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Sample records for evolutionary rate dynamically

  1. 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.

  2. 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.

  3. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory.

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-19

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.

  4. Evolutionary dynamics of language systems

    Science.gov (United States)

    Wu, Chieh-Hsi; Hua, Xia; Dunn, Michael; Levinson, Stephen C.; Gray, Russell D.

    2017-01-01

    Understanding how and why language subsystems differ in their evolutionary dynamics is a fundamental question for historical and comparative linguistics. One key dynamic is the rate of language change. While it is commonly thought that the rapid rate of change hampers the reconstruction of deep language relationships beyond 6,000–10,000 y, there are suggestions that grammatical structures might retain more signal over time than other subsystems, such as basic vocabulary. In this study, we use a Dirichlet process mixture model to infer the rates of change in lexical and grammatical data from 81 Austronesian languages. We show that, on average, most grammatical features actually change faster than items of basic vocabulary. The grammatical data show less schismogenesis, higher rates of homoplasy, and more bursts of contact-induced change than the basic vocabulary data. However, there is a core of grammatical and lexical features that are highly stable. These findings suggest that different subsystems of language have differing dynamics and that careful, nuanced models of language change will be needed to extract deeper signal from the noise of parallel evolution, areal readaptation, and contact. PMID:29073028

  5. Evolutionary dynamics in structured populations

    Science.gov (United States)

    Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor

    2010-01-01

    Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382

  6. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  7. Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

    Science.gov (United States)

    Hopkins, Melanie J.; Smith, Andrew B.

    2015-03-01

    How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

  8. Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

    Science.gov (United States)

    Hopkins, Melanie J; Smith, Andrew B

    2015-03-24

    How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

  9. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  10. Neuronal boost to evolutionary dynamics.

    Science.gov (United States)

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  11. 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....

  12. The evolutionary dynamics of language.

    Science.gov (United States)

    Steels, Luc; Szathmáry, Eörs

    2018-02-01

    The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, and points to open problems. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Organisations’ evolutionary dynamics: a group dynamics approach

    Directory of Open Access Journals (Sweden)

    Germán Eduardo Vargas

    2010-04-01

    Full Text Available Colombian entrepreneurs’ straggling, reactionary and inertial orientation has been inconsistently lustified by the availability of internal and leveraged resources, a concept intensifying deficient technological capacity. Company activity (seen as being a socioeconomic unit has been integrally orientated within an evolutionary framework by company identity and cohesion as well as adaptation and evolutionary mechanisms. The present document uses a group dynamics’ model to illustrate how knowledge-based strategic orientation and integration for innovation have become an imperative for development, from slight leverage, distinguishing between two evolutionary company forms: traditional economic (inertial, as they introduce sporadic incremental improvements and modern companies (dynamic and radical innovators. Revealing conclusions obtained from such model may be used for intervening in and modernising company activity.

  14. 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.

  15. Evolutionary dynamics of group fairness.

    Science.gov (United States)

    Santos, Fernando P; Santos, Francisco C; Paiva, Ana; Pacheco, Jorge M

    2015-08-07

    The emergence and impact of fairness is commonly studied in the context of 2-person games, notably the Ultimatum Game. Often, however, humans face problems of collective action involving more than two individuals where fairness is known to play a very important role, and whose dynamics cannot be inferred from what is known from 2-person games. Here, we propose a generalization of the Ultimatum Game for an arbitrary number of players--the Multiplayer Ultimatum Game. Proposals are made to a group of responders who must individually reject or accept the proposal. If the total number of individual acceptances stands below a given threshold, the offer will be rejected; otherwise, the offer will be accepted, and equally shared by all responders. We investigate the evolution of fairness in populations of individuals by means of evolutionary game theory, providing both analytical insights and results from numerical simulations. We show how imposing stringent consensuses significantly increases the value of the proposals, leading to fairer outcomes and more tolerant players. Furthermore, we show how stochastic effects--such as imitation errors and/or errors when assessing the fitness of others--may further enhance the overall success in reaching fair collective action. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Genome-scale rates of evolutionary change in bacteria.

    Science.gov (United States)

    Duchêne, Sebastian; Holt, Kathryn E; Weill, François-Xavier; Le Hello, Simon; Hawkey, Jane; Edwards, David J; Fourment, Mathieu; Holmes, Edward C

    2016-11-01

    Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with 'ancient DNA' data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10-5 to 10-8 nucleotide substitutions per site year-1. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

  17. Investigating Evolutionary Dynamics of RHA1 Operons

    OpenAIRE

    Yong Chen; Dandan Geng; Kristina Ehrhardt; Shaoqiang Zhang

    2016-01-01

    Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed...

  18. On evolutionary ray-projection dynamics

    NARCIS (Netherlands)

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

    2011-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman

  19. Generalized projection dynamics in evolutionary game theory

    NARCIS (Netherlands)

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

    2009-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative �tness (vector) function both locally and globally. By global (local) ray projection we mean a projection of the vector (close to the unit simplex) unto the unit simplex along a ray

  20. 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

  1. Investigating Evolutionary Dynamics of RHA1 Operons.

    Science.gov (United States)

    Chen, Yong; Geng, Dandan; Ehrhardt, Kristina; Zhang, Shaoqiang

    2016-01-01

    Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.

  2. Individual heterogeneity in life histories and eco-evolutionary dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Langangen, Øystein

    2015-05-01

    Individual heterogeneity in life history shapes eco-evolutionary processes, and unobserved heterogeneity can affect demographic outputs characterising life history and population dynamical properties. Demographic frameworks like matrix models or integral projection models represent powerful approaches to disentangle mechanisms linking individual life histories and population-level processes. Recent developments have provided important steps towards their application to study eco-evolutionary dynamics, but so far individual heterogeneity has largely been ignored. Here, we present a general demographic framework that incorporates individual heterogeneity in a flexible way, by separating static and dynamic traits (discrete or continuous). First, we apply the framework to derive the consequences of ignoring heterogeneity for a range of widely used demographic outputs. A general conclusion is that besides the long-term growth rate lambda, all parameters can be affected. Second, we discuss how the framework can help advance current demographic models of eco-evolutionary dynamics, by incorporating individual heterogeneity. For both applications numerical examples are provided, including an empirical example for pike. For instance, we demonstrate that predicted demographic responses to climate warming can be reversed by increased heritability. We discuss how applications of this demographic framework incorporating individual heterogeneity can help answer key biological questions that require a detailed understanding of eco-evolutionary dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

  3. Across-environment genetic correlations and the frequency of selective environments shape the evolutionary dynamics of growth rate in Impatiens capensis.

    Science.gov (United States)

    Stinchcombe, John R; Izem, Rima; Heschel, M Shane; McGoey, Brechann V; Schmitt, Johanna

    2010-10-01

    Trade-offs can exist within and across environments, and constrain evolutionary trajectories. To examine the effects of competition and resource availability on trade-offs, we grew individuals of recombinant inbred lines of Impatiens capensis in a factorial combination of five densities with two light environments (full light and neutral shade) and used a Bayesian logistic growth analysis to estimate intrinsic growth rates. To estimate across-environment constraints, we developed a variance decomposition approach to principal components analysis, which accounted for sample size, model-fitting, and within-RIL variation prior to eigenanalysis. We detected negative across-environment genetic covariances in intrinsic growth rates, although only under full-light. To evaluate the potential importance of these covariances, we surveyed natural populations of I. capensis to measure the frequency of different density environments across space and time. We combined our empirical estimates of across-environment genetic variance-covariance matrices and frequency of selective environments with hypothetical (yet realistic) selection gradients to project evolutionary responses in multiple density environments. Selection in common environments can lead to correlated responses to selection in rare environments that oppose and counteract direct selection in those rare environments. Our results highlight the importance of considering both the frequency of selective environments and the across-environment genetic covariances in traits simultaneously. © 2010 The Author(s). Journal compilation © 2010 The Society for the Study of Evolution.

  4. The Evolutionary Dynamics of Biofuel Value Chains

    DEFF Research Database (Denmark)

    Ponte, Stefano

    2014-01-01

    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 value chains (in Brazil, the US, and the EU); then, I provide evidence to support a trend towards the increasing but still partial formation of a global biofuel value chain and examine its governance traits....

  5. Cenozoic climate change influences mammalian evolutionary dynamics

    OpenAIRE

    Figueirido, Borja; Janis, Christine M.; Pérez-Claros, Juan A.; Renzi, Miquel de; Palmqvist, Paul

    2011-01-01

    Global climate change is having profound impacts on the natural world. However, climate influence on faunal dynamics at macroevolutionary scales remains poorly understood. In this paper we investigate the influence of climate over deep time on the diversity patterns of Cenozoic North American mammals. We use factor analysis to identify temporally correlated assemblages of taxa, or major evolutionary faunas that we can then study in relation to climatic change over the past 65 million years. T...

  6. Evolutionary dynamics on any population structure

    Science.gov (United States)

    Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

    2017-03-01

    Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

  7. 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.

  8. From prelife to life: how chemical kinetics become evolutionary dynamics.

    Science.gov (United States)

    Chen, Irene A; Nowak, Martin A

    2012-12-18

    Life is that which evolves. Living systems are the products of evolutionary processes and can undergo further evolution. A crucial question for the origin of life is the following: when do chemical kinetics become evolutionary dynamics? In this Account, we review properties of "prelife" and discuss the transition from prelife to life. We describe prelife as a chemical system where activated monomers can copolymerize into macromolecules such as RNA. These macromolecules carry information, and their physical and chemical properties depend to a certain extent on their particular sequence of monomers. We consider prelife as a logical precursor of life, where macromolecules are formed by copolymerization, but they cannot replicate. Prelife can undergo "prevolutionary dynamics", including processes such as mutation, selection, and cooperation. Prelife selection, however, is blunt: small differences in rate constants lead to small differences in abundance. Life emerges with the ability of replication. In the resulting evolutionary dynamics, selection is sharp: small differences in rate constants can lead to large differences in abundance. We also study the competition of different "prelives" and find that there can be selection for those systems that ultimately give rise to replication. The transition from prelife to life can occur over an extended period of time. Instead of a single moment that marks the origin of life, prelife may have seeded many attempts for the origin of life. Eventually life takes over and destroys prelife.

  9. Evolutionary dynamics of fairness on graphs with migration.

    Science.gov (United States)

    Wang, Xiaofeng; Chen, Xiaojie; Wang, Long

    2015-09-07

    Individual migration plays a crucial role in evolutionary dynamics of population on networks. In this paper, we generalize the networked ultimatum game by diluting population structures as well as endowing individuals with migration ability, and investigate evolutionary dynamics of fairness on graphs with migration in the ultimatum game. We first revisit the impact of node degree on the evolution of fairness. Interestingly, numerical simulations reveal that there exists an optimal value of node degree resulting in the maximal offer level of populations. Then we explore the effects of dilution and migration on the evolution of fairness, and find that both the dilution of population structures and the endowment of migration ability to individuals would lead to the drop of offer level, while the rise of acceptance level of populations. Notably, natural selection even favors the evolution of self-incompatible strategies, when either vacancy rate or migration rate exceeds a critical threshold. To confirm our simulation results, we also propose an analytical method to study the evolutionary dynamics of fairness on graphs with migration. This method can be applied to explore any games governed by pairwise interactions in finite populations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Evolutionary conservation of protein vibrational dynamics.

    Science.gov (United States)

    Maguid, Sandra; Fernandez-Alberti, Sebastian; Echave, Julian

    2008-10-01

    The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.

  11. Cenozoic climate change influences mammalian evolutionary dynamics.

    Science.gov (United States)

    Figueirido, Borja; Janis, Christine M; Pérez-Claros, Juan A; De Renzi, Miquel; Palmqvist, Paul

    2012-01-17

    Global climate change is having profound impacts on the natural world. However, climate influence on faunal dynamics at macroevolutionary scales remains poorly understood. In this paper we investigate the influence of climate over deep time on the diversity patterns of Cenozoic North American mammals. We use factor analysis to identify temporally correlated assemblages of taxa, or major evolutionary faunas that we can then study in relation to climatic change over the past 65 million years. These taxa can be grouped into six consecutive faunal associations that show some correspondence with the qualitative mammalian chronofaunas of previous workers. We also show that the diversity pattern of most of these chronofaunas can be correlated with the stacked deep-sea benthic foraminiferal oxygen isotope (δ(18)O) curve, which strongly suggests climatic forcing of faunal dynamics over a large macroevolutionary timescale. This study demonstrates the profound influence of climate on the diversity patterns of North American terrestrial mammals over the Cenozoic.

  12. Evolutionary epistemology and dynamical virtual learning networks.

    Science.gov (United States)

    Giani, Umberto

    2004-01-01

    This paper is an attempt to define the main features of a new educational model aimed at satisfying the needs of a rapidly changing society. The evolutionary epistemology paradigm of culture diffusion in human groups could be the conceptual ground for the development of this model. Multidimensionality, multi-disciplinarity, complexity, connectivity, critical thinking, creative thinking, constructivism, flexible learning, contextual learning, are the dimensions that should characterize distance learning models aimed at increasing the epistemological variability of learning communities. Two multimedia educational software, Dynamic Knowledge Networks (DKN) and Dynamic Virtual Learning Networks (DVLN) are described. These two complementary tools instantiate these dimensions, and were tested in almost 150 online courses. Even if the examples are framed in the medical context, the analysis of the shortcomings of the traditional educational systems and the proposed solutions can be applied to the vast majority of the educational contexts.

  13. Ancient hyaenas highlight the old problem of estimating evolutionary rates.

    Science.gov (United States)

    Shapiro, Beth; Ho, Simon Y W

    2014-02-01

    Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitochondrial DNA sequences isolated from a combination of ancient and present-day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification. © 2013 John Wiley & Sons Ltd.

  14. The evolutionary rate of citrus tristeza virus ranks among the rates of the slowest RNA viruses.

    Science.gov (United States)

    Silva, Gonçalo; Marques, Natália; Nolasco, Gustavo

    2012-02-01

    Citrus tristeza virus (CTV) has been studied intensively at the molecular level. However, knowledge regarding the dynamics of its evolution is practically non-existent. In the past, diverse authors have referred to CTV as a highly variable virus, implying rapid evolution. Others have, in recent times, referred to CTV as an exceptionally slowly evolving virus. In this work, we used the capsid protein (CP) gene to estimate the rate of evolution. This was obtained from a large set of heterochronous CP gene sequences using a bayesian coalescent approach. The best-fitting evolutionary and population models pointed to an evolutionary rate of 1.58×10(-4) nt per site year(-1) (95 % highest posterior density, 1.73×10(-5)-3.16×10(-4) nt per site year(-1)). For an unbiased comparison with other plant and animal viruses, the evolutionary rate of synonymous substitutions was considered. In a series of 88 synonymous evolutionary rates, ranging from 5.2×10(-6) to 6.2×10(-2) nt per site year(-1), CTV ranks in the 10th percentile, embedded among the slowest animal RNA viruses. At the time of citrus dissemination to Europe and the New World, the major clades that led to the current phylogenetic groups were already defined, which may explain the absence nowadays of geographical speciation.

  15. Evolutionary dynamics in a simple model of self-assembly

    Science.gov (United States)

    Johnston, Iain G.; Ahnert, Sebastian E.; Doye, Jonathan P. K.; Louis, Ard A.

    2011-06-01

    We investigate the evolutionary dynamics of an idealized model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model’s rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterized, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.

  16. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed

    2017-01-05

    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 games, namely so-called “stable games”. In particular, it was shown that a combination of stable games and (an analogue of) passive evolutionary dynamics results in stable convergence to Nash equilibrium. This paper considers the converse question of necessary conditions for evolutionary dynamics to exhibit stable behaviors for all generalized stable games. Using methods from robust control analysis, we show that if an evolutionary dynamic does not satisfy a passivity property, then it is possible to construct a generalized stable game that results in instability. The results are illustrated on selected evolutionary dynamics with particular attention to replicator dynamics, which are also shown to be lossless, a special class of passive systems.

  17. Geometric evolutionary dynamics of protein interaction networks.

    Science.gov (United States)

    Przulj, Natasa; Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne

    2010-01-01

    Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different network models have been proposed, from those that follow power-law degree distributions and those that model complementarity of protein binding domains, to those that have geometric properties. Here, we introduce a new model for PPI network (and thus gene) evolution that produces well-fitting network models for currently available PPI networks. The model integrates geometric network properties with evolutionary dynamics of PPI network evolution.

  18. Evolutionary vaccination dynamics with internal support mechanisms

    Science.gov (United States)

    Tang, Guo-Mei; Cai, Chao-Ran; Wu, Zhi-Xi

    2017-05-01

    This paper reports internal support mechanisms (i.e., without external intervention) to enhance the vaccine coverage in the evolutionary vaccination dynamics. We present two internal support mechanisms, one is global support mechanism in which each individual pays a support cost to build up a public fund and then the public fund is divided by all vaccinated individuals, while another is local support mechanism in which each individual pays a support cost and then this support cost will be divided by its immediate vaccinated neighbors. By means of extensive computer simulations, we show that, in the same strength of support cost, the heterogeneous (local) support mechanism can encourage more people to take vaccination than the homogeneous (global) support mechanism. And then, we study the most general case that includes supporters and troublemakers together, where supporters (troublemakers) mean that the individuals join (do not join) the internal support mechanism, in the population. We surprisingly find that, in scale-free networks, the voluntary vaccination dynamics with the local support mechanism will not degrade into the original voluntary vaccination dynamics, and the vaccination level can still be effectively improved. In view of most social networks are of scale-free degree distribution, we study further in empirical networks and find that the vaccination level can still be improved in the absence of external intervention.

  19. Evolutionary dynamics of nationalism and migration

    Science.gov (United States)

    Barreira da Silva Rocha, André

    2013-08-01

    I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.

  20. Shapes in the Shadow: Evolutionary Dynamics of Morphogenesis

    NARCIS (Netherlands)

    Hogeweg, P.

    2000-01-01

    This article investigates the evolutionary dynamics of morphogenesis. In this study, morphogenesis arises as a side-effect of maximization of number of cell types. Thus, it investigates the evolutionary dynamics of side-effects. Morphogenesis is governed by the interplay between differential

  1. The genomic basis of eco-evolutionary dynamics.

    Science.gov (United States)

    Rodríguez-Verdugo, Alejandra; Buckley, James; Stapley, Jessica

    2017-03-01

    Recent recognition that ecological and evolutionary processes can operate on similar timescales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields, the centre for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics. In this review, we use the work of the invited speakers to summarize eco-evolutionary dynamics and discuss how they are relevant for understanding and predicting responses to contemporary environmental change. Then, we show how recent advances in genomics are contributing to our understanding of eco-evolutionary dynamics. Finally, we highlight the gaps in our understanding of eco-evolutionary dynamics and recommend future avenues of research in eco-evolutionary dynamics. © 2017 John Wiley & Sons Ltd.

  2. Conversion Rate Optimization through Evolutionary Computation

    OpenAIRE

    Miikkulainen, Risto; Iscoe, Neil; Shagrin, Aaron; Cordell, Ron; Nazari, Sam; Schoolland, Cory; Brundage, Myles; Epstein, Jonathan; Dean, Randy; Lamba, Gurmeet

    2017-01-01

    Conversion optimization means designing a web interface so that as many users as possible take a desired action on it, such as register or purchase. Such design is usually done by hand, testing one change at a time through A/B testing, or a limited number of combinations through multivariate testing, making it possible to evaluate only a small fraction of designs in a vast design space. This paper describes Sentient Ascend, an automatic conversion optimization system that uses evolutionary op...

  3. Eco-evolutionary dynamics in an urbanizing planet.

    Science.gov (United States)

    Alberti, Marina

    2015-02-01

    A great challenge for ecology in the coming decades is to understand the role humans play in eco-evolutionary dynamics. If, as emerging evidence shows, rapid evolutionary change affects ecosystem functioning and stability, current rapid environmental change and its evolutionary effects might have significant implications for ecological and human wellbeing on a relatively short time scale. Humans are major selective agents with potential for unprecedented evolutionary consequences for Earth's ecosystems, especially as cities expand rapidly. In this review, I identify emerging hypotheses on how urbanization drives eco-evolutionary dynamics. Studying how human-driven micro-evolutionary changes interact with ecological processes offers us the chance to advance our understanding of eco-evolutionary feedbacks and will provide new insights for maintaining biodiversity and ecosystem function over the long term. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 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

  5. 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

  6. Evolutionary dynamics of Newcastle disease virus

    Science.gov (United States)

    Miller, P.J.; Kim, L.M.; Ip, Hon S.; Afonso, C.L.

    2009-01-01

    A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution. ?? 2009 Elsevier Inc.

  7. 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.

  8. Coupling between evolutionary and population dynamics in experimental microbial populations

    Science.gov (United States)

    Sanchez, Alvaro; Gore, Jeff

    2012-02-01

    It has been often been assumed that population dynamics and evolutionary dynamics occur at such different timescales that they are effectively de-coupled. This view has been challenged recently, due to observations of evolutionary changes occurring in short timescales. This has led to a growing interest in understanding eco-evolutionary dynamics of populations. In this context, recent theoretical models have predicted that coupling between population dynamics and evolutionary dynamics can have important effects for the evolution and stability of cooperation, and lead to extremely rich and varied dynamics. Here, we report our investigation of the eco-evolutionary dynamics of a cooperative social behavior, sucrose metabolism, in experimental yeast populations. We have devised an experimental strategy to visualize trajectories in the phase space formed by the population size (N) and the fraction of cooperator cells in the population (f). Our measurements confirm a strong coupling between evolutionary and population dynamics, and allowed us to characterize the bifurcation plots. We used this approach to investigate how sudden environmental changes affect the stability and recovery of populations, and therefore the stability of cooperation.

  9. High mitogenomic evolutionary rates and time dependency.

    NARCIS (Netherlands)

    Subramanian, S.; Denver, D.R.; Millar, C.D.; Heupink, T.; Aschrafi, A.; Emslie, S.D.; Baroni, C.; Lambert, D.M.

    2009-01-01

    Using entire modern and ancient mitochondrial genomes of Adelie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of

  10. 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.

  11. Evolutionary rate patterns of the Gibberellin pathway genes

    Directory of Open Access Journals (Sweden)

    Zhang Fu-min

    2009-08-01

    Full Text Available Abstract Background Analysis of molecular evolutionary patterns of different genes within metabolic pathways allows us to determine whether these genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution of proteins in an interacting system. Although previous studies found that upstream genes in the pathway evolved more slowly than downstream genes, the correlation between evolutionary rate and position of the genes in metabolic pathways as well as its implications in molecular evolution are still less understood. Results We sequenced and characterized 7 core structural genes of the gibberellin biosynthetic pathway from 8 representative species of the rice tribe (Oryzeae to address alternative hypotheses regarding evolutionary rates and patterns of metabolic pathway genes. We have detected significant rate heterogeneity among 7 GA pathway genes for both synonymous and nonsynonymous sites. Such rate variation is mostly likely attributed to differences of selection intensity rather than differential mutation pressures on the genes. Unlike previous argument that downstream genes in metabolic pathways would evolve more slowly than upstream genes, the downstream genes in the GA pathway did not exhibited the elevated substitution rate and instead, the genes that encode either the enzyme at the branch point (GA20ox or enzymes catalyzing multiple steps (KO, KAO and GA3ox in the pathway had the lowest evolutionary rates due to strong purifying selection. Our branch and codon models failed to detect signature of positive selection for any lineage and codon of the GA pathway genes. Conclusion This study suggests that significant heterogeneity of evolutionary rate of the GA pathway genes is mainly ascribed to differential constraint relaxation rather than the positive selection and supports the pathway flux theory that predicts that natural selection primarily targets enzymes that have the greatest control on fluxes.

  12. Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

    Science.gov (United States)

    Hanski, Ilkka A

    2011-08-30

    Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

  13. Evolutionary rescue of a parasite population by mutation rate evolution.

    Science.gov (United States)

    Greenspoon, Philip B; Mideo, Nicole

    2017-10-01

    The risk of antibiotic resistance evolution in parasites is a major problem for public health. Identifying factors which promote antibiotic resistance evolution is thus a priority in evolutionary medicine. The rate at which new mutations enter the parasite population is one important predictor; however, mutation rate is not necessarily a fixed quantity, as is often assumed, but can itself evolve. Here we explore the possible impacts of mutation rate evolution on the fate of a disease circulating in a host population, which is being treated with drugs, the use of which varies over time. Using an evolutionary rescue framework, we find that mutation rate evolution provides a dramatic increase in the probability that a parasite population survives treatment in only a limited region, while providing little or no advantage in other regions. Both epidemiological features, such as the virulence of infection, and population genetic parameters, such as recombination rate, play important roles in determining the probability of evolutionary rescue and whether mutation rate evolution enhances the probability of evolutionary rescue or not. While efforts to curtail mutation rate evolution in parasites may be worthwhile under some circumstances, our results suggest that this need not always be the case. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Behavioral variability in an evolutionary theory of behavior dynamics.

    Science.gov (United States)

    Popa, Andrei; McDowell, J J

    2016-03-01

    McDowell's evolutionary theory of behavior dynamics (McDowell, 2004) instantiates populations of behaviors (abstractly represented by integers) that evolve under the selection pressure of the environment in the form of positive reinforcement. Each generation gives rise to the next via low-level Darwinian processes of selection, recombination, and mutation. The emergent patterns can be analyzed and compared to those produced by biological organisms. The purpose of this project was to explore the effects of high mutation rates on behavioral variability in environments that arranged different reinforcer rates and magnitudes. Behavioral variability increased with the rate of mutation. High reinforcer rates and magnitudes reduced these effects; low reinforcer rates and magnitudes augmented them. These results are in agreement with live-organism research on behavioral variability. Various combinations of mutation rates, reinforcer rates, and reinforcer magnitudes produced similar high-level outcomes (equifinality). These findings suggest that the independent variables that describe an experimental condition interact; that is, they do not influence behavior independently. These conclusions have implications for the interpretation of high levels of variability, mathematical undermatching, and the matching theory. The last part of the discussion centers on a potential biological counterpart for the rate of mutation, namely spontaneous fluctuations in the brain's default mode network. © 2016 Society for the Experimental Analysis of Behavior.

  15. An evolutionary economics approach to ecosystem dynamics

    NARCIS (Netherlands)

    Blijleven, V.B; Angeren, van J.; Brinkkemper, S.

    2013-01-01

    Biology and evolution lie at the heart of the ecosystem metaphor that is recurrently applied in the digital era. Although the evolution and analogy with evolutionary biology is acknowledged within the research domains of business ecosystems and digital ecosystems, several key definitions and

  16. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B; Andersen, E S; Damgaard, Christian Kroun

    2004-01-01

    of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem......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....... In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly...

  17. Evolutionary dynamics of bacteria in a human host environment

    DEFF Research Database (Denmark)

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

    2011-01-01

    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....... In contrast to predictions based on in vitro evolution experiments, we document limited diversification of the evolving lineage despite a highly structured and complex host environment. Notably, the lineage went through an initial period of rapid adaptation caused by a small number of mutations...... 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....

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

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Witt, Carsten; Gießen, Christian

    2017-01-01

    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......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...... 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...

  19. Integrated assessment of genomic correlates of protein evolutionary rate.

    Directory of Open Access Journals (Sweden)

    Yu Xia

    2009-06-01

    Full Text Available Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the genomic correlates of protein evolutionary rate. However, dissecting the correlations among evolutionary rate and these genomic features remains a major challenge. Here, we use an integrated probabilistic modeling approach to study genomic correlates of protein evolutionary rate in Saccharomyces cerevisiae. We measure and rank degrees of association between (i an approximate measure of protein evolutionary rate with high genome coverage, and (ii a diverse list of protein properties (sequence, structural, functional, network, and phenotypic. We observe, among many statistically significant correlations, that slowly evolving proteins tend to be regulated by more transcription factors, deficient in predicted structural disorder, involved in characteristic biological functions (such as translation, biased in amino acid composition, and are generally more abundant, more essential, and enriched for interaction partners. Many of these results are in agreement with recent studies. In addition, we assess information contribution of different subsets of these protein properties in the task of predicting slowly evolving proteins. We employ a logistic regression model on binned data that is able to account for intercorrelation, non-linearity, and heterogeneity within features. Our model considers features both individually and in natural ensembles ("meta-features" in order to assess joint information contribution and degree of contribution independence. Meta-features based on protein abundance and amino acid composition make strong, partially independent contributions to the task of predicting slowly evolving proteins; other meta-features make additional minor contributions. The combination of all meta-features yields predictions

  20. Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

    Science.gov (United States)

    Holmes, Ian H

    2017-04-15

    Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com.

  1. The intriguing evolutionary dynamics of plant mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Galtier Nicolas

    2011-09-01

    Full Text Available Abstract The mitochondrial genome of plants is-in every respect and for yet unclear reasons-very different from the well-studied one of animals. Thanks to next-generation sequencing technologies, Davila et al. precisely characterized the role played by recombination and DNA repair in controlling mitochondrial variations in Arabidopsis thaliana, thus opening new perspectives on the long-term evolution of this intriguing genome. See research article: http://www.biomedcentral.com/1741-7007/9/64 The mitochondrial genome of plants is a challenge to molecular evolutionary biologists. Its content is highly dynamic: plant mitochondrial DNA (mtDNA is large and variable in size (200 to 2,500 kb, contains many introns and repeated elements (typically 90% of the total sequence, and experiences frequent gene gain/loss/transfer/duplication, and genome rearrangements 1. Its nucleotide substitution rate, paradoxically, is remarkably low-even lower than for nuclear DNA. These features are in sharp contrast with the highly studied mtDNA of animals, which is small-sized, structurally conserved, devoid of selfish elements, and has a very fast nucleotide substitution rate 2. Why these two genomes behave so differently is one of the most head-scratching questions of current comparative genomics. The study by Davila et al. 3 contributes a potentially decisive argument by connecting the plant mtDNA mutation rate to yet another intriguing feature of this organellar genome-recombination.

  2. Bridging Developmental Systems Theory and Evolutionary Psychology Using Dynamic Optimization

    Science.gov (United States)

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

    2013-01-01

    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…

  3. Testability of evolutionary game dynamics based on experimental economics data

    Science.gov (United States)

    Wang, Yijia; Chen, Xiaojie; Wang, Zhijian

    2017-11-01

    Understanding the dynamic processes of a real game system requires an appropriate dynamics model, and rigorously testing a dynamics model is nontrivial. In our methodological research, we develop an approach to testing the validity of game dynamics models that considers the dynamic patterns of angular momentum and speed as measurement variables. Using Rock-Paper-Scissors (RPS) games as an example, we illustrate the geometric patterns in the experiment data. We then derive the related theoretical patterns from a series of typical dynamics models. By testing the goodness-of-fit between the experimental and theoretical patterns, we show that the validity of these models can be evaluated quantitatively. Our approach establishes a link between dynamics models and experimental systems, which is, to the best of our knowledge, the most effective and rigorous strategy for ascertaining the testability of evolutionary game dynamics models.

  4. A stochastic evolutionary model for survival dynamics

    Science.gov (United States)

    Fenner, Trevor; Levene, Mark; Loizou, George

    2014-09-01

    The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. In our model, the only implicit assumption made is that the longer an actor has been in the system, the more likely it is to have failed. We derive a power-law distribution for the process and provide preliminary empirical evidence for the validity of the model from two well-known survival analysis data sets.

  5. Credit rating dynamics and competition

    DEFF Research Database (Denmark)

    Hirth, Stefan

    2014-01-01

    I analyze the market for credit ratings with competition between more than two rating agencies. How can honest rating behavior be achieved, and under which conditions can a new honest rating agency successfully invade a market with inflating incumbents? My model predicts cyclic dynamics if sophis......I analyze the market for credit ratings with competition between more than two rating agencies. How can honest rating behavior be achieved, and under which conditions can a new honest rating agency successfully invade a market with inflating incumbents? My model predicts cyclic dynamics...

  6. Evolutionary Dynamics of Cryptophyte Plastid Genomes.

    Science.gov (United States)

    Kim, Jong Im; Moore, Christa E; Archibald, John M; Bhattacharya, Debashish; Yi, Gangman; Yoon, Hwan Su; Shin, Woongghi

    2017-07-01

    Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch. placoidea, Cryptomonas curvata, and Storeatula sp. CCMP1868 share a number of features including synteny and gene content with the previously sequenced genomes of Cryptomonas paramecium, Rhodomonas salina, Teleaulax amphioxeia, and Guillardia theta. Our analysis of these plastid genomes reveals examples of gene loss and intron insertion. In particular, the chlB/chlL/chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss and pseudogenization in cryptophytes. Comparison of phylogenetic trees based on plastid and nuclear genome data sets show the introduction, via secondary endosymbiosis, of a red algal derived plastid in a lineage of chlorophyll-c containing algae. This event was followed by additional rounds of eukaryotic endosymbioses that spread the red lineage plastid to diverse groups such as haptophytes and stramenopiles. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Evolutionary Stability of Minimal Mutation Rates in an Evo-epidemiological Model.

    Science.gov (United States)

    Birch, Michael; Bolker, Benjamin M

    2015-11-01

    We consider the evolution of mutation rate in a seasonally forced, deterministic, compartmental epidemiological model with a transmission-virulence trade-off. We model virulence as a quantitative genetic trait in a haploid population and mutation as continuous diffusion in the trait space. There is a mutation rate threshold above which the pathogen cannot invade a wholly susceptible population. The evolutionarily stable (ESS) mutation rate is the one which drives the lowest average density, over the course of one forcing period, of susceptible individuals at steady state. In contrast with earlier eco-evolutionary models in which higher mutation rates allow for better evolutionary tracking of a dynamic environment, numerical calculations suggest that in our model the minimum average susceptible population, and hence the ESS, is achieved by a pathogen strain with zero mutation. We discuss how this result arises within our model and how the model might be modified to obtain a nonzero optimum.

  8. Generalized projection dynamics in evolutionary game theory

    NARCIS (Netherlands)

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

    2008-01-01

    We introduce a new kind of projection dynamics by employing a ray-projection both locally and globally. By global (local) we mean a projection of a vector (close to the unit simplex) unto the unit simplex along a ray through the origin. Using a correspondence between local and global ray-projection

  9. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees.

    Science.gov (United States)

    Crawford, Forrest W; Suchard, Marc A

    2013-05-01

    The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes the evolutionary relationships of the organisms of interest. The probability of the observed trait data can be computed by assuming a model for trait evolution, such as Brownian motion, over the branches of this fixed tree. However, the phylogenetic tree itself contributes statistical uncertainty to estimates of rates of phenotypic evolution, and many comparative evolutionary biologists regard the tree as a nuisance parameter. In this article, we present a framework for analytically integrating over unknown phylogenetic trees in comparative evolutionary studies by assuming that the tree arises from a continuous-time Markov branching model called the Yule process. To do this, we derive a closed-form expression for the distribution of phylogenetic diversity (PD), which is the sum of branch lengths connecting the species in a clade. We then present a generalization of PD which is equivalent to the expected trait disparity in a set of taxa whose evolutionary relationships are generated by a Yule process and whose traits evolve by Brownian motion. We find expressions for the distribution of expected trait disparity under a Yule tree. Given one or more observations of trait disparity in a clade, we perform fast likelihood-based estimation of the Brownian variance for unresolved clades. Our method does not require simulation or a fixed phylogenetic tree. We conclude with a brief example illustrating Brownian rate estimation for 12 families in the mammalian order Carnivora, in which the phylogenetic tree for each family is unresolved.

  10. MEASURING THE EVOLUTIONARY RATE OF COOLING OF ZZ Ceti

    Energy Technology Data Exchange (ETDEWEB)

    Mukadam, Anjum S.; Fraser, Oliver; Riecken, T. S.; Kronberg, M. E. [Department of Astronomy, University of Washington, Seattle, WA 98195 (United States); Bischoff-Kim, Agnes [Georgia College and State University, Milledgeville, GA 31061 (United States); Corsico, A. H. [Facultad de Ciencias Astronomicas y Geofisicas, Universidad Nacional de La Plata (Argentina); Montgomery, M. H.; Winget, D. E.; Hermes, J. J.; Winget, K. I.; Falcon, Ross E.; Reaves, D. [Department of Astronomy, University of Texas at Austin, Austin, TX 78759 (United States); Kepler, S. O.; Romero, A. D. [Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS (Brazil); Chandler, D. W. [Meyer Observatory, Central Texas Astronomical Society, 3409 Whispering Oaks, Temple, TX 76504 (United States); Kuehne, J. W. [McDonald Observatory, Fort Davis, TX 79734 (United States); Sullivan, D. J. [Victoria University of Wellington, P.O. Box 600, Wellington (New Zealand); Von Hippel, T. [Embry-Riddle Aeronautical University, 600 South Clyde Morris Boulevard, Daytona Beach, FL 32114 (United States); Mullally, F. [SETI Institute, NASA Ames Research Center, MS 244-30, Moffet Field, CA 94035 (United States); Shipman, H. [Delaware Asteroseismic Research Center, Mt. Cuba Observatory, Greenville, DE 19807 (United States); and others

    2013-07-01

    We have finally measured the evolutionary rate of cooling of the pulsating hydrogen atmosphere (DA) white dwarf ZZ Ceti (Ross 548), as reflected by the drift rate of the 213.13260694 s period. Using 41 yr of time-series photometry from 1970 November to 2012 January, we determine the rate of change of this period with time to be dP/dt = (5.2 {+-} 1.4) Multiplication-Sign 10{sup -15} s s{sup -1} employing the O - C method and (5.45 {+-} 0.79) Multiplication-Sign 10{sup -15} s s{sup -1} using a direct nonlinear least squares fit to the entire lightcurve. We adopt the dP/dt obtained from the nonlinear least squares program as our final determination, but augment the corresponding uncertainty to a more realistic value, ultimately arriving at the measurement of dP/dt = (5.5 {+-} 1.0) Multiplication-Sign 10{sup -15} s s{sup -1}. After correcting for proper motion, the evolutionary rate of cooling of ZZ Ceti is computed to be (3.3 {+-} 1.1) Multiplication-Sign 10{sup -15} s s{sup -1}. This value is consistent within uncertainties with the measurement of (4.19 {+-} 0.73) Multiplication-Sign 10{sup -15} s s{sup -1} for another similar pulsating DA white dwarf, G 117-B15A. Measuring the cooling rate of ZZ Ceti helps us refine our stellar structure and evolutionary models, as cooling depends mainly on the core composition and stellar mass. Calibrating white dwarf cooling curves with this measurement will reduce the theoretical uncertainties involved in white dwarf cosmochronometry. Should the 213.13 s period be trapped in the hydrogen envelope, then our determination of its drift rate compared to the expected evolutionary rate suggests an additional source of stellar cooling. Attributing the excess cooling to the emission of axions imposes a constraint on the mass of the hypothetical axion particle.

  11. Extinction dynamics from metastable coexistences in an evolutionary game

    Science.gov (United States)

    Park, Hye Jin; Traulsen, Arne

    2017-10-01

    Deterministic evolutionary game dynamics can lead to stable coexistences of different types. Stochasticity, however, drives the loss of such coexistences. This extinction is usually accompanied by population size fluctuations. We investigate the most probable extinction trajectory under such fluctuations by mapping a stochastic evolutionary model to a problem of classical mechanics using the Wentzel-Kramers-Brillouin (WKB) approximation. Our results show that more abundant types in a coexistence may be more likely to go extinct first, in good agreement with previous results. The distance between the coexistence and extinction points is not a good predictor of extinction either. Instead, the WKB method correctly predicts the type going extinct first.

  12. Strategy selection in evolutionary game dynamics on group interaction networks.

    Science.gov (United States)

    Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao

    2014-11-01

    Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.

  13. Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota)

    Science.gov (United States)

    2008-01-01

    Background The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended taxon sampling, we test for presence of significant rate discrepancies within and between these clades and test our a priori hypothesis that such rate discrepancies may be explained by shifts in moisture regime or other environmental conditions. Results In this paper, the first statistical evidence for accelerated evolutionary rate in lichenized ascomycetes is presented. Our results give clear evidence for a faster rate of evolution in two Hypotrachyna clades that includes species occurring in tropical and oceanic habitats in comparison with clades consisting of species occurring in semi-arid and temperate habitats. Further we explore potential links between evolutionary rates and shifts in habitat by comparing alternative Ornstein-Uhlenbeck models. Conclusion Although there was only weak support for a shift at the base of a second tropical clade, where the observed nucleotide substitution rate is high, overall support for a shift in environmental conditions at cladogenesis is very strong. This suggests that speciation in some lichen clades has proceeded by dispersal into a novel environment, followed by radiation within that environment. We found moderate support for a shift in moisture regime at the base of one tropical clade and a clade occurring in semi-arid regions and a shift in minimum temperature at the base of a boreal-temperate clade. PMID:18808710

  14. Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota

    Directory of Open Access Journals (Sweden)

    Blanco Oscar

    2008-09-01

    Full Text Available Abstract Background The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended taxon sampling, we test for presence of significant rate discrepancies within and between these clades and test our a priori hypothesis that such rate discrepancies may be explained by shifts in moisture regime or other environmental conditions. Results In this paper, the first statistical evidence for accelerated evolutionary rate in lichenized ascomycetes is presented. Our results give clear evidence for a faster rate of evolution in two Hypotrachyna clades that includes species occurring in tropical and oceanic habitats in comparison with clades consisting of species occurring in semi-arid and temperate habitats. Further we explore potential links between evolutionary rates and shifts in habitat by comparing alternative Ornstein-Uhlenbeck models. Conclusion Although there was only weak support for a shift at the base of a second tropical clade, where the observed nucleotide substitution rate is high, overall support for a shift in environmental conditions at cladogenesis is very strong. This suggests that speciation in some lichen clades has proceeded by dispersal into a novel environment, followed by radiation within that environment. We found moderate support for a shift in moisture regime at the base of one tropical clade and a clade occurring in semi-arid regions and a shift in minimum temperature at the base of a boreal-temperate clade.

