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Sample records for evolutionary programming planeacion

  1. Evolving evolutionary algorithms using linear genetic programming.

    PubMed

    Oltean, Mihai

    2005-01-01

    A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

  2. Evolutionary program induction directed by logic grammars

    PubMed

    Wong; Leung

    1997-01-01

    Program induction generates a computer program that can produce the desired behavior for a given set of situations. Two of the approaches in program induction are inductive logic programming (ILP) and genetic programming (GP). Since their formalisms are so different, these two approaches cannot be integrated easily, although they share many common goals and functionalities. A unification will greatly enhance their problem-solving power. Moreover, they are restricted in the computer languages in which programs can be induced. In this paper, we present a flexible system called LOGENPRO (The LOgic gramar-based GENetic PROgramming system) that uses some of the techniques of GP and ILP. It is based on a formalism of logic grammars. The system applies logic grammars to control the evolution of programs in various programming languages and represent context-sensitive information and domain-dependent knowledge. Experiments have been performed to demonstrate that LOGENPRO can emulate GP and GP with automatically defined functions (ADFs). Moreover, LOGENPRO can employ knowledge such as argument types in a unified framework. The experiments show that LOGENPRO has superior performance to that of GP and GP with ADFs when more domain-dependent knowledge is available. We have applied LOGENPRO to evolve general recursive functions for the even-n-parity problem from noisy training examples. A number of experiments have been performed to determine the impact of domain-specific knowledge and noise in training examples on the speed of learning.

  3. Multi-Output System Identification Using Evolutionary Programming

    DTIC Science & Technology

    1991-11-04

    Evolutionary programming (EP) has been demonstrated to be an effective method of system identification of single-input-single-output (SISO) systems...This paper investigates the use of EP in system identification of single-input-multioutput (SIMO) systems. EP is used to identify parameters of a

  4. Modern evolutionary mechanics theories and resolving the programmed/non-programmed aging controversy.

    PubMed

    Goldsmith, Theodore C

    2014-10-01

    Modern programmed (adaptive) theories of biological aging contend that organisms including mammals have generally evolved mechanisms that purposely limit their lifespans in order to obtain an evolutionary benefit. Modern non-programmed theories contend that mammal aging generally results from natural deteriorative processes, and that lifespan differences between species are explained by differences in the degree to which they resist those processes. Originally proposed in the 19th century, programmed aging in mammals has historically been widely summarily rejected as obviously incompatible with the mechanics of the evolution process. However, relatively recent and continuing developments described here have dramatically changed this situation, and programmed mammal aging now has a better evolutionary basis than non-programmed aging. Resolution of this issue is critically important to medical research because the two theories predict that very different biological mechanisms are ultimately responsible for age-related diseases and conditions.

  5. Optimal lunar soft landing trajectories using taboo evolutionary programming

    NASA Astrophysics Data System (ADS)

    Mutyalarao, M.; Raj, M. Xavier James

    A safe lunar landing is a key factor to undertake an effective lunar exploration. Lunar lander consists of four phases such as launch phase, the earth-moon transfer phase, circumlunar phase and landing phase. The landing phase can be either hard landing or soft landing. Hard landing means the vehicle lands under the influence of gravity without any deceleration measures. However, soft landing reduces the vertical velocity of the vehicle before landing. Therefore, for the safety of the astronauts as well as the vehicle lunar soft landing with an acceptable velocity is very much essential. So it is important to design the optimal lunar soft landing trajectory with minimum fuel consumption. Optimization of Lunar Soft landing is a complex optimal control problem. In this paper, an analysis related to lunar soft landing from a parking orbit around Moon has been carried out. A two-dimensional trajectory optimization problem is attempted. The problem is complex due to the presence of system constraints. To solve the time-history of control parameters, the problem is converted into two point boundary value problem by using the maximum principle of Pontrygen. Taboo Evolutionary Programming (TEP) technique is a stochastic method developed in recent years and successfully implemented in several fields of research. It combines the features of taboo search and single-point mutation evolutionary programming. Identifying the best unknown parameters of the problem under consideration is the central idea for many space trajectory optimization problems. The TEP technique is used in the present methodology for the best estimation of initial unknown parameters by minimizing objective function interms of fuel requirements. The optimal estimation subsequently results into an optimal trajectory design of a module for soft landing on the Moon from a lunar parking orbit. Numerical simulations demonstrate that the proposed approach is highly efficient and it reduces the minimum fuel

  6. Evolutionary Evaluation: implications for evaluators, researchers, practitioners, funders and the evidence-based program mandate.

