologically significant differences in thermodynamics...

Part E: Evolutionary Computation

DEFF Research Database (Denmark)

2015-01-01

of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...

Contemporary issues in evolutionary biology

Indian Academy of Sciences (India)

These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

Research traditions and evolutionary explanations in medicine.

Science.gov (United States)

Méthot, Pierre-Olivier

2011-02-01

In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

Applications of evolutionary economic geography

NARCIS (Netherlands)

Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx

2008-01-01

This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of

Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory.

Directory of Open Access Journals (Sweden)

Alessandro Di Stefano

Full Text Available Nature shows as human beings live and grow inside social structures. This assumption allows us to explain and explore how it may shape most of our behaviours and choices, and why we are not just blindly driven by instincts: our decisions are based on more complex cognitive reasons, based on our connectedness on different spaces. Thus, human cooperation emerges from this complex nature of social network. Our paper, focusing on the evolutionary dynamics, is intended to explore how and why it happens, and what kind of impact is caused by homophily among people. We investigate the evolution of human cooperation using evolutionary game theory on multiplex. Multiplexity, as an extra dimension of analysis, allows us to unveil the hidden dynamics and observe non-trivial patterns within a population across network layers. More importantly, we find a striking role of homophily, as the higher the homophily between individuals, the quicker is the convergence towards cooperation in the social dilemma. The simulation results, conducted both macroscopically and microscopically across the network layers in the multiplex, show quantitatively the role of homophily in human cooperation.

An application of evolutionary game theory to social dilemmas: the traveler's dilemma and the minimum effort coordination game.

Directory of Open Access Journals (Sweden)

Swami Iyer

Full Text Available The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.

An application of evolutionary game theory to social dilemmas: the traveler's dilemma and the minimum effort coordination game.

Science.gov (United States)

Iyer, Swami; Reyes, Joshua; Killingback, Timothy

2014-01-01

The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.

An Application of Evolutionary Game Theory to Social Dilemmas: The Traveler's Dilemma and the Minimum Effort Coordination Game

Science.gov (United States)

Iyer, Swami; Reyes, Joshua; Killingback, Timothy

2014-01-01

The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games. PMID:24709851

Protecting the larger fish: an ecological, economical and evolutionary analysis using a demographic model

DEFF Research Database (Denmark)

Verdiell, Nuria Calduch

. Recently, there is increasing evidence that this size-selective fishing reduces the chances of maintaining populations at levels sufficient to produce maximum sustainable yields, the chances of recovery/rebuilding populations that have been depleted/collapsed and may causes rapid evolutionary changes...... and the consequent changes in yield. We attempt to evaluate the capability of the larger fish to mitigate the evolutionary change on life-history traits caused by fishing, while also maintaining a sustainable annual yield. This is achieved by calculating the expected selection response on three life-history traits......Many marine fish stocks are reported as overfished on a global scale. This overfishing not only removes fish biomass, but also causes dramatic changes in the age and size structure of fish stocks. In particular, targeting of the larger individuals truncates the age and size structure of stocks...

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy.

Science.gov (United States)

Landau, Dan A; Sun, Clare; Rosebrock, Daniel; Herman, Sarah E M; Fein, Joshua; Sivina, Mariela; Underbayev, Chingiz; Liu, Delong; Hoellenriegel, Julia; Ravichandran, Sarangan; Farooqui, Mohammed Z H; Zhang, Wandi; Cibulskis, Carrie; Zviran, Asaf; Neuberg, Donna S; Livitz, Dimitri; Bozic, Ivana; Leshchiner, Ignaty; Getz, Gad; Burger, Jan A; Wiestner, Adrian; Wu, Catherine J

2017-12-19

Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by targeted therapy in CLL, we perform serial exome and transcriptome sequencing for 61 ibrutinib-treated CLLs. Here, we report clonal shifts (change >0.1 in clonal cancer cell fraction, Q < 0.1) in 31% of patients during the first year of therapy, associated with adverse outcome. We also observe transcriptional downregulation of pathways mediating energy metabolism, cell cycle, and B cell receptor signaling. Known and previously undescribed mutations in BTK and PLCG2, or uncommonly, other candidate alterations are present in seventeen subjects at the time of progression. Thus, the frequently observed clonal shifts during the early treatment period and its potential association with adverse outcome may reflect greater evolutionary capacity, heralding the emergence of drug-resistant clones.