  15. Cognitive Architecture with Evolutionary Dynamics Solves Insight Problem.

    Science.gov (United States)

    Fedor, Anna; Zachar, István; Szilágyi, András; Öllinger, Michael; de Vladar, Harold P; Szathmáry, Eörs

    2017-01-01

    In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al. (2013)'s experiment. In the second experiment, we further investigated the effects of pretraining and priming in a two-by-two design and found a beginner's luck type of effect: solution rate was highest in the condition that was primed, but not pretrained with patterns relevant for the task. In the third experiment, we showed that deficits in computational capacity and learning abilities decreased the performance of the model, as expected. We conclude that Darwinian Neurodynamics is a promising model of human problem solving that deserves further investigation.

  16. Evolutionary dynamics of nematode operons: easy come, slow go.

    Science.gov (United States)

    Qian, Wenfeng; Zhang, Jianzhi

    2008-03-01

    Operons are widespread in prokaryotes, but are uncommon in eukaryotes, except nematode worms, where approximately 15% of genes reside in over 1100 operons in the model organism Caenorhabditis elegans. It is unclear how operons have become abundant in nematode genomes. The "one-way street" hypothesis asserts that once formed by chance, operons are very difficult to break, because the breakage would leave downstream genes in an operon without a promoter, and hence, unexpressed. To test this hypothesis, we analyzed the presence and absence of C. elegans operons in Caenorhabditis briggsae, Caenorhabditis remanei, and Caenorhabditis brenneri, using Pristionchus pacificus and Brugia malayi as outgroups, and identified numerous operon gains and losses. Coupled with experimental examination of trans-splicing patterns, our comparative genomic analysis revealed diverse molecular mechanisms of operon losses, including inversion, insertion, and relocation, but the presence of internal promoters was not found to facilitate operon losses. In several cases, the data allowed inference of mechanisms by which downstream genes are expressed after operon breakage. We found that the rate of operon gain is approximately 3.3 times that of operon loss. Thus, the evolutionary dynamics of nematode operons is better described as "easy come, slow go," rather than a "one-way street." Based on a mathematic model of operon gains and losses and additional assumptions, we projected that the number of operons in C. elegans will continue to rise by 6%-18% in future evolution before reaching equilibrium between operon gains and losses.

  17. Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

    Science.gov (United States)

    Ho, Simon Y W; Duchêne, Sebastián; Duchêne, David

    2015-07-01

    Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed-clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets. © 2014 John Wiley & Sons Ltd.

  18. Impact of transcriptional properties on essentiality and evolutionary rate.

    Science.gov (United States)

    Choi, Jung Kyoon; Kim, Sang Cheol; Seo, Jungmin; Kim, Sangsoo; Bhak, Jong

    2007-01-01

    We characterized general transcriptional activity and variability of eukaryotic genes from global expression profiles of human, mouse, rat, fly, plants, and yeast. The variability shows a higher degree of divergence between distant species, implying that it is more closely related to phenotypic evolution, than the activity. More specifically, we show that transcriptional variability should be a true indicator of evolutionary rate. If we rule out the effect of translational selection, which seems to operate only in yeast, the apparent slow evolution of highly expressed genes should be attributed to their low variability. Meanwhile, rapidly evolving genes may acquire a high level of transcriptional variability and contribute to phenotypic variations. Essentiality also seems to be correlated with the variability, not the activity. We show that indispensable or highly interactive proteins tend to be present in high abundance to maintain a low variability. Our results challenge the current theory that highly expressed genes are essential and evolve slowly. Transcriptional variability, rather than transcriptional activity, might be a common indicator of essentiality and evolutionary rate, contributing to the correlation between the two variables.

  19. Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus.

    Science.gov (United States)

    Ohshima, Kazusato; Nomiyama, Rei; Mitoma, Shinichiro; Honda, Yuki; Yasaka, Ryosuke; Tomimura, Kenta

    2016-11-01

    There is no attempt to evaluate evolutionary rates, timescales and diversities of viruses collected from mixedly infected hosts in nature. Plants of the genus Narcissus are a monocotyledon and are susceptible to several viruses. In this study, narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected in Japan, and these were investigated for potyvirus infections using potyvirus-specific primers. Individual narcissus plants were found frequently to be mixedly infected with different potyviruses, different isolates and quasispecies of same virus. The viruses were potyviruses and a macluravirus in the family Potyviridae, namely Narcissus late season yellows virus (NLSYV), Narcissus yellow stripe virus (NYSV), Narcissus degeneration virus (NDV), Cyrtanthus elatus virus A (CyEVA) and Narcissus latent virus (NLV). Genetic diversities of coat protein coding region of different virus species were different; NYSV and CyEVA were most diverse whereas NDV was least. Evolutionary rates of all five narcissus viruses were 1.33-7.15×10-3nt/site/year and were similar. The most recent common ancestors (TMRCAs) varied between virus species; NYSV and CyEVA were the oldest whereas NDV was the youngest. Thus, the oldness of TMRCAs of the viruses correlated well with the greatness of nucleotide diversities. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Quantitative evolutionary dynamics using high-resolution lineage tracking.

    Science.gov (United States)

    Levy, Sasha F; Blundell, Jamie R; Venkataram, Sandeep; Petrov, Dmitri A; Fisher, Daniel S; Sherlock, Gavin

    2015-03-12

    Evolution of large asexual cell populations underlies ∼30% of deaths worldwide, including those caused by bacteria, fungi, parasites, and cancer. However, the dynamics underlying these evolutionary processes remain poorly understood because they involve many competing beneficial lineages, most of which never rise above extremely low frequencies in the population. To observe these normally hidden evolutionary dynamics, we constructed a sequencing-based ultra high-resolution lineage tracking system in Saccharomyces cerevisiae that allowed us to monitor the relative frequencies of ∼500,000 lineages simultaneously. In contrast to some expectations, we found that the spectrum of fitness effects of beneficial mutations is neither exponential nor monotonic. Early adaptation is a predictable consequence of this spectrum and is strikingly reproducible, but the initial small-effect mutations are soon outcompeted by rarer large-effect mutations that result in variability between replicates. These results suggest that early evolutionary dynamics may be deterministic for a period of time before stochastic effects become important.

  1. Characterization of evolutionary rates and constraints in three mammalian genomes

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, Gregory M.; Brudno, Michael; Stone, Eric A.; Dubchak, Inna; Batzoglou, Serafim; Sidow, Arend

    2004-02-15

    We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the mutational spectrum between the mouse and rat lineages, with the net effect being a relative increase in GC content in the rat genome. Our estimate for the neutral point substitution rate separating the two rodents is 0.196 substitutions per site, and 0.65 substitutions per site for the tree relating all three mammals. Small insertions and deletions of 1-10 bp in length (''microindels'') occur at approximately 5 percent of the point substitution rate. Inferred regional correlations in evolutionary rates between lineages and between types of sites support the idea that rates of evolution are influenced by local genomic or cell biological context. No substantial correlations between rates of point substitutions and rates of microindels are found, however, implying that the influences that affect these processes are distinct. Finally, we have identified those regions in the human genome that are evolving slowly, which are likely to include functional elements important to human biology. At least 5 percent of the human genome is under substantial constraint, most of which is noncoding.

  2. Coevolution of slow-fast populations: evolutionary sliding, evolutionary pseudo-equilibria and complex Red Queen dynamics.

    Science.gov (United States)

    Dercole, F; Ferrière, R; Gragnani, A; Rinaldi, S

    2006-04-22

    We study the interplay of ecological and evolutionary dynamics in communities composed of populations with contrasting time-scales. In such communities, genetic variation of individual traits can cause population transitions between stationary and cyclic ecological regimes, hence abrupt variations in fitness. Such abrupt variations raise ridges in the adaptive landscape, where the populations are poised between equilibrium and cyclic coexistence and along which evolutionary trajectories can remain sliding for long times or halt at special points called evolutionary pseudo-equilibria. These novel phenomena should be generic to all systems in which ecological interactions cause fitness to vary discontinuously. They are demonstrated by the analysis of a predator-prey community, with one adaptive trait for each population. The eco-evolutionary dynamics of the system show a number of other distinctive features, including evolutionary extinction and two forms of Red Queen dynamics. One of them is characterized by intermittent bouts of cyclic oscillations of the two populations.

  3. Dynamical Clustering of Exchange Rates

    OpenAIRE

    Fenn, Daniel J.; Porter, Mason A.; Mucha, Peter J; Mark McDonald; Stacy Williams; Johnson, Neil F.; Jones, Nick S

    2009-01-01

    We use techniques from network science to study correlations in the foreign exchange (FX) market over the period 1991--2008. We consider an FX market network in which each node represents an exchange rate and each weighted edge represents a time-dependent correlation between the rates. To provide insights into the clustering of the exchange rate time series, we investigate dynamic communities in the network. We show that there is a relationship between an exchange rate's functional role withi...

  4. Eco-evolutionary dynamics, coding structure and the information threshold

    Directory of Open Access Journals (Sweden)

    Hogeweg Paulien

    2010-11-01

    Full Text Available Abstract Background The amount of information that can be maintained in an evolutionary system of replicators is limited by genome length, the number of errors during replication (mutation rate and various external factors that influence the selection pressure. To date, this phenomenon, known as the information threshold, has been studied (both genotypically and phenotypically in a constant environment and with respect to maintenance (as opposed to accumulation of information. Here we take a broader perspective on this problem by studying the accumulation of information in an ecosystem, given an evolvable coding structure. Moreover, our setup allows for individual based as well as ecosystem based solutions. That is, all functions can be performed by individual replicators, or complementing functions can be performed by different replicators. In this setup, where both the ecosystem and the individual genomes can evolve their structure, we study how populations cope with high mutation rates and accordingly how the information threshold might be alleviated. Results We observe that the first response to increased mutation rates is a change in coding structure. At moderate mutation rates evolution leads to longer genomes with a higher diversity than at high mutation rates. Thus, counter-intuitively, at higher mutation rates diversity is reduced and the efficacy of the evolutionary process is decreased. Therefore, moderate mutation rates allow for more degrees of freedom in exploring genotype space during the evolutionary trajectory, facilitating the emergence of solutions. When an individual based solution cannot be attained due to high mutation rates, spatial structuring of the ecosystem can accommodate the evolution of ecosystem based solutions. Conclusions We conclude that the evolutionary freedom (eg. the number of genotypes that can be reached by evolution is increasingly restricted by higher mutation rates. In the case of such severe mutation

  5. A Dynamic Evolutionary Game Model of Modular Production Network

    Directory of Open Access Journals (Sweden)

    Wei He

    2016-01-01

    Full Text Available As a new organization mode of production in the 21st century, modular production network is deemed extensively to be a source of competitiveness for lead firms in manufacturing industries. However, despite the abundant studies on the modular production network, there are very few studies from a dynamic perspective to discuss the conditions on which a modular production network develops. Based on the dynamic evolutionary game theory, this paper constructs a model, which incorporates several main factors influencing the development of modular production network. By calculating the replicator dynamics equations and analyzing the evolutionary stable strategies, this paper discusses the evolution process of cooperation strategies of member enterprises in a modular production network. Furthermore, by using NetLogo software to simulate the model, this paper verifies the effectiveness of the model. From the model, we can find that the final stable equilibrium strategy is related to such factors as the initial cost, the extra payoff, the cooperation willingness of both parties, the cooperation efforts, and the proportion each party can get from the extra payoff. To encourage the cooperation of production integrator and modular supplier, some suggestions are also provided.

  6. 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

  7. Evolutionary game dynamics in populations with heterogenous structures.

    Directory of Open Access Journals (Sweden)

    Wes Maciejewski

    2014-04-01

    Full Text Available Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours. In this article we show that such a conclusion largely depends on the individual-level interactions that take place. In particular, averaging payoffs garnered through game interactions rather than accumulating the payoffs can altogether remove the cooperative advantage of heterogeneous graphs while such a difference does not affect the outcome on homogeneous structures. In addition, the rate at which game interactions occur can alter the evolutionary outcome. Less interactions allow heterogeneous graphs to support more cooperation than homogeneous graphs, while higher rates of interactions make homogeneous and heterogeneous graphs virtually indistinguishable in their ability to support cooperation. Most importantly, we show that common measures of evolutionary advantage used in homogeneous populations, such as a comparison of the fixation probability of a rare mutant to that of the resident type, are no longer valid in heterogeneous populations. Heterogeneity causes a bias in where mutations occur in the population which affects the mutant's fixation probability. We derive the appropriate measures for heterogeneous populations that account for this bias.

  8. Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation.

    Science.gov (United States)

    Feyertag, Felix; Berninsone, Patricia M; Alvarez-Ponce, David

    2017-03-01

    The rates of evolution of the proteins of any organism vary across orders of magnitude. A primary factor influencing rates of protein evolution is expression. A strong negative correlation between expression levels and evolutionary rates (the so-called E-R anticorrelation) has been observed in virtually all studied organisms. This effect is currently attributed to the abundance-dependent fitness costs of misfolding and unspecific protein-protein interactions, among other factors. Secreted proteins are folded in the endoplasmic reticulum, a compartment where chaperones, folding catalysts, and stringent quality control mechanisms promote their correct folding and may reduce the fitness costs of misfolding. In addition, confinement of secreted proteins to the extracellular space may reduce misinteractions and their deleterious effects. We hypothesize that each of these factors (the secretory pathway quality control and extracellular location) may reduce the strength of the E-R anticorrelation. Indeed, here we show that among human proteins that are secreted to the extracellular space, rates of evolution do not correlate with protein abundances. This trend is robust to controlling for several potentially confounding factors and is also observed when analyzing protein abundance data for 6 human tissues. In addition, analysis of mRNA abundance data for 32 human tissues shows that the E-R correlation is always less negative, and sometimes nonsignificant, in secreted proteins. Similar observations were made in Caenorhabditis elegans and in Escherichia coli, and to a lesser extent in Drosophila melanogaster, Saccharomyces cerevisiae and Arabidopsis thaliana. Our observations contribute to understand the causes of the E-R anticorrelation. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    Indian Academy of Sciences (India)

    2Present Address: National Institute of Malaria Research (ICMR), 22 Sham Nath Marg. New Delhi 110 054, India. 3Evolutionary Biology Laboratory, Evolutionary and Organismal .... To minimize nongenetic parental effects caused by dif- ferent maintenance regimes, the selected and control popu- lations were maintained ...

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

    Indian Academy of Sciences (India)

    Behaviour, Ecology and Evolution Laboratory, Biology Department, Poornaprajna Institute of Scientific Research, P.O. Box No. 18, Devanahalli, Bangalore 562 110, India; National Institute of Malaria Research (ICMR), 22 Sham Nath Marg. New Delhi 110 054, India; Evolutionary Biology Laboratory, Evolutionary and ...

  11. Fast evolutionary rates associated with functional loss in class I glucose transporters of Schistosoma mansoni.

    Science.gov (United States)

    Cabezas-Cruz, Alejandro; Valdés, James J; Lancelot, Julien; Pierce, Raymond J

    2015-11-19

    The trematode parasite, Schistosoma mansoni, has evolved to switch from oxidative phosphorylation to glycolysis in the presence of glucose immediately after invading the human host. This metabolic switch is dependent on extracellular glucose concentration. Four glucose transporters are encoded in the genome of S. mansoni, however, only two were shown to facilitate glucose diffusion. By modeling the phase of human host infection, we showed that transporter transcript expression profiles of recently transformed schistosomula have two opposing responses to increased glucose concentrations. Concurring with the transcription profiles, our phylogenetic analyses revealed that S. mansoni glucose transporters belong to two separate clusters, one associated with class I glucose transporters from vertebrates and insects, and the other specific to parasitic Platyhelminthes. To study the evolutionary paths of both groups and their functional implications, we determined evolutionary rates, relative divergence times, genomic organization and performed structural analyses with the protein sequences. We finally used the modelled structures of the S. mansoni glucose transporters to biophysically (i) analyze the dynamics of key residues during glucose binding, (ii) test glucose stability within the active site, and (iii) demonstrate glucose diffusion. The two S. mansoni Platyhelminthes-specific glucose transporters, which seem to be younger than the other two, exhibit slower rates of molecular evolution, are encoded by intron-poor genes, and transport glucose. Interestingly, our molecular dynamic analyses suggest that S. mansoni class I glucose transporters are not able to transport glucose. The glucose transporter family in S. mansoni exhibit different evolutionary histories. Our results suggested that S. mansoni class I glucose transporters lost their capacity to transport glucose and that this function evolved independently in the Platyhelminthes-specific glucose transporters

  12. Developmental dynamics: toward a biologically plausible evolutionary psychology.

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    There has been a conceptual revolution in the biological sciences over the past several decades. Evidence from genetics, embryology, and developmental biology has converged to offer a more epigenetic, contingent, and dynamic view of how organisms develop. Despite these advances, arguments for the heuristic value of a gene-centered, predeterministic approach to the study of human behavior and development have become increasingly evident in the psychological sciences during this time. In this article, the authors review recent advances in genetics, embryology, and developmental biology that have transformed contemporary developmental and evolutionary theory and explore how these advances challenge gene-centered explanations of human behavior that ignore the complex, highly coordinated system of regulatory dynamics involved in development and evolution.

  13. Bidirectional Dynamic Diversity Evolutionary Algorithm for Constrained Optimization

    Directory of Open Access Journals (Sweden)

    Weishang Gao

    2013-01-01

    Full Text Available Evolutionary algorithms (EAs were shown to be effective for complex constrained optimization problems. However, inflexible exploration-exploitation and improper penalty in EAs with penalty function would lead to losing the global optimum nearby or on the constrained boundary. To determine an appropriate penalty coefficient is also difficult in most studies. In this paper, we propose a bidirectional dynamic diversity evolutionary algorithm (Bi-DDEA with multiagents guiding exploration-exploitation through local extrema to the global optimum in suitable steps. In Bi-DDEA potential advantage is detected by three kinds of agents. The scale and the density of agents will change dynamically according to the emerging of potential optimal area, which play an important role of flexible exploration-exploitation. Meanwhile, a novel double optimum estimation strategy with objective fitness and penalty fitness is suggested to compute, respectively, the dominance trend of agents in feasible region and forbidden region. This bidirectional evolving with multiagents can not only effectively avoid the problem of determining penalty coefficient but also quickly converge to the global optimum nearby or on the constrained boundary. By examining the rapidity and veracity of Bi-DDEA across benchmark functions, the proposed method is shown to be effective.

  14. Trust Dynamics in WSNs: An Evolutionary Game-Theoretic Approach

    Directory of Open Access Journals (Sweden)

    Shigen Shen

    2016-01-01

    Full Text Available A sensor node (SN in Wireless Sensor Networks (WSNs can decide whether to collaborate with others based on a trust management system (TMS by making a trust decision. In this paper, we study the trust decision and its dynamics that play a key role to stabilize the whole network using evolutionary game theory. When SNs are making their decisions to select action Trust or Mistrust, a WSNs trust game is created to reflect their utilities. An incentive mechanism bound with one SN’s trust degree is incorporated into this trust game and effectively promotes SNs to select action Trust. The replicator dynamics of SNs’ trust evolution, illustrating the evolutionary process of SNs selecting their actions, are given. We then propose and prove the theorems indicating that evolutionarily stable strategies can be attained under different parameter values, which supply theoretical foundations to devise a TMS for WSNs. Moreover, we can find out the conditions that will lead SNs to choose action Trust as their final behavior. In this manner, we can assure WSNs’ security and stability by introducing a trust mechanism to satisfy these conditions. Experimental results have confirmed the proposed theorems and the effects of the incentive mechanism.

  15. Disease ecology. Ecological and evolutionary effects of fragmentation on infectious disease dynamics.

    Science.gov (United States)

    Jousimo, Jussi; Tack, Ayco J M; Ovaskainen, Otso; Mononen, Tommi; Susi, Hanna; Tollenaere, Charlotte; Laine, Anna-Liisa

    2014-06-13

    Ecological theory predicts that disease incidence increases with increasing density of host networks, yet evolutionary theory suggests that host resistance increases accordingly. To test the combined effects of ecological and evolutionary forces on host-pathogen systems, we analyzed the spatiotemporal dynamics of a plant (Plantago lanceolata)-fungal pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000 host populations. Disease prevalence at the metapopulation level was low, with high annual pathogen extinction rates balanced by frequent (re-)colonizations. Highly connected host populations experienced less pathogen colonization and higher pathogen extinction rates than expected; a laboratory assay confirmed that this phenomenon was caused by higher levels of disease resistance in highly connected host populations. Copyright © 2014, American Association for the Advancement of Science.

  16. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

    Science.gov (United States)

    Adams, Richard H; Blackmon, Heath; Reyes-Velasco, Jacobo; Schield, Drew R; Card, Daren C; Andrew, Audra L; Waynewood, Nyimah; Castoe, Todd A

    2016-05-01

    The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.

  17. Promotion of cooperation in evolutionary game dynamics with local information.

    Science.gov (United States)

    Liu, Xuesong; Pan, Qiuhui; He, Mingfeng

    2018-01-21

    In this paper, we propose a strategy-updating rule driven by local information, which is called Local process. Unlike the standard Moran process, the Local process does not require global information about the strategic environment. By analyzing the dynamical behavior of the system, we explore how the local information influences the fixation of cooperation in two-player evolutionary games. Under weak selection, the decreasing local information leads to an increase of the fixation probability when natural selection does not favor cooperation replacing defection. In the limit of sufficiently large selection, the analytical results indicate that the fixation probability increases with the decrease of the local information, irrespective of the evolutionary games. Furthermore, for the dominance of defection games under weak selection and for coexistence games, the decreasing of local information will lead to a speedup of a single cooperator taking over the population. Overall, to some extent, the local information is conducive to promoting the cooperation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. The mathematical law of evolutionary information dynamics and an observer's evolution regularities

    CERN Document Server

    Lerner, Vladimir S

    2011-01-01

    An interactive stochastics, evaluated by an entropy functional (EF) of a random field and informational process' path functional (IPF), allows us modeling the evolutionary information processes and revealing regularities of evolution dynamics. Conventional Shannon's information measure evaluates a sequence of the process' static events for each information state and do not reveal hidden dynamic connections between these events. The paper formulates the mathematical forms of the information regularities, based on a minimax variation principle (VP) for IPF, applied to the evolution's both random microprocesses and dynamic macroprocesses. The paper shows that the VP single form of the mathematical law leads to the following evolutionary regularities: -creation of the order from stochastics through the evolutionary macrodynamics, described by a gradient of dynamic potential, evolutionary speed and the evolutionary conditions of a fitness and diversity; -the evolutionary hierarchy with growing information values a...

  19. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Directory of Open Access Journals (Sweden)

    Murat Cetinbaş

    Full Text Available Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  20. A new phylogenetic test for comparing multiple high-dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae).

    Science.gov (United States)

    Denton, John S S; Adams, Dean C

    2015-09-01

    The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best-fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high-dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development-informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best-fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life-history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  1. Ribosome dynamics and the evolutionary history of ribosomes

    Science.gov (United States)

    Fox, George E.; Paci, Maxim; Tran, Quyen; Petrov, Anton S.; Williams, Loren D.

    2015-09-01

    The ribosome is a dynamic nanomachine responsible for coded protein synthesis. Its major subsystems were essentially in place at the time of the last universal common ancestor (LUCA). Ribosome evolutionary history thus potentially provides a window into the pre- LUCA world. This history begins with the origins of the peptidyl transferase center where the actual peptide is synthesized and then continues over an extended timeframe as additional functional centers including the GTPase center are added. The large ribosomal RNAs (rRNAs) have grown over time by an accretion process and a model exists that proposes a relative age of each accreted element. We have compared atomic resolution ribosome structures before and after EF-G bound GTP hydrolysis and thereby identified the location of 23 pivot points in the large rRNAs that facilitate ribosome dynamics. Pivots in small subunit helices h28 and h44 appear to be especially central to the process and according to the accretion model significantly older than the other helices containing pivots. Overall, the results suggest that ribosomal dynamics occurred in two phases. In the first phase, an inherently mobile h28/h44 combination provided the flexibility needed to create a dynamic ribosome that was essentially a Brownian machine. This addition likely made coded peptide synthesis possible by facilitating movement of a primitive mRNA. During the second phase, addition of pivoting elements and the creation of a factor binding site allowed the regulation of the inherent motion created by h28/h44. All of these events likely occurred before LUCA.

  2. Evolutionary dynamics of general group interactions in structured populations

    Science.gov (United States)

    Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.

  3. 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.

  4. Forecasting for dynamic line rating

    DEFF Research Database (Denmark)

    Michiorri, Andrea; Nguyen, Huu-Minh; Alessandrini, Stefano

    2015-01-01

    This paper presents an overview of the state of the art on the research on Dynamic Line Rating forecasting. It is directed at researchers and decision-makers in the renewable energy and smart grids domain, and in particular at members of both the power system and meteorological community. Its aim...... sensors on the line that measure conductor temperature, tension, sag or environmental parameters such as wind speed and air temperature. Because of the conservative assumptions used to calculate static seasonal ampacity limits and the variability of weather parameters, DLRs are considerably higher than....... In order to facilitate the integration of DLR into power system operations, research has been launched into DLR forecasting, following a similar avenue to IRS production forecasting, i.e. based on a mix of statistical methods and meteorological forecasts. The development of reliable DLR forecasts...

  5. The evolutionary dynamics of operon distributions in eukaryote genomes.

    Science.gov (United States)

    Cutter, Asher D; Agrawal, Aneil F

    2010-06-01

    Genes in nematode and ascidian genomes frequently occur in operons--multiple genes sharing a common promoter to generate a polycistronic primary transcript--and such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis. Recent work in nematodes has demonstrated that the identity of genes within operons is highly conserved among species and that the unifying feature of genes within operons is that they are expressed in germline tissue. However, it is generally unknown what processes are responsible for generating the distribution of operon sizes across the genome, which are composed of up to eight genes per operon. Here we investigate several models for operon evolution to better understand their abundance, distribution of sizes, and evolutionary dynamics over time. We find that birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, nonoperon genes that likely participate in the birth-death process. This theory, and applications to C. elegans and Ciona, motivates several new and testable hypotheses about eukaryote operon evolution.

  6. 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.

  7. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

    Directory of Open Access Journals (Sweden)

    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.

  8. Evolutionary dynamics on rugged fitness landscapes: exact dynamics and information theoretical aspects.

    Science.gov (United States)

    Saakian, David B; Fontanari, José F

    2009-10-01

    The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the random energy model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three distinct regimes: pure diffusion or stasis for short times, depending on the fitness of the initial configuration, and a spin-glass regime for large times. The dynamic transition between these dynamical regimes is marked by discontinuities in the mean-fitness as well as in the overlap with the initial reference sequence. The relaxation to equilibrium is described by an inverse time decay. In the ferromagnetic REM, we find in addition to these three regimes, a ferromagnetic regime where the overlap and the mean-fitness are frozen. In this case, the system relaxes to equilibrium in a finite time. The relevance of our results to information processing aspects of evolution is discussed.

  9. 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

    Evolutionary algorithms have been frequently used for dynamic optimization problems. With this paper, we contribute to the theoretical understanding of this research area. We present the first computational complexity analysis of evolutionary algorithms for a dynamic variant of a classical...... 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...... effective in dynamically tracking changes made to the problem instance....

  10. Evolutionary dynamics in financial markets with many trader types

    NARCIS (Netherlands)

    Brock, W.A.; Hommes, C.H.; Wagener, F.O.O.

    2001-01-01

    This paper develops the notion of a Large Type Limit (LTL) describing the average behavior of adaptive evolutionary systems with many trader types. It is shown that generic and persistent features of adaptive evolutionary systems with many trader types are well described by the large type limit.

  11. Stability properties of nonlinear dynamical systems and evolutionary stable states

    Science.gov (United States)

    Gleria, Iram; Brenig, Leon; Rocha Filho, Tarcísio M.; Figueiredo, Annibal

    2017-03-01

    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.

  12. Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution.

    Directory of Open Access Journals (Sweden)

    Brian K Mannakee

    2016-07-01

    Full Text Available The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein's rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces.

  13. Evolutionary psychology and developmental dynamics: comment on Lickliter and Honeycutt (2003).

    Science.gov (United States)

    Buss, David M; Reeve, H Kern

    2003-11-01

    Evolutionary psychology provides a cogent metatheory for psychological science. It has furnished compelling theories of major domains of human functioning, including mating, parenting, kinship, morality, cooperation, conflict, aggression, and aesthetics. It has produced hundreds of empirical discoveries missed entirely by prior psychologists. Developmental dynamics, properly conceived, can add to the theoretical foundation of evolutionary psychology. But it has not provided alternative theories capable of explaining the many detailed empirical discoveries made by evolutionary' psychologists. Nor has it generated a comparable bounty of new empirical discoveries. By critical scientific standards--theoretical cogency, predictive accuracy, interdisciplinary consistency, and empirical harvest--modern evolutionary psychology fares well compared with alternatives.

  14. 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.

  15. 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...

  16. Genome-wide investigation reveals high evolutionary rates in annual model plants

    Directory of Open Access Journals (Sweden)

    Araki Hitoshi

    2010-11-01

    Full Text Available Abstract Background Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera and popular (Populus trichocarpa for perennials. Results According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. Conclusions The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from

  17. Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

    Science.gov (United States)

    Eo, Soo Hyung; DeWoody, J. Andrew

    2010-01-01

    Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings. PMID:20610427

  18. Evolutionary dynamics and the evolution of multiplayer cooperation in a subdivided population.

    Science.gov (United States)

    Pattni, Karan; Broom, Mark; Rychtář, Jan

    2017-09-21

    The classical models of evolution have been developed to incorporate structured populations using evolutionary graph theory and, more recently, a new framework has been developed to allow for more flexible population structures which potentially change through time and can accommodate multiplayer games with variable group sizes. In this paper we extend this work in three key ways. Firstly by developing a complete set of evolutionary dynamics so that the range of dynamic processes used in classical evolutionary graph theory can be applied. Secondly, by building upon previous models to allow for a general subpopulation structure, where all subpopulation members have a common movement distribution. Subpopulations can have varying levels of stability, represented by the proportion of interactions occurring between subpopulation members; in our representation of the population all subpopulation members are represented by a single vertex. In conjunction with this we extend the important concept of temperature (the temperature of a vertex is the sum of all the weights coming into that vertex; generally, the higher the temperature, the higher the rate of turnover of individuals at a vertex). Finally, we have used these new developments to consider the evolution of cooperation in a class of populations which possess this subpopulation structure using a multiplayer public goods game. We show that cooperation can evolve providing that subpopulations are sufficiently stable, with the smaller the subpopulations the easier it is for cooperation to evolve. We introduce a new concept of temperature, namely "subgroup temperature", which can be used to explain our results. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Causes of evolutionary rate variation among protein sites

    OpenAIRE

    Echave, Julian; Spielman, Stephanie J.; Wilke, Claus O.

    2016-01-01

    It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, are more conserved than are other sites. However, our understanding of rate variation among sites remains surprisingly limited. Recent progress to address this includes the development of a wide array of reliable methods to estimate site-specific substitution rates from sequence alignments. In addition, several molecular traits have been identified that correlat...

  20. 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.

  1. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns.

    Science.gov (United States)

    Grusz, Amanda L; Rothfels, Carl J; Schuettpelz, Eric

    2016-08-30

    Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

  2. Eco-evolutionary dynamics in a coevolving host-virus system.

    Science.gov (United States)

    Frickel, Jens; Sieber, Michael; Becks, Lutz

    2016-04-01

    Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.

  3. Correlated evolutionary rates across genomic compartments in Annonaceae.

    Science.gov (United States)

    Hoekstra, Paul H; Wieringa, Jan J; Smets, Erik; Brandão, Rita D; Lopes, Jenifer de Carvalho; Erkens, Roy H J; Chatrou, Lars W

    2017-09-01

    The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Causes of evolutionary rate variation among protein sites.

    Science.gov (United States)

    Echave, Julian; Spielman, Stephanie J; Wilke, Claus O

    2016-02-01

    It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, are evolutionarily more conserved than other sites. However, our understanding of rate variation among sites remains surprisingly limited. Recent progress to address this includes the development of a wide array of reliable methods to estimate site-specific substitution rates from sequence alignments. In addition, several molecular traits have been identified that correlate with site-specific mutation rates, and novel mechanistic biophysical models have been proposed to explain the observed correlations. Nonetheless, current models explain, at best, approximately 60% of the observed variance, highlighting the limitations of current methods and models and the need for new research directions.

  5. Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective

    Science.gov (United States)

    Cho, Sung-Jin; Vallès, Yvonne; Giani, Vincent C.; Seaver, Elaine C.; Weisblat, David A.

    2010-01-01

    The wnt gene family encodes a set of secreted glycoproteins involved in key developmental processes, including cell fate specification and regulation of posterior growth (Cadigan KM, Nusse R. 1997. Wnt signaling: a common theme in animal development. Genes Dev. 11:3286–3305.; Martin BL, Kimelman D. 2009. Wnt signaling and the evolution of embryonic posterior development. Curr Biol. 19:R215–R219.). As for many other gene families, evidence for expansion and/or contraction of the wnt family is available from deuterostomes (e.g., echinoderms and vertebrates [Nusse R, Varmus HE. 1992. Wnt genes. Cell. 69:1073–1087.; Schubert M, Holland LZ, Holland ND, Jacobs DK. 2000. A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Mol Biol Evol. 17:1896–1903.; Croce JC, Wu SY, Byrum C, Xu R, Duloquin L, Wikramanayake AH, Gache C, McClay DR. 2006. A genome-wide survey of the evolutionarily conserved Wnt pathways in the sea urchin Strongylocentrotus purpuratus. Dev Biol. 300:121–131.]) and ecdysozoans (e.g., arthropods and nematodes [Eisenmann DM. 2005. Wnt signaling. WormBook. 1–17.; Bolognesi R, Farzana L, Fischer TD, Brown SJ. 2008. Multiple Wnt genes are required for segmentation in the short-germ embryo of Tribolium castaneum. Curr Biol. 18:1624–1629.]), but little is known from the third major bilaterian group, the lophotrochozoans (e.g., mollusks and annelids [Prud'homme B, Lartillot N, Balavoine G, Adoutte A, Vervoort M. 2002. Phylogenetic analysis of the Wnt gene family. Insights from lophotrochozoan members. Curr Biol. 12:1395.]). To obtain a more comprehensive scenario of the evolutionary dynamics of this gene family, we exhaustively mined wnt gene sequences from the whole genome assemblies of a mollusk (Lottia gigantea) and two annelids (Capitella teleta and Helobdella robusta) and examined them by phylogenetic, genetic linkage, intron–exon structure, and embryonic

  6. Genomewide Evolutionary Rates in Laboratory and Wild Yeast

    OpenAIRE

    Ronald, James; Tang, Hua; Brem, Rachel B.

    2006-01-01

    As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

  7. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA

    Directory of Open Access Journals (Sweden)

    McDonald John F

    2008-05-01

    Full Text Available Abstract Background The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs. It is becoming increasingly apparent that many of these repetitive DNA sequence elements encode gene regulatory functions. This fact has important evolutionary implications, since repetitive DNA is the most dynamic part of the genome. We set out to assess the evolutionary rate and pattern of experimentally characterized human transcription factor binding sites (TFBS that are derived from repetitive versus non-repetitive DNA to test whether repeat-derived TFBS are in fact rapidly evolving. We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA. Results We found numerous experimentally characterized TFBS in the human genome, 7–10% of all mapped sites, which are derived from repetitive DNA sequences including simple sequence repeats (SSRs and TEs. TE-derived TFBS sequences are far less conserved between species than TFBS derived from SSRs and non-repetitive DNA. Despite their rapid evolution, several lines of evidence indicate that TE-derived TFBS are functionally constrained. First of all, ancient TE families, such as MIR and L2, are enriched for TFBS relative to younger families like Alu and L1. Secondly, functionally important positions in TE-derived TFBS, specifically those residues thought to physically interact with their cognate protein binding factors (TF, are more evolutionarily conserved than adjacent TFBS positions. Finally, TE-derived TFBS show position-specific patterns of sequence variation that are highly distinct from random patterns and similar to the variation seen for non-repeat derived sequences of the same TFBS. Conclusion The abundance of experimentally characterized human TFBS that are derived from repetitive DNA speaks to the substantial regulatory effects that this class of

  8. Reduced evolutionary rate in reemerged Ebola virus transmission chains.

    Science.gov (United States)

    Blackley, David J; Wiley, Michael R; Ladner, Jason T; Fallah, Mosoka; Lo, Terrence; Gilbert, Merle L; Gregory, Christopher; D'ambrozio, Jonathan; Coulter, Stewart; Mate, Suzanne; Balogun, Zephaniah; Kugelman, Jeffrey; Nwachukwu, William; Prieto, Karla; Yeiah, Adolphus; Amegashie, Fred; Kearney, Brian; Wisniewski, Meagan; Saindon, John; Schroth, Gary; Fakoli, Lawrence; Diclaro, Joseph W; Kuhn, Jens H; Hensley, Lisa E; Jahrling, Peter B; Ströher, Ute; Nichol, Stuart T; Massaquoi, Moses; Kateh, Francis; Clement, Peter; Gasasira, Alex; Bolay, Fatorma; Monroe, Stephan S; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Scott Laney, A; Nyenswah, Tolbert; Christie, Athalia; Palacios, Gustavo

    2016-04-01

    On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.

  9. Design games : A conceptual framework for dynamic evolutionary design

    NARCIS (Netherlands)

    Sönmez, N.O.; Erdem, A.

    2014-01-01

    Most evolutionary computation (EC) applications in design fields either assume simplified, static, performance-oriented procedures for design or focus on well-defined sub-problems, to be able to impose problem-solving and optimization schemes on design tasks, which render known EC techniques

  10. 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…

  11. 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.

  12. Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

    2013-09-01

    The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary

  13. Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage.

    Science.gov (United States)

    Subramaniam, Saravanan; Mohapatra, Jajati K; Sharma, Gaurav K; Biswal, Jitendra K; Ranjan, Rajeev; Rout, Manoranjan; Das, Biswajit; Dash, Bana B; Sanyal, Aniket; Pattnaik, Bramhadev

    2015-08-05

    Foot-and-mouth disease (FMD) virus serotype O Ind2001 lineage within the Middle East-South Asia topotype is the major cause of recent FMD incidences in India. A sub-lineage of Ind2001 caused severe outbreaks in the southern region of the country during 2013 and also reported for the first time from Libya. In this study, we conducted a detailed evolutionary analysis of Ind2001 lineage. Phylogenetic analysis of Ind2001 lineage based on maximum likelihood method revealed two major splits and three sub-lineages. The mean nucleotide substitution rate for this lineage was calculated to be 6.338×10(-3)substitutions/site/year (s/s/y), which is similar to those of PanAsian sub-lineages. Evolutionary time scale analysis indicated that the Ind2001 lineage might have originated in 1989. The sub-lineage Ind2001d that caused 2013 outbreaks seems to be relatively more divergent genetically from other Ind2001 sub-lineages. Seven codons in the VP1 region of Ind2001 were found to be under positive selection. Four out of 24 recent Ind2001 strains tested in 2D-MNT had antigenic relationship value of <0.3 with the serotype O vaccine strain indicating intra-epidemic antigenic diversity. Amino acid substitutions found in these minor variants with reference to antigenic diversity have been discussed. The dominance of antigenically homologous strains indicates absence of vaccine immunity in the majority of the affected hosts. Taken together, the evolution of Ind2001 lineage deviates from the strict molecular clock and a typical lineage evolutionary dynamics characterized by periodic emergence and re-emergence of Ind2001 and PanAsia lineage have been observed in respect of serotype O. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013-2014.

    Science.gov (United States)

    Bao, Jingyue; Wang, Qinghua; Li, Lin; Liu, Chunju; Zhang, Zhicheng; Li, Jinming; Wang, Shujuan; Wu, Xiaodong; Wang, Zhiliang

    2017-10-01

    Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013-2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10(-6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013-2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Stochastic evolutionary dynamics of minimum-effort coordination games

    CERN Document Server

    Li, Kun; Wang, Long

    2016-01-01

    The minimum-effort coordination game, having potentially important implications in both evolutionary biology and sociology, draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classic game theory. In the framework of classic game theory, any common effort level is a strict and trembling hand perfect Nash equilibrium, so that no desideratum is provided for selecting among them. Behavior experiments, however, show that the effort levels employed by subjects are inversely related to the effort costs. Here, we combine coalescence theory and evolutionary game 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, where the population structure itself is a consequence of the evolutio...