    PubMed

    Urban, Jennifer Brown; Hargraves, Monica; Trochim, William M

    2014-08-01

    Evolutionary theory, developmental systems theory, and evolutionary epistemology provide deep theoretical foundations for understanding programs, their development over time, and the role of evaluation. This paper relates core concepts from these powerful bodies of theory to program evaluation. Evolutionary Evaluation is operationalized in terms of program and evaluation evolutionary phases, which are in turn aligned with multiple types of validity. The model of Evolutionary Evaluation incorporates Chen's conceptualization of bottom-up versus top-down program development. The resulting framework has important implications for many program management and evaluation issues. The paper illustrates how an Evolutionary Evaluation perspective can illuminate important controversies in evaluation using the example of the appropriate role of randomized controlled trials that encourages a rethinking of "evidence-based programs". From an Evolutionary Evaluation perspective, prevailing interpretations of rigor and mandates for evidence-based programs pose significant challenges to program evolution. This perspective also illuminates the consequences of misalignment between program and evaluation phases; the importance of supporting both researcher-derived and practitioner-derived programs; and the need for variation and evolutionary phase diversity within portfolios of programs.

  7. Study of an evolutionary interim earth orbit program

    NASA Technical Reports Server (NTRS)

    Anderson, J. L.; Alton, L. R.; Arno, R. D.; Deerwester, J. M.; Edsinger, L. E.; Sinclair, K. F.; Tindle, E. L.; Wood, R. D.

    1971-01-01

    An evolutionary, gradual, and step-wise spacecraft systems technology development from those used on the Apollos and Skylab 1 to that required for the space station was considered. The four mission spacecraft were dry workshop versions of the Saturn 4-B stage, and each individually configured, outfitted and launched by INT-21 vehicles. These spacecraft were evaluated for crews of three, six and nine men and for mission lifetimes of one year. Two versions of the Apollo CSM, a three man and a four man crew, were considered as the logistic vehicle. The solar cell electrical power system of the first mission evolves into a light weight panel system supplemented by an operating isotope-Brayton system on the later missions. The open life support system of the first mission evolves to a system which recovers both water and oxygen on the last mission. The data handling, communications, radiation shielding, micrometeoroid protection, and orbit keeping systems were determined. The program costs were estimated and, excluding operational costs, the cost for each mission would average about $2 billion of which one-sixth would be for development, one-fourth for experiments, and the balance for vehicle acquisition.

  8. Evolutionary programming for goal-driven dynamic planning

    NASA Astrophysics Data System (ADS)

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

    2002-03-01

    Many complex artificial intelligence (IA) problems are goal- driven in nature and the opportunity exists to realize the benefits of a goal-oriented solution. In many cases, such as in command and control, a goal-oriented approach may be the only option. One of many appropriate applications for such an approach is War Gaming. War Gaming is an important tool for command and control because it provides a set of alternative courses of actions so that military leaders can contemplate their next move in the battlefield. For instance, when making decisions that save lives, it is necessary to completely understand the consequences of a given order. A goal-oriented approach provides a slowly evolving tractably reasoned solution that inherently follows one of the principles of war: namely concentration on the objective. Future decision-making will depend not only on the battlefield, but also on a virtual world where military leaders can wage wars and determine their options by playing computer war games much like the real world. The problem with these games is that the built-in AI does not learn nor adapt and many times cheats, because the intelligent player has access to all the information, while the user has access to limited information provided on a display. These games are written for the purpose of entertainment and actions are calculated a priori and off-line, and are made prior or during their development. With these games getting more sophisticated in structure and less domain specific in scope, there needs to be a more general intelligent player that can adapt and learn in case the battlefield situations or the rules of engagement change. One such war game that might be considered is Risk. Risk incorporates the principles of war, is a top-down scalable model, and provides a good application for testing a variety of goal- oriented AI approaches. By integrating a goal-oriented hybrid approach, one can develop a program that plays the Risk game effectively and move

  9. Effective Technology Insertion: The Key to Evolutionary Acquisition Program

    DTIC Science & Technology

    2004-05-03

    Army War College, 7 April 2003. 47Orazia A. Di Marca ; Rejto, Stephen B. Rejto and Thomas Gomez, “ Open System Design and Evolutionary Acquisition...to Military Applications-Report No. D-2002-107. 14 June 2002. Di Marca , Orazia A.; Rejto, StephenB., and Gomez, Thomas, “ Open System Design and

  10. Aberration correction of zoom lenses using evolutionary programming.

    PubMed

    Pal, Sourav

    2013-08-10

    A systematic approach for the aberration correction of zoom systems is presented. It is assumed that the powers and movements of the components of the zoom systems are known. Each component is considered as a system of thin lenses in contact. An evolutionary algorithm is developed to explore the multivariate hyperspace of design variables formed by spherical aberration, central coma, and longitudinal chromatic aberration of each component for infinite conjugate. The primary aberrations for each component at any zoom position are deduced from three central aberration coefficients of the component for infinite conjugate using conjugate shift formulas. Overall system aberrations of the zoom systems are determined by using stop shift formulas. In most of the zoom lens systems it is important to achieve stability in the primary aberrations of the system over the zoom range. This is facilitated by proper formulation of the merit function for the optimization process. Investigations have been carried out on four-component zoom lenses, and an ab initio structure of a four-component zoom lens is presented.