Ni-MH batteries state-of-charge prediction based on immune evolutionary network

International Nuclear Information System (INIS)

Cheng Bo; Zhou Yanlu; Zhang Jiexin; Wang Junping; Cao Binggang

2009-01-01

Based on clonal selection theory, an improved immune evolutionary strategy is presented. Compared with conventional evolutionary strategy algorithm (CESA) and immune monoclonal strategy algorithm (IMSA), experimental results show that the proposed algorithm is of high efficiency and can effectively prevent premature convergence. A three-layer feed-forward neural network is presented to predict state-of-charge (SOC) of Ni-MH batteries. Initially, partial least square regression (PLSR) is used to select input variables. Then, five variables, battery terminal voltage, voltage derivative, voltage second derivative, discharge current and battery temperature, are selected as the inputs of NN. In order to overcome the weakness of BP algorithm, the new algorithm is adopted to train weights. Finally, under the state of dynamic power cycle, the predicted SOC and the actual SOC are compared to verify the proposed neural network with acceptable accuracy (5%).

Evolutionary model of an anonymous consumer durable market

Science.gov (United States)

Kaldasch, Joachim

2011-07-01

An analytic model is presented that considers the evolution of a market of durable goods. The model suggests that after introduction goods spread always according to a Bass diffusion. However, this phase will be followed by a diffusion process for durable consumer goods governed by a variation-selection-reproduction mechanism and the growth dynamics can be described by a replicator equation. The theory suggests that products play the role of species in biological evolutionary models. It implies that the evolution of man-made products can be arranged into an evolutionary tree. The model suggests that each product can be characterized by its product fitness. The fitness space contains elements of both sites of the market, supply and demand. The unit sales of products with a higher product fitness compared to the mean fitness increase. Durables with a constant fitness advantage replace other goods according to a logistic law. The model predicts in particular that the mean price exhibits an exponential decrease over a long time period for durable goods. The evolutionary diffusion process is directly related to this price decline and is governed by Gompertz equation. Therefore it is denoted as Gompertz diffusion. Describing the aggregate sales as the sum of first, multiple and replacement purchase the product life cycle can be derived. Replacement purchase causes periodic variations of the sales determined by the finite lifetime of the good (Juglar cycles). The model suggests that both, Bass- and Gompertz diffusion may contribute to the product life cycle of a consumer durable. The theory contains the standard equilibrium view of a market as a special case. It depends on the time scale, whether an equilibrium or evolutionary description is more appropriate. The evolutionary framework is used to derive also the size, growth rate and price distribution of manufacturing business units. It predicts that the size distribution of the business units (products) is lognormal

Evolutionary Exploration of the Finitely Repeated Prisoners’ Dilemma—The Effect of Out-of-Equilibrium Play

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Kristian Lindgren

2013-01-01

Full Text Available The finitely repeated Prisoners’ Dilemma is a good illustration of the discrepancy between the strategic behaviour suggested by a game-theoretic analysis and the behaviour often observed among human players, where cooperation is maintained through most of the game. A game-theoretic reasoning based on backward induction eliminates strategies step by step until defection from the first round is the only remaining choice, reflecting the Nash equilibrium of the game. We investigate the Nash equilibrium solution for two different sets of strategies in an evolutionary context, using replicator-mutation dynamics. The first set consists of conditional cooperators, up to a certain round, while the second set in addition to these contains two strategy types that react differently on the first round action: The ”Convincer” strategies insist with two rounds of initial cooperation, trying to establish more cooperative play in the game, while the ”Follower” strategies, although being first round defectors, have the capability to respond to an invite in the first round. For both of these strategy sets, iterated elimination of strategies shows that the only Nash equilibria are given by defection from the first round. We show that the evolutionary dynamics of the first set is always characterised by a stable fixed point, corresponding to the Nash equilibrium, if the mutation rate is sufficiently small (but still positive. The second strategy set is numerically investigated, and we find that there are regions of parameter space where fixed points become unstable and the dynamics exhibits cycles of different strategy compositions. The results indicate that, even in the limit of very small mutation rate, the replicator-mutation dynamics does not necessarily bring the system with Convincers and Followers to the fixed point corresponding to the Nash equilibrium of the game. We also perform a detailed analysis of how the evolutionary behaviour depends on