  16. 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...

  17. 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).

  18. Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

    Science.gov (United States)

    Firth, Cadhla; Kitchen, Andrew; Shapiro, Beth; Suchard, Marc A.; Holmes, Edward C.; Rambaut, Andrew

    2010-01-01

    Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 × 10−5 substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses. PMID:20363828

  19. Metabolic Rate Calibrates the Molecular Clock: Reconciling Molecular and Fossil Estimates of Evolutionary Divergence

    OpenAIRE

    Gillooly, James F.; Andrew P. Allen; West, Geoffrey B.; Brown, James H.

    2004-01-01

    Observations that rates of molecular evolution vary widely within and among lineages have cast doubts upon the existence of a single molecular clock. Differences in the timing of evolutionary events estimated from genetic and fossil evidence have raised further questions about the existence of molecular clocks and their use. Here we present a model of nucleotide substitution that combines new theory on metabolic rate with the now classic neutral theory of molecular evolution. The model quanti...

  20. Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

    Directory of Open Access Journals (Sweden)

    Hsiung Chao

    2011-10-01

    Full Text Available Abstract Background Changes in transcriptional orientation (“CTOs” occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Methods Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS and nonsynonymous (dN substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, “COGs” and those that do not (same-orientation genes, “SOGs”. The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. Results We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Conclusions Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the

  1. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

    Directory of Open Access Journals (Sweden)

    Alvaro Sanchez

    Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the

  2. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

    Directory of Open Access Journals (Sweden)

    Yasir H. Ahmed-Braimah

    2017-09-01

    Full Text Available Postcopulatory sexual selection (PCSS is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis. We find that the majority of male reproductive transcripts are testes-biased, accounting for ∼15% of all annotated genes. Ejaculatory bulb (EB-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation.

  3. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup.

    Science.gov (United States)

    Ahmed-Braimah, Yasir H; Unckless, Robert L; Clark, Andrew G

    2017-09-07

    Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis We find that the majority of male reproductive transcripts are testes-biased, accounting for ∼15% of all annotated genes. Ejaculatory bulb (EB)-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation. Copyright © 2017 Ahmed-Braimah et al.

  4. Evolutionary Dynamics of Tumor-Stroma Interactions in Multiple Myeloma.

    Directory of Open Access Journals (Sweden)

    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.

  5. Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota.

    Science.gov (United States)

    Wang, Haiying; Guo, Shouyu; Huang, Manrong; Thorsten, Lumbsch H; Wei, Jiangchun

    2010-10-01

    Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.

  6. Non-Payoff Monotonic Dynamics in an Evolutionary Game of Courtship

    CERN Document Server

    Chacoma, Andrés; Zanette, Damián H

    2015-01-01

    We propose an evolutionary coordination game to formalize a simplified model of the evolution of strategies during human courtship. The dynamics, derived from the consideration of experimental observations on human social behavior driven by self-esteem, turns out to be non-payoff monotonic. This property gives rise to nontrivial evolution in the players' strategies, which we study both numerically and analytically.

  7. 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.

  8. Evolutionary Dynamics While Trapped in Resonance: A Keplerian Binary System Perturbed by Gravitational Radiation

    OpenAIRE

    Chicone, Carmen; Mashhoon, Bahram; Retzloff, David

    1996-01-01

    The method of averaging is used to investigate the phenomenon of capture into resonance for a model that describes a Keplerian binary system influenced by radiation damping and external normally incident periodic gravitational radiation. The dynamical evolution of the binary orbit while trapped in resonance is elucidated using the second order partially averaged system. This method provides a theoretical framework that can be used to explain the main evolutionary dynamics of a physical system...

  9. Adaptation to fragmentation: evolutionary dynamics driven by human influences.

    Science.gov (United States)

    Cheptou, Pierre-Olivier; Hargreaves, Anna L; Bonte, Dries; Jacquemyn, Hans

    2017-01-19

    Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

  10. Evolutionary multiobjective optimization for dynamic hospital resource management

    NARCIS (Netherlands)

    A.K. Hutzschenreuter (Anke Kristine); P.A.N. Bosman (Peter); J.A. La Poutré (Han); M. Ehrgott; C.M. Fonseca; X. Gandibleux; J.-K. Hao; M. Sevaux

    2009-01-01

    htmlabstractAllocating resources to hospital units is a major managerial issue as the relationship between resources, utilization and patient flow of different patient groups is complex. Furthermore, the problem is dynamic as patient arrival and treatment processes are stochastic. In this paper we

  11. Dynamic routing problems with fruitful regions: models and evolutionary computation

    NARCIS (Netherlands)

    J.I. van Hemert; J.A. La Poutré (Han)

    2004-01-01

    textabstractWe introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the

  12. Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations.

    Science.gov (United States)

    Haafke, Julia; Abou Chakra, Maria; Becks, Lutz

    2016-03-01

    Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  13. The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate

    Directory of Open Access Journals (Sweden)

    Stone Eric A

    2011-08-01

    Full Text Available Abstract Background Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation. Results Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends. Conclusions We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may

  14. Dynamic Line Rating: Research and Policy Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Jake P. Gentle; Kurt S. Myers; Michael R. West

    2014-07-01

    Dynamic Line Rating (DLR) is a smart grid technology that allows the rating of electrical conductors to be increased based on local weather conditions. Overhead lines are conventionally given a conservative rating based on worst case scenarios. We demonstrate that observing the conditions in real time leads to additional capacity and safer operation. This paper provides a report of a pioneering scheme in the United States of America in which DLR has been applied. Thereby, we demonstrate that observing the local weather conditions in real time leads to additional capacity and safer operation. Secondly, we discuss limitations involved. In doing so, we arrive at novel insights which will inform and improve future DLR projects. Third, we provide a policy background and discussion to clarify the technology’s potential and identifies barriers to the imminent adoption of dynamic line rating systems. We provide suggestions for regulatory bodies about possible improvements in policy to encourage adoption of this beneficial technology.

  15. A Runtime Analysis of Parallel Evolutionary Algorithms in Dynamic Optimization

    DEFF Research Database (Denmark)

    Lissovoi, Andrei; Witt, Carsten

    2017-01-01

    A simple island model with (Formula presented.) islands and migration occurring after every (Formula presented.) iterations is studied on the dynamic fitness function Maze. This model is equivalent to a (Formula presented.) EA if (Formula presented.), i. e., migration occurs during every iteration....... It is proved that even for an increased offspring population size up to (Formula presented.), the (Formula presented.) EA is still not able to track the optimum of Maze. If the migration interval is chosen carefully, the algorithm is able to track the optimum even for logarithmic (Formula presented...

  16. An evolutionary computational approach for the dynamic Stackelberg competition problems

    Directory of Open Access Journals (Sweden)

    Lorena Arboleda-Castro

    2016-06-01

    Full Text Available Stackelberg competition models are an important family of economical decision problems from game theory, in which the main goal is to find optimal strategies between two competitors taking into account their hierarchy relationship. Although these models have been widely studied in the past, it is important to note that very few works deal with uncertainty scenarios, especially those that vary over time. In this regard, the present research studies this topic and proposes a computational method for solving efficiently dynamic Stackelberg competition models. The computational experiments suggest that the proposed approach is effective for problems of this nature.

  17. Particle creation rate for dynamical black holes

    Energy Technology Data Exchange (ETDEWEB)

    Firouzjaee, Javad T. [School of Astronomy, Institute for Research in Fundamental Sciences (IPM), Tehran (Iran, Islamic Republic of); University of Oxford, Department of Physics (Astrophysics), Oxford (United Kingdom); Ellis, George F.R. [University of Cape Town, Mathematics and Applied Mathematics Department, Rondebosch (South Africa)

    2016-11-15

    We present the particle creation probability rate around a general black hole as an outcome of quantum fluctuations. Using the uncertainty principle for these fluctuation, we derive a new ultraviolet frequency cutoff for the radiation spectrum of a dynamical black hole. Using this frequency cutoff, we define the probability creation rate function for such black holes. We consider a dynamical Vaidya model and calculate the probability creation rate for this case when its horizon is in a slowly evolving phase. Our results show that one can expect the usual Hawking radiation emission process in the case of a dynamical black hole when it has a slowly evolving horizon. Moreover, calculating the probability rate for a dynamical black hole gives a measure of when Hawking radiation can be killed off by an incoming flux of matter or radiation. Our result strictly suggests that we have to revise the Hawking radiation expectation for primordial black holes that have grown substantially since they were created in the early universe. We also infer that this frequency cut off can be a parameter that shows the primordial black hole growth at the emission moment. (orig.)

  18. Colicin Diversity: a Result of Eco!evolutionary Dynamics

    NARCIS (Netherlands)

    Pagie, L.; Hogeweg, P.

    1998-01-01

    Colicins are plasmids that are carried in Escherichia coli. They code for a toxic protein and for proteins that confer on the host immunity against this toxin. When bacteria carry plasmids their growth rate is reduced. At the same time, the production of toxins makes it possible for colicinogenic

  19. Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

    Directory of Open Access Journals (Sweden)

    Christopher Jacobs

    Full Text Available System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution. Here we show that this negative correlation does exist, and can be exposed by revisiting a broadly employed assumption of flux balance models. In particular, we introduce a new metric that we call "function-loss cost", which estimates the cost of a gene loss event as the total potential functional impairment caused by that loss. This new metric displays significant negative correlation with evolutionary rate, across several thousand minimal environments. We demonstrate that the improvement gained using function-loss cost over gene-loss cost is explained by replacing the base assumption that isoenzymes provide unlimited capacity for backup with the assumption that isoenzymes are completely non-redundant. We further show that this change of the assumption regarding isoenzymes increases the recall of epistatic interactions predicted by the flux balance model at the cost of a reduction in the precision of the predictions. In addition to suggesting that the gene-to-reaction mapping in genome-scale flux balance models should be used with caution, our analysis provides new evidence that evolutionary gene importance captures much more than strict essentiality.

  20. A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility.

    Science.gov (United States)

    Huang, Tsun-Tsao; del Valle Marcos, María Laura; Hwang, Jenn-Kang; Echave, Julian

    2014-04-09

    Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site's rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site's Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site's LPD with its rate of evolution. We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein's potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant's active conformation.We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship

  1. Cancer-stroma evolutionary dynamics in stress-gradient microenvironment

    Science.gov (United States)

    Wu, Amy; Lambert, Guillaume; Austin, Robert; Sturm, James; Khin, Zayar; Silva, Ariosto

    2012-02-01

    In order to study the evolution of drug resistance in cancer, it is important to mimic the tumor microenvironment, in which cells are exposed to not uniform concentrations but rather gradients of drugs, nutrients, and other factors Compared to traditional in-vitro methods, microfluidic structure enables better control of the temporal and spatial profile of gradients. Here we demonstrate a microfluidic Doxorubicin gradient environment with heterogeneous landscape, and culture multiple myeloma (8226-S, expressing RFP) and bone marrow stroma (HS-5, expressing GFP) cell lines together. The myeloma cells are not directly motile, but they are able to migrate via the adhesion to motile stroma cells. The indirect motility mechanism of the myeloma cells is crucial for the adaptation to stress environment. Finally, we will report the co-culture dynamics under the stress of doxorubicin gradients, observing for cellular migrations and growth

  2. Evolutionary dynamics of sporophytic self-incompatibility alleles in plants

    DEFF Research Database (Denmark)

    Schierup, M H; Vekemans, X; Christiansen, F B

    1997-01-01

    The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act...... of gametophytic self-incompatibility, but the selection intensity is stronger. With dominance, dominant alleles invade the population more easily than recessive alleles and have a lower frequency at equilibrium. In the SSIdom model, recessive alleles have both a higher allele frequency and higher expected life...... is closely approximated by a random walk on a dominance ladder. Implications of the results for experimental studies of sporophytic self-incompatibility in natural populations are discussed. Udgivelsesdato: 1997-Oct...

  3. Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

    Science.gov (United States)

    Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas

    2016-05-20

    The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.

  4. A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming.

    Science.gov (United States)

    Cotto, Olivier; Wessely, Johannes; Georges, Damien; Klonner, Günther; Schmid, Max; Dullinger, Stefan; Thuiller, Wilfried; Guillaume, Frédéric

    2017-05-05

    Withstanding extinction while facing rapid climate change depends on a species' ability to track its ecological niche or to evolve a new one. Current methods that predict climate-driven species' range shifts use ecological modelling without eco-evolutionary dynamics. Here we present an eco-evolutionary forecasting framework that combines niche modelling with individual-based demographic and genetic simulations. Applying our approach to four endemic perennial plant species of the Austrian Alps, we show that accounting for eco-evolutionary dynamics when predicting species' responses to climate change is crucial. Perennial species persist in unsuitable habitats longer than predicted by niche modelling, causing delayed range losses; however, their evolutionary responses are constrained because long-lived adults produce increasingly maladapted offspring. Decreasing population size due to maladaptation occurs faster than the contraction of the species range, especially for the most abundant species. Monitoring of species' local abundance rather than their range may likely better inform on species' extinction risks under climate change.

  5. 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.

  6. Evolutionary dynamics of satellite DNA repeats from Phaseolus beans.

    Science.gov (United States)

    Ribeiro, Tiago; Dos Santos, Karla G B; Richard, Manon M S; Sévignac, Mireille; Thareau, Vincent; Geffroy, Valérie; Pedrosa-Harand, Andrea

    2017-03-01

    Common bean (Phaseolus vulgaris) subtelomeres are highly enriched for khipu, the main satellite DNA identified so far in this genome. Here, we comparatively investigate khipu genomic organization in Phaseolus species from different clades. Additionally, we identified and characterized another satellite repeat, named jumper, associated to khipu. A mixture of P. vulgaris khipu clones hybridized in situ confirmed the presence of khipu-like sequences on subterminal chromosome regions in all Phaseolus species, with differences in the number and intensity of signals between species and when species-specific clones were used. Khipu is present as multimers of ∼500 bp and sequence analyses of cloned fragments revealed close relationship among khipu repeats. The new repeat, named jumper, is a 170-bp satellite sequence present in all Phaseolus species and inserted into the nontranscribed spacer (NTS) of the 5S rDNA in the P. vulgaris genome. Nevertheless, jumper was found as a high-copy repeat at subtelomeres and/or pericentromeres in the Phaseolus microcarpus lineage only. Our data argue for khipu as an important subtelomeric satellite DNA in the genus and for a complex satellite repeat composition of P. microcarpus subtelomeres, which also contain jumper. Furthermore, the differential amplification of these repeats in subtelomeres or pericentromeres reinforces the presence of a dynamic satellite DNA library in Phaseolus.

  7. Why is the correlation between gene importance and gene evolutionary rate so weak?

    Directory of Open Access Journals (Sweden)

    Zhi Wang

    2009-01-01

    Full Text Available One of the few commonly believed principles of molecular evolution is that functionally more important genes (or DNA sequences evolve more slowly than less important ones. This principle is widely used by molecular biologists in daily practice. However, recent genomic analysis of a diverse array of organisms found only weak, negative correlations between the evolutionary rate of a gene and its functional importance, typically measured under a single benign lab condition. A frequently suggested cause of the above finding is that gene importance determined in the lab differs from that in an organism's natural environment. Here, we test this hypothesis in yeast using gene importance values experimentally determined in 418 lab conditions or computationally predicted for 10,000 nutritional conditions. In no single condition or combination of conditions did we find a much stronger negative correlation, which is explainable by our subsequent finding that always-essential (enzyme genes do not evolve significantly more slowly than sometimes-essential or always-nonessential ones. Furthermore, we verified that functional density, approximated by the fraction of amino acid sites within protein domains, is uncorrelated with gene importance. Thus, neither the lab-nature mismatch nor a potentially biased among-gene distribution of functional density explains the observed weakness of the correlation between gene importance and evolutionary rate. We conclude that the weakness is factual, rather than artifactual. In addition to being weakened by population genetic reasons, the correlation is likely to have been further weakened by the presence of multiple nontrivial rate determinants that are independent from gene importance. These findings notwithstanding, we show that the principle of slower evolution of more important genes does have some predictive power when genes with vastly different evolutionary rates are compared, explaining why the principle can be

  8. Mutation and evolutionary rates in adélie penguins from the antarctic.

    Directory of Open Access Journals (Sweden)

    Craig D Millar

    2008-10-01

    Full Text Available Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (micro of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29-0.88 mutations/site/Myrs after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17. Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.

  9. Evolutionary dynamics of HBV-D7 subgenotype in Tunisia.

    Science.gov (United States)

    Ciccozzi, Massimo; Chaouch, Houda; Lo Presti, Alessandra; Taffon, Stefania; Villano, Umbertina; Equestre, Michele; Bruni, Roberto; Marcantonio, Cinzia; Tritarelli, Elena; Cella, Eleonora; Blasi, Aletheia; Aouni, Mahjoub; Letaief, Amel; Ciccaglione, Anna Rita

    2017-03-01

    Hepatitis B virus (HBV) is the main cause of diseases liver related infecting more than 200 milion persons worldwide. HBV infection shows high level of prevalence in South-East Europe and in Mediterranean basin. In Tunisia, a country with an intermediate level endemicity, HbsAg prevalence ranges from 2 to 5%. Most of the HBV isolates from Tunisia were classified as subgenotype D7 whose circulation is restricted to a specific area of North Africa including Maghreb region. In this paper, the phylogeny of HBV-D7 isolated from 38 Tunisian patients was investigated by analyzing the S gene region of HBV. A Bayesian coalescent-based framework was used to estimate the origin of the HBV-D7 in the country. The Tunisian D7 isolates were found to share a common ancestor whose origin was traced back to 1958. Population dynamics indicated that HBV-D7 epidemic in Tunisia grew exponentially from 1960s to 1990s. After that, the curve reached a plateau around the years 2000 likely due to the implementation of the infant vaccination program in 1996. Epidemiological data suggested that the exponential growth phase was likely sustained by intra-familial transmission events occurring during infancy. Further characterization of HBV-D7 isolates should be performed to evaluate, in the post-vaccination era, the emergence of new transmission routes, and to monitor the efficacy of the vaccination program. J. Med. Virol. 89:469-475, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. The Tangled Nature Model of evolutionary dynamics reconsidered

    DEFF Research Database (Denmark)

    Andersen, Christian Walther; Sibani, Paolo

    2016-01-01

    The Tangled Nature Model of biological and cultural evolution features interacting agents which compete for limited resources and reproduce in an error prone fashion and at a rate depending on the `tangle' of interactions they maintain with others. The set of interactions linking a TNM individual...... all the interactions, while increasing $K$ up to the length of the genome ensures an increasing level of trait inheritance. We show that the distribution of the interactions generated by our rule is nearly independent of the value of $K$. Changing $K$ strengthens the core structure of the ecology......, leads to population abundance distributions which are better approximated by log-normal probability densities and increases the probability that a species extant at time $t_{\\rm w}$ is also extant at a later time $t$. In particular, survival probabilities are shown to decay as powers of the ratio $t...

  11. Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.

    Science.gov (United States)

    Sydykova, Dariya K; Wilke, Claus O

    2017-01-01

    Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation-selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferred dN∕dS values on the same alignments. We find that Rate4Site scores generally correlate well with true dN∕dS, and the correlation strengths increase in alignments with greater sequence divergence and more taxa. Moreover, Rate4Site scores correlate very well with inferred (as opposed to true) dN∕dS values, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site and dN∕dS in a variety of empirical datasets. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield very similar inferences.

  12. Heart Rate Fragmentation: A Symbolic Dynamical Approach

    Directory of Open Access Journals (Sweden)

    Madalena D. Costa

    2017-11-01

    Full Text Available Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability.Objective: The objectives of this study were to: (1 introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2 evaluate how the distribution of the different dynamical patterns (“words” varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD; and (3 quantify the differences in the fragmentation patterns between the two sample populations.Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW.Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed “soft” inflection points. In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to

  13. Heart Rate Fragmentation: A Symbolic Dynamical Approach.

    Science.gov (United States)

    Costa, Madalena D; Davis, Roger B; Goldberger, Ary L

    2017-01-01

    Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability. Objective: The objectives of this study were to: (1) introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2) evaluate how the distribution of the different dynamical patterns ("words") varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD); and (3) quantify the differences in the fragmentation patterns between the two sample populations. Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words) with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW). Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed "soft" inflection points). In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to deceleration and vice

  14. Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana.

    Science.gov (United States)

    Fournier-Level, Alexandre; Perry, Emily O; Wang, Jonathan A; Braun, Peter T; Migneault, Andrew; Cooper, Martha D; Metcalf, C Jessica E; Schmitt, Johanna

    2016-05-17

    Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.

  15. An improved shuffled frog leaping algorithm based evolutionary framework for currency exchange rate prediction

    Science.gov (United States)

    Dash, Rajashree

    2017-11-01

    Forecasting purchasing power of one currency with respect to another currency is always an interesting topic in the field of financial time series prediction. Despite the existence of several traditional and computational models for currency exchange rate forecasting, there is always a need for developing simpler and more efficient model, which will produce better prediction capability. In this paper, an evolutionary framework is proposed by using an improved shuffled frog leaping (ISFL) algorithm with a computationally efficient functional link artificial neural network (CEFLANN) for prediction of currency exchange rate. The model is validated by observing the monthly prediction measures obtained for three currency exchange data sets such as USD/CAD, USD/CHF, and USD/JPY accumulated within same period of time. The model performance is also compared with two other evolutionary learning techniques such as Shuffled frog leaping algorithm and Particle Swarm optimization algorithm. Practical analysis of results suggest that, the proposed model developed using the ISFL algorithm with CEFLANN network is a promising predictor model for currency exchange rate prediction compared to other models included in the study.

  16. Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Jose Manuel C Tubio

    Full Text Available Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.

  17. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis

    Science.gov (United States)

    Fokas, Alexander S.; Cole, Daniel J.; Ahnert, Sebastian E.; Chin, Alex W.

    2016-09-01

    Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.

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

    Science.gov (United States)

    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.

  19. An Improved Co-evolutionary Particle Swarm Optimization for Wireless Sensor Networks with Dynamic Deployment

    Directory of Open Access Journals (Sweden)

    Jun-Jie Ma

    2007-03-01

    Full Text Available The effectiveness of wireless sensor networks (WSNs depends on the coverage and target detection probability provided by dynamic deployment, which is usually supported by the virtual force (VF algorithm. However, in the VF algorithm, the virtual force exerted by stationary sensor nodes will hinder the movement of mobile sensor nodes. Particle swarm optimization (PSO is introduced as another dynamic deployment algorithm, but in this case the computation time required is the big bottleneck. This paper proposes a dynamic deployment algorithm which is named “virtual force directed co-evolutionary particle swarm optimization” (VFCPSO, since this algorithm combines the co-evolutionary particle swarm optimization (CPSO with the VF algorithm, whereby the CPSO uses multiple swarms to optimize different components of the solution vectors for dynamic deployment cooperatively and the velocity of each particle is updated according to not only the historical local and global optimal solutions, but also the virtual forces of sensor nodes. Simulation results demonstrate that the proposed VFCPSO is competent for dynamic deployment in WSNs and has better performance with respect to computation time and effectiveness than the VF, PSO and VFPSO algorithms.

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

    Science.gov (United States)

    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.

  1. Geometrical envelopes: Extending graphical contemporary niche theory to communities and eco-evolutionary dynamics.

    Science.gov (United States)

    Koffel, Thomas; Daufresne, Tanguy; Massol, François; Klausmeier, Christopher A

    2016-10-21

    Contemporary niche theory is a powerful structuring framework in theoretical ecology. First developed in the context of resource competition, it has been extended to encompass other types of regulating factors such as shared predators, parasites or inhibitors. A central component of contemporary niche theory is a graphical approach popularized by Tilman that illustrates the different outcomes of competition along environmental gradients, like coexistence and competitive exclusion. These food web modules have been used to address species sorting in community ecology, as well as adaptation and coexistence on eco-evolutionary time scales in adaptive dynamics. Yet, the associated graphical approach has been underused so far in the evolutionary context. In this paper, we provide a rigorous approach to extend this graphical method to a continuum of interacting strategies, using the geometrical concept of the envelope. Not only does this approach provide community and eco-evolutionary bifurcation diagrams along environmental gradients, it also sheds light on the similarities and differences between those two perspectives. Adaptive dynamics naturally merges with this ecological framework, with a close correspondence between the classification of singular strategies and the geometrical properties of the envelope. Finally, this approach provides an integrative tool to study adaptation between levels of organization, from the individual to the ecosystem. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Dynamic Properties of Evolutionary Multi-player Games in Finite Populations

    Directory of Open Access Journals (Sweden)

    Bin Wu

    2013-05-01

    Full Text Available William D. Hamilton famously stated that “human life is a many person game and not just a disjoined collection of two person games”. However, most of the theoretical results in evolutionary game theory have been developed for two player games. In spite of a multitude of examples ranging from humans to bacteria, multi-player games have received less attention than pairwise games due to their inherent complexity. Such complexities arise from the fact that group interactions cannot always be considered as a sum of multiple pairwise interactions. Mathematically, multi-player games provide a natural way to introduce non-linear, polynomial fitness functions into evolutionary game theory, whereas pairwise games lead to linear fitness functions. Similarly, studying finite populations is a natural way of introducing intrinsic stochasticity into population dynamics. While these topics have been dealt with individually, few have addressed the combination of finite populations and multi-player games so far. We are investigating the dynamical properties of evolutionary multi-player games in finite populations. Properties of the fixation probability and fixation time, which are relevant for rare mutations, are addressed in well mixed populations. For more frequent mutations, the average abundance is investigated in well mixed as well as in structured populations. While the fixation properties are generalizations of the results from two player scenarios, addressing the average abundance in multi-player games gives rise to novel outcomes not possible in pairwise games.

  3. Heterogeneous evolutionary rates of Pi2/9 homologs in rice

    Directory of Open Access Journals (Sweden)

    Wu Kejing

    2012-08-01

    Full Text Available Abstract Background The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR genes in the rice genome. Although three functional R-genes have been cloned from this locus, little is known about the origin and evolutionary history of these genes. Herein, an extensive genome-wide survey of Pi2/9 homologs in rice, sorghum, Brachypodium and Arabidopsis, was conducted to explore this theme. Results In our study, 1, 1, 5 and 156 Pi2/9 homologs were detected in Arabidopsis, Brachypodium, sorghum and rice genomes, respectively. Two distinct evolutionary patterns of Pi2/9 homologs, Type I and Type II, were observed in rice lines. Type I Pi2/9 homologs showed evidence of rapid gene diversification, including substantial copy number variations, obscured orthologous relationships, high levels of nucleotide diversity or/and divergence, frequent sequence exchanges and strong positive selection, whereas Type II Pi2/9 homologs exhibited a fairly slow evolutionary rate. Interestingly, the three cloned R-genes from the Pi2/9 locus all belonged to the Type I genes. Conclusions Our data show that the Pi2/9 locus had an ancient origin predating the common ancestor of gramineous species. The existence of two types of Pi2/9 homologs suggest that diversifying evolution should be an important strategy of rice to cope with different types of pathogens. The relationship of cloned Pi2/9 genes and Type I genes also suggests that rapid gene diversification might facilitate rice to adapt quickly to the changing spectrum of the fungal pathogen M. grisea. Based on these criteria, other potential candidate genes that might confer novel resistance specificities to rice blast could be predicted.

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

    Science.gov (United States)

    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.

  5. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ.

    Science.gov (United States)

    Philip, Siby; Machado, João Paulo; Maldonado, Emanuel; Vasconcelos, Vítor; O'Brien, Stephen J; Johnson, Warren E; Antunes, Agostinho

    2012-12-01

    The mechanosensory lateral line, found only in fishes and amphibians, is an important sense organ associated with aquatic life. Lateral line patterns differ among teleost, the most diverse vertebrate taxa, hypothetically in response to selective pressures from different aquatic habitats. In this article, we conduct evolutionary genomic analyses of 34 genes associated with lateral line system development in teleosts to elucidate the significance of contrasting evolutionary rates and changes in the protein coding sequences. We find that duplicated copies of these genes are preferentially retained in the teleost genomes and that episodic events of positive selection have occurred in 22 of the 30 postduplication branches. In general, teleost genes evolved at a faster rate relative to their tetrapod counterparts, and the mutation rates of 26 of the 34 genes differed among teleosts and tetrapods. We conclude that following whole genome duplication, evolutionary rates and episodic events of positive selection on the lateral line system development genes might have been one of the factors favoring the subsequent adaptive radiation of teleosts into diverse habitats. These results provide the foundation for further detailed explorations into lateral line system genes and the evolution of diverse phenotypes and adaptations.

  6. Minimizing the symbol-error-rate for amplify-and-forward relaying systems using evolutionary algorithms

    KAUST Repository

    Ahmed, Qasim Zeeshan

    2015-02-01

    In this paper, a new detector is proposed for an amplify-and-forward (AF) relaying system. The detector is designed to minimize the symbol-error-rate (SER) of the system. The SER surface is non-linear and may have multiple minimas, therefore, designing an SER detector for cooperative communications becomes an optimization problem. Evolutionary based algorithms have the capability to find the global minima, therefore, evolutionary algorithms such as particle swarm optimization (PSO) and differential evolution (DE) are exploited to solve this optimization problem. The performance of proposed detectors is compared with the conventional detectors such as maximum likelihood (ML) and minimum mean square error (MMSE) detector. In the simulation results, it can be observed that the SER performance of the proposed detectors is less than 2 dB away from the ML detector. Significant improvement in SER performance is also observed when comparing with the MMSE detector. The computational complexity of the proposed detector is much less than the ML and MMSE algorithms. Moreover, in contrast to ML and MMSE detectors, the computational complexity of the proposed detectors increases linearly with respect to the number of relays.

  7. Island colonisation and the evolutionary rates of body size in insular neonate snakes

    Science.gov (United States)

    Aubret, F

    2015-01-01

    Island colonisation by animal populations is often associated with dramatic shifts in body size. However, little is known about the rates at which these evolutionary shifts occur, under what precise selective pressures and the putative role played by adaptive plasticity on driving such changes. Isolation time played a significant role in the evolution of body size in island Tiger snake populations, where adaptive phenotypic plasticity followed by genetic assimilation fine-tuned neonate body and head size (hence swallowing performance) to prey size. Here I show that in long isolated islands (>6000 years old) and mainland populations, neonate body mass and snout-vent length are tightly correlated with the average prey body mass available at each site. Regression line equations were used to calculate body size values to match prey size in four recently isolated populations of Tiger snakes. Rates of evolution in body mass and snout-vent length, calculated for seven island snake populations, were significantly correlated with isolation time. Finally, rates of evolution in body mass per generation were significantly correlated with levels of plasticity in head growth rates. This study shows that body size evolution occurs at a faster pace in recently isolated populations and suggests that the level of adaptive plasticity for swallowing abilities may correlate with rates of body mass evolution. I hypothesise that, in the early stages of colonisation, adaptive plasticity and directional selection may combine and generate accelerated evolution towards an ‘optimal' phenotype. PMID:25074570

  8. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    Science.gov (United States)

    Ahsan, Syed Amir

    forces are reviewed culminating with the research manuscript in section 3.4 of the development of the two-state worm-like chain, modeling the overstretching transition of B-DNA to S-DNA. Chapter 4 considers the behavior of DNA in an electric field, first reviewing DNA as a polyelectrolyte and of DNA electrophoresis in free solution and it's polarization and resulting stretched conformation as context for the study of the contrasting behavior of DNA in an AC electric field presented in the research manuscripts of the final two sections of chapter 4. In section 4.3 the collapse of DNA in ac electric fields is investigated with the experimental results and possible models for collapse presented with a scaling analysis of the frequency- and confinement-dependent critical field for collapse presented in section 4.4, contrasting a mean-field Flory-type model and a continuum, wormlike chain model. Chapter 5 investigates viral RNA; reviewing the encapsidation, life cycle and the evolutionary dynamics of single-stranded RNA viruses including the quasispecies model and it's prediction of the information or error catastrophe, providing context for the models developed in the research manuscripts presented in sections 2.5 and 5.3. In section 5.3, a simple ODE model of the evolution of positive-sense single-stranded RNA viruses is developed, adopting the two-state mean-field quasispecies model, to characterize the selection pressure associated with the encapsidation and independently, the degradation by RNAi of the wild-type relative to the mutant population and demonstrate their capacity to induce an information catastrophe and consequently support the evolution of intermediate encapsidation rates and of viral suppressors of RNA silencing, in addition to providing support for antiviral therapeutic pathways.

  9. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia.

    Science.gov (United States)

    Lovsin, N; Gubensek, F; Kordi, D

    2001-12-01

    The evolution of the novel L2 clade of non-long terminal repeat (LTR) retrotransposons and their evolutionary dynamics in Deuterostomia has been examined. The short-term evolution of long interspersed nuclear element 2s (LINE2s) has been studied in 18 reptilian species by analysis of a PCR amplified 0.7-kb fragment encoding the palm/fingers subdomain of reverse transcriptase (RT). Most of the reptilian LINE2s examined are inactive since they contain multiple stop codons, indels, or frameshift mutations that disrupt the RT. Analysis of reptilian LINE2s has shown a high degree of sequence divergence and an unexpectedly large number of deletions. The evolutionary dynamics of LINE2s in reptiles has been found to be complex. LINE2s are shown to form a novel clade of non-LTR retrotransposons that is well separated from the CR1 clade. This novel L2 clade is more widely distributed than previously thought, and new representatives have been discovered in echinoderms, insects, teleost fishes, Xenopus, Squamata, and marsupials. There is an apparent absence of LINE2s from different vertebrate classes, such as cartilaginous fishes, Archosauria (birds and crocodiles), and turtles. Whereas the LINE2s are present in echinoderms and teleost fishes in a conserved form, in most tetrapods only highly degenerated pseudogenes can be found. The predominance of inactive LINE2s in Tetrapoda indicates that, in the host genomes, only inactive copies are still present. The present data indicate that the vertical inactivation of LINE2s might have begun at the time of Tetrapoda origin, 400 MYA. The evolutionary dynamics of the L2 clade in Deuterostomia can be described as a gradual vertical inactivation in Tetrapoda, stochastic loss in Archosauria and turtles, and strict vertical transmission in echinoderms and teleost fishes.

  10. Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

    Directory of Open Access Journals (Sweden)

    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.

  11. 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)

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Exchange Rate Dynamics under Alternative Optimal Interest Rate Rules

    OpenAIRE

    Binici, Mahir; Cheung, Yin-Wong

    2011-01-01

    We explore the role of interest rate policy in the exchange rate determination process. Specifically, we derive exchange rate equations from interest rate rules that are theoretically optimal under a few alternative settings. The exchange rate equation depends on its underlying interest rate rule and its performance could vary across evaluation criteria and sample periods. The exchange rate equation implied by the interest rate rule that allows for interest rate and inflation inertia under co...

  14. 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

  15. 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.

  16. Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons.

    OpenAIRE

    Miyata, T.; Hayashida, H

    1981-01-01

    Comparisons of nucleotide sequences of several pseudogenes described to date, including alpha- and beta-globin and immunoglobulin kappa-type variable domain pseudogenes, with those of functional counterparts revealed that pseudogenes accumulate mutations at an extremely high rate uniformly over their entirety. It is remarkable that the evolutionary rate exceeds the rate of changes between synonymous codons, the highest known rate, in functional genes. Because no pseudogenes appear to function...

  17. Phenotypic engineering of sperm-production rate confirms evolutionary predictions of sperm competition theory.

    Science.gov (United States)

    Sekii, Kiyono; Vizoso, Dita B; Kuales, Georg; De Mulder, Katrien; Ladurner, Peter; Schärer, Lukas

    2013-04-22

    Sperm production is a key male reproductive trait and an important parameter in sperm competition theory. Under sperm competition, paternity success is predicted to depend strongly on male allocation to sperm production. Furthermore, because sperm production is inherently costly, individuals should economize in sperm expenditure, and conditional adjustment of the copulation frequency according to their sperm availability may be expected. However, experimental studies showing effects of sperm production on mating behaviour and paternity success have so far been scarce, mainly because sperm production is difficult to manipulate directly in animals. Here, we used phenotypic engineering to manipulate sperm-production rate, by employing dose-dependent RNA interference (RNAi) of a spermatogenesis-specific gene, macbol1, in the free-living flatworm Macrostomum lignano. We demonstrate (i) that our novel dose-dependent RNAi approach allows us to induce high variability in sperm-production rate; (ii) that a reduced sperm-production rate is associated with a decreased copulation frequency, suggesting conditional adjustment of mating behaviour; and (iii) that both sperm production and copulation frequency are important determinants of paternity success in a competitive situation, as predicted by sperm competition theory. Our study clearly documents the potential of phenotypic engineering via dose-dependent RNAi to test quantitative predictions of evolutionary theory.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

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

    Science.gov (United States)

    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 1.3<γin<3 coinciding with social networks.

  1. Multiple HIV-1 infection of cells and the evolutionary dynamics of cytotoxic T lymphocyte escape mutants.

    Science.gov (United States)

    Wodarz, Dominik; Levy, David N

    2009-09-01

    Cytotoxic T lymphocytes (CTL) are an important branch of the immune system, killing virus-infected cells. Many viruses can mutate so that infected cells are not killed by CTL anymore. This escape can contribute to virus persistence and disease. A prominent example is HIV-1. The evolutionary dynamics of CTL escape mutants in vivo have been studied experimentally and mathematically, assuming that a cell can only be infected with one HIV particle at a time. However, according to data, multiple virus particles frequently infect the same cell, a process called coinfection. Here, we study the evolutionary dynamics of CTL escape mutants in the context of coinfection. A mathematical model suggests that an intermediate strength of the CTL response against the wild-type is most detrimental for an escape mutant, minimizing overall virus load and even leading to its extinction. A weaker or, paradoxically, stronger CTL response against the wild-type both lead to the persistence of the escape mutant and higher virus load. It is hypothesized that an intermediate strength of the CTL response, and thus the suboptimal virus suppression observed in HIV-1 infection, might be adaptive to minimize the impact of existing CTL escape mutants on overall virus load.

  2. 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.

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

    DEFF Research Database (Denmark)

    Lissovoi, Andrei

    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...... exist more complex oscillations that cannot be tracked with a polynomial-size colony. MMAS and (μ+1) EA on Maze We analyse the behaviour of a (μ + 1) EA with genotype diversity on a dynamic fitness function Maze, extended to a finite-alphabet search space. We prove that the (μ + 1) EA is able to track...... 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...

  4. Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.

    Directory of Open Access Journals (Sweden)

    Carlos Peña

    Full Text Available The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.

  5. Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.

    Science.gov (United States)

    Peña, Carlos; Espeland, Marianne

    2015-01-01

    The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.

  6. Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily

    Directory of Open Access Journals (Sweden)

    Bagnato S

    2014-04-01

    Full Text Available Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily. The aim of this paper is to evaluate the dynamics of Etna birch stands (Betula aetnensis Rafin following the cessation of silvicultural activities in the Etna Regional Park (Sicily. We investigated forest structure, natural regeneration, vegetation and deadwood in different forest types. Our findings highlighted three different dynamics for birch populations: stable birch stands in the high mountain area which might represent an edapho-climax forest; progressive dynamic birch stands in the intermediate mountain area, showing a gradual depletion of birch and a concomitant replacement with monospecific stands (calabrian pine, beech, oaks or mixed ones (with birch; pure birch stands (typical that tend to be regressive - especially under stressful conditions - and to be replaced by xerophilous grasslands. Following the cessation of coppicing and with stand ageing, the stumps transformation into more homogeneous stand structures have been increasing. Within the context of protected areas the restoration of coppice selection system (with appropriate adaptations could help to maintain the traditional forest landscape, acting as a silvicultural technique with low environmental and landscape impact.

  7. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

    Science.gov (United States)

    Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L.

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. 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.

  11. Against matching theory: predictions of an evolutionary theory of behavior dynamics.

    Science.gov (United States)

    McDowell, J J; Calvin, Nicholas T

    2015-05-01

    A selectionist theory of adaptive behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of resource acquisition or threat escape or avoidance. The theory is implemented by a computer program that creates an artificial organism and animates it with a population of potential behaviors. The population undergoes selection, recombination, and mutation across generations, or ticks of time, which produces a continuous stream of behavior that can be studied as if it were the behavior of a live organism. Novel predictions of the evolutionary theory can be compared to predictions of matching theory in a critical experiment that arranges concurrent schedules with reinforcer magnitudes that vary across conditions in one component of the schedules but not the other. Matching theory and the evolutionary theory make conflicting predictions about the outcome of this critical experiment, such that the results must disconfirm at least one of the theories. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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

  13. Chromosomal evolutionary dynamics of four multigene families in Coreidae and Pentatomidae (Heteroptera) true bugs.

    Science.gov (United States)

    Bardella, Vanessa Bellini; Fernandes, José Antônio Marin; Cabral-de-Mello, Diogo Cavalcanti

    2016-10-01

    Previous chromosome mapping of multigene families in Pentatomomorpha (Heteroptera) insects, which was restricted to the major rDNA, revealed remarkable conservation of number of clusters and chromosomal positions. Aiming to understand the chromosomal organization and evolutionary patterns of multigene families in karyotypes of Heteroptera, we performed a chromosomal mapping using four distinct multigene families in representatives of Coreidae (ten species) and Pentatomidae (five species). A single pair of the major rDNA cluster (18S rDNA probe) and a single pair of the minor rDNA cluster (5S rDNA probe), both terminally located were primarily observed, being, in most species, located in distinct chromosomes. However, some alternative patterns were also observed. In species in which the U2 snDNA and H4 gene clusters were mapped, they were mainly located in one autosomal pair each, wherein the H4 gene cluster was located in different positions. Our data suggest that the karyotype diversity reported in Coreidae is not reflected in the distribution diversity of multigene families. This contrasts with the data for Pentatomidae, with a conserved gross karyotype but a discrete diversity in the location of the clusters of multigene families, indicating genome dynamics for these markers. The findings are discussed to shed light on the possible causes for the conservation or variation observed and to assist in understanding the chromosomal evolutionary trends in the group.