  11. Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

    PubMed Central

    McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E

    2008-01-01

    Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637

  12. Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

    PubMed Central

    Brodersen, Jakob; Seehausen, Ole

    2014-01-01

    While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061

  13. Training the Millennial learner through experiential evolutionary scaffolding: implications for clinical supervision in graduate education programs.

    PubMed

    Venne, Vickie L; Coleman, Darrell

    2010-12-01

    They are the Millennials--Generation Y. Over the next few decades, they will be entering genetic counseling graduate training programs and the workforce. As a group, they are unlike previous youth generations in many ways, including the way they learn. Therefore, genetic counselors who teach and supervise need to understand the Millennials and explore new ways of teaching to ensure that the next cohort of genetic counselors has both skills and knowledge to represent our profession well. This paper will summarize the distinguishing traits of the Millennial generation as well as authentic learning and evolutionary scaffolding theories of learning that can enhance teaching and supervision. We will then use specific aspects of case preparation during clinical rotations to demonstrate how incorporating authentic learning theory into evolutionary scaffolding results in experiential evolutionary scaffolding, a method that potentially offers a more effective approach when teaching Millennials. We conclude with suggestions for future research.

  14. The new image segmentation algorithm using adaptive evolutionary programming and fuzzy c-means clustering

    NASA Astrophysics Data System (ADS)

    Liu, Fang

    2011-06-01

    Image segmentation remains one of the major challenges in image analysis and computer vision. Fuzzy clustering, as a soft segmentation method, has been widely studied and successfully applied in mage clustering and segmentation. The fuzzy c-means (FCM) algorithm is the most popular method used in mage segmentation. However, most clustering algorithms such as the k-means and the FCM clustering algorithms search for the final clusters values based on the predetermined initial centers. The FCM clustering algorithms does not consider the space information of pixels and is sensitive to noise. In the paper, presents a new fuzzy c-means (FCM) algorithm with adaptive evolutionary programming that provides image clustering. The features of this algorithm are: 1) firstly, it need not predetermined initial centers. Evolutionary programming will help FCM search for better center and escape bad centers at local minima. Secondly, the spatial distance and the Euclidean distance is also considered in the FCM clustering. So this algorithm is more robust to the noises. Thirdly, the adaptive evolutionary programming is proposed. The mutation rule is adaptively changed with learning the useful knowledge in the evolving process. Experiment results shows that the new image segmentation algorithm is effective. It is providing robustness to noisy images.

  15. Recurring two-stage evolutionary programming: a novel approach for numeric optimization.

    PubMed

    Alam, Mohammad Shafiul; Islam, Md Monirul; Yao, Xin; Murase, Kazuyuki

    2011-10-01

    In the application of evolutionary algorithms (EAs) to complex problem solving, it is essential to maintain proper balance between global exploration and local exploitation to achieve a good near-optimum solution to the problem. This paper presents a recurring two-stage evolutionary programming (RTEP) to balance the explorative and exploitative features of the conventional EAs. Unlike most previous works, RTEP is based on repeated and alternated execution of two different stages, namely, the exploration and exploitation stages, each with its own mutation operator, selection strategy, and explorative/exploitative objective. Both analytical and empirical studies have been carried out to understand the necessity of repeated and alternated exploration and exploitation operations in EAs. A suite of 48 benchmark numerical optimization problems has been used in the empirical studies. The experimental results show the remarkable effectiveness of the repeated exploration and exploitation operations employed by RTEP.

  16. Ab initio synthesis of linearly compensated zoom lenses by evolutionary programming.

    PubMed

    Pal, Sourav; Hazra, Lakshminarayan

    2011-04-01

    An approach for ab initio synthesis of the thin lens structure of linearly compensated zoom lenses is reported. This method uses evolutionary programming that explores the available configuration space formed by powers of the individual components, the intercomponent separations, and the relative movement parameters of the moving components. Useful thin lens structures of optically and linearly compensated zoom lens systems are obtained by suitable formulation of the merit function of optimization. This paper reports our investigations on three-component zoom lens structures. Illustrative numerical results are presented.