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

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Duchêne, Sebastian; Lanfear, Robert

2015-09-01

Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. © 2015 Wiley Periodicals, Inc.

Models for Evolutionary Algorithms and Their Applications in System Identification and Control Optimization

DEFF Research Database (Denmark)

Ursem, Rasmus Kjær

population and many generations, which essentially turns the problem into a series of related static problems. To our surprise, the control problem could easily be solved when optimized like this. To further examine this, we compared the EA with a particle swarm and a local search approach, which we...... simulate an evolutionary process where the goal is to evolve solutions by means of crossover, mutation, and selection based on their quality (fitness) with respect to the optimization problem at hand. Evolutionary algorithms (EAs) are highly relevant for industrial applications, because they are capable...... of handling problems with non-linear constraints, multiple objectives, and dynamic components – properties that frequently appear in real-world problems. This thesis presents research in three fundamental areas of EC; fitness function design, methods for parameter control, and techniques for multimodal...

Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota.

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Bagley, Justin C; Sandel, Michael; Travis, Joseph; Lozano-Vilano, María de Lourdes; Johnson, Jerald B

2013-10-09

Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). Evidence for such range dynamics and refugia in the unglaciated Gulf-Atlantic Coastal Plain stems largely from terrestrial species, and aquatic species Pleistocene responses remain relatively uninvestigated. Heterandria formosa, a wide-ranging regional endemic, presents an ideal system to test the expansion-contraction model within this biota. By integrating ecological niche modeling and phylogeography, we infer the Pleistocene history of this livebearing fish (Poeciliidae) and test for several predicted distributional and genetic effects of the last glaciation. Paleoclimatic models predicted range contraction to a single southwest Florida peninsula refugium during the Last Glacial Maximum, followed by northward expansion. We inferred spatial-population subdivision into four groups that reflect genetic barriers outside this refuge. Several other features of the genetic data were consistent with predictions derived from an expansion-contraction model: limited intraspecific divergence (e.g. mean mtDNA p-distance = 0.66%); a pattern of mtDNA diversity (mean Hd = 0.934; mean π = 0.007) consistent with rapid, recent population expansion; a lack of mtDNA isolation-by-distance; and clinal variation in allozyme diversity with higher diversity at lower latitudes near the predicted refugium. Statistical tests of mismatch distributions and coalescent simulations of the gene tree lent greater support to a scenario of post-glacial expansion and diversification from a single refugium than to any other model examined (e.g. multiple-refugia scenarios). Congruent results from diverse data indicate H. formosa fits the classic Pleistocene

Evolutionary economics and industry location

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Boschma, R.A.; Frenken, K.

2003-01-01

This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both

Evolutionary institutionalism.

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Fürstenberg, Dr Kai

Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

Multi-step-prediction of chaotic time series based on co-evolutionary recurrent neural network

International Nuclear Information System (INIS)

Ma Qianli; Zheng Qilun; Peng Hong; Qin Jiangwei; Zhong Tanwei

2008-01-01

This paper proposes a co-evolutionary recurrent neural network (CERNN) for the multi-step-prediction of chaotic time series, it estimates the proper parameters of phase space reconstruction and optimizes the structure of recurrent neural networks by co-evolutionary strategy. The searching space was separated into two subspaces and the individuals are trained in a parallel computational procedure. It can dynamically combine the embedding method with the capability of recurrent neural network to incorporate past experience due to internal recurrence. The effectiveness of CERNN is evaluated by using three benchmark chaotic time series data sets: the Lorenz series, Mackey-Glass series and real-world sun spot series. The simulation results show that CERNN improves the performances of multi-step-prediction of chaotic time series

Evolutionary foundations for cancer biology.