  14. Female orgasm rates are largely independent of other traits: implications for "female orgasmic disorder" and evolutionary theories of orgasm.

    Science.gov (United States)

    Zietsch, Brendan P; Miller, Geoffrey F; Bailey, J Michael; Martin, Nicholas G

    2011-08-01

    The criteria for "female orgasmic disorder" (FOD) assume that low rates of orgasm are dysfunctional, implying that high rates are functional. Evolutionary theories about the function of female orgasm predict correlations of orgasm rates with sexual attitudes and behavior and other fitness-related traits. To test hypothesized evolutionary functions of the female orgasm. We examined such correlations in a community sample of 2,914 adult female Australian twins who reported their orgasm rates during masturbation, intercourse, and other sexual activities, and who completed demographic, personality, and sexuality questionnaires. Orgasm rates during intercourse, other sex, and masturbation. Although orgasm rates showed high variance across women and substantial heritability, they were largely phenotypically and genetically independent of other important traits. We found zero to weak phenotypic correlations between all three orgasm rates and all other 19 traits examined, including occupational status, social class, educational attainment, extraversion, neuroticism, psychoticism, impulsiveness, childhood illness, maternal pregnancy stress, marital status, political liberalism, restrictive attitudes toward sex, libido, lifetime number of sex partners, risky sexual behavior, masculinity, orientation toward uncommitted sex, age of first intercourse, and sexual fantasy. Furthermore, none of the correlations had significant genetic components. These findings cast doubt on most current evolutionary theories about female orgasm's adaptive functions, and on the validity of FOD as a psychiatric construct. © 2011 International Society for Sexual Medicine.

  15. Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology.

    Directory of Open Access Journals (Sweden)

    Lydia Tan

    Full Text Available Human respiratory syncytial virus (RSV is an important cause of severe lower respiratory tract infections in infants and the elderly. In the vast majority of cases, however, RSV infections run mild and symptoms resemble those of a common cold. The immunological, clinical, and epidemiological profile of severe RSV infections suggests a disease caused by a virus with typical seasonal transmission behavior, lacking clear-cut virulence factors, but instead causing disease by modifying the host's immune response in a way that stimulates pathogenesis. Yet, the interplay between RSV-evoked immune responses and epidemic behavior, and how this affects the genomic evolutionary dynamics of the virus, remains poorly understood. Here, we present a comprehensive collection of 33 novel RSV subgroup A genomes from strains sampled over the last decade, and provide the first measurement of RSV-A genomic diversity through time in a phylodynamic framework. In addition, we map amino acid substitutions per protein to determine mutational hotspots in specific domains. Using Bayesian genealogical inference, we estimated the genomic evolutionary rate to be 6.47 × 10(-4 (credible interval: 5.56 × 10(-4, 7.38 × 10(-4 substitutions/site/year, considerably slower than previous estimates based on G gene sequences only. The G gene is however marked by elevated substitution rates compared to other RSV genes, which can be attributed to relaxed selective constraints. In line with this, site-specific selection analyses identify the G gene as the major target of diversifying selection. Importantly, statistical analysis demonstrates that the immune driven positive selection does not leave a measurable imprint on the genome phylogeny, implying that RSV lineage replacement mainly follows nonselective epidemiological processes. The roughly 50 years of RSV-A genomic evolution are characterized by a constant population size through time and general co-circulation of lineages over

  16. Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates.

    Directory of Open Access Journals (Sweden)

    Zhao Zhang

    Full Text Available Vertebrate interferon-induced transmembrane (IFITM genes have been demonstrated to have extensive and diverse functions, playing important roles in the evolution of vertebrates. Despite observance of their functionality, the evolutionary dynamics of this gene family are complex and currently unknown. Here, we performed detailed evolutionary analyses to unravel the evolutionary history of the vertebrate IFITM family. A total of 174 IFITM orthologous genes and 112 pseudogenes were identified from 27 vertebrate genome sequences. The vertebrate IFITM family can be divided into immunity-related IFITM (IR-IFITM, IFITM5 and IFITM10 sub-families in phylogeny, implying origins from three different progenitors. In general, vertebrate IFITM genes are located in two loci, one containing the IFITM10 gene, and the other locus containing IFITM5 and various numbers of IR-IFITM genes. Conservation of evolutionary synteny was observed in these IFITM genes. Significant functional divergence was detected among the three IFITM sub-families. No gene duplication or positive selection was found in IFITM5 sub-family, implying the functional conservation of IFITM5 in vertebrate evolution, which is involved in bone formation. No IFITM5 locus was identified in the marmoset genome, suggesting a potential association with the tiny size of this monkey. The IFITM10 sub-family was divided into two groups: aquatic and terrestrial types. Functional divergence was detected between the two groups, and five IFITM10-like genes from frog were dispersed into the two groups. Both gene duplication and positive selection were observed in aquatic vertebrate IFITM10-like genes, indicating that IFITM10 might be associated with the adaptation to aquatic environments. A large number of lineage- and species-specific gene duplications were observed in IR-IFITM sub-family and positive selection was detected in IR-IFITM of primates and rodents. Because primates have experienced a long history of

  17. 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.

  18. An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses

    Directory of Open Access Journals (Sweden)

    Drake John M

    2011-03-01

    Full Text Available Abstract Background Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to complex dynamical systems that are too cumbersome to analyse. Results Here, we develop an Individual-Based Model (IBM in order to address simultaneously the ecology, epidemiology and evolution of strain-polymorphic pathogens, using Influenza A viruses as an illustrative example. Conclusions We carry out careful validation of our IBM against comparable mathematical models to demonstrate the robustness of our algorithm and the sound basis for this novel framework. We discuss how this new approach can give critical insights in the study of influenza evolution.

  19. An agent-based model to study the epidemiological and evolutionary dynamics of Influenza viruses.

    Science.gov (United States)

    Roche, Benjamin; Drake, John M; Rohani, Pejman

    2011-03-30

    Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to complex dynamical systems that are too cumbersome to analyse. Here, we develop an Individual-Based Model (IBM) in order to address simultaneously the ecology, epidemiology and evolution of strain-polymorphic pathogens, using Influenza A viruses as an illustrative example. We carry out careful validation of our IBM against comparable mathematical models to demonstrate the robustness of our algorithm and the sound basis for this novel framework. We discuss how this new approach can give critical insights in the study of influenza evolution.

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

    Science.gov (United States)

    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.

  1. Transmission Expansion Planning – A Multiyear Dynamic Approach Using a Discrete Evolutionary Particle Swarm Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Saraiva J. T.

    2012-10-01

    Full Text Available The basic objective of Transmission Expansion Planning (TEP is to schedule a number of transmission projects along an extended planning horizon minimizing the network construction and operational costs while satisfying the requirement of delivering power safely and reliably to load centres along the horizon. This principle is quite simple, but the complexity of the problem and the impact on society transforms TEP on a challenging issue. This paper describes a new approach to solve the dynamic TEP problem, based on an improved discrete integer version of the Evolutionary Particle Swarm Optimization (EPSO meta-heuristic algorithm. The paper includes sections describing in detail the EPSO enhanced approach, the mathematical formulation of the TEP problem, including the objective function and the constraints, and a section devoted to the application of the developed approach to this problem. Finally, the use of the developed approach is illustrated using a case study based on the IEEE 24 bus 38 branch test system.

  2. Evolutionary dynamics in the two-locus two-allele model with weak selection.

    Science.gov (United States)

    Pontz, Martin; Hofbauer, Josef; Bürger, Reinhard

    2018-01-01

    Two-locus two-allele models are among the most studied models in population genetics. The reason is that they are the simplest models to explore the role of epistasis for a variety of important evolutionary problems, including the maintenance of polymorphism and the evolution of genetic incompatibilities. Many specific types of models have been explored. However, due to the mathematical complexity arising from the fact that epistasis generates linkage disequilibrium, few general insights have emerged. Here, we study a simpler problem by assuming that linkage disequilibrium can be ignored. This is a valid approximation if selection is sufficiently weak relative to recombination. The goal of our paper is to characterize all possible equilibrium structures, or more precisely and general, all robust phase portraits or evolutionary flows arising from this weak-selection dynamics. For general fitness matrices, we have not fully accomplished this goal, because some cases remain undecided. However, for many specific classes of fitness schemes, including additive fitnesses, purely additive-by-additive epistasis, haploid selection, multilinear epistasis, marginal overdominance or underdominance, and the symmetric viability model, we obtain complete characterizations of the possible equilibrium structures and, in several cases, even of all possible phase portraits. A central point in our analysis is the inference of the number and stability of fully polymorphic equilibria from the boundary flow, i.e., from the dynamics at the four marginal single-locus subsystems. The key mathematical ingredient for this is index theory. The specific form of epistasis has both a big influence on the possible boundary flows as well as on the internal equilibrium structure admitted by a given boundary flow.

  3. Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

    Science.gov (United States)

    Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

    2011-01-01

    Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

  4. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.

    Science.gov (United States)

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G; Drummond, Alexei J

    2014-05-06

    The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible-infected-removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth-death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.

  5. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model

    Science.gov (United States)

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G.; Drummond, Alexei J.

    2014-01-01

    The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible–infected–removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth–death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970. PMID:24573331

  6. Density Dependence and Growth Rate: Evolutionary Effects on Resistance Development to Bt (Bacillus thuringiensis).

    Science.gov (United States)

    Martinez, Jeannette C; Caprio, Michael A; Friedenberg, Nicholas A

    2018-02-09

    It has long been recognized that pest population dynamics can affect the durability of a pesticide, but dose remains the primary component of insect resistance management (IRM). For transgenic pesticidal traits such as Bt (Bacillus thuringiensis Berliner (Bacillales: Bacillaceae)), dose (measured as the mortality of susceptibles caused by a toxin) is a relatively fixed characteristic and often falls below the standard definition of high dose. Hence, it is important to understand how pest population dynamics modify durability and what targets they present for IRM. We used a deterministic model of a generic arthropod pest to examine how timing and strength of density dependence interacted with population growth rate and Bt mortality to affect time to resistance. As in previous studies, durability typically reached a minimum at intermediate doses. However, high population growth rates could eliminate benefits of high dose. The timing of density dependence had a more subtle effect. If density dependence operated simultaneously with Bt mortality, durability was insensitive to its strengths. However, if density dependence was driven by postselection densities, decreasing its strength could increase durability. The strength of density dependence could affect durability of both single traits and pyramids, but its influence depended on the timing of density dependence and size of the refuge. Our findings suggest the utility of a broader definition of high dose, one that incorporates population-dynamic context. That maximum growth rates and timing and strength of interactions causing density dependent mortality can all affect durability, also highlights the need for ecologically integrated approaches to IRM research. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. 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...

  8. The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

    Directory of Open Access Journals (Sweden)

    Fabio Luciani

    2009-11-01

    Full Text Available Many pathogens associated with chronic infections evolve so rapidly that strains found late in an infection have little in common with the initial strain. This raises questions at different levels of analysis because rapid within-host evolution affects the course of an infection, but it can also affect the possibility for natural selection to act at the between-host level. We present a nested approach that incorporates within-host evolutionary dynamics of a rapidly mutating virus (hepatitis C virus targeted by a cellular cross-reactive immune response, into an epidemiological perspective. The viral trait we follow is the replication rate of the strain initiating the infection. We find that, even for rapidly evolving viruses, the replication rate of the initial strain has a strong effect on the fitness of an infection. Moreover, infections caused by slowly replicating viruses have the highest infection fitness (i.e., lead to more secondary infections, but strains with higher replication rates tend to dominate within a host in the long-term. We also study the effect of cross-reactive immunity and viral mutation rate on infection life history traits. For instance, because of the stochastic nature of our approach, we can identify factors affecting the outcome of the infection (acute or chronic infections. Finally, we show that anti-viral treatments modify the value of the optimal initial replication rate and that the timing of the treatment administration can have public health consequences due to within-host evolution. Our results support the idea that natural selection can act on the replication rate of rapidly evolving viruses at the between-host level. It also provides a mechanistic description of within-host constraints, such as cross-reactive immunity, and shows how these constraints affect the infection fitness. This model raises questions that can be tested experimentally and underlines the necessity to consider the evolution of quantitative

  9. Linear and evolutionary polynomial regression models to forecast coastal dynamics: Comparison and reliability assessment

    Science.gov (United States)

    Bruno, Delia Evelina; Barca, Emanuele; Goncalves, Rodrigo Mikosz; de Araujo Queiroz, Heithor Alexandre; Berardi, Luigi; Passarella, Giuseppe

    2018-01-01

    In this paper, the Evolutionary Polynomial Regression data modelling strategy has been applied to study small scale, short-term coastal morphodynamics, given its capability for treating a wide database of known information, non-linearly. Simple linear and multilinear regression models were also applied to achieve a balance between the computational load and reliability of estimations of the three models. In fact, even though it is easy to imagine that the more complex the model, the more the prediction improves, sometimes a "slight" worsening of estimations can be accepted in exchange for the time saved in data organization and computational load. The models' outcomes were validated through a detailed statistical, error analysis, which revealed a slightly better estimation of the polynomial model with respect to the multilinear model, as expected. On the other hand, even though the data organization was identical for the two models, the multilinear one required a simpler simulation setting and a faster run time. Finally, the most reliable evolutionary polynomial regression model was used in order to make some conjecture about the uncertainty increase with the extension of extrapolation time of the estimation. The overlapping rate between the confidence band of the mean of the known coast position and the prediction band of the estimated position can be a good index of the weakness in producing reliable estimations when the extrapolation time increases too much. The proposed models and tests have been applied to a coastal sector located nearby Torre Colimena in the Apulia region, south Italy.

  10. Ancestor of the new archetypal biology: Goethe's dynamic typology as a model for contemporary evolutionary developmental biology.

    Science.gov (United States)

    Riegner, Mark F

    2013-12-01

    As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo). Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Co-evolutionary dynamics of collective action with signaling for a quorum.

    Directory of Open Access Journals (Sweden)

    Jorge M Pacheco

    2015-02-01

    Full Text Available Collective signaling for a quorum is found in a wide range of organisms that face collective action problems whose successful solution requires the participation of some quorum of the individuals present. These range from humans, to social insects, to bacteria. The mechanisms involved, the quorum required, and the size of the group may vary. Here we address the general question of the evolution of collective signaling at a high level of abstraction. We investigate the evolutionary dynamics of a population engaging in a signaling N-person game theoretic model. Parameter settings allow for loners and cheaters, and for costly or costless signals. We find a rich dynamics, showing how natural selection, operating on a population of individuals endowed with the simplest strategies, is able to evolve a costly signaling system that allows individuals to respond appropriately to different states of Nature. Signaling robustly promotes cooperative collective action, in particular when coordinated action is most needed and difficult to achieve. Two different signaling systems may emerge depending on Nature's most prevalent states.

  12. Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

    Directory of Open Access Journals (Sweden)

    Jingjing Ma

    2014-01-01

    Full Text Available Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

    Science.gov (United States)

    Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

    2014-01-01

    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420

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

    Science.gov (United States)

    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

  16. The Evolutionary History and Spatiotemporal Dynamics of the NC Lineage of Citrus Tristeza Virus.

    Science.gov (United States)

    Benítez-Galeano, María José; Castells, Matías; Colina, Rodney

    2017-10-12

    Citrus tristeza virus (CTV) is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV's evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the aim to delve deeper into the CTV-NC (New Clade) genotype evolution, we estimated an evolution rate of 1.19 × 10(-3) subs/site/year and the most common recent ancestor in 1977. Furthermore, the place of origin of the genotype was in the United States, and a great expansion of the population was observed in Uruguay. This expansion phase could be a consequence of the increment in the number of naïve citrus trees in Uruguayan orchards encompassing citrus industry growth in the past years.

  17. The Evolutionary History and Spatiotemporal Dynamics of the NC Lineage of Citrus Tristeza Virus

    Directory of Open Access Journals (Sweden)

    María José Benítez-Galeano

    2017-10-01

    Full Text Available Citrus tristeza virus (CTV is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV’s evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the aim to delve deeper into the CTV-NC (New Clade genotype evolution, we estimated an evolution rate of 1.19 × 10−3 subs/site/year and the most common recent ancestor in 1977. Furthermore, the place of origin of the genotype was in the United States, and a great expansion of the population was observed in Uruguay. This expansion phase could be a consequence of the increment in the number of naïve citrus trees in Uruguayan orchards encompassing citrus industry growth in the past years.

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

    Science.gov (United States)

    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.

  19. Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms.

    Science.gov (United States)

    Chenuil, Anne; Egea, Emilie; Rocher, Caroline; Touzet, Hélène; Féral, Jean-Pierre

    2008-11-01

    The divergent domain D8 of the large ribosomal RNA is very variable and extended in vertebrates compared to other eukaryotes. We provide data from 31 species of echinoderms and present the first comparative analysis of the D8 in nonvertebrate deuterostomes. In addition, we obtained 16S mitochondrial DNA sequences for the sea urchin taxa and analyzed single-strand conformation polymorphism (SSCP) of D8 in several populations within the species complex Echinocardium cordatum. A common secondary structure supported by compensatory substitutions and indels is inferred for echinoderms. Variation mostly arises at the tip of the longest stem (D8a), and the most variable taxa also display the longest and most stable D8. The most stable variants are the only ones displaying bulges in the terminal part of the stem, suggesting that selection, rather than maximizing stability of the D8 secondary structure, maintains it in a given range. Striking variation in D8 evolutionary rates was evidenced among sea urchins, by comparison with both 16S mitochondrial DNA and paleontological data. In Echinocardium cordatum and Strongylocentrotus pallidus and S. droebachiensis, belonging to very distant genera, the increase in D8 evolutionary rate is extreme. Their highly stable D8 secondary structures rule out the possibility of pseudogenes. These taxa are the only ones in which interspecific hybridization was reported. We discuss how evolutionary rates may be affected in nuclear relative to mitochondrial genes after hybridization, by selective or mutational processes such as gene silencing and concerted evolution.

  20. Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis.

    Directory of Open Access Journals (Sweden)

    Germán Añez

    Full Text Available West Nile virus (WNV, an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03. We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006-2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999-2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006-2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10(-4 substitutions/site/year (s/s/y. The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific

  1. Further Results on Dynamic Additive Hazard Rate Model

    Directory of Open Access Journals (Sweden)

    Zhengcheng Zhang

    2014-01-01

    Full Text Available In the past, the proportional and additive hazard rate models have been investigated in the works. Nanda and Das (2011 introduced and studied the dynamic proportional (reversed hazard rate model. In this paper we study the dynamic additive hazard rate model, and investigate its aging properties for different aging classes. The closure of the model under some stochastic orders has also been investigated. Some examples are also given to illustrate different aging properties and stochastic comparisons of the model.

  2. The effect of network structure on innovation initiation process: an evolutionary dynamics approach

    CERN Document Server

    Jafari, Afshin; Zolfagharzadeh, Mohammad Mahdi; Mohammadi, Mehdi

    2016-01-01

    In this paper we have proposed a basic agent-based model based on evolutionary dynamics for investigating innovation initiation process. In our model we suppose each agent will represent a firm which is interacting with other firms through a given network structure. We consider a two-hit process for presenting a potentially successful innovation in this model and therefore at each time step each firm can be in on of three different stages which are respectively, Ordinary, Innovative, and Successful. We design different experiments in order to investigate how different interaction networks may affect the process of presenting a successful innovation to the market. In this experiments, we use five different network structures, i.e. Erd\\H{o}s and R\\'enyi, Ring Lattice, Small World, Scale-Free and Distance-Based networks. According to the results of the simulations, for less frequent innovations like radical innovation, local structures are showing a better performance comparing to Scale-Free and Erd\\H{o}s and R\\...

  3. Firms' Decision Making Process in an Evolutionary Model of Industrial Dynamics

    Science.gov (United States)

    Kwasnicki, Witold

    Evolutionary model of industrial dynamics, presented in this paper, can be classified as Schumpeterian one. The model describes the behaviour of a number of competing firms producing functionally equivalent products. Each firm tries to improve its position in the industry and in the market by introducing innovations in order to minimize the unit costs of production, maximize the productivity of capital, and maximize the competitiveness of its products on the market. The problem how decisions are made seems to be crucial for relevant modelling of socio-economic processes. The main aim of the simulations presented in the second part of the paper is to show how fluctuations and discontinuities occurs in economic processes due to boundedly rational decisions of competing firms. It is shown how fluctuation of 3-6 years and of 10 years periodicity can occur in an industry development because of firms' bounded rationality. Long waves of development of 50-60 years period (Kondratieff cycles) occur in the model because of radical innovation emergence at the maturity phase of an `old' technology.

  4. Evolutionary dynamics of strategic behavior in a collective-risk dilemma.

    Directory of Open Access Journals (Sweden)

    Maria Abou Chakra

    Full Text Available A collective-risk social dilemma arises when a group must cooperate to reach a common target in order to avoid the risk of collective loss while each individual is tempted to free-ride on the contributions of others. In contrast to the prisoners' dilemma or public goods games, the collective-risk dilemma encompasses the risk that all individuals lose everything. These characteristics have potential relevance for dangerous climate change and other risky social dilemmas. Cooperation is costly to the individual and it only benefits all individuals if the common target is reached. An individual thus invests without guarantee that the investment is worthwhile for anyone. If there are several subsequent stages of investment, it is not clear when individuals should contribute. For example, they could invest early, thereby signaling their willingness to cooperate in the future, constantly invest their fair share, or wait and compensate missing contributions. To investigate the strategic behavior in such situations, we have simulated the evolutionary dynamics of such collective-risk dilemmas in a finite population. Contributions depend individually on the stage of the game and on the sum of contributions made so far. Every individual takes part in many games and successful behaviors spread in the population. It turns out that constant contributors, such as constant fair sharers, quickly lose out against those who initially do not contribute, but compensate this in later stages of the game. In particular for high risks, such late contributors are favored.

  5. Pre- versus post-mass extinction divergence of Mesozoic marine reptiles dictated by time-scale dependence of evolutionary rates.

    Science.gov (United States)

    Motani, Ryosuke; Jiang, Da-Yong; Tintori, Andrea; Ji, Cheng; Huang, Jian-Dong

    2017-05-17

    The fossil record of a major clade often starts after a mass extinction even though evolutionary rates, molecular or morphological, suggest its pre-extinction emergence (e.g. squamates, placentals and teleosts). The discrepancy is larger for older clades, and the presence of a time-scale-dependent methodological bias has been suggested, yet it has been difficult to avoid the bias using Bayesian phylogenetic methods. This paradox raises the question of whether ecological vacancies, such as those after mass extinctions, prompt the radiations. We addressed this problem by using a unique temporal characteristic of the morphological data and a high-resolution stratigraphic record, for the oldest clade of Mesozoic marine reptiles, Ichthyosauromorpha. The evolutionary rate was fastest during the first few million years of ichthyosauromorph evolution and became progressively slower over time, eventually becoming six times slower. Using the later slower rates, estimates of divergence time become excessively older. The fast, initial rate suggests the emergence of ichthyosauromorphs after the end-Permian mass extinction, matching an independent result from high-resolution stratigraphic confidence intervals. These reptiles probably invaded the sea as a new ecosystem was formed after the end-Permian mass extinction. Lack of information on early evolution biased Bayesian clock rates. © 2017 The Author(s).

  6. Exchange rate movements and export market dynamics: evidence from China

    National Research Council Canada - National Science Library

    Xiaobing Huang

    2017-01-01

    This paper highlights the relationship between foreign exchange rate fluctuations and firms' export market dynamics using a Chinese firm-level production data and a firm-level trade data over the period of 2000-2006...

  7. Portfolio separation and the dynamics of bank Iiterest rates

    NARCIS (Netherlands)

    Dia, E.; Giuliodori, M.

    2012-01-01

    We develop a dynamic model of the interest rates of a monopolistic bank, providing both intermediation and payment services. We obtain testable restrictions on portfolio separation from the dynamic terms of the reduced-form solutions, and test the model using balance-sheet data from large banks of

  8. Temporal dynamics of high repetition rate pulsed single longitudinal ...

    Indian Academy of Sciences (India)

    Theoretical and experimental studies of temporal dynamics of grazing incidence grating (GIG) cavity, single-mode dye laser pumped by high repetition rate copper vapour laser (CVL) are presented. Spectral chirp of the dye laser as they evolve in the cavity due to transient phase dynamics of the amplifier gain medium is ...

  9. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data

    Science.gov (United States)

    Xu, Kuipeng; Tang, Xianghai; Wang, Lu; Yu, Xinzi; Sun, Peipei; Mao, Yunxiang

    2017-08-01

    Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology ((( Bangia, Porphyra ) Pyropia ) Wildemania ). Molecular dating indicates that Bangiales diversified approximately 246.40 million years ago (95% highest posterior density (HPD)= 194.78u2013318.24 Ma, posterior probability (PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland (currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversification in Bangiales relative to Florideophyceae. Compared with Viridiplantae (green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome (ptDNA) and 15-fold for mitochondrial genome (mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.

  10. Heterogeneous evolutionary rates of Pi2/9 homologs in rice

    OpenAIRE

    Wu, Kejing; Xu, Ting; Guo, Changjiang; Zhang, Xiaohui; Yang, Sihai

    2012-01-01

    Abstract Background The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome. Although three functional R-genes have been cloned from this locus, little is known about the origin and evolutionary history of these genes. Herein, an extensive genome-wide survey of Pi2/9 homologs in rice, sorghum, Brachypodium and Arabidopsis, was conducted to explore this theme. Results In our study, 1, 1, 5 and 156 Pi2/9 homologs were detected in Arabidop...

  11. Effective dynamics along given reaction coordinates, and reaction rate theory.

    Science.gov (United States)

    Zhang, Wei; Hartmann, Carsten; Schütte, Christof

    2016-12-22

    In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: we first show that if we start with an ergodic diffusion process whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Mori-Zwanzig, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.

  12. Dynamically weighted evolutionary ordinal neural network for solving an imbalanced liver transplantation problem.

    Science.gov (United States)

    Dorado-Moreno, Manuel; Pérez-Ortiz, María; Gutiérrez, Pedro A; Ciria, Rubén; Briceño, Javier; Hervás-Martínez, César

    2017-03-01

    Create an efficient decision-support model to assist medical experts in the process of organ allocation in liver transplantation. The mathematical model proposed here uses different sources of information to predict the probability of organ survival at different thresholds for each donor-recipient pair considered. Currently, this decision is mainly based on the Model for End-stage Liver Disease, which depends only on the severity of the recipient and obviates donor-recipient compatibility. We therefore propose to use information concerning the donor, the recipient and the surgery, with the objective of allocating the organ correctly. The database consists of information concerning transplants conducted in 7 different Spanish hospitals and the King's College Hospital (United Kingdom). The state of the patients is followed up for 12 months. We propose to treat the problem as an ordinal classification one, where we predict the organ survival at different thresholds: less than 15 days, between 15 and 90 days, between 90 and 365 days and more than 365 days. This discretization is intended to produce finer-grain survival information (compared with the common binary approach). However, it results in a highly imbalanced dataset in which more than 85% of cases belong to the last class. To solve this, we combine two approaches, a cost-sensitive evolutionary ordinal artificial neural network (ANN) (in which we propose to incorporate dynamic weights to make more emphasis on the worst classified classes) and an ordinal over-sampling technique (which adds virtual patterns to the minority classes and thus alleviates the imbalanced nature of the dataset). The results obtained by our proposal are promising and satisfactory, considering the overall accuracy, the ordering of the classes and the sensitivity of minority classes. In this sense, both the dynamic costs and the over-sampling technique improve the base results of the considered ANN-based method. Comparing our model with

  13. Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus.

    Science.gov (United States)

    Zhu, Henan; Hughes, Joseph; Murcia, Pablo R

    2015-05-01

    Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼ 700 million. Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating

  14. Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus

    Science.gov (United States)

    Black, Allison; Breyta, Rachel; Bedford, Trevor; Kurath, Gael

    2016-01-01

    Infectious hematopoietic necrosis virus (IHNV) is a negative-sense RNA virus that infects wild and cultured salmonids throughout the Pacific Coastal United States and Canada, from California to Alaska. Although infection of adult fish is usually asymptomatic, juvenile infections can result in high mortality events that impact salmon hatchery programs and commercial aquaculture. We used epidemiological case data and genetic sequence data from a 303 nt portion of the viral glycoprotein gene to study the evolutionary dynamics of U genogroup IHNV in the Pacific Northwestern United States from 1971 to 2013. We identified 114 unique genotypes among 1,219 U genogroup IHNV isolates representing 619 virus detection events. We found evidence for two previously unidentified, broad subgroups within the U genogroup, which we designated ‘UC’ and ‘UP’. Epidemiologic records indicated that UP viruses were detected more frequently in sockeye salmon (Oncorhynchus nerka) and in coastal waters of Washington and Oregon, whereas UC viruses were detected primarily in Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, which is a large, complex watershed extending throughout much of interior Washington, Oregon, and Idaho. These findings were supported by phylogenetic analysis and by FST. Ancestral state reconstruction indicated that early UC viruses in the Columbia River Basin initially infected sockeye salmon but then emerged via host shifts into Chinook salmon and steelhead trout sometime during the 1980s. We postulate that the development of these subgroups within U genogroup was driven by selection pressure for viral adaptation to Chinook salmon and steelhead trout within the Columbia River Basin.

  15. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014

    Science.gov (United States)

    Pang, Yong Kek; Chan, Kok Gan; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012–2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors—total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012–2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013–2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion

  16. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.

    Science.gov (United States)

    Oong, Xiang Yong; Ng, Kim Tien; Lam, Tommy Tsan-Yuk; Pang, Yong Kek; Chan, Kok Gan; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore

  17. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.

    Directory of Open Access Journals (Sweden)

    Xiang Yong Oong

    Full Text Available Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1% patients infected with at least one respiratory virus, 287 (14.3% and 183 (9.1% samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10. Phylogenetic reconstruction of haemagglutinin (HA gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%, Yamagata Clade 2 (48, 28.6% and Victoria Clade 1 (55, 32.7%. With neuraminidase (NA phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1 and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013, and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014. Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013, with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and

  18. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  19. Evolutionary dynamics and temporal/geographical correlates of recombination in the human enterovirus echovirus types 9, 11, and 30.

    Science.gov (United States)

    McWilliam Leitch, E C; Cabrerizo, M; Cardosa, J; Harvala, H; Ivanova, O E; Kroes, A C M; Lukashev, A; Muir, P; Odoom, J; Roivainen, M; Susi, P; Trallero, G; Evans, D J; Simmonds, P

    2010-09-01

    The relationship between virus evolution and recombination in species B human enteroviruses was investigated through large-scale genetic analysis of echovirus type 9 (E9) and E11 isolates (n = 85 and 116) from 16 European, African, and Asian countries between 1995 and 2008. Cluster 1 E9 isolates and genotype D5 and A E11 isolates showed evidence of frequent recombination between the VP1 and 3Dpol regions, the latter falling into 23 (E9) and 43 (E11) clades interspersed phylogenetically with 46 3Dpol clades of E30 and with those of other species B serotypes. Remarkably, only 2 of the 112 3Dpol clades were shared by more than one serotype (E11 and E30), demonstrating an extremely large and genetically heterogeneous recombination pool of species B nonstructural-region variants. The likelihood of recombination increased with geographical separation and time, and both were correlated with VP1 divergence, whose substitution rates allowed recombination half-lives of 1.3, 9.8, and 3.1 years, respectively, for E9, E11, and E30 to be calculated. These marked differences in recombination dynamics matched epidemiological patterns of periodic epidemic cycles of 2 to 3 (E9) and 5 to 6 (E30) years and the longer-term endemic pattern of E11 infections. Phylotemporal analysis using a Bayesian Markov chain Monte Carlo method, which placed recombination events within the evolutionary reconstruction of VP1, showed a close relationship with VP1 lineage expansion, with defined recombination events that correlated with their epidemiological periodicity. Whether recombination events contribute directly to changes in transmissibility that drive epidemic behavior or occur stochastically during periodic population bottlenecks is an unresolved issue vital to future understanding of enterovirus molecular epidemiology and pathogenesis.

  20. Evolutionary Dynamics and Temporal/Geographical Correlates of Recombination in the Human Enterovirus Echovirus Types 9, 11, and 30▿

    Science.gov (United States)

    McWilliam Leitch, E. C.; Cabrerizo, M.; Cardosa, J.; Harvala, H.; Ivanova, O. E.; Kroes, A. C. M.; Lukashev, A.; Muir, P.; Odoom, J.; Roivainen, M.; Susi, P.; Trallero, G.; Evans, D. J.; Simmonds, P.

    2010-01-01

    The relationship between virus evolution and recombination in species B human enteroviruses was investigated through large-scale genetic analysis of echovirus type 9 (E9) and E11 isolates (n = 85 and 116) from 16 European, African, and Asian countries between 1995 and 2008. Cluster 1 E9 isolates and genotype D5 and A E11 isolates showed evidence of frequent recombination between the VP1 and 3Dpol regions, the latter falling into 23 (E9) and 43 (E11) clades interspersed phylogenetically with 46 3Dpol clades of E30 and with those of other species B serotypes. Remarkably, only 2 of the 112 3Dpol clades were shared by more than one serotype (E11 and E30), demonstrating an extremely large and genetically heterogeneous recombination pool of species B nonstructural-region variants. The likelihood of recombination increased with geographical separation and time, and both were correlated with VP1 divergence, whose substitution rates allowed recombination half-lives of 1.3, 9.8, and 3.1 years, respectively, for E9, E11, and E30 to be calculated. These marked differences in recombination dynamics matched epidemiological patterns of periodic epidemic cycles of 2 to 3 (E9) and 5 to 6 (E30) years and the longer-term endemic pattern of E11 infections. Phylotemporal analysis using a Bayesian Markov chain Monte Carlo method, which placed recombination events within the evolutionary reconstruction of VP1, showed a close relationship with VP1 lineage expansion, with defined recombination events that correlated with their epidemiological periodicity. Whether recombination events contribute directly to changes in transmissibility that drive epidemic behavior or occur stochastically during periodic population bottlenecks is an unresolved issue vital to future understanding of enterovirus molecular epidemiology and pathogenesis. PMID:20610722

  1. Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus.

    Science.gov (United States)

    Suzuki, Yutaro; Tomozawa, Morihiko; Koizumi, Yuki; Tsuchiya, Kimiyuki; Suzuki, Hitoshi

    2015-09-15

    Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7-10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11-16 % and 22-32 %, respectively, for A. argenteus, and 12-17 % and 17-24 %, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1 %/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11-17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1 %/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. The faster and slower evolutionary rates of Cytb can account for

  2. Co-Evolutionary Mechanisms of Emotional Bursts in Online Social Dynamics and Networks

    Directory of Open Access Journals (Sweden)

    Bosiljka Tadić

    2013-11-01

    Full Text Available Collective emotional behavior of users is frequently observed on various Web portals; however, its complexity and the role of emotions in the acting mechanisms are still not thoroughly understood. In this work, using the empirical data and agent-based modeling, a parallel analysis is performed of two archetypal systems—Blogs and Internet-Relayed-Chats—both of which maintain self-organized dynamics but not the same communication rules and time scales. The emphasis is on quantifying the collective emotions by means of fractal analysis of the underlying processes as well as topology of social networks, which arise and co-evolve in these stochastic processes. The results reveal that two distinct mechanisms, which are based on different use of emotions (an emotion is characterized by two components, arousal and valence, are intrinsically associated with two classes of emergent social graphs. Their hallmarks are the evolution of communities in accordance with the excess of the negative emotions on popular Blogs, on one side, and smooth spreading of the Bot’s emotional impact over the entire hierarchical network of chats, on the other. Another emphasis of this work is on the understanding of nonextensivity of the emotion dynamics; it was found that, in its own way, each mechanism leads to a reduced phase space of the emotion components when the collective dynamics takes place. That a non-additive entropy describes emotion dynamics, is further confirmed by computing the q-generalized Kolmogorov-Sinai entropy rate in the empirical data of chats as well as in the simulations of interacting emotional agents and Bots.

  3. Augmented Ehrenfest dynamics yields a rate for surface hopping

    Science.gov (United States)

    Subotnik, Joseph E.

    2010-04-01

    We present a new algorithm for mixed quantum-classical dynamics that helps bridge the gap between mean-field (Ehrenfest) and surface-hopping dynamics by defining a natural rate of decoherence. In order to derive this decoherence result, we have expanded the number of independent variables in the usual Ehrenfest routine so that mixed quantum-classical derivatives are now propagated in time alongside the usual Ehrenfest variables. Having done so, we compute a unique rate of decoherence using two independent approaches: (i) by comparing the equations of motion for the joint nuclear-electronic probability density in phase space according to Ehrenfest dynamics versus partial Wigner transform dynamics and (ii) by introducing a frozen Gaussian interpretation of Ehrenfest dynamics which allows nuclear wave packets to separate. The first consequence of this work is a means to rigorously check the accuracy of standard Ehrenfest dynamics. Second, this paper suggests a nonadiabatic dynamics algorithm, whereby the nuclei are propagated on the mean-field (Ehrenfest) potential energy surface and undergo stochastic decoherence events. Our work resembles the surface-hopping algorithm of Schwartz and co-workers [J. Chem. Phys. 123, 234106 (2005)]—only now without any adjustable parameters. For the case of two electronic states, we present numerical results on the so-called "Tully problems" and emphasize that future numerical benchmarking is still needed. Future work will also treat the problem of three or more electronic states.

  4. Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia, a carnivorous plant with a minimal genome

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    Herrera-Estrella Alfredo

    2011-06-01

    Full Text Available Abstract Background The carnivorous plant Utricularia gibba (bladderwort is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of Arabidopsis. Bladderworts show an incredible diversity of forms surrounding a defined theme: tiny, bladder-like suction traps on terrestrial, epiphytic, or aquatic plants with a diversity of unusual vegetative forms. Utricularia plants, which are rootless, are also anomalous in physiological features (respiration and carbon distribution, and highly enhanced molecular evolutionary rates in chloroplast, mitochondrial and nuclear ribosomal sequences. Despite great interest in the genus, no genomic resources exist for Utricularia, and the substitution rate increase has received limited study. Results Here we describe the sequencing and analysis of the Utricularia gibba transcriptome. Three different organs were surveyed, the traps, the vegetative shoot bodies, and the inflorescence stems. We also examined the bladderwort transcriptome under diverse stress conditions. We detail aspects of functional classification, tissue similarity, nitrogen and phosphorus metabolism, respiration, DNA repair, and detoxification of reactive oxygen species (ROS. Long contigs of plastid and mitochondrial genomes, as well as sequences for 100 individual nuclear genes, were compared with those of other plants to better establish information on molecular evolutionary rates. Conclusion The Utricularia transcriptome provides a detailed genomic window into processes occurring in a carnivorous plant. It contains a deep representation of the complex metabolic pathways that characterize a putative minimal plant genome, permitting its use as a source of genomic information to explore the structural, functional, and evolutionary diversity of the genus. Vegetative shoots and traps are the most similar organs by functional classification of their transcriptome, the traps expressing hydrolytic enzymes for prey

  5. Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates.

    Science.gov (United States)

    Matos-Maraví, Pável

    2016-07-01

    Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. © 2016 The Author(s).

  6. Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.

    Science.gov (United States)

    Prudent, Xavier; Parra, Genis; Schwede, Peter; Roscito, Juliana G; Hiller, Michael

    2016-08-01

    The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3) computing a statistical significance. We demonstrate on large-scale simulated data and on real data that both new methods substantially improve the sensitivity to detect associations between phenotypic and genomic differences. We applied these new methods to detect genomic differences involved in the loss of vision in the blind mole rat and the cape golden mole, two independent subterranean mammals. Forward Genomics identified several genes that are enriched in functions related to eye development and the perception of light, as well as genes involved in the circadian rhythm. These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species. Source code: https://github.com/hillerlab/ForwardGenomics/. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  8. Molecular evolutionary and epidemiological dynamics of genotypes 1G and 2B of rubella virus.

    Directory of Open Access Journals (Sweden)

    Abinash Padhi

    Full Text Available Rubella Virus (RV, which causes measles-like rashes in children, puts millions of infants at risk of congenital defects across the globe. Employing phylogenetic approaches to the whole genome sequence data and E1 glycoprotein sequence data, the present study reports the substitution rates and dates of emergence of all thirteen previously described rubella genotypes, and gains important insights into the epidemiological dynamics of two geographically widely distributed genotypes 1G and 2B. The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10-3 substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family. Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD. Viral strains within the respective genotypes began diverging between the year 1930 s and 1980 s. Both genotype 1G and 2B have shown a decline in effective number of infections since 1990 s, a period during which mass immunization programs against RV were adapted across the globe. Although both genotypes showed some extent of spatial genetic structuring, the analyses also depicted an inter-continental viral dispersal. Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.

  9. 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......, the GSCM diffusion process is simulated by the model with a case study on Chinese automotive manufacturing industry. The results show that the subsidies for manufacturers are better than that for consumers to promote GSCM diffusion, and the environmental awareness is another influential key factor....

  10. 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...

  11. 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...

  12. An evolutionary model of energy transitions with interactive innovation-selection dynamics

    NARCIS (Netherlands)

    Safarzynska, K.E.; van den Bergh, J.C.J.M.

    2013-01-01

    We develop a stylized application of a new evolutionary model to study an energy transition in electricity production. The framework describes a population of boundedly rational electricity producers who decide each period on the allocation of profits among different energy technologies. They tend

  13. Polarization and Segregation through Conformity Pressure and Voluntary Migration: Simulation Analysis of Co-Evolutionary Dynamics

    Directory of Open Access Journals (Sweden)

    Dai Zusai

    2017-11-01

    Full Text Available While conformity pressures people to assimilate in a community, an individual occasionally migrates among communities when the individual feels discomfort. These two factors cause segregation and cultural diversity within communities in the society. By embedding a migration dynamic into Kuran and Sandholm’s model (2008 of preference evolution, we build an agent-based model to see how the variance of preferences in the entire society quantitatively changes over time. We find from the Monte-Carlo simulations that, while preferences assimilate within a community, self-selected migrations enlarge the diversity of preferences over communities in the society. We further study how the arrival rate of migration opportunities and the degree of conformity pressures affect the variance of preferences.

  14. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.

    Science.gov (United States)

    Katz, Lee S; Petkau, Aaron; Beaulaurier, John; Tyler, Shaun; Antonova, Elena S; Turnsek, Maryann A; Guo, Yan; Wang, Susana; Paxinos, Ellen E; Orata, Fabini; Gladney, Lori M; Stroika, Steven; Folster, Jason P; Rowe, Lori; Freeman, Molly M; Knox, Natalie; Frace, Mike; Boncy, Jacques; Graham, Morag; Hammer, Brian K; Boucher, Yan; Bashir, Ali; Hanage, William P; Van Domselaar, Gary; Tarr, Cheryl L

    2013-07-02

    Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics. Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to

  15. The evolutionary synchronization of the exchange rate system in ASEAN+6

    Science.gov (United States)

    Feng, Xiaobing; Hu, Haibo; Wang, Xiaofan

    2010-12-01

    Although there are extensive researches on the behavior of the world currency network, the complexity of the Asian regional currency system is not well understood regardless of its importance. Using daily exchange rates this paper examines exchange rate co-movements in the region before and after the China exchange rate reform. It was found that the correlation between Asian currencies and the US Dollar, the previous regional key currency has become weaker and intra-Asia interactions have increased. Cross sample entropy and cross entropy approaches are also applied to examine the synchrony behavior among the Asian currencies. The study also shows that the Asian exchange rate markets featured are neither stochastic nor efficient. These findings may shed some light on the in-depth understanding of collective behaviors in a regional currency network; they will also lay a theoretical foundation for further policy formulation in Asian currency integration.

  16. Comparison of pitch rate history effects on dynamic stall

    Science.gov (United States)

    Chandrasekhara, M. S.; Carr, Lawrence W.; Ahmed, S.

    1992-01-01

    Dynamic stall of an airfoil is a classic case of forced unsteady separated flow. Flow separation is brought about by large incidences introduced by the large amplitude unsteady pitching motion of an airfoil. One of the parameters that affects the dynamic stall process is the history of the unsteady motion. In addition, the problem is complicated by the effects of compressibility that rapidly appear over the airfoil even at low Mach numbers at moderately high angles of attack. Consequently, it is of interest to know the effects of pitch rate history on the dynamic stall process. This abstract compares the results of a flow visualization study of the problem with two different pitch rate histories, namely, oscillating airfoil motion and a linear change in the angle of attack due to a transient pitching motion.

  17. Implications of Exchange Rate Dynamics and External Reserve for ...

    African Journals Online (AJOL)

    In this paper, we examined the impact of exchange rate dynamics and external reserve on inflation and investment in Nigeria between the period 1970 – 2009, using a combination of ordinary least squares, augmented dickey fuller unit root test and the co- integration test. The changes in external reserve had a positive ...

  18. The growth rates and population dynamics of bivalves in estuaries ...

    African Journals Online (AJOL)

    The growth rates and population dynamics of bivalves in estuaries and shallow seas in the. Northern Hemisphere have been extensively studied. In these regions bivalves occur in densities up to 7 fm/ml (Stephen 1928) and densities of 1 fm/ml are common. Further, growth studies on these animals have been facilitated by ...

  19. Population dynamics of metastable growth-rate phenotypes.

    Directory of Open Access Journals (Sweden)

    Lindsay S Moore

    Full Text Available Neo-Darwinian evolution has presented a paradigm for population dynamics built on random mutations and selection with a clear separation of time-scales between single-cell mutation rates and the rate of reproduction. Laboratory experiments on evolving populations until now have concentrated on the fixation of beneficial mutations. Following the Darwinian paradigm, these experiments probed populations at low temporal resolution dictated by the rate of rare mutations, ignoring the intermediate evolving phenotypes. Selection however, works on phenotypes rather than genotypes. Research in recent years has uncovered the complexity of genotype-to-phenotype transformation and a wealth of intracellular processes including epigenetic inheritance, which operate on a wide range of time-scales. Here, by studying the adaptation dynamics of genetically rewired yeast cells, we show a novel type of population dynamics in which the intracellular processes intervene in shaping the population structure. Under constant environmental conditions, we measure a wide distribution of growth rates that coexist in the population for very long durations (>100 generations. Remarkably, the fastest growing cells do not take over the population on the time-scale dictated by the width of the growth-rate distributions and simple selection. Additionally, we measure significant fluctuations in the population distribution of various phenotypes: the fraction of exponentially-growing cells, the distributions of single-cell growth-rates and protein content. The observed fluctuations relax on time-scales of many generations and thus do not reflect noisy processes. Rather, our data show that the phenotypic state of the cells, including the growth-rate, for large populations in a constant environment is metastable and varies on time-scales that reflect the importance of long-term intracellular processes in shaping the population structure. This lack of time-scale separation between the

  20. The Pharmaco –, Population and Evolutionary Dynamics of Multi-drug Therapy: Experiments with S. aureus and E. coli and Computer Simulations

    Science.gov (United States)

    Ankomah, Peter; Johnson, Paul J. T.; Levin, Bruce R.

    2013-01-01

    There are both pharmacodynamic and evolutionary reasons to use multiple rather than single antibiotics to treat bacterial infections; in combination antibiotics can be more effective in killing target bacteria as well as in preventing the emergence of resistance. Nevertheless, with few exceptions like tuberculosis, combination therapy is rarely used for bacterial infections. One reason for this is a relative dearth of the pharmaco-, population- and evolutionary dynamic information needed for the rational design of multi-drug treatment protocols. Here, we use in vitro pharmacodynamic experiments, mathematical models and computer simulations to explore the relative efficacies of different two-drug regimens in clearing bacterial infections and the conditions under which multi-drug therapy will prevent the ascent of resistance. We estimate the parameters and explore the fit of Hill functions to compare the pharmacodynamics of antibiotics of four different classes individually and in pairs during cidal experiments with pathogenic strains of Staphylococcus aureus and Escherichia coli. We also consider the relative efficacy of these antibiotics and antibiotic pairs in reducing the level of phenotypically resistant but genetically susceptible, persister, subpopulations. Our results provide compelling support for the proposition that the nature and form of the interactions between drugs of different classes, synergy, antagonism, suppression and additivity, has to be determined empirically and cannot be inferred from what is known about the pharmacodynamics or mode of action of these drugs individually. Monte Carlo simulations of within-host treatment incorporating these pharmacodynamic results and clinically relevant refuge subpopulations of bacteria indicate that: (i) the form of drug-drug interactions can profoundly affect the rate at which infections are cleared, (ii) two-drug therapy can prevent treatment failure even when bacteria resistant to single drugs are present

  1. 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

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

    Directory of Open Access Journals (Sweden)

    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

  3. 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

  4. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  5. An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses

    OpenAIRE

    Drake John M; Roche Benjamin; Rohani Pejman

    2011-01-01

    Abstract Background Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to co...

  6. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

    OpenAIRE

    Yasir H. Ahmed-Braimah; Unckless, Robert L.; Clark, Andrew G.

    2017-01-01

    Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of P...

  7. Asymmetric acceleration/deceleration dynamics in heart rate variability

    Science.gov (United States)

    Alvarez-Ramirez, J.; Echeverria, J. C.; Meraz, M.; Rodriguez, E.

    2017-08-01

    The heart rate variability (HRV) is an important physiological signal used either to assess the risk of cardiac death or to model the cardiovascular regulatory dynamics. Asymmetries in HRV data have been observed using 2D Poincare plots, which have been linked to a non-equilibrium operation of the cardiac autonomic system. This work further explores the presence of asymmetries but in the serial correlations of the dynamics of HRV data. To this end, detrended fluctuation analysis (DFA) was used to estimate the Hurst exponent both when the heart rate is accelerating and when it is decelerating. The analysis is conducted using data collected from subjects under normal sinus rhythm (NSR), congestive heart failure (CHF) and atrial fibrillation (AF) . For the NSR cases, it was found that correlations are stronger (p behavior was detected for the CHF and AF patients. Possible links between asymmetric correlations in the dynamics and the mechanisms controlling the operation of the heart rate are discussed, as well as their implications for modeling the cardiovascular regulatory dynamics.

  8. Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility.

    Science.gov (United States)

    Fischer, Valentin; Bardet, Nathalie; Benson, Roger B J; Arkhangelsky, Maxim S; Friedman, Matt

    2016-03-08

    Despite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.

  9. Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation

    Directory of Open Access Journals (Sweden)

    Yi Soojin V

    2009-05-01

    Full Text Available Abstract Background Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes. Results We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential amplicons from putatively neutral, non-coding, non-repetitive regions of these genomes. Subsequently we amplified, using experimental methods, many of these amplicons from diverse primate taxa, including a ring-tailed lemur, which is distantly related to the genomic resources. Using a subset of 10 markers, we demonstrate the utility of the developed markers in phylogenetic and evolutionary rate analyses. Particularly, we uncovered substantial evolutionary rate variation among lineages, some of which are previously not reported. Conclusion We successfully developed numerous markers from putatively neutral regions of primate genomes using a strategy combining computational and experimental methods. Applying these markers to phylogenetic and evolutionary rate variation analyses exemplifies the utility of these markers. Diverse ecological and evolutionary analyses will benefit from these markers. Importantly, methods similar to those presented here can be applied to other taxa in the near future.

  10. Evolutionary sequences for Nova V1974 Cygni using new nuclear reaction rates and opacities

    Science.gov (United States)

    Starrfield, S.; Truran, J. W.; Wiescher, M. C.; Sparks, W. M.

    1998-05-01

    The outburst of Nova V1974 Cyg 1992 is arguably the best observed of this century, with realistic estimates now available for the amount of mass ejected, the composition of the ejecta and the total energy budget. These data strongly support the conclusion that this was indeed a `neon' nova that occurred on an oxygen, neon, magnesium white dwarf. In addition, X-ray studies of its outburst imply that the mass of the white dwarf is about 1.25Msolar. We, therefore, report on the results of new calculations of thermonuclear runaways on 1.25-Msolar oxygen, neon, magnesium white dwarfs, using our one-dimensional, fully implicit, hydrodynamic stellar evolution code that includes a large nuclear reaction network. We have updated the nuclear reaction network, with the inclusion of new and improved experimental and theoretical determinations of the nuclear reaction rates. We have also incorporated the OPAL carbon rich tables and have investigated the effects of changes in convective efficiency on the evolution. Our results show that the changes in the reaction rates and opacities that we have introduced produce important changes with respect to our previous studies. For example, relevant to nucleosynthesis considerations, a smaller amount of ^26Al is produced, while the abundances of ^31P and ^32S increase by factors of more than two. This change is attributed to the increased proton-capture reaction rates for some of the intermediate mass nuclei near ^26Al and beyond, such that nuclear fusion to higher mass nuclei is enhanced. The characteristics of our models are then compared to observations of the outburst of V1974 Cyg 1992 and we find that the predicted amount of mass ejected is at least a factor of 10 less than observed. The low values for the amount of ejected mass are a consequence of the fact that the OPAL opacities are larger than those we previously used, which results in less mass being accreted on to the white dwarf. This is a general problem with respect to the

  11. Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes.

    Science.gov (United States)

    Yokoyama, Shozo; Starmer, William T; Liu, Yang; Tada, Takashi; Britt, Lyle

    2014-01-15

    Aquatic organisms such as cichlids, coelacanths, seals, and cetaceans are active in UV-blue color environments, but many of them mysteriously lost their abilities to detect these colors. The loss of these functions is a consequence of the pseudogenization of their short wavelength-sensitive (SWS1) opsin genes without gene duplication. We show that the SWS1 gene (BdenS1ψ) of the deep-sea fish, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years ago (Mya) yet it is still transcribed. The rates of nucleotide substitution (~1.4 × 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes. © 2013 Elsevier B.V. All rights reserved.

  12. The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions.

    Directory of Open Access Journals (Sweden)

    Manqiong Yuan

    Full Text Available Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance.176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10(-3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure.Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.

  13. Short-run Exchange-Rate Dynamics: Theory and Evidence

    DEFF Research Database (Denmark)

    Carlson, John A.; Dahl, Christian Møller; Osler, Carol L.

    Recent research has revealed a wealth of information about the microeconomics of currency markets and thus the determination of exchange rates at short horizons. This information is valuable to us as scientists since, like evidence of macroeconomic regularities, it can provide critical guidance...... for designing exchange-rate models. This paper presents an optimizing model of short-run exchange-rate dynamics consistent with both the micro evidence and the macro evidence, the first such model of which we are aware. With respect to microeconomics, the model is consistent with the institutional structure...... of currency markets, it accurately reflects the constraints and objectives faced by the major participants, and it fits key stylized facts concerning returns and order flow. With respect to macroeconomics, the model is consistent with most of the major puzzles that have emerged under floating rates....

  14. Peptide dimerization-dissociation rates from replica exchange molecular dynamics

    Science.gov (United States)

    Leahy, Cathal T.; Kells, Adam; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

    2017-10-01

    We show how accurate rates of formation and dissociation of peptide dimers can be calculated using direct transition counting (DTC) from replica-exchange molecular dynamics (REMD) simulations. First, continuous trajectories corresponding to system replicas evolving at different temperatures are used to assign conformational states. Second, we analyze the entire REMD data to calculate the corresponding rates at each temperature directly from the number of transition counts. Finally, we compare the kinetics extracted directly, using the DTC method, with indirect estimations based on trajectory likelihood maximization using short-time propagators and on decay rates of state autocorrelation functions. For systems with relatively low-dimensional intrinsic conformational dynamics, the DTC method is simple to implement and leads to accurate temperature-dependent rates. We apply the DTC rate-extraction method to all-atom REMD simulations of dimerization of amyloid-forming NNQQ tetrapetides in explicit water. In an assessment of the REMD sampling efficiency with respect to standard MD, we find a gain of more than a factor of two at the lowest temperature.

  15. Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability.

    Science.gov (United States)

    Fernandez-Rodriguez, Jesus; Yang, Lei; Gorochowski, Thomas E; Gordon, D Benjamin; Voigt, Christopher A

    2015-12-18

    Genetic memory can be implemented using enzymes that catalyze DNA inversions, where each orientation corresponds to a "bit". Here, we use two DNA invertases (FimE and HbiF) that reorient DNA irreversibly between two states with opposite directionality. First, we construct memory that is set by FimE and reset by HbiF. Next, we build a NOT gate where the input promoter drives FimE and in the absence of signal the reverse state is maintained by the constitutive expression of HbiF. The gate requires ∼3 h to turn on and off. The evolutionary stabilities of these circuits are measured by passaging cells while cycling function. The memory switch is stable over 400 h (17 days, 14 state changes); however, the gate breaks after 54 h (>2 days) due to continuous invertase expression. Genome sequencing reveals that the circuit remains intact, but the host strain evolves to reduce invertase expression. This work highlights the need to evaluate the evolutionary robustness and failure modes of circuit designs, especially as more complex multigate circuits are implemented.

  16. 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.

  17. 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

  18. Testability of evolutionary game dynamics models based on experimental economics data

    CERN Document Server

    Wang, Yijia; Wang, Zhijian

    2016-01-01

    In order to better understand the dynamic processes of a real game system, we need an appropriate dynamics model, so to evaluate the validity of a model is not a trivial task. Here, we demonstrate an approach, considering the dynamic patterns of angular momentum and speed as the measurement variables, for evaluating the validity of various dynamics models. Using the data in real time Rock-Paper-Scissors (RPS) games experiments, we obtain the experimental patterns, and then derive the related theoretical patterns from a series of typical dynamics models respectively. By testing the goodness-of-fit between the experimental and theoretical patterns, the validity of the models can be evaluated. One of the results is that, among all the non-parametric models tested, the best-known Replicator dynamics model performs almost worst, while the Projection dynamics model performs best. Besides providing new empirical patterns of social dynamics, we demonstrate that the approach can be an effective and rigorous method to ...

  19. Dynamics of Two Populations with Different Birth Rates

    Science.gov (United States)

    Hoffmann, Julia; Pekalski, Andrzej

    We propose a simple model describing the dynamics of a system of two populations — more numerous natives and less numerous immigrants. The immigrants' birth rate is higher than that of the natives. Several modifications of this model taking into account changes of the birth rates due to external factors and/or possibility of contacts between the populations, are also introduced. The model is studied within two approaches — by solving a set of differential equations and through a Monte Carlo simulations. We show that the question of which population will eventually dominate depends on such factors as the probability of producing offsprings of mixed origin, assimilation of the immigrants, the ratio of the birth rates, initial numbers of the populations and the average age of an individual. In all, but two extreme cases, both populations will survive.

  20. Evolutionary dynamics of rRNA gene clusters in cichlid fish

    Directory of Open Access Journals (Sweden)

    Nakajima Rafael T

    2012-10-01

    Full Text Available Abstract Background Among multigene families, ribosomal RNA (rRNA genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. Results The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. Conclusions The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a

  1. The coordination aspect of institutions in the context of an evolutionary approach to economic dynamics

    Directory of Open Access Journals (Sweden)

    Zoran Stefanovic

    2015-08-01

    Full Text Available The paper provides an insight into the dominant trends of contemporary evolutionary economics and outlines the important issues related to the articulation of this approach in thinking about the economy. The paper also affirms a proposition on institutions as carrier structures of socio-economic evolution, whose numerous effects at the societal level are decoded through the coordination function. In addition to the market, the process of coordination also employs other non-market institutional structures, whose profile and operational principles are the product of the trajectories of cultural and historical evolution, different among social orders. Projects aimed at the transformation of the economic system are to be sensitized to an objectively conditioned diversity of the institutional structures of the world economy, and in this sense, should be very careful in the installation of „universal” reform solutions.

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

    Science.gov (United States)

    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 extending the memory for past happiness are both stronger in an environment where food is scarce; (ii) that in such an environment "relative consumption," in which the agent's well-being is negatively affected by that of its neighbors, is more detrimental to survival when food is scarce; and (iii) that having a positive outlook, under which agents' longer-term happiness is increased by positive events more than it is decreased by negative ones, is generally advantageous.

  3. Evolutionary dynamics of an at-rich satellite DNA and its contribution to karyotype differentiation in wild diploid Arachis species.

    Science.gov (United States)

    Samoluk, Sergio Sebastián; Robledo, Germán; Bertioli, David; Seijo, José Guillermo

    2017-04-01

    Satellite DNA (satDNA) is a major component of the heterochromatic regions of eukaryote genomes and usually shows a high evolutionary dynamic, even among closely related species. Section Arachis (genus Arachis) is composed of species belonging to six different genomes (A, B, D, F, G and K). The most distinguishing features among these genomes are the amount and distribution of the heterochromatin in the karyotypes. With the objective of gaining insight into the sequence composition and evolutionary dynamics of the heterochromatin fraction in Arachis, we investigated here the sequence diversity, genomic abundance, and chromosomal distribution of a satDNA family (ATR-2) among seven diploid species of section Arachis. All of the isolated sequences were AT-rich and highly conserved at both intraspecific and interspecific levels, without any species-specific polymorphism. Pairwise comparisons of isolated ATR-2 monomers revealed that most of the nucleotide sites were in the first two transitional stages of Strachan's model. However, the abundance of ATR-2 was significantly different among genomes according to the 'library hypothesis'. Fluorescent in situ hybridization revealed that ATR-2 is a main component of the DAPI + centromeric heterochromatin of the A, F, and K genomes. Thus, the evolution of the different heterochromatin patterns observed in Arachis genomes can be explained, at least in part, by the differential representation of ATR-2 among the different species or even among the chromosomes of the same complement. These findings are the first to demonstrate the participation of satDNA sequences in the karyotype diversification of wild diploid Arachis species.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate

    Science.gov (United States)

    Donaher, Natalie; Tanifuji, Goro; Onodera, Naoko T.; Malfatti, Stephanie A.; Chain, Patrick S. G.; Hara, Yoshiaki

    2009-01-01

    The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species Cryptomonas paramecium CCAP977/2a. The ∼78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 transfer RNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa, and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G + C content (38%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae and reveals features shared with the plastid genomes of other secondarily nonphotosynthetic eukaryotes. PMID:20333213

  6. Rowing Crew Coordination Dynamics at Increasing Stroke Rates.

    Science.gov (United States)

    Cuijpers, Laura S; Zaal, Frank T J M; de Poel, Harjo J

    2015-01-01

    In rowing, perfect synchronisation is important for optimal performance of a crew. Remarkably, a recent study on ergometers demonstrated that antiphase crew coordination might be mechanically more efficient by reducing the power lost to within-cycle velocity fluctuations of the boat. However, coupled oscillator dynamics predict the stability of the coordination to decrease with increasing stroke rate, which in case of antiphase may eventually yield breakdowns to in-phase. Therefore, this study examined the effects of increasing stroke rate on in- and antiphase crew coordination in rowing dyads. Eleven experienced dyads rowed on two mechanically coupled ergometers on slides, which allowed the ergometer system to move back and forth as one 'boat'. The dyads performed a ramp trial in both in- and antiphase pattern, in which stroke rates gradually increased from 30 strokes per minute (spm) to as fast as possible in steps of 2 spm. Kinematics of rowers, handles and ergometers were captured. Two dyads showed a breakdown of antiphase into in-phase coordination at the first stroke rate of the ramp trial. The other nine dyads reached between 34-42 spm in antiphase but achieved higher rates in in-phase. As expected, the coordinative accuracy in antiphase was worse than in in-phase crew coordination, while, somewhat surprisingly, the coordinative variability did not differ between the patterns. Whereas crew coordination did not substantially deteriorate with increasing stroke rate, stroke rate did affect the velocity fluctuations of the ergometers: fluctuations were clearly larger in the in-phase pattern than in the antiphase pattern, and this difference significantly increased with stroke rate. Together, these results suggest that although antiphase rowing is less stable (i.e., less resistant to perturbation), potential on-water benefits of antiphase over in-phase rowing may actually increase with stroke rate.

  7. Turning Rate Dynamics of Zebrafish Exposed to Ethanol

    Science.gov (United States)

    Mwaffo, Violet; Porfiri, Maurizio

    2015-06-01

    Zebrafish is emerging as a species of choice in alcohol-related pharmacological studies. In these studies, zebrafish are often exposed to acute ethanol treatments and their activity scored during behavioral assays. Computational modeling of zebrafish behavior is expected to positively impact these efforts by offering a predictive toolbox to plan hypothesis-driven studies, reduce the number of subjects, perform pilot trials, and refine behavioral screening. In this work, we demonstrate the use of the recently proposed jump persistent turning walker to model the turning rate dynamics of zebrafish exposed to acute ethanol administration. This modeling framework is based on a stochastic mean reverting jump process to capture the sudden and large changes in orientation of swimming zebrafish. The model is calibrated on an available experimental dataset of 40 subjects, tested at different ethanol concentrations. We demonstrate that model parameters are modulated by ethanol administration, whereby both the relaxation rate and jump frequency of the turning rate dynamics are influenced by ethanol concentration. This effort offers a first evidence for the possibility of complementing zebrafish pharmacological research with computational modeling of animal behavior.

  8. Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

    Directory of Open Access Journals (Sweden)

    Li Chun

    2012-01-01

    Full Text Available Abstract Background Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes, were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

  9. Nonparametric analysis of nonexponential and multidimensional kinetics. I. Quantifying rate dispersion, rate heterogeneity, and exchange dynamics

    Science.gov (United States)

    Berg, Mark A.; Kaur, Harveen

    2017-02-01

    The quantification of nonexponential (dispersed) kinetics has relied on empirical functions, which yield parameters that are neither unique nor easily related to the underlying mechanism. Multidimensional kinetics provide more information on dispersed processes, but a good approach to their analysis is even less clear than for standard, one-dimensional kinetics. This paper is the first in a series that analyzes kinetic data in one or many dimensions with a scheme that is nonparametric: it quantifies nonexponential decays without relying on a specific functional form. The quantities obtained are directly related to properties of the mechanism causing the rate dispersion. Log-moments of decays, which parallel the standard moments of distributions (mean, standard deviation, etc.), are introduced for both one- and multi-dimensional decays. Kinetic spectra are defined to visualize the data. The utility of this approach is demonstrated on a simple, but general, model of dispersed kinetics—a nonexponential homogeneous decay combined with slowly exchanging rate heterogeneity. The first log-moments give a geometric-mean relaxation time. Second log-moments quantify the magnitude of rate dispersion, the fraction of the dispersion due to heterogeneity, and the dynamics of exchange between different rate subensembles. A suitable combination of these moments isolates exchange dynamics from three-dimensional kinetics without contamination by the rate-filtering effects that were identified in a recent paper [M. A. Berg and J. R. Darvin, J. Chem. Phys. 145, 054119 (2016)].

  10. Dynamics of intrarenal pressures and glomerular filtration rate after acetazolamide

    DEFF Research Database (Denmark)

    Leyssac, P P; Karlsen, F M; Skøtt, O

    1991-01-01

    The dynamics of intrarenal pressures, early distal tubular fluid conductivity (EDC), and renal flood flow (RBF) were studied in rats given acetazolamide (ACZ), an inhibitor of proximal reabsorption. Glomerular filtration rate (GFR) and end-proximal flow were estimated by clearances of 51Cr......-EDTA and lithium. Proximal tubular pressure (Pprox) increased initially by 1.7 +/- 0.1 mmHg after ACZ, causing a decrease in the hydrostatic pressure difference across the glomerular membrane (delta P). EDC increased, and then RBF, glomerular capillary pressure (Pgc), Pprox, and star vessel pressures (Psv) dropped...

  11. Detecting brain dynamics during resting state: a tensor based evolutionary clustering approach

    Science.gov (United States)

    Al-sharoa, Esraa; Al-khassaweneh, Mahmood; Aviyente, Selin

    2017-08-01

    Human brain is a complex network with connections across different regions. Understanding the functional connectivity (FC) of the brain is important both during resting state and task; as disruptions in connectivity patterns are indicators of different psychopathological and neurological diseases. In this work, we study the resting state functional connectivity networks (FCNs) of the brain from fMRI BOLD signals. Recent studies have shown that FCNs are dynamic even during resting state and understanding the temporal dynamics of FCNs is important for differentiating between different conditions. Therefore, it is important to develop algorithms to track the dynamic formation and dissociation of FCNs of the brain during resting state. In this paper, we propose a two step tensor based community detection algorithm to identify and track the brain network community structure across time. First, we introduce an information-theoretic function to reduce the dynamic FCN and identify the time points that are similar topologically to combine them into a tensor. These time points will be used to identify the different FC states. Second, a tensor based spectral clustering approach is developed to identify the community structure of the constructed tensors. The proposed algorithm applies Tucker decomposition to the constructed tensors and extract the orthogonal factor matrices along the connectivity mode to determine the common subspace within each FC state. The detected community structure is summarized and described as FC states. The results illustrate the dynamic structure of resting state networks (RSNs), including the default mode network, somatomotor network, subcortical network and visual network.

  12. Unraveling the evolutionary dynamics of ancient and recent polypoidization events in Avena (Poaceae).

    Science.gov (United States)

    Liu, Qing; Lin, Lei; Zhou, Xiangying; Peterson, Paul M; Wen, Jun

    2017-02-03

    Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat.

  13. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum fiber transcriptome.

    Directory of Open Access Journals (Sweden)

    Mi-Jeong Yoo

    2014-01-01

    Full Text Available The single-celled cotton (Gossypium hirsutum fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ~5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution.

  14. A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

    Directory of Open Access Journals (Sweden)

    Guoqin Mai

    2016-01-01

    Full Text Available Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.

  15. The dynamic evolutionary history of genome size in North American woodland salamanders.

    Science.gov (United States)

    Newman, Catherine E; Gregory, T Ryan; Austin, Christopher C

    2017-04-01

    The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

  16. Unraveling the evolutionary dynamics of ancient and recent polypoidization events in Avena (Poaceae)

    Science.gov (United States)

    Liu, Qing; Lin, Lei; Zhou, Xiangying; Peterson, Paul M.; Wen, Jun

    2017-01-01

    Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat. PMID:28157193

  17. Extreme Selection Unifies Evolutionary Game Dynamics in Finite and Infinite Populations.

    Science.gov (United States)

    Della Rossa, Fabio; Dercole, Fabio; Vicini, Cristina

    2017-05-01

    We show that when selection is extreme-the fittest strategy always reproduces or is imitated-the unequivalence between the possible evolutionary game scenarios in finite and infinite populations resolves, in the sense that the three generic outcomes-dominance, coexistence, and mutual exclusion-emerge in well-mixed populations of any size. We consider the simplest setting of a 2-player-2-strategy symmetric game and the two most common microscopic definitions of strategy spreading-the frequency-dependent Moran process and the imitation process by pairwise comparison-both in the case allowing any intensity of selection. We show that of the seven different invasion and fixation scenarios that are generically possible in finite populations-fixation being more or less likely to occur and rapid compared to the neutral game-the three that are possible in large populations are the same three that occur for sufficiently strong selection: (1) invasion and fast fixation of one strategy; (2) mutual invasion and slow fixation of one strategy; (3) no invasion and no fixation. Moreover (and interestingly), in the limit of extreme selection 2 becomes mutual invasion and no fixation, a case not possible for finite intensity of selection that better corresponds to the deterministic case of coexistence. In the extreme selection limit, we also derive the large population deterministic limit of the two considered stochastic processes.

  18. Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens.

    Science.gov (United States)

    Wininger, Kerry; Rank, Nathan

    2017-11-01

    Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research. © 2017 New York Academy of Sciences.

  19. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

    Science.gov (United States)

    2010-01-01

    Background Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online. Results By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of γ-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed. Conclusions We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far. PMID:20181243

  20. The architecture of river networks can drive the evolutionary dynamics of aquatic populations.

    Science.gov (United States)

    Thomaz, Andréa T; Christie, Mark R; Knowles, L Lacey

    2016-03-01

    It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures and downstream flow regimes affect the genetic structure of populations situated within river networks. Irrespective of the river length, our results illustrate that the extent of river branching, confluence position, and levels of asymmetric downstream migration dictate patterns of genetic variation in riverine populations. Comparisons between simple and highly branched rivers show a 20-fold increase in the overall genetic diversity and a sevenfold increase in the genetic differentiation between local populations. Given that most rivers have complex architectures, these results highlight the importance of incorporating riverscape information into evolutionary models of aquatic species and could help explain why riverine fishes represent a disproportionately large amount of global vertebrate diversity per unit of habitable area. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  1. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

    Directory of Open Access Journals (Sweden)

    Luis eRubio

    2013-06-01

    Full Text Available RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. I A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. II Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. III Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. IV Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. V Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

  2. Understanding the dynamics of technological transitions. A co-evolutionary and socio-technical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Geels, F.W.

    2002-11-01

    This thesis is about Technological Transitions (TT), which are long-term and large-scale changes in socio- technical systems at the level of societal functions (e.g. transportation, communication, housing). The main research question is how TT come about. The thesis develops a conceptual perspective to understand TT. This perspective is multi-disciplinary, using insights from evolutionary economics, technology studies, and innovation studies. Insights from different disciplines are combined into a multi-level perspective, consisting of three levels: a micro-level of technological niches, a meso-level of socio-technical regimes and a macro-level of socio- technical landscape. The conceptual perspective is qualitative and appreciative. Another contribution of the thesis is to distinguish different patterns and mechanisms in TT. The conceptual perspective is illustrated with three case- studies: (a) the transition in aviation from propeller-piston engine aircraft to turbojets (1926-1975), (b) the transition in oceanic shipping from sailing ships to steamships (1780-1914), and (c) the transition in urban land transportation from horse-and-carriage to automobiles (1860-1930). These case-studies are not only used to illustrate the perspective, but also function as a source for further development of ideas.

  3. Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

    Directory of Open Access Journals (Sweden)

    Vanessa Rodrigues Paixão-Côrtes

    Full Text Available Paired box (PAX genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.

  4. Phylogenetic distribution and evolutionary dynamics of the sex determination genes doublesex and transformer in insects.

    Science.gov (United States)

    Geuverink, E; Beukeboom, L W

    2014-01-01

    Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects. © 2013 S. Karger AG, Basel.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Comparison of multiobjective evolutionary algorithms for optimization of externalities by using dynamic traffic management measures.

    NARCIS (Netherlands)

    Wismans, Luc Johannes Josephus; van Berkum, Eric C.; Bliemer, M.C.J.

    2011-01-01

    The externalities of traffic are increasingly important for policy decisions related to design of a road network. Optimization of externalities with dynamic traffic management measures influencing the supply of infrastructure is a multiobjective network design problem, which in turn is a bi-level

  7. Host-pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

    Czech Academy of Sciences Publication Activity Database

    Streicker, D. G.; Winternitz, Jamie Caroline; Satterfield, D. A.; Condori-Condori, R. E.; Broos, A.; Tello, C.; Recuenco, S.; Velasco-Villa, A.; Altizer, S.; Valderrama, W.

    2016-01-01

    Roč. 113, č. 39 (2016), s. 10926-10931 ISSN 0027-8424 Institutional support: RVO:68081766 Keywords : Desmodus * zoonotic disease * forecasting * sex bias * spatial dynamics Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 9.661, year: 2016

  8. Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system.

    Science.gov (United States)

    Bonachela, Juan A; Wortel, Meike T; Stenseth, Nils Chr

    2017-12-15

    The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.

  9. Host?pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

    OpenAIRE

    Streicker, Daniel G.; Winternitz, Jamie C.; Satterfield, Dara A.; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andr?s; Altizer, Sonia; Valderrama, William

    2016-01-01

    Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared complete...

  10. Toward a Mechanics of Adaptive Behavior: Evolutionary Dynamics and Matching Theory Statics

    Science.gov (United States)

    McDowell, J. J.; Popa, Andrei

    2010-01-01

    One theory of behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of reinforcement. This computational theory implements Darwinian principles of selection, reproduction, and mutation, which operate on a population of potential behaviors by means of a genetic algorithm.…

  11. Confirming Time-reversal Symmetry of a Directed Percolation Phase Transition in a Model of Neutral Evolutionary Dynamics

    Science.gov (United States)

    Ordway, Stephen; King, Dawn; Bahar, Sonya

    Reaction-diffusion processes, such as branching-coalescing random walks, can be used to describe the underlying dynamics of nonequilibrium phase transitions. In an agent-based, neutral model of evolutionary dynamics, we have previously shown that our system undergoes a continuous, nonequilibrium phase transition, from extinction to survival, as various system parameters were tuned. This model was shown to belong to the directed percolation (DP) universality class, by measuring the critical exponents corresponding to correlation length ξ⊥, correlation time ξ| |, and particle density β. The fourth critical exponent that defines the DP universality class is β', which measures the survival probability of growth from a single seed organism. Since DP universality is theorized to have time-reversal symmetry, it is assumed that β = β '. In order to confirm the existence of time-reversal symmetry in our model, we evaluate the system growth from a single asexually reproducing organism. Importantly, the critical exponent β' could be useful for comparison to experimental studies of phase transitions in biological systems, since observing growth of microbial populations is significantly easier than observing death. This research was supported by funding from the James S. McDonnell Foundation.

  12. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary ' genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history, evolution, the evolutionary genetics of biological clocks, the evolution of ecological specialization dynamics. He.

  13. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Directory of Open Access Journals (Sweden)

    Ana Zafra Ruano

    2016-05-01

    Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

  14. Quantification of fetal heart rate regularity using symbolic dynamics

    Science.gov (United States)

    van Leeuwen, P.; Cysarz, D.; Lange, S.; Geue, D.; Groenemeyer, D.

    2007-03-01

    Fetal heart rate complexity was examined on the basis of RR interval time series obtained in the second and third trimester of pregnancy. In each fetal RR interval time series, short term beat-to-beat heart rate changes were coded in 8bit binary sequences. Redundancies of the 28 different binary patterns were reduced by two different procedures. The complexity of these sequences was quantified using the approximate entropy (ApEn), resulting in discrete ApEn values which were used for classifying the sequences into 17 pattern sets. Also, the sequences were grouped into 20 pattern classes with respect to identity after rotation or inversion of the binary value. There was a specific, nonuniform distribution of the sequences in the pattern sets and this differed from the distribution found in surrogate data. In the course of gestation, the number of sequences increased in seven pattern sets, decreased in four and remained unchanged in six. Sequences that occurred less often over time, both regular and irregular, were characterized by patterns reflecting frequent beat-to-beat reversals in heart rate. They were also predominant in the surrogate data, suggesting that these patterns are associated with stochastic heart beat trains. Sequences that occurred more frequently over time were relatively rare in the surrogate data. Some of these sequences had a high degree of regularity and corresponded to prolonged heart rate accelerations or decelerations which may be associated with directed fetal activity or movement or baroreflex activity. Application of the pattern classes revealed that those sequences with a high degree of irregularity correspond to heart rate patterns resulting from complex physiological activity such as fetal breathing movements. The results suggest that the development of the autonomic nervous system and the emergence of fetal behavioral states lead to increases in not only irregular but also regular heart rate patterns. Using symbolic dynamics to

  15. Dynamic Line Rating Oncor Electric Delivery Smart Grid Program

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Justin; Smith, Cale; Young, Mike; Donohoo, Ken; Owen, Ross; Clark, Eddit; Espejo, Raul; Aivaliotis, Sandy; Stelmak, Ron; Mohr, Ron; Barba, Cristian; Gonzalez, Guillermo; Malkin, Stuart; Dimitrova, Vessela; Ragsdale, Gary; Mitchem, Sean; Jeirath, Nakul; Loomis, Joe; Trevino, Gerardo; Syracuse, Steve; Hurst, Neil; Mereness, Matt; Johnson, Chad; Bivens, Carrie

    2013-05-04

    Electric transmission lines are the lifeline of the electric utility industry, delivering its product from source to consumer. This critical infrastructure is often constrained such that there is inadequate capacity on existing transmission lines to efficiently deliver the power to meet demand in certain areas or to transport energy from high-generation areas to high-consumption regions. When this happens, the cost of the energy rises; more costly sources of power are used to meet the demand or the system operates less reliably. These economic impacts are known as congestion, and they can amount to substantial dollars for any time frame of reference: hour, day or year. There are several solutions to the transmission constraint problem, including: construction of new generation, construction of new transmission facilities, rebuilding and reconductoring of existing transmission assets, and Dynamic Line Rating (DLR). All of these options except DLR are capital intensive, have long lead times and often experience strong public and regulatory opposition. The Smart Grid Demonstration Program (SGDP) project co-funded by the Department of Energy (DOE) and Oncor Electric Delivery Company developed and deployed the most extensive and advanced DLR installation to demonstrate that DLR technology is capable of resolving many transmission capacity constraint problems with a system that is reliable, safe and very cost competitive. The SGDP DLR deployment is the first application of DLR technology to feed transmission line real-time dynamic ratings directly into the system operation’s State Estimator and load dispatch program, which optimizes the matching of generation with load demand on a security, reliability and economic basis. The integrated Dynamic Line Rating (iDLR)1 collects transmission line parameters at remote locations on the lines, calculates the real-time line rating based on the equivalent conductor temperature, ambient temperature and influence of wind and solar

  16. Physical mechanism or evolutionary trade-off? Factors dictating the relationship between metabolic rate and ambient temperature in carabid beetles.