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Aktipis, C Athena; Nesse, Randolph M

2013-01-01

New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

Rapid post-seismic landslide evacuation boosted by dynamic river width

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Croissant, Thomas; Lague, Dimitri; Steer, Philippe; Davy, Philippe

2017-09-01

Mass wasting caused by large-magnitude earthquakes chokes mountain rivers with several cubic kilometres of sediment. The timescale and mechanisms by which rivers evacuate small to gigantic landslide deposits are poorly known, but are critical for predicting post-seismic geomorphic hazards, interpreting the signature of earthquakes in sedimentary archives and deciphering the coupling between erosion and tectonics. Here, we use a new 2D hydro-sedimentary evolution model to demonstrate that river self-organization into a narrower alluvial channel overlying the bedrock valley dramatically increases sediment transport capacity and reduces export time of gigantic landslides by orders of magnitude compared with existing theory. Predicted export times obey a universal non-linear relationship of landslide volume and pre-landslide valley transport capacity. Upscaling these results to realistic populations of landslides shows that removing half of the total coarse sediment volume introduced by large earthquakes in the fluvial network would typically take 5 to 25 years in various tectonically active mountain belts, with little impact of earthquake magnitude and climate. Dynamic alluvial channel narrowing is therefore a key, previously unrecognized mechanism by which mountain rivers rapidly digest extreme events and maintain their capacity to incise uplifted rocks.

Holistic Darwinism: the new evolutionary paradigm and some implications for political science.

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Corning, Peter A

2008-03-01

Holistic Darwinism is a candidate name for a major paradigm shift that is currently underway in evolutionary biology and related disciplines. Important developments include (1) a growing appreciation for the fact that evolution is a multilevel process, from genes to ecosystems, and that interdependent coevolution is a ubiquitous phenomenon in nature; (2) a revitalization of group selection theory, which was banned (prematurely) from evolutionary biology over 30 years ago (groups may in fact be important evolutionary units); (3) a growing respect for the fact that the genome is not a "bean bag" (in biologist Ernst Mayr's caricature), much less a gladiatorial arena for competing selfish genes, but a complex, interdependent, cooperating system; (4) an increased recognition that symbiosis is an important phenomenon in nature and that symbiogenesis is a major source of innovation in evolution; (5) an array of new, more advanced game theory models, which support the growing evidence that cooperation is commonplace in nature and not a rare exception; (6) new research and theoretical work that stresses the role of nurture in evolution, including developmental processes, phenotypic plasticity, social information transfer (culture), and especially the role of behavioral innovations as pacemakers of evolutionary change (e.g., niche construction theory, which is concerned with the active role of organisms in shaping the evolutionary process, and gene-culture coevolution theory, which relates especially to the dynamics of human evolution); (7) and, not least, a broad effort to account for the evolution of biological complexity--from major transition theory to the "Synergism Hypothesis." Here I will briefly review these developments and will present a case for the proposition that this paradigm shift has profound implications for the social sciences, including specifically political theory, economic theory, and political science as a discipline. Interdependent superorganisms, it

Evolutionary principles and their practical application

DEFF Research Database (Denmark)

Hendry, A. P.; Kinnison, M. T.; Heino, M.

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...

Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus

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Fan, Wentao; Sun, Zhaoyu; Shen, Tongtong; Xu, Danning; Huang, Kehe; Zhou, Jiyong; Song, Suquan; Yan, Liping

2017-01-01

Waterfowl parvoviruses are classified into goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) according to their antigenic features and host preferences. A novel duck parvovirus (NDPV), identified as a new variant of GPV, is currently infecting ducks, thus causing considerable economic loss. This study analyzed the molecular evolution and population dynamics of the emerging parvovirus capsid gene to investigate the evolutionary processes concerning the host shift of NDPV. Two important amino acids changes (Asn-489 and Asn-650) were identified in NDPV, which may be responsible for host shift of NDPV. Phylogenetic analysis indicated that the currently circulating NDPV originated from the GPV lineage. The Bayesian Markov chain Monte Carlo tree indicated that the NDPV diverged from GPV approximately 20 years ago. Evolutionary rate analyses demonstrated that GPV evolved with 7.674 × 10-4 substitutions/site/year, and the data for MDPV was 5.237 × 10-4 substitutions/site/year, whereas the substitution rate in NDPV branch was 2.25 × 10-3 substitutions/site/year. Meanwhile, viral population dynamics analysis revealed that the GPV major clade, including NDPV, grew exponentially at a rate of 1.717 year-1. Selection pressure analysis showed that most sites are subject to strong purifying selection and no positively selected sites were found in NDPV. The unique immune-epitopes in waterfowl parvovirus were also estimated, which may be helpful for the prediction of antibody binding sites against NDPV in ducks. PMID:28352261

Selectionist and evolutionary approaches to brain function: a critical appraisal

Directory of Open Access Journals (Sweden)

Chrisantha Thomas Fernando

2012-04-01

Full Text Available We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity and variability as the most powerful mechanism in a sparsely occupied search space. Examples of why parallel competitive search with information transfer among the units is efficient are given. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.

"Asia's missing women" as a problem in applied evolutionary psychology?

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Brooks, Robert

2012-12-20

In many parts of Asia, the Middle East and North Africa, women and children are so undervalued, neglected, abused, and so often killed, that sex ratios are now strongly male biased. In recent decades, sex-biased abortion has exacerbated the problem. In this article I highlight several important insights from evolutionary biology into both the origin and the severe societal consequences of "Asia's missing women", paying particular attention to interactions between evolution, economics and culture. Son preferences and associated cultural practices like patrilineal inheritance, patrilocality and the Indian Hindu dowry system arise among the wealthy and powerful elites for reasons consistent with models of sex-biased parental investment. Those practices then spread via imitation as technology gets cheaper and economic development allows the middle class to grow rapidly. I will consider evidence from India, China and elsewhere that grossly male-biased sex ratios lead to increased crime, violence, local warfare, political instability, drug abuse, prostitution and trafficking of women. The problem of Asia's missing women presents a challenge for applied evolutionary psychology to help us understand and ameliorate sex ratio biases and their most severe consequences.

Rapid changes in genetic architecture of behavioural syndromes following colonization of a novel environment.

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Karlsson Green, K; Eroukhmanoff, F; Harris, S; Pettersson, L B; Svensson, E I

2016-01-01

Behavioural syndromes, that is correlated behaviours, may be a result from adaptive correlational selection, but in a new environmental setting, the trait correlation might act as an evolutionary constraint. However, knowledge about the quantitative genetic basis of behavioural syndromes, and the stability and evolvability of genetic correlations under different ecological conditions, is limited. We investigated the quantitative genetic basis of correlated behaviours in the freshwater isopod Asellus aquaticus. In some Swedish lakes, A. aquaticus has recently colonized a novel habitat and diverged into two ecotypes, presumably due to habitat-specific selection from predation. Using a common garden approach and animal model analyses, we estimated quantitative genetic parameters for behavioural traits and compared the genetic architecture between the ecotypes. We report that the genetic covariance structure of the behavioural traits has been altered in the novel ecotype, demonstrating divergence in behavioural correlations. Thus, our study confirms that genetic correlations behind behaviours can change rapidly in response to novel selective environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

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Maslo, Brooke; Fefferman, Nina H

2015-08-01

Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation. © 2015 Society for Conservation

Older partner selection promotes the prevalence of cooperation in evolutionary games.

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Yang, Guoli; Huang, Jincai; Zhang, Weiming

2014-10-21

Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. Copyright © 2014 Elsevier Ltd. All rights reserved.