    Science.gov (United States)

    Gudowska, Agnieszka; Schramm, Bartosz W; Czarnoleski, Marcin; Kozłowski, Jan; Bauchinger, Ulf

    2017-08-01

    The tight association between ambient temperature (T) and metabolic rate (MR) is a common occurrence in ectotherms, but the determinants of this association are not fully understood. This study examined whether the relationship between MR and T is the same among individuals, as predicted by the Universal Temperature Dependence hypothesis, or whether this relationship differs between them. We used flow-through respirometry to measure standard MR and to determine gas exchange patterns for 111 individuals of three Carabidae species which differ in size (Abax ovalis, Carabus linnei and C. coriaceus), exposed to four different temperatures (ten individuals of each species measured at 6, 11, 16 and 21°C). We found a significant interaction between ln body mass and the inverse of temperature, indicating that in a given species, the effect of temperature on MR was weaker in larger individuals than in smaller individuals. Overall, this finding shows that the thermal dependence of MR is not body mass invariant. We observed three types of gas exchange patterns among beetles: discontinuous, cyclic and continuous. Additionally, the appearance of these patterns was associated with MR and T. Evolution in diverse terrestrial environments could affect diverse ventilation patterns, which accommodate changes in metabolism in response to temperature variation. In conclusion, explaining the variance in metabolism only through fundamental physical laws of thermodynamics, as predicted by the Universal Temperature Dependence hypothesis, appears to oversimplify the complexity of nature, ignoring evolutionary trade-offs that should be taken into account in the temperature - metabolism relationship. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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.

  18. Evolutionary genomics of environmental pollution.

    Science.gov (United States)

    Whitehead, Andrew

    2014-01-01

    Chemical toxins have been a persistent source of evolutionary challenges throughout the history of life, and deep within the genomic storehouse of evolutionary history lay ancient adaptations to diverse chemical poisons. However, the rate of change of contemporary environments mediated by human-introduced pollutants is rapidly screening this storehouse and severely testing the adaptive potential of many species. In this chapter, we briefly review the deep history of evolutionary adaptation to environmental toxins, and then proceed to describe the attributes of stressors and populations that may facilitate contemporary adaptation to pollutants introduced by humans. We highlight that phenotypes derived to enable persistence in polluted habitats may be multi-dimensional, requiring global genome-scale tools and approaches to uncover their mechanistic basis, and include examples of recent progress in the field. The modern tools of genomics offer promise for discovering how pollutants interact with genomes on physiological timescales, and also for discovering what genomic attributes of populations may enable resistance to pollutants over evolutionary timescales. Through integration of these sophisticated genomics tools and approaches with an understanding of the deep historical forces that shaped current populations, a more mature understanding of the mechanistic basis of contemporary ecological-evolutionary dynamics should emerge.

  19. Evolutionary constraints on visual cortex architecture from the dynamics of hallucinations.

    Science.gov (United States)

    Butler, Thomas Charles; Benayoun, Marc; Wallace, Edward; van Drongelen, Wim; Goldenfeld, Nigel; Cowan, Jack

    2012-01-10

    In the cat or primate primary visual cortex (V1), normal vision corresponds to a state where neural excitation patterns are driven by external visual stimuli. A spectacular failure mode of V1 occurs when such patterns are overwhelmed by spontaneously generated spatially self-organized patterns of neural excitation. These are experienced as geometric visual hallucinations. The problem of identifying the mechanisms by which V1 avoids this failure is made acute by recent advances in the statistical mechanics of pattern formation, which suggest that the hallucinatory state should be very robust. Here, we report how incorporating physiologically realistic long-range connections between inhibitory neurons changes the behavior of a model of V1. We find that the sparsity of long-range inhibition in V1 plays a previously unrecognized but key functional role in preserving the normal vision state. Surprisingly, it also contributes to the observed regularity of geometric visual hallucinations. Our results provide an explanation for the observed sparsity of long-range inhibition in V1--this generic architectural feature is an evolutionary adaptation that tunes V1 to the normal vision state. In addition, it has been shown that exactly the same long-range connections play a key role in the development of orientation preference maps. Thus V1's most striking long-range features--patchy excitatory connections and sparse inhibitory connections--are strongly constrained by two requirements: the need for the visual state to be robust and the developmental requirements of the orientational preference map.

  20. Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system

    OpenAIRE

    Bonachela, Juan A.; Wortel, Meike T.; Stenseth, Nils Chr.

    2017-01-01

    The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setup...

  1. Discussing the distance bias in the estimation of Hi-GAL compact source physical properties - II. Evolutionary status and star formation rate

    Science.gov (United States)

    Baldeschi, Adriano; Molinari, S.; Elia, D.; Pezzuto, S.; Schisano, E.

    2017-12-01

    The derivation of the evolutionary stage and rate of star formation of star-forming sites from Galactic single-dish far-infrared and submillimetre surveys suffers from the relatively limited spatial resolution that prevents access to `core' scales (r ≤ 0.1 pc) for heliocentric distances d ≳ 1 kpc. In a previous article, we studied the implications of this `distance bias' for the mass-radius relationship and its ability to diagnose potential sites for high-mass star formation, using a method that simulates the appearance at large distances of nearby and well-resolved star-forming regions mapped with Herschel. In the present article, we use the same method to quantify the bias introduced in the estimate of the evolutionary stage of dense `clumps' (r ≥ 0.1 pc) revealed from the Herschel Hi-GAL survey, focusing in particular on the Lbol/Menv ratio, which is widely used as an evolutionary indicator. Furthermore, we discuss how the star formation rate (SFR) and efficiency (SFE) change with distance. The location of sources extracted from the virtual distance-displaced maps in the Lbol versus Menv diagram provides evolutionary indications that are consistent with those derived from the underlying population of cores and do not fluctuate substantially with distance. We also show that estimates of the SFR from integrated clump properties are consistent with estimates from the underlying resolved source population and show only minor variations with virtual distance. We conclude that methodologies commonly used to infer evolutionary indicators from clump-integrated quantities from large-scale single-dish Galactic far-infrared and submillimetre surveys are robust against distance and angular-resolution bias.

  2. Sectoral dynamics and technological convergence: an evolutionary analysis of eco-innovation in the automotive sector

    DEFF Research Database (Denmark)

    Faria, Lourenco; Andersen, Maj Munch

    2017-01-01

    1965 to 2012, focusing on powertrain technologies. The empirical analysis is based on patent data amongst big car producers and focuses on identifying changes in two main aspects: (1) the convergence/divergence of firms’ green strategies and technologies within the automotive sector; and (2...... to understanding green industrial dynamics and the greening of the economy. This paper investigates to what degree the economy is greening horizontally (sector-wise). Starting with a sectoral case study, we undertake a longitudinal analysis of the breath and strength of the greening of the automotive sector from...

  3. Developmental dynamics and contemporary evolutionary psychology: status quo or irreconcilable views? Reply to Bjorklund (2003), Krebs (2003), Buss and Reeve (2003), Crawford (2003), and Tooby et Al. (2003).

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    The authors address commentaries by D. F. Bjorklund (2003); D. M. Buss and H. K. Reeve (2003); C. B. Crawford (2003); D. L. Krebs (2003); and J. Tooby, L. Cosmides, and H. C. Barrett (2003) on their analysis of the underlying assumptions of contemporary evolutionary psychology (R. Lickliter & H. Honeycutt, 2003). The authors argue that evolutionary psychology currently offers no coherent framework for how to integrate genetic, environmental, and experiential factors into a theory of behavioral or cognitive phenotypes. The authors propose that this absence is due to a lack of developmental analysis in the major works of evolutionary psychology, resulting in an almost exclusive focus on adaptationist accounts of evolution by natural selection rather than a more broad-based focus on the process and products of evolution by epigenetic developmental dynamics.

  4. Nucleation rate analysis of methane hydrate from molecular dynamics simulations.

    Science.gov (United States)

    Yuhara, Daisuke; Barnes, Brian C; Suh, Donguk; Knott, Brandon C; Beckham, Gregg T; Yasuoka, Kenji; Wu, David T; Sum, Amadeu K

    2015-01-01

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

  5. Extended inclusive fitness theory: synergy and assortment drives the evolutionary dynamics in biology and economics.

    Science.gov (United States)

    Jaffe, Klaus

    2016-01-01

    W.D. Hamilton's Inclusive Fitness Theory explains the conditions that favor the emergence and maintenance of social cooperation. Today we know that these include direct and indirect benefits an agent obtains by its actions, and through interactions with kin and with genetically unrelated individuals. That is, in addition to kin-selection, assortation or homophily, and social synergies drive the evolution of cooperation. An Extended Inclusive Fitness Theory (EIFT) synthesizes the natural selection forces acting on biological evolution and on human economic interactions by assuming that natural selection driven by inclusive fitness produces agents with utility functions that exploit assortation and synergistic opportunities. This formulation allows to estimate sustainable cost/benefit threshold ratios of cooperation among organisms and/or economic agents, using existent analytical tools, illuminating our understanding of the dynamic nature of society, the evolution of cooperation among kin and non-kin, inter-specific cooperation, co-evolution, symbioses, division of labor and social synergies. EIFT helps to promote an interdisciplinary cross fertilization of the understanding of synergy by, for example, allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics. Another example is a bio-economic understanding of the motivations of terrorists, which identifies different forms of terrorism.

  6. The population and evolutionary dynamics of homologous gene recombination in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Bruce R Levin

    2009-08-01

    Full Text Available In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination -- broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT -- plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1 the contribution of HGR to the rate of adaptive evolution in these populations and (2 the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1 HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2 once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent

  7. Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms.

    Science.gov (United States)

    Killeen, Joshua; Gougat-Barbera, Claire; Krenek, Sascha; Kaltz, Oliver

    2017-04-01

    Evolutionary rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23 to 32 °C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35, 37 °C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23 °C) and high-temperature (32 °C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9 °C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche. © 2017 John Wiley & Sons Ltd.

  8. Heart rate variability and blood pressure during dynamic and static exercise at similar heart rate levels.

    Science.gov (United States)

    Weippert, Matthias; Behrens, Kristin; Rieger, Annika; Stoll, Regina; Kreuzfeld, Steffi

    2013-01-01

    Aim was to elucidate autonomic responses to dynamic and static (isometric) exercise of the lower limbs eliciting the same moderate heart rate (HR) response. 23 males performed two kinds of voluntary exercise in a supine position at similar heart rates: static exercise (SE) of the lower limbs (static leg press) and dynamic exercise (DE) of the lower limbs (cycling). Subjective effort, systolic (SBP) and diastolic blood pressure (DBP), mean arterial pressure (MAP), rate pressure product (RPP) and the time between consecutive heart beats (RR-intervals) were measured. Time-domain (SDNN, RMSSD), frequency-domain (power in the low and high frequency band (LFP, HFP)) and geometric measures (SD1, SD2) as well as non-linear measures of regularity (approximate entropy (ApEn), sample entropy (SampEn) and correlation dimension D2) were calculated. Although HR was similar during both exercise conditions (88±10 bpm), subjective effort, SBP, DBP, MAP and RPP were significantly enhanced during SE. HRV indicators representing overall variability (SDNN, SD 2) and vagal modulated variability (RMSSD, HFP, SD 1) were increased. LFP, thought to be modulated by both autonomic branches, tended to be higher during SE. ApEn and SampEn were decreased whereas D2 was enhanced during SE. It can be concluded that autonomic control processes during SE and DE were qualitatively different despite similar heart rate levels. The differences were reflected by blood pressure and HRV indices. HRV-measures indicated a stronger vagal cardiac activity during SE, while blood pressure response indicated a stronger sympathetic efferent activity to the vessels. The elevated vagal cardiac activity during SE might be a response mechanism, compensating a possible co-activation of sympathetic cardiac efferents, as HR and LF/HF was similar and LFP tended to be higher. However, this conclusion must be drawn cautiously as there is no HRV-marker reflecting "pure" sympathetic cardiac activity.

  9. Evolutionary dynamics of a sexual ornament in the house sparrow (Passer domesticus): the role of indirect selection within and between sexes.

    Science.gov (United States)

    Jensen, Henrik; Steinsland, Ingelin; Ringsby, Thor Harald; Saether, Bernt-Erik

    2008-06-01

    The relative contribution of sexual and natural selection to evolution of sexual ornaments has rarely been quantified under natural conditions. In this study we used a long-term dataset of house sparrows in which parents and offspring were matched genetically to estimate the within- and across-sex genetic basis for variation and covariation among morphological traits. By applying two-sex multivariate "animal models" to estimate genetic parameters, we estimated evolutionary changes in a male sexual ornament, badge size, from the contribution of direct and indirect selection on correlated traits within males and females, after accounting for overlapping generations and age-structure. Indirect natural selection on genetically correlated traits in males and females was the major force causing evolutionary change in the male ornament. Thus, natural selection on female morphology may cause indirect evolutionary changes in male ornaments. We observed however no directional phenotypic change in the ornament size of one-year-old males during the study period. On the other hand, changes were recorded in other morphological characters of both sexes. Our analyses of evolutionary dynamics in sexual characters require application of appropriate two-sex models to account for how selection on correlated traits in both sexes affects the evolutionary outcome of sexual selection.

  10. Kinetic model of mass exchange with dynamic Arrhenius transition rates

    Science.gov (United States)

    Hristopulos, Dionissios T.; Muradova, Aliki

    2016-02-01

    We study a nonlinear kinetic model of mass exchange between interacting grains. The transition rates follow the Arrhenius equation with an activation energy that depends dynamically on the grain mass. We show that the activation parameter can be absorbed in the initial conditions for the grain masses, and that the total mass is conserved. We obtain numerical solutions of the coupled, nonlinear, ordinary differential equations of mass exchange for the two-grain system, and we compare them with approximate theoretical solutions in specific neighborhoods of the phase space. Using phase plane methods, we determine that the system exhibits regimes of diffusive and growth-decay (reverse diffusion) kinetics. The equilibrium states are determined by the mass equipartition and separation nullcline curves. If the transfer rates are perturbed by white noise, numerical simulations show that the system maintains the diffusive and growth-decay regimes; however, the noise can reverse the sign of equilibrium mass difference. Finally, we present theoretical analysis and numerical simulations of a system with many interacting grains. Diffusive and growth-decay regimes are established as well, but the approach to equilibrium is considerably slower. Potential applications of the mass exchange model involve coarse-graining during sintering and wealth exchange in econophysics.

  11. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.

    Science.gov (United States)

    Noel, Jeffrey K; Morcos, Faruck; Onuchic, Jose N

    2016-01-01

    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.

  12. Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes.

    Science.gov (United States)

    Radzvilavicius, Arunas L

    2016-09-07

    Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of multi-copy mitochondrial genomes. Here I develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations under strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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.

  15. 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.

  16. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

    Science.gov (United States)

    Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

    2013-01-01

    WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

  17. Analysis of the Dynamic Evolutionary Behavior of American Heating Oil Spot and Futures Price Fluctuation Networks

    Directory of Open Access Journals (Sweden)

    Huan Chen

    2017-04-01

    Full Text Available Heating oil is an extremely important heating fuel to consumers in northeastern United States. This paper studies the fluctuations law and dynamic behavior of heating oil spot and futures prices by setting up their complex network models based on the data of America in recent 30 years. Firstly, modes are defined by the method of coarse graining, the spot price fluctuation network of heating oil (HSPFN and its futures price fluctuation network (HFPFN in different periods are established to analyze the transformation characteristics between the modes. Secondly, several indicators are investigated: average path length, node strength and strength distribution, betweeness, etc. In addition, a function is established to measure and analyze the network similarity. The results show the cumulative time of new nodes appearing in either spot or futures price network is not random but exhibits a growth trend of straight line. Meanwhile, the power law distributions of spot and futures price fluctuations in different periods present regularity and complexity. Moreover, these prices are strongly correlated in stable fluctuation period but weak in the phase of sharp fluctuation. Finally, the time distribution characteristics of important modes in the networks and the evolution results of the topological properties mentioned above are obtained.

  18. Host–pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

    Science.gov (United States)

    Streicker, Daniel G.; Winternitz, Jamie C.; Satterfield, Dara A.; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andrés; Altizer, Sonia; Valderrama, William

    2016-01-01

    Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared completely isolated. In contrast, greater population connectivity in biparentally inherited nuclear microsatellites explained the historical limits of invasions, suggesting that dispersing male bats spread VBRV between genetically isolated female populations. Host nuclear DNA further indicated unanticipated gene flow through the Andes mountains connecting the VBRV-free Pacific coast to the VBRV-endemic Amazon rainforest. By combining Bayesian phylogeography with landscape resistance models, we projected invasion routes through northern Peru that were validated by real-time livestock rabies mortality data. The first outbreaks of VBRV on the Pacific coast of South America could occur by June 2020, which would have serious implications for agriculture, wildlife conservation, and human health. Our results show that combining host and pathogen genetic data can identify sex biases in pathogen spatial spread, which may be a widespread but underappreciated phenomenon, and demonstrate that genetic forecasting can aid preparedness for impending viral invasions. PMID:27621441

  19. Host-pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies.

    Science.gov (United States)

    Streicker, Daniel G; Winternitz, Jamie C; Satterfield, Dara A; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andrés; Altizer, Sonia; Valderrama, William

    2016-09-27

    Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared completely isolated. In contrast, greater population connectivity in biparentally inherited nuclear microsatellites explained the historical limits of invasions, suggesting that dispersing male bats spread VBRV between genetically isolated female populations. Host nuclear DNA further indicated unanticipated gene flow through the Andes mountains connecting the VBRV-free Pacific coast to the VBRV-endemic Amazon rainforest. By combining Bayesian phylogeography with landscape resistance models, we projected invasion routes through northern Peru that were validated by real-time livestock rabies mortality data. The first outbreaks of VBRV on the Pacific coast of South America could occur by June 2020, which would have serious implications for agriculture, wildlife conservation, and human health. Our results show that combining host and pathogen genetic data can identify sex biases in pathogen spatial spread, which may be a widespread but underappreciated phenomenon, and demonstrate that genetic forecasting can aid preparedness for impending viral invasions.

  20. Universal effect of dynamical reinforcement learning mechanism in spatial evolutionary games

    Science.gov (United States)

    Zhang, Hai-Feng; Wu, Zhi-Xi; Wang, Bing-Hong

    2012-06-01

    One of the prototypical mechanisms in understanding the ubiquitous cooperation in social dilemma situations is the win-stay, lose-shift rule. In this work, a generalized win-stay, lose-shift learning model—a reinforcement learning model with dynamic aspiration level—is proposed to describe how humans adapt their social behaviors based on their social experiences. In the model, the players incorporate the information of the outcomes in previous rounds with time-dependent aspiration payoffs to regulate the probability of choosing cooperation. By investigating such a reinforcement learning rule in the spatial prisoner's dilemma game and public goods game, a most noteworthy viewpoint is that moderate greediness (i.e. moderate aspiration level) favors best the development and organization of collective cooperation. The generality of this observation is tested against different regulation strengths and different types of network of interaction as well. We also make comparisons with two recently proposed models to highlight the importance of the mechanism of adaptive aspiration level in supporting cooperation in structured populations.

  1. Predation and resource fluctuations drive eco-evolutionary dynamics of a bacterial community

    Science.gov (United States)

    Hiltunen, Teppo; Friman, Ville-Petri; Kaitala, Veijo; Mappes, Johanna; Laakso, Jouni

    2012-01-01

    Predation and temporal resource availability are among the most important factors determining prey community dynamics and composition. Both factors have been shown to affect prey diversity, but less is known about their interactive effects, especially in rapidly evolving prey communities. In a laboratory microcosm experiment, we manipulated the presence of the predatory protozoan Tetrahymena thermophila and the temporal patterns in the availability of resources for a bacterial prey community. We found that both predation and temporal fluctuations in prey resources resulted in a more even prey community, and these factors also interacted so that the effect of predation was only seen in a fluctuating environment. One possible explanation for this finding could be differences in prey species grazing resistance and resource use abilities, which likely had the greatest effect on prey community structure in fluctuating environments with periodical resource limitation. We also found that prey communities evolved to be more grazing-resistant during the experiment, and that this effect was due to a clear increase in the grazing resistance of the bacterium Serratia marcescens. Our results demonstrate that temporal variability in prey resources and predation can promote more even prey species proportions by allowing the existence of both defensive and competitive prey life-history strategies.

  2. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents

    Directory of Open Access Journals (Sweden)

    Niimura Yoshihito

    2009-12-01

    Full Text Available Abstract Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs, which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution.

  3. A CRITICAL AND COMPARATIVE ANALYSIS OF THE INDUSTRIAL CORPORATIONS IN THEIR EVOLUTIONARY DYNAMIC

    Directory of Open Access Journals (Sweden)

    GHERGHEL Sabina

    2017-05-01

    Full Text Available Since the 2000s, a series of mergers and acquisitions of brand at industrial corporations’ level has been observed in the global industry landscape, and an even more pronounced dynamism was manifested in Europe. The wave of mergers and acquisitions continues nowadays, when the concentration of the dominant "actors" on the industrial stage is followed by a similar process of creating enterprises able to compete with the first ones, either by the size of production or financial strength, or by innovativeness and introduction of new and competitive products. The existence of the Common Market and the EU on our continent has contributed enormously to the process of restructuring the "old" Europe. In the first phase of the European construction, the stage where national markets were still dominant, but there could be noticed a serious growth of competition, in Europe there has been produced a huge wave of mergers, for many surprising. Once with the consolidation of the European Community, a new phase begins, in which enterprises begin to adopt "continental" strategies and policies, reasoning according to the logic of a market area. Through international mergers means, is implemented a strategy that adapts the minimization of costs and simultaneously an insurance policy against a future possible currency devaluation. Today we are witnessing the third stage, with rules that tend quickly towards a complete unification and a single currency. The agreements between the European enterprises can be considered favorable because they often lead to high levels of efficiency without decreasing elements that make them competitive.

  4. Evolutionary history and spatiotemporal dynamics of DENV-1 genotype V in the Americas.

    Science.gov (United States)

    de Bruycker-Nogueira, Fernanda; Mir, Daiana; Dos Santos, Flavia Barreto; Bello, Gonzalo

    2016-11-01

    The genotype V has been the most prevalent dengue virus type 1 (DENV-1) clade circulating in the Americas over the last 40years. In this study, we investigate the spatiotemporal pattern of emergence and dissemination of DENV-1 lineages in the continent. We applied phylogenetic and phylogeographic approaches to a comprehensive data set of 836 DENV-1 E gene sequences of the genotype V isolated from 46 different countries around the world over a period of 50years (1962 to 2014). Our study reveals that genetic diversity of DENV-1 genotype V in the Americas resulted from two independent introductions of this genotype from India. The first genotype V strain was most probably introduced into the Lesser Antilles at around the early 1970s and this Caribbean region becomes the source population of several DENV-1 lineages that spread in the Americas during the 1970s and 1980s. Most of those lineages appear to become extinct during the 1990s, except one that persisted in Venezuela and later spread to other American countries, dominating the DENV-1 epidemics in the region from the early 2000s onwards. The second genotype V strain of Indian origin was also most probably introduced into the Lesser Antilles at around the early 1980s. This lineage remained almost undetected for nearly 15years, until it was introduced in Northern Brazil around the middle 1990s and later spread to other country regions. These results demonstrate that different geographic regions have played a role in maintaining and spreading the DENV-1 genotype V in the Americas over time. DENV-1 genotype V lineages have originated, spread and died out in the Americas with very different dynamics and the phenomenon of lineage replacement across successive DENV-1 epidemic outbreaks was a common characteristic in most American countries. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids

    Directory of Open Access Journals (Sweden)

    Fernandes António MG

    2008-10-01

    Full Text Available Abstract Background Segmental duplications (SDs are euchromatic portions of genomic DNA (≥ 1 kb that occur at more than one site within the genome, and typically share a high level of sequence identity (>90%. Approximately 5% of the human genome is composed of such duplicated sequences. Here we report the detailed investigation of CHEK2 duplications. CHEK2 is a multiorgan cancer susceptibility gene encoding a cell cycle checkpoint kinase acting in the DNA-damage response signalling pathway. The continuous presence of the CHEK2 gene in all eukaryotes and its important role in maintaining genome stability prompted us to investigate the duplicative evolution and phylogeny of CHEK2 and its paralogs during anthropoid evolution. Results To study CHEK2 duplicon evolution in anthropoids we applied a combination of comparative FISH and in silico analyses. Our comparative FISH results with a CHEK2 fosmid probe revealed the single-copy status of CHEK2 in New World monkeys, Old World monkeys and gibbons. Whereas a single CHEK2 duplication was detected in orangutan, a multi-site signal pattern indicated a burst of duplication in African great apes and human. Phylogenetic analysis of paralogous and ancestral CHEK2 sequences in human, chimpanzee and rhesus macaque confirmed this burst of duplication, which occurred after the radiation of orangutan and African great apes. In addition, we used inter-species quantitative PCR to determine CHEK2 copy numbers. An amplification of CHEK2 was detected in African great apes and the highest CHEK2 copy number of all analysed species was observed in the human genome. Furthermore, we detected variation in CHEK2 copy numbers within the analysed set of human samples. Conclusion Our detailed analysis revealed the highly dynamic nature of CHEK2 duplication during anthropoid evolution. We determined a burst of CHEK2 duplication after the radiation of orangutan and African great apes and identified the highest CHEK2 copy number

  6. Current Evolutionary Adaptiveness of Psychiatric Disorders: Fertility Rates, Parent-Child Relationship Quality, and Psychiatric Disorders across the Lifespan

    OpenAIRE

    Jacobson, Nicholas C.

    2016-01-01

    This study sought to evaluate the current evolutionary adaptiveness of psychopathology by examining whether these disorders impact the quantity of offspring or the quality of the parent-child relationship across the lifespan. Using the National Comorbidity Survey, this study examined whether DSM-III-R anxiety, posttraumatic stress, depressive, bipolar, substance use, antisocial, and psychosis disorders predicted later fertility and the quality of parent-child relationships across the lifespan...

  7. Functionally dissociable influences on learning rate in a dynamic environment.

    Science.gov (United States)

    McGuire, Joseph T; Nassar, Matthew R; Gold, Joshua I; Kable, Joseph W

    2014-11-19

    Maintaining accurate beliefs in a changing environment requires dynamically adapting the rate at which one learns from new experiences. Beliefs should be stable in the face of noisy data but malleable in periods of change or uncertainty. Here we used computational modeling, psychophysics, and fMRI to show that adaptive learning is not a unitary phenomenon in the brain. Rather, it can be decomposed into three computationally and neuroanatomically distinct factors that were evident in human subjects performing a spatial-prediction task: (1) surprise-driven belief updating, related to BOLD activity in visual cortex; (2) uncertainty-driven belief updating, related to anterior prefrontal and parietal activity; and (3) reward-driven belief updating, a context-inappropriate behavioral tendency related to activity in ventral striatum. These distinct factors converged in a core system governing adaptive learning. This system, which included dorsomedial frontal cortex, responded to all three factors and predicted belief updating both across trials and across individuals. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Eco-Evolutionary Trophic Dynamics: Loss of Top Predators Drives Trophic Evolution and Ecology of Prey

    Science.gov (United States)

    Palkovacs, Eric P.; Wasserman, Ben A.; Kinnison, Michael T.

    2011-01-01

    Ecosystems are being altered on a global scale by the extirpation of top predators. The ecological effects of predator removal have been investigated widely; however, predator removal can also change natural selection acting on prey, resulting in contemporary evolution. Here we tested the role of predator removal on the contemporary evolution of trophic traits in prey. We utilized a historical introduction experiment where Trinidadian guppies (Poecilia reticulata) were relocated from a site with predatory fishes to a site lacking predators. To assess the trophic consequences of predator release, we linked individual morphology (cranial, jaw, and body) to foraging performance. Our results show that predator release caused an increase in guppy density and a “sharpening” of guppy trophic traits, which enhanced food consumption rates. Predator release appears to have shifted natural selection away from predator escape ability and towards resource acquisition ability. Related diet and mesocosm studies suggest that this shift enhances the impact of guppies on lower trophic levels in a fashion nuanced by the omnivorous feeding ecology of the species. We conclude that extirpation of top predators may commonly select for enhanced feeding performance in prey, with important cascading consequences for communities and ecosystems. PMID:21526156

  9. Eco-evolutionary trophic dynamics: loss of top predators drives trophic evolution and ecology of prey.

    Science.gov (United States)

    Palkovacs, Eric P; Wasserman, Ben A; Kinnison, Michael T

    2011-04-19

    Ecosystems are being altered on a global scale by the extirpation of top predators. The ecological effects of predator removal have been investigated widely; however, predator removal can also change natural selection acting on prey, resulting in contemporary evolution. Here we tested the role of predator removal on the contemporary evolution of trophic traits in prey. We utilized a historical introduction experiment where Trinidadian guppies (Poecilia reticulata) were relocated from a site with predatory fishes to a site lacking predators. To assess the trophic consequences of predator release, we linked individual morphology (cranial, jaw, and body) to foraging performance. Our results show that predator release caused an increase in guppy density and a "sharpening" of guppy trophic traits, which enhanced food consumption rates. Predator release appears to have shifted natural selection away from predator escape ability and towards resource acquisition ability. Related diet and mesocosm studies suggest that this shift enhances the impact of guppies on lower trophic levels in a fashion nuanced by the omnivorous feeding ecology of the species. We conclude that extirpation of top predators may commonly select for enhanced feeding performance in prey, with important cascading consequences for communities and ecosystems.

  10. Eco-evolutionary trophic dynamics: loss of top predators drives trophic evolution and ecology of prey.

    Directory of Open Access Journals (Sweden)

    Eric P Palkovacs

    Full Text Available Ecosystems are being altered on a global scale by the extirpation of top predators. The ecological effects of predator removal have been investigated widely; however, predator removal can also change natural selection acting on prey, resulting in contemporary evolution. Here we tested the role of predator removal on the contemporary evolution of trophic traits in prey. We utilized a historical introduction experiment where Trinidadian guppies (Poecilia reticulata were relocated from a site with predatory fishes to a site lacking predators. To assess the trophic consequences of predator release, we linked individual morphology (cranial, jaw, and body to foraging performance. Our results show that predator release caused an increase in guppy density and a "sharpening" of guppy trophic traits, which enhanced food consumption rates. Predator release appears to have shifted natural selection away from predator escape ability and towards resource acquisition ability. Related diet and mesocosm studies suggest that this shift enhances the impact of guppies on lower trophic levels in a fashion nuanced by the omnivorous feeding ecology of the species. We conclude that extirpation of top predators may commonly select for enhanced feeding performance in prey, with important cascading consequences for communities and ecosystems.

  11. Evolutionary dynamics of HBV-D1 genotype epidemic in Turkey.

    Science.gov (United States)

    Ciccozzi, Massimo; Ciccaglione, Anna Rita; Lo Presti, Alessandra; Equestre, Michele; Cella, Eleonora; Ebranati, Erika; Gabanelli, Elena; Villano, Umbertina; Bruni, Roberto; Yalcinkaya, Tulay; Tanzi, Elisabetta; Zehender, Gianguglielmo

    2014-01-01

    Hepatitis B virus (HBV), is the leading cause of liver diseases infecting an estimated 240 million persons worldwide. The HBV prevalence rates are variables between different countries, with an high level of endemicity in the south-eastern part of Europe. Seven main HBV-D subgenotypes have been described until now (D1-D7). Turkey, seems to have played an important role in the penetration of HBV-D1 in the Mediterranean area. The importance of Turkey in the European epidemiology of HBV is also suggested by the observation that the highest spread of HBV infection in the Continent are reported in Turkey with Romania, Bulgaria, Greece, Albania and some southern regions of Italy. In this paper the molecular epidemiology and the epidemiological history of HBV-D in Turkey was studied, by characterizing 34 new Turkish isolates and performing a phylogeographic reconstruction. By using a phylodynamic and phylogeographic Bayesian approach, the analysis suggested that HBV-D1 originated in Turkey about in the early 1940s. The large prevalence of D1 in comparison to the other subgenotypes in Turkey confirms the importance of this Country as epidemiological reservoir of HBV-D1 dispersion. The phylogeny suggests that after each initial introduction of the virus in a specific population, separate transmission clusters have been evolving along independent phylogenetic lineages. Better characterization and continuous monitoring of such groups are going to be crucial to understand in detail the epidemiology of HBV-D1 subgenotype in Turkey and to assess the efficacy of prevention, vaccination and therapy in controlling the epidemic. © 2013 Wiley Periodicals, Inc.

  12. Evolutionary mechanics: new engineering principles for the emergence of flexibility in a dynamic and uncertain world.

    Science.gov (United States)

    Whitacre, James M; Rohlfshagen, Philipp; Bender, Axel; Yao, Xin

    2012-09-01

    Engineered systems are designed to deftly operate under predetermined conditions yet are notoriously fragile when unexpected perturbations arise. In contrast, biological systems operate in a highly flexible manner; learn quickly adequate responses to novel conditions, and evolve new routines and traits to remain competitive under persistent environmental change. A recent theory on the origins of biological flexibility has proposed that degeneracy-the existence of multi-functional components with partially overlapping functions-is a primary determinant of the robustness and adaptability found in evolved systems. While degeneracy's contribution to biological flexibility is well documented, there has been little investigation of degeneracy design principles for achieving flexibility in systems engineering. Actually, the conditions that can lead to degeneracy are routinely eliminated in engineering design. With the planning of transportation vehicle fleets taken as a case study, this article reports evidence that degeneracy improves the robustness and adaptability of a simulated fleet towards unpredicted changes in task requirements without incurring costs to fleet efficiency. We find that degeneracy supports faster rates of design adaptation and ultimately leads to better fleet designs. In investigating the limitations of degeneracy as a design principle, we consider decision-making difficulties that arise from degeneracy's influence on fleet complexity. While global decision-making becomes more challenging, we also find degeneracy accommodates rapid distributed decision-making leading to (near-optimal) robust system performance. Given the range of conditions where favorable short-term and long-term performance outcomes are observed, we propose that degeneracy may fundamentally alter the propensity for adaptation and is useful within different engineering and planning contexts.

  13. Comparative Analysis of the Complete Plastomes ofApostasia wallichiiandNeuwiedia singapureana(Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.

    Science.gov (United States)

    Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

    2017-01-01

    Apostasioideae, consists of only two genera, Apostasia and Neuwiedia , which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla ), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase ( ndh ) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci- ndhA intron, matK-5'trnK , clpP-psbB , rps8-rpl14 , trnT-trnL , 3'trnK-matK , clpP intron , psbK-trnK , trnS-psbC , and ndhF-rpl32 -that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

  14. Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

    Directory of Open Access Journals (Sweden)

    Zhitao Niu

    2017-10-01

    Full Text Available Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla, the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

  15. 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.

  16. Benchmark Generator for the IEEE WCCI-2014 Competition on Evolutionary Computation for Dynamic Optimization Problems: Dynamic Rotation Peak Benchmark Generator (DRPBG) and Dynamic Composition Benchmark Generator (DCBG)

    OpenAIRE

    Li, Changhe; Mavrovouniotis, Michalis; Yang, Shengxiang; Yao, Xin

    2013-01-01

    Based on our previous benchmark generator for the IEEE CEC’12 Competition on Dynamic Optimization, this report updates the two benchmark instances where two new features have 1been developed as well as a constraint to the benchmark instance of the dynamic rotation peak benchmark generator. The source code in C++ language for the two benchmark instances is included in the library of EAlib, which is an open platform to test and compare the performances of EAs.

  17. Dynamic Optimization Design of Cranes Based on Human–Crane–Rail System Dynamics and Annoyance Rate

    Directory of Open Access Journals (Sweden)

    Yunsheng Xin

    2017-01-01

    Full Text Available The operators of overhead traveling cranes experience discomfort as a result of the vibrations of crane structures. These vibrations are produced by defects in the rails on which the cranes move. To improve the comfort of operators, a nine-degree-of-freedom (nine-DOF mathematical model of a “human–crane–rail” system was constructed. Based on the theoretical guidance provided in ISO 2631-1, an annoyance rate model was established, and quantization results were determined. A dynamic optimization design method for overhead traveling cranes is proposed. A particle swarm optimization (PSO algorithm was used to optimize the crane structural design, with the structure parameters as the basic variables, the annoyance rate model as the objective function, and the acceleration amplitude and displacement amplitude of the crane as the constraint conditions. The proposed model and method were used to optimize the design of a double-girder 100 t–28.5 m casting crane, and the optimal parameters are obtained. The results show that optimization decreases the human annoyance rate from 28.3% to 9.8% and the root mean square of the weighted acceleration of human vibration from 0.59 m/s2 to 0.38 m/s2. These results demonstrate the effectiveness and practical applicability of the models and method proposed in this paper.

  18. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

    Directory of Open Access Journals (Sweden)

    Buschiazzo Emmanuel

    2012-01-01

    Full Text Available Background Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis and loblolly pine (Pinus taeda, together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa, offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Results Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Conclusions Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.

  19. Effect of orbital and ionic dynamics coupling in barrier crossing rates for Car-Parrinello molecular dynamics

    Science.gov (United States)

    Mohanam, L. N.; Ong, S. W.; Tok, E. S.; Kang, H. C.

    2015-02-01

    Even though the Car-Parrinello molecular dynamics (CPMD) method provides excellent sampling for thermal equilibrium, coupling between ionic motion and the fictitious orbital dynamics leads to an underestimation of ionic vibration frequencies In this letter we examine how this coupling affects calculated rates of energy-barrier crossing. Simulating double-well potentials in 'toy' models based on H3O2- and H5O2+ complexes, we demonstrate that barrier crossing rates can be dramatically affected depending upon how orbitals evolve at the top of the reaction barrier. Thus, it is important that calculated dynamical quantities such as chemical reaction rates be assessed for this coupling effect.

  20. Current evolutionary adaptiveness of psychiatric disorders: Fertility rates, parent-child relationship quality, and psychiatric disorders across the lifespan.

    Science.gov (United States)

    Jacobson, Nicholas C

    2016-08-01

    This study sought to evaluate the current evolutionary adaptiveness of psychopathology by examining whether these disorders impact the quantity of offspring or the quality of the parent-child relationship across the life span. Using the National Comorbidity Survey, this study examined whether DSM-III-R anxiety, posttraumatic stress, depressive, bipolar, substance use, antisocial, and psychosis disorders predicted later fertility and the quality of parent-child relationships across the life span in a national sample (N = 8,098). Using latent variable and varying coefficient models, the results suggested that anxiety in males and bipolar pathology in males and females were associated with increased fertility at younger ages. The results suggested almost all other psychopathology was associated with decreased fertility in middle to late adulthood. The results further suggested that all types of psychopathology had negative impacts on the parent-child relationship quality (except for antisocial pathology in males). Nevertheless, for all disorders, the impact of psychopathology on both fertility and the parent-child relationship quality was affected by the age of the participant. The results also showed that anxiety pathology is associated with a high-quantity, low-quality parenting strategy followed by a low-quantity, low-quality parenting strategy. Further, the results suggest that bipolar pathology is associated with an early high-quantity and a continued low-quality parenting strategy. Posttraumatic stress, depression, substance use, antisocial personality, and psychosis pathology are each associated with a low-quantity, low-quality parenting strategy, particularly in mid to late adulthood. These findings suggest that the evolutionary impact of psychopathology depends on the developmental context. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

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

    Science.gov (United States)

    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

  2. Fluctuation Dynamics of Exchange Rates on Indian Financial Market

    Science.gov (United States)

    Sarkar, A.; Barat, P.

    Here we investigate the scaling behavior and the complexity of the average daily exchange rate returns of the Indian Rupee against four foreign currencies namely US Dollar, Euro, Great Britain Pound and Japanese Yen. Our analysis revealed that the average daily exchange rate return of the Indian Rupee against the US Dollar exhibits a persistent scaling behavior and follow Levy stable distribution. On the contrary the average daily exchange rate returns of the other three foreign currencies show randomness and follow Gaussian distribution. Moreover, it is seen that the complexity of the average daily exchange rate return of the Indian Rupee against US Dollar is less than the other three exchange rate returns.

  3. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

    Science.gov (United States)

    Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël; Willison, John C; Lenski, Richard E; Soyer, Orkun S; Schneider, Dominique

    2016-08-20

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.

  4. Mean field ring polymer molecular dynamics for electronically nonadiabatic reaction rates.

    Science.gov (United States)

    Duke, Jessica Ryan; Ananth, Nandini

    2016-12-22

    We present a mean field ring polymer molecular dynamics method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. Our approach involves calculating a transition state theory (TST) estimate to the rate using an exact path integral in discrete electronic states and continuous Cartesian nuclear coordinates. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory. Further, we show that using a reaction coordinate based on electronic state populations allows us to capture the turnover in rates for ET in the Marcus inverted regime.

  5. Temporal dynamics of high repetition rate pulsed single longitudinal ...

    Indian Academy of Sciences (India)

    tion dynamics closely affects both spectral and temporal behaviour of the dye laser. The frequency chirp of the dye laser during the evolution due to pulsation of population is studied for our cavity and the results are presented. 2. Experimental method. Figure 1 shows the schematic of the single longitudinal mode (SLM) dye ...

  6. 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...

  7. Program participation, labor force dynamics, and accepted wage rates

    DEFF Research Database (Denmark)

    Munch, Jakob Roland; Skipper, Lars

    2008-01-01

    transition rate from unemployment to employment upon completion. Most programs, therefore, increase the expected duration of unemployment spells. However, we find that the training undertaken while unemployed successfully increases the expected duration of subsequent spells of employment for many...... subpopulations. These longer spells of employment come at a cost of lower accepted hourly wage rates...

  8. Catecholaminergic Regulation of Learning Rate in a Dynamic Environment

    Science.gov (United States)

    Jepma, Marieke; Nassar, Matthew R.; Rangel-Gomez, Mauricio; Meeter, Martijn; Nieuwenhuis, Sander

    2016-01-01

    Adaptive behavior in a changing world requires flexibly adapting one’s rate of learning to the rate of environmental change. Recent studies have examined the computational mechanisms by which various environmental factors determine the impact of new outcomes on existing beliefs (i.e., the ‘learning rate’). However, the brain mechanisms, and in particular the neuromodulators, involved in this process are still largely unknown. The brain-wide neurophysiological effects of the catecholamines norepinephrine and dopamine on stimulus-evoked cortical responses suggest that the catecholamine systems are well positioned to regulate learning about environmental change, but more direct evidence for a role of this system is scant. Here, we report evidence from a study employing pharmacology, scalp electrophysiology and computational modeling (N = 32) that suggests an important role for catecholamines in learning rate regulation. We found that the P3 component of the EEG—an electrophysiological index of outcome-evoked phasic catecholamine release in the cortex—predicted learning rate, and formally mediated the effect of prediction-error magnitude on learning rate. P3 amplitude also mediated the effects of two computational variables—capturing the unexpectedness of an outcome and the uncertainty of a preexisting belief—on learning rate. Furthermore, a pharmacological manipulation of catecholamine activity affected learning rate following unanticipated task changes, in a way that depended on participants’ baseline learning rate. Our findings provide converging evidence for a causal role of the human catecholamine systems in learning-rate regulation as a function of environmental change. PMID:27792728

  9. Evaluation of Instrumentation and Dynamic Thermal Ratings for Overhead Lines

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, A. [New York Power Authority, White Plains, NY (United States)

    2013-01-31

    In 2010, a project was initiated through a partnership between the Department of Energy (DOE) and the New York Power Authority (NYPA) to evaluate EPRI's rating technology and instrumentation that can be used to monitor the thermal states of transmission lines and provide the required real-time data for real-time rating calculations. The project included the installation and maintenance of various instruments at three 230 kV line sites in northern New York. The instruments were monitored, and data collection and rating calculations were performed for about a three year period.

  10. The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis

    Science.gov (United States)

    2008-01-01

    Background The bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion. Results Phylogenetic concordance between mitochondrial and nuclear genes at the base of the bananaquit phylogeny supported a West Indian origin for continental populations. Multi-gene analysis showing genetic remnants of successive colonization events in the Lesser Antilles reinforced earlier research demonstrating that bananaquits alternate periods of invasiveness and colonization with biogeographic quiescence. Although nuclear genes provided insufficient information at the tips of the tree to further evaluate relationships of closely allied but strongly supported mitochondrial DNA clades, the discrepancy between mitochondrial and nuclear data in the population of Dominican Republic suggested that the mitochondrial genome was recently acquired by introgression from Jamaica. Conclusion This study represents one of the most complete phylogeographic analyses of its kind and reveals three patterns that are not commonly appreciated in birds: (1) island to mainland colonization, (2) multiple expansion phases, and (3) mitochondrial genome replacement. The detail revealed by this analysis will guide evolutionary analyses of populations in archipelagos such as the West Indies, which include islands varying in size, age, and geological history. Our results suggest that

  11. The dynamic evolutionary history of the bananaquit (Coereba flaveola in the Caribbean revealed by a multigene analysis

    Directory of Open Access Journals (Sweden)

    Ricklefs Robert E

    2008-08-01

    Full Text Available Abstract Background The bananaquit (Coereba flaveola is a small nectivorous and frugivorous emberizine bird (order Passeriformes that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs and three nuclear genes (2049 base pairs for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion. Results Phylogenetic concordance between mitochondrial and nuclear genes at the base of the bananaquit phylogeny supported a West Indian origin for continental populations. Multi-gene analysis showing genetic remnants of successive colonization events in the Lesser Antilles reinforced earlier research demonstrating that bananaquits alternate periods of invasiveness and colonization with biogeographic quiescence. Although nuclear genes provided insufficient information at the tips of the tree to further evaluate relationships of closely allied but strongly supported mitochondrial DNA clades, the discrepancy between mitochondrial and nuclear data in the population of Dominican Republic suggested that the mitochondrial genome was recently acquired by introgression from Jamaica. Conclusion This study represents one of the most complete phylogeographic analyses of its kind and reveals three patterns that are not commonly appreciated in birds: (1 island to mainland colonization, (2 multiple expansion phases, and (3 mitochondrial genome replacement. The detail revealed by this analysis will guide evolutionary analyses of populations in archipelagos such as the West Indies, which include islands varying in size, age, and geological history. Our

  12. 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.

  13. Strain rate sensitivity analysis in phase-field dislocation dynamics

    OpenAIRE

    Cao, Lei; Koslowski, Marisol

    2014-01-01

    We present dislocation simulations involving the collective behavior of partials and extended full dislocations in nanocrystalline (nc) materials. Although atomistic simulations have shown the importance of including partial dislocations in high strain rate simulations, the behavior of partial dislocations in complex geometries with low strain rates has not been explored. To account for the dissociation of dislocations into partials we include the full representation of the gamma surface for ...

  14. Scaling laws in the dynamics of crime growth rate

    Science.gov (United States)

    Alves, Luiz G. A.; Ribeiro, Haroldo V.; Mendes, Renio S.

    2013-06-01

    The increasing number of crimes in areas with large concentrations of people have made cities one of the main sources of violence. Understanding characteristics of how crime rate expands and its relations with the cities size goes beyond an academic question, being a central issue for contemporary society. Here, we characterize and analyze quantitative aspects of murders in the period from 1980 to 2009 in Brazilian cities. We find that the distribution of the annual, biannual and triannual logarithmic homicide growth rates exhibit the same functional form for distinct scales, that is, a scale invariant behavior. We also identify asymptotic power-law decay relations between the standard deviations of these three growth rates and the initial size. Further, we discuss similarities with complex organizations.

  15. Scaling laws in the dynamics of crime growth rate

    CERN Document Server

    Alves, Luiz Gustavo de Andrade; Mendes, Renio dos Santos

    2013-01-01

    The increasing number of crimes in areas with large concentrations of people have made cities one of the main source of violence. Understanding characteristics of how crime rate expands and its relations with the cities size goes beyond an academic question, being a central issue for the contemporary society. Here, we characterize and analyze quantitative aspects of murders in the period from 1980 to 2009 in Brazilian cities. We find that the distribution of the annual, biannual and triannual logarithmic homicide growth rates exhibit the same functional form for distinct scales, that is, a scale invariant behaviour. We also identify asymptotic power-law decay relations between the standard deviations of these three growth rates and the initial size. Further, we discuss similarities with complex organizations.

  16. Comparison of diurnal dynamics in evaporation rate between bare ...

    Indian Academy of Sciences (India)

    between bare soil and moss-crusted soil are expected to be predicted by soil water content. 1. ... face for evaporation due to their high water reten- tion (West 1990 ..... demand (Allen et al. 1998). While, when soil water content was in a lower level (Day 3–6), the evap- oration rate was evidently reduced. We considered.

  17. Dynamic Relationship between Crude Oil Price, Exchange Rate and ...

    African Journals Online (AJOL)

    DrNneka

    stock market performance (Adebiyi et al., 2009). This study contributed to the study of linkage between crude oil price movements, exchange rate behaviour and stock market performance of African oil-exporting countries. The increased integration of financial markets in the world today provides investors with new ways to ...

  18. Dynamic Relationship between Crude Oil Price, Exchange Rate and ...

    African Journals Online (AJOL)

    This study employed a multivariate Vector Error Correction Model (VECM) that uses the Granger causality test and generalized variance decomposition analysis to study the relationship between crude oil prices, exchange rate and stock market performance in Nigeria from January 1995 to December 2014. As expected ...

  19. High Dynamic Optimized Carrier Loop Improvement for Tracking Doppler Rates

    Directory of Open Access Journals (Sweden)

    Amirhossein Fereidountabar

    2015-01-01

    Full Text Available Mathematical analysis and optimization of a carrier tracking loop are presented. Due to fast changing of the carrier frequency in some satellite systems, such as Low Earth Orbit (LEO or Global Positioning System (GPS, or some planes like Unmanned Aerial Vehicles (UAVs, high dynamic tracking loops play a very important role. In this paper an optimized tracking loop consisting of a third-order Phase Locked Loop (PLL assisted by a second-order Frequency Locked Loop (FLL for UAVs is proposed and discussed. Based on this structure an optimal loop has been designed. The main advantages of this approach are the reduction of the computation complexity and smaller phase error. The paper shows the simulation results, comparing them with a previous work.

  20. Organizational Dynamics and the Evolutionary Dilemma between Diversity and Standardization in Mission-Oriented Research Programmes: An Illustration

    OpenAIRE

    Conesa, E.

    1998-01-01

    The American NASP programme -- National Aero Space Plane -- is a good illustration of the evolutionary dilemma between variety and standardization in management of mission-oriented R&D. This dilemma relates to the trade-off between the need to explore the technological diversity in order to avoid the risk of being locked-in on the wrong technological option, and the need to share the knowledge produce through the experiments. In this regard, two main organizational designs can be considered: ...

  1. Growth rate in the dynamical dark energy models.

    Science.gov (United States)

    Avsajanishvili, Olga; Arkhipova, Natalia A; Samushia, Lado; Kahniashvili, Tina

    Dark energy models with a slowly rolling cosmological scalar field provide a popular alternative to the standard, time-independent cosmological constant model. We study the simultaneous evolution of background expansion and growth in the scalar field model with the Ratra-Peebles self-interaction potential. We use recent measurements of the linear growth rate and the baryon acoustic oscillation peak positions to constrain the model parameter [Formula: see text] that describes the steepness of the scalar field potential.

  2. An Abstract Multi-Rate Method for Vehicle Dynamics Simulation

    Science.gov (United States)

    2012-01-01

    a single macro multi-rate step from initial to final time. TODO : There are time domain multigrid approaches. This should be mentioned here with...simplified faster than real-time models such as those employed in first order design optimization tools [ TODO : citations]. Increasing in detail one...training [ TODO : citations]. Next are vehicle models of modest detail which support off-line analysis of vehicle handling, virtual kinematics and

  3. Observing ultrasound stimulated microbubble dynamics at MHz framing rates.

    Science.gov (United States)

    Prentice, P A; Campbell, P A

    2008-01-01

    Microbubble contrast agents were originally developed to enhance echogenicity in diagnostic sonography. However, their somewhat unique acoustic response and facility to transduct energy into spatially focussed regimes, together with the clinical demand for non-invasive adjuncts and options to conventional therapy, have seen interest in exploring the therapeutic potential of microbubbbles grow steadily within this past decade. For the purposes of the present study, we examined the ultrasonically stimulated response of many such microbubbles by controlling their spatial placement with bespoke optical traps. The objective was to improve our understanding of their statistical behaviour and to feed this information into realistic computational models so that processes might be more easily optimised. Hence, individual microbubbles of commercial [low-index] ultrasound contrast agent were isolated from a parent population by selection using a Laguerre-Gaussian optical trap, and subsequently manipulated to controllable micrometer level displacements from a solid surface. This configuration was then insonated using a 60ms burst of 1MHz ultrasound at a nominal peak pressure of 6.5MPa, and the subsequent bubble dynamics recorded using ultra high speed micro-photography at microsecond temporal resolutions. Any resultant damage induced at the target surface was also observed and characterised using atomic force microscopy.

  4. A new approach to estimate ice dynamic rates using satellite observations in East Antarctica

    Science.gov (United States)

    Kallenberg, Bianca; Tregoning, Paul; Fabian Hoffmann, Janosch; Hawkins, Rhys; Purcell, Anthony; Allgeyer, Sébastien

    2017-05-01

    Mass balance changes of the Antarctic ice sheet are of significant interest due to its sensitivity to climatic changes and its contribution to changes in global sea level. While regional climate models successfully estimate mass input due to snowfall, it remains difficult to estimate the amount of mass loss due to ice dynamic processes. It has often been assumed that changes in ice dynamic rates only need to be considered when assessing long-term ice sheet mass balance; however, 2 decades of satellite altimetry observations reveal that the Antarctic ice sheet changes unexpectedly and much more dynamically than previously expected. Despite available estimates on ice dynamic rates obtained from radar altimetry, information about ice sheet changes due to changes in the ice dynamics are still limited, especially in East Antarctica. Without understanding ice dynamic rates, it is not possible to properly assess changes in ice sheet mass balance and surface elevation or to develop ice sheet models. In this study we investigate the possibility of estimating ice sheet changes due to ice dynamic rates by removing modelled rates of surface mass balance, firn compaction, and bedrock uplift from satellite altimetry and gravity observations. With similar rates of ice discharge acquired from two different satellite missions we show that it is possible to obtain an approximation of the rate of change due to ice dynamics by combining altimetry and gravity observations. Thus, surface elevation changes due to surface mass balance, firn compaction, and ice dynamic rates can be modelled and correlated with observed elevation changes from satellite altimetry.

  5. A new approach to estimate ice dynamic rates using satellite observations in East Antarctica

    Directory of Open Access Journals (Sweden)

    B. Kallenberg

    2017-05-01

    Full Text Available Mass balance changes of the Antarctic ice sheet are of significant interest due to its sensitivity to climatic changes and its contribution to changes in global sea level. While regional climate models successfully estimate mass input due to snowfall, it remains difficult to estimate the amount of mass loss due to ice dynamic processes. It has often been assumed that changes in ice dynamic rates only need to be considered when assessing long-term ice sheet mass balance; however, 2 decades of satellite altimetry observations reveal that the Antarctic ice sheet changes unexpectedly and much more dynamically than previously expected. Despite available estimates on ice dynamic rates obtained from radar altimetry, information about ice sheet changes due to changes in the ice dynamics are still limited, especially in East Antarctica. Without understanding ice dynamic rates, it is not possible to properly assess changes in ice sheet mass balance and surface elevation or to develop ice sheet models. In this study we investigate the possibility of estimating ice sheet changes due to ice dynamic rates by removing modelled rates of surface mass balance, firn compaction, and bedrock uplift from satellite altimetry and gravity observations. With similar rates of ice discharge acquired from two different satellite missions we show that it is possible to obtain an approximation of the rate of change due to ice dynamics by combining altimetry and gravity observations. Thus, surface elevation changes due to surface mass balance, firn compaction, and ice dynamic rates can be modelled and correlated with observed elevation changes from satellite altimetry.

  6. Dynamic mathematical model of high rate algal ponds (HRAP).

    Science.gov (United States)

    Jupsin, H; Praet, E; Vasel, J L

    2003-01-01

    This article presents a mathematical model to describe High-Rate Algal Ponds (HRAPs). The hydrodynamic behavior of the reactor is described as completely mixed tanks in series with recirculation. The hydrodynamic pattern is combined with a subset of River Water Quality Model 1 (RWQM1), including the main processes in liquid phase. Our aim is to develop models for WSPs and aerated lagoons, too, but we focused on HRAPs first for several reasons: Sediments are usually less abundant in HRAP and can be neglected, Stratification is not observed and state variables are constant in a reactor cross section, Due to the system's geometry, the reactor is quite similar to a plugflow type reactor with recirculation, with a simple advection term. The model is based on mass balances and includes the following processes: *Phytoplankton growth with NO3-, NO2- and death, *Aerobic growth of heterotrophs with NO3-, NH4+ and respiration, *Anoxic growth of heterotrophs with NO3-, NO2- and anoxic respiration, *Growth of nitrifiers (two stages) and respiration. The differences with regard to RWQM1 are that we included a limiting term associated with inorganic carbon on the growth rate of algae and nitrifiers, gas transfers are taken into account by the familiar Adeney equation, and a subroutine calculates light intensity at the water surface. This article presents our first simulations.

  7. Nonlinear dynamical effects on reaction rates in thermally fluctuating environments.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2010-07-21

    A framework to calculate the rate constants of condensed phase chemical reactions of manybody systems is presented without relying on the concept of transition state. The theory is based on a framework we developed recently adopting a multidimensional underdamped Langevin equation in the region of a rank-one saddle. The theory provides a reaction coordinate expressed as an analytical nonlinear functional of the position coordinates and velocities of the system (solute), the friction constants, and the random force of the environment (solvent). Up to moderately high temperature, the sign of the reaction coordinate can determine the final destination of the reaction in a thermally fluctuating media, irrespective of what values the other (nonreactive) coordinates may take. In this paper, it is shown that the reaction probability is analytically derived as the probability of the reaction coordinate being positive, and that the integration with the Boltzmann distribution of the initial conditions leads to the exact reaction rate constant when the local equilibrium holds and the quantum effect is negligible. Because of analytical nature of the theory taking into account all nonlinear effects and their combination with fluctuation and dissipation, the theory naturally provides us with the firm mathematical foundation of the origin of the reactivity of the reaction in a fluctuating media.

  8. Gender- and age-related differences in heart rate dynamics: are women more complex than men?

    Science.gov (United States)

    Ryan, S. M.; Goldberger, A. L.; Pincus, S. M.; Mietus, J.; Lipsitz, L. A.

    1994-01-01

    OBJECTIVES. This study aimed to quantify the complex dynamics of beat-to-beat sinus rhythm heart rate fluctuations and to determine their differences as a function of gender and age. BACKGROUND. Recently, measures of heart rate variability and the nonlinear "complexity" of heart rate dynamics have been used as indicators of cardiovascular health. Because women have lower cardiovascular risk and greater longevity than men, we postulated that there are important gender-related differences in beat-to-beat heart rate dynamics. METHODS. We analyzed heart rate dynamics during 8-min segments of continuous electrocardiographic recording in healthy young (20 to 39 years old), middle-aged (40 to 64 years old) and elderly (65 to 90 years old) men (n = 40) and women (n = 27) while they performed spontaneous and metronomic (15 breaths/min) breathing. Relatively high (0.15 to 0.40 Hz) and low (0.01 to 0.15 Hz) frequency components of heart rate variability were computed using spectral analysis. The overall "complexity" of each heart rate time series was quantified by its approximate entropy, a measure of regularity derived from nonlinear dynamics ("chaos" theory). RESULTS. Mean heart rate did not differ between the age groups or genders. High frequency heart rate power and the high/low frequency power ratio decreased with age in both men and women (p cardiovascular disease risk and greater longevity in women requires further study.

  9. 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.

  10. 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

  11. Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer.

    Science.gov (United States)

    Chiara, Matteo; Caruso, Marta; D'Erchia, Anna Maria; Manzari, Caterina; Fraccalvieri, Rosa; Goffredo, Elisa; Latorre, Laura; Miccolupo, Angela; Padalino, Iolanda; Santagada, Gianfranco; Chiocco, Doriano; Pesole, Graziano; Horner, David S; Parisi, Antonio

    2015-07-15

    Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. Simulation of dynamic behavior of quasi-brittle materials with new rate dependent damage model

    NARCIS (Netherlands)

    Magalhaes Pereira, L.F.; Weerheijm, J.; Sluijs, Lambertus J.; Saouma, V.; Bolander, J.; Landis, E.

    2016-01-01

    Stress-based nonlocal model, Damage, Rate dependency, Dynamic crack-branching Abstract. In concrete often complex fracture and fragmentation patterns develop when subjected to high straining loads. The proper simulation of the dynamic cracking process in concrete is crucial for good predictions of

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Evolution of dengue virus type 3 genotype III in Venezuela: diversification, rates and population dynamics.

    Science.gov (United States)

    Ramírez, Alvaro; Fajardo, Alvaro; Moros, Zoila; Gerder, Marlene; Caraballo, Gerson; Camacho, Daria; Comach, Guillermo; Alarcón, Victor; Zambrano, Julio; Hernández, Rosa; Moratorio, Gonzalo; Cristina, Juan; Liprandi, Ferdinando

    2010-11-18

    Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV are comprised of four distinct serotypes (DENV-1 through DENV-4) and each serotype can be divided in different genotypes. Currently, there is a dramatic emergence of DENV-3 genotype III in Latin America. Nevertheless, we still have an incomplete understanding of the evolutionary forces underlying the evolution of this genotype in this region of the world. In order to gain insight into the degree of genetic variability, rates and patterns of evolution of this genotype in Venezuela and the South American region, phylogenetic analysis, based on a large number (n = 119) of envelope gene sequences from DENV-3 genotype III strains isolated in Venezuela from 2001 to 2008, were performed. Phylogenetic analysis revealed an in situ evolution of DENV-3 genotype III following its introduction in the Latin American region, where three different genetic clusters (A to C) can be observed among the DENV-3 genotype III strains circulating in this region. Bayesian coalescent inference analyses revealed an evolutionary rate of 8.48 x 10⁻⁴ substitutions/site/year (s/s/y) for strains of cluster A, composed entirely of strains isolated in Venezuela. Amino acid substitution at position 329 of domain III of the E protein (A→V) was found in almost all E proteins from Cluster A strains. A significant evolutionary change between DENV-3 genotype III strains that circulated in the initial years of the introduction in the continent and strains isolated in the Latin American region in recent years was observed. The presence of DENV-3 genotype III strains belonging to different clusters was observed in Venezuela, revealing several introduction events into this country. The evolutionary rate found for Cluster A strains circulating in Venezuela is similar to the others previously established for this genotype in other regions of the world. This suggests a lack of correlation among DENV genotype III

  15. Evolutionary dynamics of the American African genotype of dengue type 1 virus in India (1962-2005).

    Science.gov (United States)

    Patil, J A; Cherian, S; Walimbe, A M; Patil, B R; Sathe, P S; Shah, P S; Cecilia, D

    2011-08-01

    Dengue is a major health problem in India with all four serotypes represented. Recently there has been an increase in the occurrence of dengue-1 outbreaks. It is possible that there have been changes in the genetics of dengue virus-1 (DENV-1), either by fresh introductions or by evolution in situ. The studies on DENV-1 evolution so far have no Indian sequences included. To gain insight into the dynamics of DENV-1 in India, the envelope (E) gene of thirteen virus isolates representative of the period 1962-2005 were sequenced and analyzed together with the available sequences of 40 globally representative isolates. All the Indian DENV-1 isolates were found to belong to the American African (AMAF) genotype. With the addition of 13 Indian isolates, the AMAF genotype can now be called Cosmopolitan. The Indian isolates were distributed into four lineages, India I, II, III and the Africa lineage, now called Afro-India. Of these, India III was the oldest and extinct lineage; the Afro-India was a transient lineage while India I, imported from Singapore and India II, evolving in situ, were the circulating lineages. Despite the extinction and introduction of lineages, no specific codon site was observed to be under selection pressure. The rate of nucleotide substitution estimated for DENV-1 was 6.5 × 10(-4) substitutions/site/year, and the time to the most recent common ancestor (tMRCA) was estimated to be 78-180 years (1825-1925), similar to previous estimates. The tMRCA for the AMAF/Cosmopolitan genotype was 56-98 years (1907-1949), a period that covers World War I and II. The two imports from Africa (1953-1968) and Singapore (1964-1975) and an export to the Americas (1955-1965) prove that there have been changes in the lineage of the DENV-1 viruses circulating in India which has contributed to the global dynamics of DENV-1 evolution and perhaps to the changing epidemiology of dengue in India. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. An Evolutionary Explanation for the Perturbation of the Dynamics of Metastatic Tumors Induced by Surgery and Acute Inflammation

    Energy Technology Data Exchange (ETDEWEB)

    Bayonas, Alberto Carmona [Department of Hematology and Medical Oncology, Hospital Morales Meseguer, Murcia (Spain)

    2011-03-02

    Surgery has contributed to unveil a tumor behavior that is difficult to reconcile with the models of tumorigenesis based on gradualism. The postsurgical patterns of progression include unexpected features such as distant interactions and variable rhythms. The underlying evidence can be summarized as follows: (1) the resection of the primary tumor is able to accelerate the evolution of micrometastasis in early stages, and (2) the outcome is transiently opposed in advanced tumors. The objective of this paper is to give some insight into tumorigenesis and surgery-related effects, by applying the concepts of the evolutionary theory in those tumor behaviors that gompertzian and tissular-centered models are unable to explain. According to this view, tumors are the consequence of natural selection operating at the somatic level, which is the basic mechanism of tumorigenesis, notwithstanding the complementary role of the intrinsic constrictions of complex networks. A tumor is a complicated phenomenon that entails growth, evolution and development simultaneously. So, an evo-devo perspective can explain how and why tumor subclones are able to translate competition from a metabolic level into neoangiogenesis and the immune response. The paper proposes that distant interactions are an extension of the ecological events at the local level. This notion explains the evolutionary basis for tumor dormancy, and warns against the teleological view of tumorigenesis as a process directed towards the maximization of a concrete trait such as aggressiveness.

  17. The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae.

    Science.gov (United States)

    Markova, Dragomira N; Mason-Gamer, Roberta J

    2015-01-01

    PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF.

  18. Transient Duplication-Dependent Divergence and Horizontal Transfer Underlie the Evolutionary Dynamics of Bacterial Cell-Cell Signaling.

    Directory of Open Access Journals (Sweden)

    Eran Even-Tov

    2016-12-01

    Full Text Available Evolutionary expansion of signaling pathway families often underlies the evolution of regulatory complexity. Expansion requires the acquisition of a novel homologous pathway and the diversification of pathway specificity. Acquisition can occur either vertically, by duplication, or through horizontal transfer, while divergence of specificity is thought to occur through a promiscuous protein intermediate. The way by which these mechanisms shape the evolution of rapidly diverging signaling families is unclear. Here, we examine this question using the highly diversified Rap-Phr cell-cell signaling system, which has undergone massive expansion in the genus Bacillus. To this end, genomic sequence analysis of >300 Bacilli genomes was combined with experimental analysis of the interaction of Rap receptors with Phr autoinducers and downstream targets. Rap-Phr expansion is shown to have occurred independently in multiple Bacillus lineages, with >80 different putative rap-phr alleles evolving in the Bacillius subtilis group alone. The specificity of many rap-phr alleles and the rapid gain and loss of Rap targets are experimentally demonstrated. Strikingly, both horizontal and vertical processes were shown to participate in this expansion, each with a distinct role. Horizontal gene transfer governs the acquisition of already diverged rap-phr alleles, while intralocus duplication and divergence of the phr gene create the promiscuous intermediate required for the divergence of Rap-Phr specificity. Our results suggest a novel role for transient gene duplication and divergence during evolutionary shifts in specificity.

  19. Evolutionary dynamics ofEnterococcus faeciumreveals complex genomic relationships between isolates with independent emergence of vancomycin resistance.

    Science.gov (United States)

    van Hal, Sebastiaan J; Ip, Camilla L C; Ansari, M Azim; Wilson, Daniel J; Espedido, Bjorn A; Jensen, Slade O; Bowden, Rory

    2016-01-19

    Enterococcus faecium , a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn 1549 -like element- vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies.

  20. Indirect evolutionary rescue: prey adapts, predator avoids extinction

    Science.gov (United States)

    Yamamichi, Masato; Miner, Brooks E

    2015-01-01

    Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator–prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term ‘indirect evolutionary rescue’, has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change. PMID:26366196

  1. Gender- and age-related differences in heart rate dynamics: are women more complex than men?

    Science.gov (United States)

    Ryan, S. M.; Goldberger, A. L.; Pincus, S. M.; Mietus, J.; Lipsitz, L. A.

    1994-01-01

    OBJECTIVES. This study aimed to quantify the complex dynamics of beat-to-beat sinus rhythm heart rate fluctuations and to determine their differences as a function of gender and age. BACKGROUND. Recently, measures of heart rate variability and the nonlinear "complexity" of heart rate dynamics have been used as indicators of cardiovascular health. Because women have lower cardiovascular risk and greater longevity than men, we postulated that there are important gender-related differences in beat-to-beat heart rate dynamics. METHODS. We analyzed heart rate dynamics during 8-min segments of continuous electrocardiographic recording in healthy young (20 to 39 years old), middle-aged (40 to 64 years old) and elderly (65 to 90 years old) men (n = 40) and women (n = 27) while they performed spontaneous and metronomic (15 breaths/min) breathing. Relatively high (0.15 to 0.40 Hz) and low (0.01 to 0.15 Hz) frequency components of heart rate variability were computed using spectral analysis. The overall "complexity" of each heart rate time series was quantified by its approximate entropy, a measure of regularity derived from nonlinear dynamics ("chaos" theory). RESULTS. Mean heart rate did not differ between the age groups or genders. High frequency heart rate power and the high/low frequency power ratio decreased with age in both men and women (p gender-as well as age-related differences in heart rate dynamics. Whether these gender differences are related to lower cardiovascular disease risk and greater longevity in women requires further study.

  2. 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...... from a herd, and an intervention effect on a given day. The model was constructed to handle any number of cows, experimental interventions, different data sources, or presence of control groups. In this study, data from 2 commercial Danish herds were used. In herd 1, data on 98,046 and 12,133 milkings......,471) were used. In herd 1, the manager wanted to explore the possibility of reducing the amount of concentrate provided to the cows in an AMS. In herd 2, the manager wanted to know if the milk yield could be increased by elevating the energy level provided to the cows in a total mixed ration. The experiment...

  3. An evolutionary model for collapsing molecular clouds and their star formation activity. II. Mass dependence of the star formation rate

    Energy Technology Data Exchange (ETDEWEB)

    Zamora-Avilés, Manuel; Vázquez-Semadeni, Enrique [Centro de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Apdo. Postal 3-72, Morelia, Michoacán 58089 (Mexico)

    2014-10-01

    We discuss the evolution and dependence on cloud mass of the star formation rate (SFR) and efficiency (SFE) of star-forming molecular clouds (MCs) within the scenario that clouds are undergoing global collapse and that the SFR is controlled by ionization feedback. We find that low-mass clouds (M {sub max} ≲ 10{sup 4} M {sub ☉}) spend most of their evolution at low SFRs, but end their lives with a mini-burst, reaching a peak SFR ∼10{sup 4} M {sub ☉} Myr{sup –1}, although their time-averaged SFR is only (SFR) ∼ 10{sup 2} M {sub ☉} Myr{sup –1}. The corresponding efficiencies are SFE{sub final} ≲ 60% and (SFE) ≲ 1%. For more massive clouds (M {sub max} ≳ 10{sup 5} M {sub ☉}), the SFR first increases and then reaches a plateau because the clouds are influenced by stellar feedback since earlier in their evolution. As a function of cloud mass, (SFR) and (SFE) are well represented by the fits (SFR) ≈ 100(1 + M {sub max}/1.4 × 10{sup 5} M {sub ☉}){sup 1.68} M {sub ☉} Myr{sup –1} and (SFE) ≈ 0.03(M {sub max}/2.5 × 10{sup 5} M {sub ☉}){sup 0.33}, respectively. Moreover, the SFR of our model clouds follows closely the SFR-dense gas mass relation recently found by Lada et al. during the epoch when their instantaneous SFEs are comparable to those of the clouds considered by those authors. Collectively, a Monte Carlo integration of the model-predicted SFR(M) over a Galactic giant molecular cloud mass spectrum yields values for the total Galactic SFR that are within half an order of magnitude of the relation obtained by Gao and Solomon. Our results support the scenario that star-forming MCs may be in global gravitational collapse and that the low observed values of the SFR and SFE are a result of the interruption of each SF episode, caused primarily by the ionizing feedback from massive stars.

  4. Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum.

    Directory of Open Access Journals (Sweden)

    Oliver Ratmann

    2007-11-01

    Full Text Available Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene

  5. Dynamic Line Rating - Technologies and Challenges of PMU on Overhead Lines: A Survey

    DEFF Research Database (Denmark)

    Alvarez, David; Rosero, Javier; Silva, Filipe Miguel Faria da

    2016-01-01

    for line rating computation and monitoring are identified, these are: sensors, communications, management information system and information analysis tools, which are part of integral dynamic line rating systems. Finally, the benefits and challenges of using phasor measurement units for real time capacity...

  6. Dynamic Asset Allocation with Stochastic Income and Interest Rates

    DEFF Research Database (Denmark)

    Munk, Claus; Sørensen, Carsten

    2010-01-01

    We solve for optimal portfolios when interest rates and labor income are stochastic with the expected income growth being affine in the short-term interest rate in order to encompass business cycle variations in wages. Our calibration based on the Panel Study of Income Dynamics (PSID) data supports...

  7. Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids

    Czech Academy of Sciences Publication Activity Database

    Čertner, Martin; Fenclová, E.; Kúr, P.; Kolář, Filip; Koutecký, P.; Krahulcová, Anna; Suda, Jan

    2017-01-01

    Roč. 120, č. 2 (2017), s. 303-315 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : cytotype coesxistence * flow cytometry * temporal dynamics Subject RIV: EF - Botanics Impact factor: 4.041, year: 2016

  8. 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.

  9. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    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......, 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......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...

  10. [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.

  11. Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection.

    Directory of Open Access Journals (Sweden)

    Nils Poulicard

    2016-08-01

    Full Text Available This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin. Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound

  12. Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection.

    Science.gov (United States)

    Poulicard, Nils; Pacios, Luis Fernández; Gallois, Jean-Luc; Piñero, Daniel; García-Arenal, Fernando

    2016-08-01

    This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the

  13. DYPHORA—a dynamic model for the rate of photosynthesis of algae

    OpenAIRE

    Pahl-Wostl, C.; Imboden, D.M.

    2017-01-01

    Experimental data obtained from different cultures of phytoplankton indicate that photosynthesis (P) depends on light intensity (I) in a dynamic way. Therefore, static P/I curves relating photosynthesis to the instantaneous light may not be adequate to describe the activity of algal cells in lakes or oceans where mixing can cause a complex pattern of light variation. The model DYPHORA (DYnamic model for the PHOtosynthetic Rate of Algae) describes the response of photosynthesis to light using ...

  14. The evolutionary strategies of plant defenses have a dynamic impact on the adaptations and interactions of vectors and pathogens.

    Science.gov (United States)

    Huot, Ordom Brian; Nachappa, Punya; Tamborindeguy, Cecilia

    2013-06-01

    Plants have evolved and diversified to reduce the damages imposed by infectious pathogens and herbivorous insects. Living in a sedentary lifestyle, plants are constantly adapting to their environment. They employ various strategies to increase performance and fitness. Thus, plants developed cost-effective strategies to defend against specific insects and pathogens. Plant defense, however, imposes selective pressure on insects and pathogens. This selective pressure provides incentives for pathogens and insects to diversify and develop strategies to counter plant defense. This results in an evolutionary arms race among plants, pathogens and insects. The ever-changing adaptations and physiological alterations among these organisms make studying plant-vector-pathogen interactions a challenging and fascinating field. Studying plant defense and plant protection requires knowledge of the relationship among organisms and the adaptive strategies each organism utilize. Therefore, this review focuses on the integral parts of plant-vector-pathogen interactions in order to understand the factors that affect plant defense and disease development. The review addresses plant-vector-pathogen co-evolution, plant defense strategies, specificity of plant defenses and plant-vector-pathogen interactions. Improving the comprehension of these factors will provide a multi-dimensional perspective for the future research in pest and disease management. © 2012 Institute of Zoology, Chinese Academy of Sciences.

  15. Short- and long-term variations in non-linear dynamics of heart rate variability

    DEFF Research Database (Denmark)

    Kanters, J K; Højgaard, M V; Agner, E

    1996-01-01

    variability. METHODS: Twelve healthy subjects were investigated by 3-h ambulatory ECG recordings repeated on 3 separate days. Correlation dimension, non-linear predictability, mean heart rate, and heart rate variability in the time and frequency domains were measured and compared with the results from......OBJECTIVES: The purpose of the study was to investigate the short- and long-term variations in the non-linear dynamics of heart rate variability, and to determine the relationships between conventional time and frequency domain methods and the newer non-linear methods of characterizing heart rate...... corresponding surrogate time series. RESULTS: A small significant amount of non-linear dynamics exists in heart rate variability. Correlation dimensions and non-linear predictability are relatively specific parameters for each individual examined. The correlation dimension is inversely correlated to the heart...

  16. The Dynamics of an Eco-Epidemiological Model with Nonlinear Incidence Rate

    Directory of Open Access Journals (Sweden)

    Raid Kamel Naji

    2012-01-01

    Full Text Available This paper treats the dynamical behavior of eco-epidemiological model with nonlinear incidence rate. A Holling type II prey-predator model with SI-type of disease in prey has been proposed and analyzed. The existence, uniqueness, and boundedness of the solution of the system are studied. The local and global dynamical behaviors are investigated. The conditions, which guarantee the occurring of Hopf bifurcation of the system, are established. Finally, further investigations for the global dynamics of the proposed system are carried out with the help of numerical simulations.

  17. Application of biomarkers in cancer risk management: evaluation from stochastic clonal evolutionary and dynamic system optimization points of view.

    Directory of Open Access Journals (Sweden)

    Xiaohong Li

    2011-02-01

    Full Text Available Aside from primary prevention, early detection remains the most effective way to decrease mortality associated with the majority of solid cancers. Previous cancer screening models are largely based on classification of at-risk populations into three conceptually defined groups (normal, cancer without symptoms, and cancer with symptoms. Unfortunately, this approach has achieved limited successes in reducing cancer mortality. With advances in molecular biology and genomic technologies, many candidate somatic genetic and epigenetic "biomarkers" have been identified as potential predictors of cancer risk. However, none have yet been validated as robust predictors of progression to cancer or shown to reduce cancer mortality. In this Perspective, we first define the necessary and sufficient conditions for precise prediction of future cancer development and early cancer detection within a simple physical model framework. We then evaluate cancer risk prediction and early detection from a dynamic clonal evolution point of view, examining the implications of dynamic clonal evolution of biomarkers and the application of clonal evolution for cancer risk management in clinical practice. Finally, we propose a framework to guide future collaborative research between mathematical modelers and biomarker researchers to design studies to investigate and model dynamic clonal evolution. This approach will allow optimization of available resources for cancer control and intervention timing based on molecular biomarkers in predicting cancer among various risk subsets that dynamically evolve over time.

  18. The Seasonal Dynamics of Artificial Nest Predation Rates along Edges in a Mosaic Managed Reedbed.

    Directory of Open Access Journals (Sweden)

    Iain Malzer

    Full Text Available Boundaries between different habitats can be responsible for changes in species interactions, including modified rates of encounter between predators and prey. Such 'edge effects' have been reported in nesting birds, where nest predation rates can be increased at habitat edges. The literature concerning edge effects on nest predation rates reveals a wide variation in results, even within single habitats, suggesting edge effects are not fixed, but dynamic throughout space and time. This study demonstrates the importance of considering dynamic mechanisms underlying edge effects and their relevance when undertaking habitat management. In reedbed habitats, management in the form of mosaic winter reed cutting can create extensive edges which change rapidly with reed regrowth during spring. We investigate the seasonal dynamics of reedbed edges using an artificial nest experiment based on the breeding biology of a reedbed specialist. We first demonstrate that nest predation decreases with increasing distance from the edge of cut reed blocks, suggesting edge effects have a pivotal role in this system. Using repeats throughout the breeding season we then confirm that nest predation rates are temporally dynamic and decline with the regrowth of reed. However, effects of edges on nest predation were consistent throughout the season. These results are of practical importance when considering appropriate habitat management, suggesting that reed cutting may heighten nest predation, especially before new growth matures. They also contribute directly to an overall understanding of the dynamic processes underlying edge effects and their potential role as drivers of time-dependent habitat use.

  19. The Seasonal Dynamics of Artificial Nest Predation Rates along Edges in a Mosaic Managed Reedbed.

    Science.gov (United States)

    Malzer, Iain; Helm, Barbara

    2015-01-01

    Boundaries between different habitats can be responsible for changes in species interactions, including modified rates of encounter between predators and prey. Such 'edge effects' have been reported in nesting birds, where nest predation rates can be increased at habitat edges. The literature concerning edge effects on nest predation rates reveals a wide variation in results, even within single habitats, suggesting edge effects are not fixed, but dynamic throughout space and time. This study demonstrates the importance of considering dynamic mechanisms underlying edge effects and their relevance when undertaking habitat management. In reedbed habitats, management in the form of mosaic winter reed cutting can create extensive edges which change rapidly with reed regrowth during spring. We investigate the seasonal dynamics of reedbed edges using an artificial nest experiment based on the breeding biology of a reedbed specialist. We first demonstrate that nest predation decreases with increasing distance from the edge of cut reed blocks, suggesting edge effects have a pivotal role in this system. Using repeats throughout the breeding season we then confirm that nest predation rates are temporally dynamic and decline with the regrowth of reed. However, effects of edges on nest predation were consistent throughout the season. These results are of practical importance when considering appropriate habitat management, suggesting that reed cutting may heighten nest predation, especially before new growth matures. They also contribute directly to an overall understanding of the dynamic processes underlying edge effects and their potential role as drivers of time-dependent habitat use.

  20. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

    Directory of Open Access Journals (Sweden)

    Olivier Arnaiz

    Full Text Available Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a

  1. Random walk in genome space: A key ingredient of intermittent dynamics of community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke

    2010-06-01

    Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species, while migrants have no correlation with the resident species. It is found that the dynamics of community assembly with mutations are quite different from the case with migrations. In contrast to mutation models, which show intermittent dynamics of quasi-steady states interrupted by sudden reorganizations of the community, migration models show smooth and gradual renewal of the community. As a consequence, instead of the 1/f diversity fluctuations found for the mutation models, 1/f2, random-walk like fluctuations are observed for the migration models. In addition, a characteristic species-lifetime distribution is found: a power law that is cut off by a "skewed" distribution in the long-lifetime regime. The latter has a longer tail than a simple exponential function, which indicates an age-dependent species-mortality function. Since this characteristic profile has been observed, both in fossil data and in several other mathematical models, we conclude that it is a universal feature of macroevolution. © 2010 Elsevier Ltd.

  2. Paradoxical persistence through mixed-system dynamics: towards a unified perspective of reversal behaviours in evolutionary ecology

    Science.gov (United States)

    Williams, Paul David; Hastings, Alan

    2011-01-01

    Counterintuitive dynamics of various biological phenomena occur when composite system dynamics differ qualitatively from that of their component systems. Such composite systems typically arise when modelling situations with time-varying biotic or abiotic conditions, and examples range from metapopulation dynamics to population genetic models. These biological, and related physical, phenomena can often be modelled as simple financial games, wherein capital is gained and lost through gambling. Such games have been developed and used as heuristic devices to elucidate the processes at work in generating seemingly paradoxical outcomes across a spectrum of disciplines, albeit in a field-specific, ad hoc fashion. Here, we propose that studying these simple games can provide a much deeper understanding of the fundamental principles governing paradoxical behaviours in models from a diversity of topics in evolution and ecology in which fluctuating environmental effects, whether deterministic or stochastic, are an essential aspect of the phenomenon of interest. Of particular note, we find that, for a broad class of models, the ecological concept of equilibrium reactivity provides an intuitive necessary condition that must be satisfied in order for environmental variability to promote population persistence. We contend that further investigations along these lines promise to unify aspects of the study of a range of topics, bringing questions from genetics, species persistence and coexistence and the evolution of bet-hedging strategies, under a common theoretical purview. PMID:21270032

  3. Dynamic Mechanical Response of Biomedical 316L Stainless Steel as Function of Strain Rate and Temperature.

    Science.gov (United States)

    Lee, Woei-Shyan; Chen, Tao-Hsing; Lin, Chi-Feng; Luo, Wen-Zhen

    2011-01-01

    A split Hopkinson pressure bar is used to investigate the dynamic mechanical properties of biomedical 316L stainless steel under strain rates ranging from 1 × 10(3) s(-1) to 5 × 10(3) s(-1) and temperatures between 25°C and 800°C. The results indicate that the flow stress, work-hardening rate, strain rate sensitivity, and thermal activation energy are all significantly dependent on the strain, strain rate, and temperature. For a constant temperature, the flow stress, work-hardening rate, and strain rate sensitivity increase with increasing strain rate, while the thermal activation energy decreases. Catastrophic failure occurs only for the specimens deformed at a strain rate of 5 × 10(3) s(-1) and temperatures of 25°C or 200°C. Scanning electron microscopy observations show that the specimens fracture in a ductile shear mode. Optical microscopy analyses reveal that the number of slip bands within the grains increases with an increasing strain rate. Moreover, a dynamic recrystallisation of the deformed microstructure is observed in the specimens tested at the highest temperature of 800°C.

  4. Incorporating evolutionary processes into population viability models.

    Science.gov (United States)

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

  5. Bilateral interactions in disease dynamics - Decreasing epidemic thresholds with facilitated contact rates

    Science.gov (United States)

    Morales Gallardo, Alejandro; Brockmann, Dirk; Geisel, Theo

    2008-03-01

    Compartmental epidemiological models are very successful modeling paradigms in epidemiology. Typically, they are employed for quantitative assessments of key parameters such as the basic reproduction number R0. These models rest on two key assumptions: 1.) a population is well mixed 2.) transmission is triggered by a population averaged contact rate. However, experimental evidence shows that contact rates vary substantially, and it has been hypothesized that this variability can change the dynamics of population relevant disease dynamics. However, for inhomogeneous populations the translation of distributed contact rates into effective disease transmission events is non-trivial. Transmission may either depend only on the contact rate of the transmitting individual alone (unilateral transmission), or on the contact rates of transmitting and receiving individual (bilateral transmission). In the SIS model we show that in either systems the endemic state of a disease can be stable for values of R0<1 unlike homogeneous systems with a critical value R0=1. Furthermore, bilateral contact dynamics entail parameter regimes in which a stable endemic state can cease to exist if the mean contact rate is increased, an unexpected effect absent in homogeneous populations.

  6. Nonparametric modeling of US interest rate term structure dynamics and implications on the prices of derivative securities

    NARCIS (Netherlands)

    Jiang, GJ

    1998-01-01

    This paper develops a nonparametric model of interest rate term structure dynamics based an a spot rate process that permits only positive interest rates and a market price of interest rate risk that precludes arbitrage opportunities. Both the spot rate process and the market price of interest rate

  7. Adaptation and habitat selection in the eco-evolutionary process.

    Science.gov (United States)

    Morris, Douglas W

    2011-08-22

    The struggle for existence occurs through the vital rates of population growth. This basic fact demonstrates the tight connection between ecology and evolution that defines the emerging field of eco-evolutionary dynamics. An effective synthesis of the interdependencies between ecology and evolution is grounded in six principles. The mechanics of evolution specifies the origin and rules governing traits and evolutionary strategies. Traits and evolutionary strategies achieve their selective value through their functional relationships with fitness. Function depends on the underlying structure of variation and the temporal, spatial and organizational scales of evolution. An understanding of how changes in traits and strategies occur requires conjoining ecological and evolutionary dynamics. Adaptation merges these five pillars to achieve a comprehensive understanding of ecological and evolutionary change. I demonstrate the value of this world-view with reference to the theory and practice of habitat selection. The theory allows us to assess evolutionarily stable strategies and states of habitat selection, and to draw the adaptive landscapes for habitat-selecting species. The landscapes can then be used to forecast future evolution under a variety of climate change and other scenarios.

  8. Dynamics of Rate of Returns for Postgraduate Education in Taiwan: The Impact of Higher Education Expansion

    Science.gov (United States)

    Yang, Chih-Hai; Lin, Chun-Hung A.; Lin, Chien-Ru

    2011-01-01

    This paper analyzes the dynamics of rate of returns for postgraduate education and the determinants of wage premiums for postgraduate labor, especially for the impact of higher education expansions, in terms of quantity and quality, since the late 1990s in Taiwan. Utilizing quasi-panel data over the 1990-2004 period and employing the double fixed…

  9. Reduced Sensitivity to Slow-Rate Dynamic Auditory Information in Children with Dyslexia

    Science.gov (United States)

    Poelmans, Hanne; Luts, Heleen; Vandermosten, Maaike; Boets, Bart; Ghesquiere, Pol; Wouters, Jan

    2011-01-01

    The etiology of developmental dyslexia remains widely debated. An appealing theory postulates that the reading and spelling problems in individuals with dyslexia originate from reduced sensitivity to slow-rate dynamic auditory cues. This low-level auditory deficit is thought to provoke a cascade of effects, including inaccurate speech perception…

  10. Selection Dynamics in Joint Matching to Rate and Magnitude of Reinforcement

    Science.gov (United States)

    McDowell, J. J.; Popa, Andrei; Calvin, Nicholas T.

    2012-01-01

    Virtual organisms animated by a selectionist theory of behavior dynamics worked on concurrent random interval schedules where both the rate and magnitude of reinforcement were varied. The selectionist theory consists of a set of simple rules of selection, recombination, and mutation that act on a population of potential behaviors by means of a…

  11. Quantifying collective effervescence: Heart-rate dynamics at a fire-walking ritual

    DEFF Research Database (Denmark)

    Xygalatas, Dimitris; Konvalinka, Ivana; Roepstorff, Andreas

    2011-01-01

    solidarity, yet quantitative evidence for these conjectures is scarce. Our recent study measured the physiological effects of a highly arousing Spanish fire-walking ritual, revealing shared patterns in heart-rate dynamics between participants and related spectators. We briefly describe our results...

  12. State Anxiety and Nonlinear Dynamics of Heart Rate Variability in Students.

    Directory of Open Access Journals (Sweden)

    Dimitriy A Dimitriev

    Full Text Available Clinical and experimental research studies have demonstrated that the emotional experience of anxiety impairs heart rate variability (HRV in humans. The present study investigated whether changes in state anxiety (SA can also modulate nonlinear dynamics of heart rate.A group of 96 students volunteered to participate in the study. For each student, two 5-minute recordings of beat intervals (RR were performed: one during a rest period and one just before a university examination, which was assumed to be a real-life stressor. Nonlinear analysis of HRV was performed. The Spielberger's State-Trait Anxiety Inventory was used to assess the level of SA.Before adjusting for heart rate, a Wilcoxon matched pairs test showed significant decreases in Poincaré plot measures, entropy, largest Lyapunov exponent (LLE, and pointwise correlation dimension (PD2, and an increase in the short-term fractal-like scaling exponent of detrended fluctuation analysis (α1 during the exam session, compared with the rest period. A Pearson analysis indicated significant negative correlations between the dynamics of SA and Poincaré plot axes ratio (SD1/SD2, and between changes in SA and changes in entropy measures. A strong negative correlation was found between the dynamics of SA and LLE. A significant positive correlation was found between the dynamics of SA and α1. The decreases in Poincaré plot measures (SD1, complex correlation measure, entropy measures, and LLE were still significant after adjusting for heart rate. Corrected α1 was increased during the exam session. As before, the dynamics of adjusted LLE was significantly correlated with the dynamics of SA.The qualitative increase in SA during academic examination was related to the decrease in the complexity and size of the Poincaré plot through a reduction of both the interbeat interval and its variation.

  13. Blink rate, blink amplitude, and tear film integrity during dynamic visual display terminal tasks.

    Science.gov (United States)

    Cardona, Genís; García, Carles; Serés, Carme; Vilaseca, Meritxell; Gispets, Joan

    2011-03-01

    The present study aimed at investigating the influence of the level of dynamism of two different visual display terminal tasks on spontaneous eyeblink rate, blink amplitude, and tear film integrity. A total of 25 healthy, young volunteers participated in the study. Blink rate and blink amplitude were recorded in silent primary gaze conditions and while subjects were playing two computer games of similar cognitive demands but different rate of visual information presentation. For each experimental condition, tear volume was evaluated by measuring meniscus height and with the red phenol thread test. Fluorescein and non-invasive break-up time tests, as well as the observation of interference patterns and the estimation of the dry area extension, were employed to assess tear stability. Statistically significant differences were revealed in blink rate (F = 595.85, p blink amplitude (χ(2) = 34.00, p blink rate during fast- and slow-paced game play decreasing to almost 1/3 and 1/2 of baseline levels, respectively, and with a larger percentage of incomplete blinks during dynamic tasks. Fluorescein and non-invasive break-up time tests and dry area extension were able to differentiate between experimental conditions in general (F = 408.42, p Blink rate, blink amplitude, and tear film stability were compromised during the most dynamic visual display terminal task, suggesting a negative influence of not only the cognitive aspects of the task, but also of the rate at which new visual information is presented. Frequent breaks and blinking awareness training are recommended for visual display terminal users requiring prolonged periods of visually demanding dynamic computer play or work.

  14. Evolutionary institutionalism.

    Science.gov (United States)

    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.

  15. Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s

    Science.gov (United States)

    Parvez, Mohammad; Qhanya, Lehlohonolo Benedict; Mthakathi, Ntsane Trevor; Kgosiemang, Ipeleng Kopano Rosinah; Bamal, Hans Denis; Pagadala, Nataraj Sekhar; Xie, Ting; Yang, Haoran; Chen, Hengye; Theron, Chrispian William; Monyaki, Richie; Raselemane, Seiso Caiphus; Salewe, Vuyani; Mongale, Bogadi Lorato; Matowane, Retshedisitswe Godfrey; Abdalla, Sara Mohamed Hasaan; Booi, Wool Isaac; van Wyk, Mari; Olivier, Dedré; Boucher, Charlotte E.; Nelson, David R.; Tuszynski, Jack A.; Blackburn, Jonathan Michael; Yu, Jae-Hyuk; Mashele, Samson Sitheni; Chen, Wanping; Syed, Khajamohiddin

    2016-01-01

    Since the initial identification of cytochrome P450 monooxygenases (CYPs/P450s), great progress has been made in understanding their structure-function relationship, diversity and application in producing compounds beneficial to humans. However, the molecular evolution of P450s in terms of their dynamics both at protein and DNA levels and functional conservation across kingdoms still needs investigation. In this study, we analyzed 17 598 P450s belonging to 113 P450 families (bacteria −42; fungi −19; plant −28; animal −22; plant and animal −1 and common P450 family −1) and found highly conserved and rapidly evolving P450 families. Results suggested that bacterial P450s, particularly P450s belonging to mycobacteria, are highly conserved both at protein and DNA levels. Mycobacteria possess the highest P450 diversity percentage compared to other microbes and have a high coverage of P450s (≥1%) in their genomes, as found in fungi and plants. Phylogenetic and functional analyses revealed the functional conservation of P450s despite belonging to different biological kingdoms, suggesting the adherence of P450s to their innate function such as their involvement in either generation or oxidation of steroids and structurally related molecules, fatty acids and terpenoids. This study’s results offer new understanding of the dynamic structural nature of P450s. PMID:27616185

  16. Computational modeling of dynamic mechanical properties of pure polycrystalline magnesium under high loading strain rates

    Directory of Open Access Journals (Sweden)

    Li Qizhen

    2015-01-01

    Full Text Available Computational simulations were performed to investigate the dynamic mechanical behavior of pure polycrystalline magnesium under different high loading strain rates with the values of 800, 1000, 2000, and 3600 s−1. The Johnson-Cook model was utilized in the simulations based on finite element modeling. The results showed that the simulations provided well-matched predictions of the material behavior such as the strain rate-time history, the stress-strain curve, and the temperature increase. Under high loading strain rates, the tested material experienced linear strain hardening at the early stage of plastic deformation, increased strain hardening at the intermediate plastic deformation region, and decreased strain hardening at the region before fracture. The strain hardening rates for the studied high loading strain rate cases do not vary much with the change of strain rates.

  17. INVESTIGATION OF A DYNAMIC POWER LINE RATING CONCEPT FOR IMPROVED WIND ENERGY INTEGRATION OVER COMPLEX TERRAIN

    Energy Technology Data Exchange (ETDEWEB)

    Jake P. Gentle; Kurt S Myers; Tyler B Phillips; Inanc Senocak; Phil Anderson

    2014-08-01

    Dynamic Line Rating (DLR) is a smart grid technology that allows the rating of power line to be based on real-time conductor temperature dependent on local weather conditions. In current practice overhead power lines are generally given a conservative rating based on worst case weather conditions. Using historical weather data collected over a test bed area, we demonstrate there is often additional transmission capacity not being utilized with the current static rating practice. We investigate a new dynamic line rating methodology using computational fluid dynamics (CFD) to determine wind conditions along transmission lines at dense intervals. Simulated results are used to determine conductor temperature by calculating the transient thermal response of the conductor under variable environmental conditions. In calculating the conductor temperature, we use both a calculation with steady-state assumption and a transient calculation. Under low wind conditions, steady-state assumption predicts higher conductor temperatures that could lead to curtailments, whereas transient calculations produce conductor temperatures that are significantly lower, implying the availability of additional transmission capacity.

  18. Analyzing the effect of high repetition laser shock peening on dynamic corrosion rate of magnesium

    Science.gov (United States)

    Caralapatti, Vinodh Krishna; Narayanswamy, Sivakumar

    2017-08-01

    Magnesium as implant material is being investigated extensively due to its superior suitability. With corrosion rate being the major obstacle, this paper aims to determine the effects of high repetition laser shock peening (HRLSP) on the dynamic corrosion rate of magnesium. While there is lot of research on corrosion of magnesium, in this work, a specially designed test bench was used for characterization of dynamic corrosion to mimic the physiological conditions experienced by the implant inside human body. From the results, it can be inferred that corrosion rate of peened samples reduced by at least 6 times compared to unpeened sample and sample peened with 66% overlap 1 scans exhibited the least corrosion. The wettability of the samples was also determined as a measure to analyze the effects of HRLSP on biocompatibility. In addition, peening is seen to induce surface corrosion, which minimizes the risks of implant failure.

  19. Influence of forced respiration on nonlinear dynamics in heart rate variability

    DEFF Research Database (Denmark)

    Kanters, J K; Højgaard, M V; Agner, E

    1997-01-01

    of this study was to test whether the known nonlinear input from spontaneous respiration is a source for the nonlinearities in heart rate variability. Twelve healthy subjects were examined in supine position with 3-h electrocardiogram recordings during both spontaneous and forced respiration in accordance...... expressed as the nonlinear prediction error did not differ between spontaneous respiration, 32.3 +/- 3.4 ms, and forced respiration, 31.9 +/- 5.7. It is concluded that the origin of the nonlinear dynamics in heart rate variability is not a nonlinear input from the respiration into the cardiovascular...... oscillator. Additional studies are needed to elucidate the mechanisms behind the nonlinear dynamics in heart rate variability....

  20. Theory of fads: Traveling-wave solution of evolutionary dynamics in a one-dimensional trait space

    Science.gov (United States)

    Lee, Mi Jin; Yi, Su Do; Kim, Beom Jun; Baek, Seung Ki

    2015-01-01

    We consider an infinite-sized population where an infinite number of traits compete simultaneously. The replicator equation with a diffusive term describes time evolution of the probability distribution over the traits due to selection and mutation on a mean-field level. We argue that this dynamics can be expressed as a variant of the Fisher equation with high-order correction terms. The equation has a traveling-wave solution, and the phase-space method shows how the wave shape depends on the correction. We compare this solution with empirical time-series data of given names in Quebec, treating it as a descriptive model for the observed patterns. Our model explains the reason that many names exhibit a similar pattern of the rise and fall as time goes by. At the same time, we have found that their dissimilarities are also statistically significant.

  1. Theory of fads: traveling-wave solution of evolutionary dynamics in a one-dimensional trait space.

    Science.gov (United States)

    Lee, Mi Jin; Yi, Su Do; Kim, Beom Jun; Baek, Seung Ki

    2015-01-01

    We consider an infinite-sized population where an infinite number of traits compete simultaneously. The replicator equation with a diffusive term describes time evolution of the probability distribution over the traits due to selection and mutation on a mean-field level. We argue that this dynamics can be expressed as a variant of the Fisher equation with high-order correction terms. The equation has a traveling-wave solution, and the phase-space method shows how the wave shape depends on the correction. We compare this solution with empirical time-series data of given names in Quebec, treating it as a descriptive model for the observed patterns. Our model explains the reason that many names exhibit a similar pattern of the rise and fall as time goes by. At the same time, we have found that their dissimilarities are also statistically significant.

  2. How far could we make ourselves understood by the Andromedans? - an evolutionary cybernetic problem in hierarchical dynamics

    Science.gov (United States)

    Santoli, Salvatore

    1994-01-01

    The mechanistic interpretation of the communication process between cognitive hierarchical systems as an iterated pair of convolutions between the incoming discrete time series signals and the chaotic dynamics (CD) at the nm-scale of the perception (energy) wetware level, with the consequent feeding of the resulting collective properties to the CD software (symbolic) level, shows that the category of quality, largely present in Galilean quantitative-minded science, is to be increasingly made into quantity for finding optimum common codes for communication between different intelligent beings. The problem is similar to that solved by biological evolution, of communication between the conscious logic brain and the underlying unfelt ultimate extra-logical processes, as well as to the problem of the mind-body or the structure-function dichotomies. Perspective cybernated nanotechnological and/or nanobiological interfaces, and time evolution of the 'contact language' (the iterated dialogic process) as a self-organising system might improve human-alien understanding.

  3. Sodium sulfate impacts feeding, specific dynamic action, and growth rate in the freshwater bivalve Corbicula fluminea.

    Science.gov (United States)

    Soucek, David John

    2007-08-01

    Sodium sulfate is a ubiquitous salt that reaches toxic concentrations due to mining and other industrial activities, yet is currently unregulated at the Federal level in the United States. Previous studies have documented reduced growth of clams downstream of sulfate-dominated effluents, altered bioenergetics in filter-feeding invertebrates, and interactions between sulfate and other toxicants. Therefore, the purpose of this study was to determine if sodium sulfate affects the bioenergetics of the filter-feeding, freshwater bivalve, Corbicula fluminea, and the mechanism by which the effects are elicited. In addition to measuring effects on feeding, respiration and growth rates, I evaluated the relative sensitivity of a green algae consumed by clams to determine if top-down or bottom-up effects might be exhibited under field conditions. This study demonstrated that sodium sulfate had no effect on basal metabolic rates, but significantly reduced the feeding, post-feeding metabolic, and growth rates of C. fluminea. The proposed mechanism for these impacts is that filtering rates are reduced upon exposure, resulting in reduced food consumption and therefore, preventing increased metabolic rates normally associated with post-feeding specific dynamic action (SDA). In the field, these effects may cause changes in whole stream respiration rates and organic matter dynamics, as well as alter uptake rates of other food-associated contaminants like selenium, the toxicity of which is known to be antagonized by sulfate, in filter-feeding bivalves.

  4. Credit Rating via Dynamic Slack-Based Measure And It´s Optimal Investment Strategy

    Directory of Open Access Journals (Sweden)

    A. Delavarkhalafi

    2015-01-01

    Full Text Available In this paper we check the credit rating of firms applied for a loan. In this regard we introduce a model, named Dynamic Slack-Based Measure (DSBM for measuring credit rating of applicant companies. Selection of financial ratios that represent the financial state of a company -in the best possible way- is one of the most challenging parts of any credit rating analysis. At first, ranking needs to identify the appropriate variables. Therefore we introduce five financial variables to provide a ranking. As noted above, we assess the performance of these firms. Then we introduce the dynamic model of SBM and theorems, also we discuss the overall structure of DSBM. Then we will present the implementation and the simulation model. After that, we propose a stochastic controlled dynamic system model to express the optimal strategy. Banks expect companies selected with DSBM model, act in accordance with this strategy. This stochastic dynamic system is originated from the balance sheets of firms applying for a loan. Finally we evaluate the performance of the system and strategy problem.

  5. 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...

  6. Environment determines evolutionary trajectory in a constrained phenotypic space.

    Science.gov (United States)

    Fraebel, David T; Mickalide, Harry; Schnitkey, Diane; Merritt, Jason; Kuhlman, Thomas E; Kuehn, Seppe

    2017-03-27

    Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory.

  7. Dynamic Programming Optimization of Multi-rate Multicast Video-Streaming Services

    Directory of Open Access Journals (Sweden)

    Nestor Michael Caños Tiglao

    2010-06-01

    Full Text Available In large scale IP Television (IPTV and Mobile TV distributions, the video signal is typically encoded and transmitted using several quality streams, over IP Multicast channels, to several groups of receivers, which are classified in terms of their reception rate. As the number of video streams is usually constrained by both the number of TV channels and the maximum capacity of the content distribution network, it is necessary to find the selection of video stream transmission rates that maximizes the overall user satisfaction. In order to efficiently solve this problem, this paper proposes the Dynamic Programming Multi-rate Optimization (DPMO algorithm. The latter was comparatively evaluated considering several user distributions, featuring different access rate patterns. The experimental results reveal that DPMO is significantly more efficient than exhaustive search, while presenting slightly higher execution times than the non-optimal Multi-rate Step Search (MSS algorithm.

  8. Dynamics of heart rate parameters in students with various personal anxiety levels during computerized testing.

    Science.gov (United States)

    Dzhebrailova, T D; Sulejmanova, R G

    2012-09-01

    Students with low level of initial (pre-test) personal anxiety demonstrated a high level of modulating effects on the heart rate in all basic frequency ranges (VLF, LF, and HF) resulting in a greater total power of heart rate variability spectrum compared to students with high personal anxiety. The peculiarities of dynamics of heart rate variability were revealed during a real learning task, which correlated with personal anxiety level. In comparison with highly anxious students, the low-anxious group demonstrated more pronounced drop in the power of all ranges of the heart rate variability spectrum during testing followed by restoration of these power indices to initial levels after completion of the test. In contrast, the drop of the total power of the heart rate variability spectrum and in the power of its individual components persisted in students with high anxiety level even after the end of the testing.

  9. An effective chaos-geometric computational approach to analysis and prediction of evolutionary dynamics of the environmental systems: Atmospheric pollution dynamics

    Science.gov (United States)

    Buyadzhi, V. V.; Glushkov, A. V.; Khetselius, O. Yu; Bunyakova, Yu Ya; Florko, T. A.; Agayar, E. V.; Solyanikova, E. P.

    2017-10-01

    The present paper concerns the results of computational studying dynamics of the atmospheric pollutants (dioxide of nitrogen, sulphur etc) concentrations in an atmosphere of the industrial cities (Odessa) by using the dynamical systems and chaos theory methods. A chaotic behaviour in the nitrogen dioxide and sulphurous anhydride concentration time series at several sites of the Odessa city is numerically investigated. As usually, to reconstruct the corresponding attractor, the time delay and embedding dimension are needed. The former is determined by the methods of autocorrelation function and average mutual information, and the latter is calculated by means of a correlation dimension method and algorithm of false nearest neighbours. Further, the Lyapunov’s exponents spectrum, Kaplan-Yorke dimension and Kolmogorov entropy are computed. It has been found an existence of a low-D chaos in the time series of the atmospheric pollutants concentrations.

  10. Time-Scaled Evolutionary Analysis of the Transmission and Antibiotic Resistance Dynamics of Staphylococcus aureus Clonal Complex 398

    Science.gov (United States)

    Gibbons, C. L.; McAdam, P. R.; van Bunnik, B. A. D.; Girvan, E. K.; Edwards, G. F.; Fitzgerald, J. R.; Woolhouse, M. E. J.

    2014-01-01

    Staphylococcus aureus clonal complex 398 (CC398) is associated with disease in humans and livestock, and its origins and transmission have generated considerable interest. We performed a time-scaled phylogenetic analysis of CC398, including sequenced isolates from the United Kingdom (Scotland), along with publicly available genomes. Using state-of-the-art methods for mapping traits onto phylogenies, we quantified transitions between host species to identify sink and source populations for CC398 and employed a novel approach to investigate the gain and loss of antibiotic resistance in CC398 over time. We identified distinct human- and livestock-associated CC398 clades and observed multiple transmissions of CC398 from livestock to humans and between countries, lending quantitative support to previous reports. Of note, we identified a subclade within the livestock-associated clade comprised of isolates from hospital environments and newborn babies, suggesting that livestock-associated CC398 is capable of onward transmission in hospitals. In addition, our analysis revealed significant differences in the dynamics of resistance to methicillin and tetracycline related to contrasting historical patterns of antibiotic usage between the livestock industry and human medicine. We also identified significant differences in patterns of gain and loss of different tetracycline resistance determinants, which we ascribe to epistatic interactions between the resistance genes and/or differences in the modes of inheritance of the resistance determinants. PMID:25239891

  11. Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia.

    Science.gov (United States)

    Wei, K; Lin, Y; Xie, D

    2015-06-01

    Southeast Asia has been the breeding ground for many emerging diseases in the past decade, and it is in this region that new genetic variants of HPAI H5N1 viruses have been emerging. Cross-border movement of animals accelerates the spread of H5N1, and the changing environmental conditions also exert strong selective pressure on the viruses. The transboundary zoonotic diseases caused by H5N1 pose a serious and continual threat to global economy and public health. Here, we divided the H5N1 viruses isolated in Southeast Asia during 2003-2009 into four groups according to their phylogenetic relationships among HA gene sequences. Molecular evolution analysis suggests populations in expansion rather than a positive selection for group 2 and group 3, yet group 4 is under strong positive selection. Site 193 was found to be a potential glycosylation site and located in receptor-binding domain. Note that site 193 tends to appear in avian isolates instead of human strains. Population dynamics analysis reveals that the effective population size of infections in Southeast Asia has undergone three obvious increases, and the results are consistent with the epidemiological analysis. Ecological and phylogeographical analyses show that agro-ecological environments, migratory birds, domestic waterfowl, especially free-ranging ducks, are crucial in the occurrence, maintenance and spread of H5N1 virus. The epidemiological links between Indonesia and Suphanburi observed suggest that viruses in Indonesia were originated from multiple introductions. © 2013 Blackwell Verlag GmbH.

  12. Genomics of adaptation depends on the rate of environmental change in experimental yeast populations

    NARCIS (Netherlands)

    Gorter, F.A.; Derks, M.F.L.; Heuvel, van den J.; Aarts, M.G.M.; Zwaan, B.J.; Ridder, de D.; Visser, de J.A.G.M.

    2017-01-01

    The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae

  13. Invasive species as drivers of evolutionary change: cane toads in tropical Australia.

    Science.gov (United States)

    Shine, Richard

    2012-02-01

    The arrival of an invasive species can have wide-ranging ecological impacts on native taxa, inducing rapid evolutionary responses in ways that either reduce the invader's impact or exploit the novel opportunity that it provides. The invasion process itself can cause substantial evolutionary shifts in traits that influence the invader's dispersal rate (via both adaptive and non-adaptive mechanisms) and its ability to establish new populations. I briefly review the nature of evolutionary changes likely to be set in train by a biological invasion, with special emphasis on recent results from my own research group on the invasion of cane toads (Rhinella marina) through tropical Australia. The toads' invasion has caused evolutionary changes both in the toads and in native taxa. Many of those changes are adaptive, but others may result from non-adaptive evolutionary processes: for example, the evolved acceleration in toad dispersal rates may be due to spatial sorting of dispersal-enhancing genes, rather than fitness advantages to faster-dispersing individuals. Managers need to incorporate evolutionary dynamics into their conservation planning, because biological invasions can affect both the rates and the trajectories of evolutionary change.

  14. Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?

    Energy Technology Data Exchange (ETDEWEB)

    Hele, Timothy J. H., E-mail: tjhh2@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Suleimanov, Yury V. [Computation-based Science and Technology Research Center, Cyprus Institute, 20 Kavafi St., Nicosia 2121 (Cyprus); Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139 (United States)

    2015-08-21

    We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H{sub 2}, D + MuH, and F + H{sub 2}, and the prototypical polyatomic reaction H + CH{sub 4}. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.

  15. Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?

    Science.gov (United States)

    Hele, Timothy J H; Suleimanov, Yury V

    2015-08-21

    We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H2, D + MuH, and F + H2, and the prototypical polyatomic reaction H + CH4. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.

  16. Dynamic analysis of heartbeat rate signals of epileptics using multidimensional phase space reconstruction approach

    Science.gov (United States)

    Su, Zhi-Yuan; Wu, Tzuyin; Yang, Po-Hua; Wang, Yeng-Tseng

    2008-04-01

    The heartbeat rate signal provides an invaluable means of assessing the sympathetic-parasympathetic balance of the human autonomic nervous system and thus represents an ideal diagnostic mechanism for detecting a variety of disorders such as epilepsy, cardiac disease and so forth. The current study analyses the dynamics of the heartbeat rate signal of known epilepsy sufferers in order to obtain a detailed understanding of the heart rate pattern during a seizure event. In the proposed approach, the ECG signals are converted into heartbeat rate signals and the embedology theorem is then used to construct the corresponding multidimensional phase space. The dynamics of the heartbeat rate signal are then analyzed before, during and after an epileptic seizure by examining the maximum Lyapunov exponent and the correlation dimension of the attractors in the reconstructed phase space. In general, the results reveal that the heartbeat rate signal transits from an aperiodic, highly-complex behaviour before an epileptic seizure to a low dimensional chaotic motion during the seizure event. Following the seizure, the signal trajectories return to a highly-complex state, and the complex signal patterns associated with normal physiological conditions reappear.

  17. An SIRS Epidemic Model with Vital Dynamics and a Ratio-Dependent Saturation Incidence Rate

    Directory of Open Access Journals (Sweden)

    Xinli Wang

    2015-01-01

    Full Text Available This paper presents an investigation on the dynamics of an epidemic model with vital dynamics and a nonlinear incidence rate of saturated mass action as a function of the ratio of the number of the infectives to that of the susceptibles. The stabilities of the disease-free equilibrium and the endemic equilibrium are first studied. Under the assumption of nonexistence of periodic solution, the global dynamics of the model is established: either the number of infective individuals tends to zero as time evolves or it produces bistability in which there is a region such that the disease will persist if the initial position lies in the region and disappears if the initial position lies outside this region. Computer simulation shows such results.

  18. Therapist interventions using the Psychodynamic Interventions Rating Scale (PIRS) in dynamic therapy, psychoanalysis and CBT.

    Science.gov (United States)

    Banon, Elisabeth; Perry, John Christopher; Semeniuk, Trent; Bond, Michael; de Roten, Yves; Hersoug, Anne Grete; Despland, Jean-Nicolas

    2013-01-01

    One requirement for psychotherapy research is an accurate assessment of therapeutic interventions across studies. This study compared frequency and depth of therapist interventions from a dynamic perspective across four studies, conducted in four countries, including three treatment arms of psychodynamic psychotherapy, and one each of psychoanalysis and CBT. All studies used the Psychodynamic Intervention Rating Scales (PIRS) to identify 10 interventions from transcribed whole sessions early and later in treatment. The PIRS adequately categorized all interventions, except in CBT (only 91-93% categorized). As hypothesized, interpretations were present in all dynamic therapies and relatively absent in CBT. Proportions of interpretations increased over time. Defense interpretations were more common than transference interpretations, which were most prevalent in psychoanalysis. Depth of interpretations also increased over time. These data can serve as norms for measuring where on the supportive-interpretive continuum a dynamic treatment lies, as well as identify potentially mutative interventions for further process and outcome study.

  19. Influence of high strain-rates on the dynamic flexural material properties of spruce–pine–fir wood studs

    National Research Council Canada - National Science Library

    Jacques, Eric; Lloyd, Alan; Braimah, Abass; Saatcioglu, Murat; Doudak, Ghasan; Abdelalim, Omar

    2014-01-01

    ... not. Since equilibrium of the dynamic stress–strain relationship requires that one or both of the MOE and strain at rupture must be sensitive to strain-rate effects, the lack of observed rate enhancement on these material properties...

  20. Using dynamic line rating to minimize curtailment of wind power connected to rural power networks

    Energy Technology Data Exchange (ETDEWEB)

    Schell, Peter [Ampacimon SA, Angleur (Belgium); Lambin, Jean-Jacques [Elia, Brussels (Belgium); Godard, Bertrand; Nguyen, Huu-Minh; Lilien, J.L. [Liege Univ. (Belgium). ULG Montefiore Inst.

    2011-07-01

    Elia, the Belgian TSO, is aiming to minimize curtailment of wind power plants connected to its 70kV rural network to the absolute minimum by using Dynamic Line Rating in combination with advanced flow simulation. This combination allows Elia to use its network assets to their real time maximum, without increasing risk and decreasing the security of supply. In situations like the one described below, where it's possible to control the flow in near real-time via curtailment it becomes possible to use all of the extra capacity available via Dynamic Line Rating. On average more then 30% extra capacity is available but this figure can easily increase to 100% extra capacity as soon as there is more than 4 m/s wind perpendicular to the line. (orig.)

  1. Modeling the Interest Rate Term Structure: Derivatives Contracts Dynamics and Evaluation

    Directory of Open Access Journals (Sweden)

    Pedro L. Valls Pereira

    2005-06-01

    Full Text Available This article deals with a model for the term structure of interest rates and the valuation of derivative contracts directly dependent on it. The work is of a theoretical nature and deals, exclusively, with continuous time models, making ample use of stochastic calculus results and presents original contributions that we consider relevant to the development of the fixed income market modeling. We develop a new multifactorial model of the term structure of interest rates. The model is based on the decomposition of the yield curve into the factors level, slope, curvature, and the treatment of their collective dynamics. We show that this model may be applied to serve various objectives: analysis of bond price dynamics, valuation of derivative contracts and also market risk management and formulation of operational strategies which is presented in another article.

  2. Transitions in genetic toggle switches driven by dynamic disorder in rate coefficients

    Science.gov (United States)

    Chen, Hang; Thill, Peter; Cao, Jianshu

    2016-05-01

    In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes with the same stationary distribution. In one, the kinetic parameters follow a discrete Markov process and in the other they follow continuous Langevin dynamics. We find that regulation of the parameters modulating the dynamic disorder, as has been demonstrated to occur through allosteric control in bistable networks in the immune system, can be crucial in shaping the statistics of optimal transition paths, transition probabilities, and the stationary probability distribution of the network.

  3. Dynamic linear models to explore time-varying suspended sediment-discharge rating curves

    Science.gov (United States)

    Ahn, Kuk-Hyun; Yellen, Brian; Steinschneider, Scott

    2017-06-01

    This study presents a new method to examine long-term dynamics in sediment yield using time-varying sediment-discharge rating curves. Dynamic linear models (DLMs) are introduced as a time series filter that can assess how the relationship between streamflow and sediment concentration or load changes over time in response to a wide variety of natural and anthropogenic watershed disturbances or long-term changes. The filter operates by updating parameter values using a recursive Bayesian design that responds to 1 day-ahead forecast errors while also accounting for observational noise. The estimated time series of rating curve parameters can then be used to diagnose multiscale (daily-decadal) variability in sediment yield after accounting for fluctuations in streamflow. The technique is applied in a case study examining changes in turbidity load, a proxy for sediment load, in the Esopus Creek watershed, part of the New York City drinking water supply system. The results show that turbidity load exhibits a complex array of variability across time scales. The DLM highlights flood event-driven positive hysteresis, where turbidity load remained elevated for months after large flood events, as a major component of dynamic behavior in the rating curve relationship. The DLM also produces more accurate 1 day-ahead loading forecasts compared to other static and time-varying rating curve methods. The results suggest that DLMs provide a useful tool for diagnosing changes in sediment-discharge relationships over time and may help identify variability in sediment concentrations and loads that can be used to inform dynamic water quality management.

  4. The Dynamic Relationship Between Stock Prices and Exchange Rates: Evidence from Four Transition Economies

    OpenAIRE

    Morales, Lucia

    2007-01-01

    This article examines the dynamic relationship between exchange rates and stock prices in four Easter European markets, Czech Republic, Hungary, Poland and Slovakia, using stock price and exchange rate data from these countries, as well as stock prices from the United States, Germany and the United Kingdom. The data set consists of daily data over a 7 year period from 1999 to 2006. Both the long-run and the short-run association between these variables are analyzed. We employed the Johansen c...

  5. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications.

    Science.gov (United States)

    Suleimanov, Yury V; Aoiz, F Javier; Guo, Hua

    2016-11-03

    This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.

  6. Dependence of Strain Rate Sensitivity on the Slip System: A Molecular Dynamics Simulation

    Science.gov (United States)

    Movahedi-Rad, A.; Alizadeh, R.

    2017-11-01

    The strain rate of deformation might affect mechanical properties of metallic materials, especially at elevated temperatures. Due to the nature of dislocation slip, it is anticipated that strain rate sensitivity (SRS) depends on the slip system. While the dependency of SRS on the temperature and strain rate of the deformation is well recognized, its dependence on the slip system is not well understood. Accordingly, the molecular dynamics simulation was used to investigate the dependence of strain rate sensitivity of pure Al single crystals on the slip system. In this study, the embedded atom method (EAM) potential for Al was employed. SRS and shear strength of the material were studied in four different slip systems and at two temperatures of 300 and 500 K. It was found that SRS of the material depends on the slip system in addition to the temperature, and SRS was higher in less compact systems with more difficult slip. The dislocation theories were used to rationalize the simulation results.

  7. Dynamic neural networking as a basis for plasticity in the control of heart rate.

    Science.gov (United States)

    Kember, G; Armour, J A; Zamir, M

    2013-01-21

    A model is proposed in which the relationship between individual neurons within a neural network is dynamically changing to the effect of providing a measure of "plasticity" in the control of heart rate. The neural network on which the model is based consists of three populations of neurons residing in the central nervous system, the intrathoracic extracardiac nervous system, and the intrinsic cardiac nervous system. This hierarchy of neural centers is used to challenge the classical view that the control of heart rate, a key clinical index, resides entirely in central neuronal command (spinal cord, medulla oblongata, and higher centers). Our results indicate that dynamic networking allows for the possibility of an interplay among the three populations of neurons to the effect of altering the order of control of heart rate among them. This interplay among the three levels of control allows for different neural pathways for the control of heart rate to emerge under different blood flow demands or disease conditions and, as such, it has significant clinical implications because current understanding and treatment of heart rate anomalies are based largely on a single level of control and on neurons acting in unison as a single entity rather than individually within a (plastically) interconnected network. Copyright © 2012 Elsevier Ltd. All rights reserved.