  17. A Program for At-Risk High School Students Informed by Evolutionary Science

    PubMed Central

    Wilson, David Sloan; Kauffman, Richard A.; Purdy, Miriam S.

    2011-01-01

    Improving the academic performance of at-risk high school students has proven difficult, often calling for an extended day, extended school year, and other expensive measures. Here we report the results of a program for at-risk 9th and 10th graders in Binghamton, New York, called the Regents Academy that takes place during the normal school day and year. The design of the program is informed by the evolutionary dynamics of cooperation and learning, in general and for our species as a unique product of biocultural evolution. Not only did the Regents Academy students outperform their comparison group in a randomized control design, but they performed on a par with the average high school student in Binghamton on state-mandated exams. All students can benefit from the social environment provided for at-risk students at the Regents Academy, which is within the reach of most public school districts. PMID:22114703

  18. Evolutionary acquisition of a mortal genetic program: the origin of an altruistic gene.

    PubMed

    Oohashi, Tsutomu; Maekawa, Tadao; Ueno, Osamu; Kawai, Norie; Nishina, Emi; Honda, Manabu

    2014-01-01

    As part of our research on programmed self-decomposition, we formed the hypothesis that originally immortal terrestrial organisms evolve into ones that are programmed for autonomous death. We then conducted evolutionary simulation experiments in which we examined this hypothesis using an artificial ecosystem that we designed to resemble a terrestrial ecosystem endowed with artificial chemistry. Notable results corroborating our hypothesis were obtained, which showed that mortal organisms emerged from indigenous immortal organisms through mutation; such mortal organisms survived and left behind offspring, albeit very rarely, and, having survived, surpassed immortal organisms without exception. In this article, we report the details of the above findings and also discuss a background framework we previously constructed for approaching altruism.

  19. Models of performance of evolutionary program induction algorithms based on indicators of problem difficulty.

    PubMed

    Graff, Mario; Poli, Riccardo; Flores, Juan J

    2013-01-01

    Modeling the behavior of algorithms is the realm of evolutionary algorithm theory. From a practitioner's point of view, theory must provide some guidelines regarding which algorithm/parameters to use in order to solve a particular problem. Unfortunately, most theoretical models of evolutionary algorithms are difficult to apply to realistic situations. However, in recent work (Graff and Poli, 2008, 2010), where we developed a method to practically estimate the performance of evolutionary program-induction algorithms (EPAs), we started addressing this issue. The method was quite general; however, it suffered from some limitations: it required the identification of a set of reference problems, it required hand picking a distance measure in each particular domain, and the resulting models were opaque, typically being linear combinations of 100 features or more. In this paper, we propose a significant improvement of this technique that overcomes the three limitations of our previous method. We achieve this through the use of a novel set of features for assessing problem difficulty for EPAs which are very general, essentially based on the notion of finite difference. To show the capabilities or our technique and to compare it with our previous performance models, we create models for the same two important classes of problems-symbolic regression on rational functions and Boolean function induction-used in our previous work. We model a variety of EPAs. The comparison showed that for the majority of the algorithms and problem classes, the new method produced much simpler and more accurate models than before. To further illustrate the practicality of the technique and its generality (beyond EPAs), we have also used it to predict the performance of both autoregressive models and EPAs on the problem of wind speed forecasting, obtaining simpler and more accurate models that outperform in all cases our previous performance models.

  20. AI-BL1.0: a program for automatic on-line beamline optimization using the evolutionary algorithm.

    PubMed

    Xi, Shibo; Borgna, Lucas Santiago; Zheng, Lirong; Du, Yonghua; Hu, Tiandou

    2017-01-01

    In this report, AI-BL1.0, an open-source Labview-based program for automatic on-line beamline optimization, is presented. The optimization algorithms used in the program are Genetic Algorithm and Differential Evolution. Efficiency was improved by use of a strategy known as Observer Mode for Evolutionary Algorithm. The program was constructed and validated at the XAFCA beamline of the Singapore Synchrotron Light Source and 1W1B beamline of the Beijing Synchrotron Radiation Facility.

  1. Prediction of Layer Thickness in Molten Borax Bath with Genetic Evolutionary Programming

    NASA Astrophysics Data System (ADS)

    Taylan, Fatih

    2011-04-01

    In this study, the vanadium carbide coating in molten borax bath process is modeled by evolutionary genetic programming (GEP) with bath composition (borax percentage, ferro vanadium (Fe-V) percentage, boric acid percentage), bath temperature, immersion time, and layer thickness data. Five inputs and one output data exist in the model. The percentage of borax, Fe-V, and boric acid, temperature, and immersion time parameters are used as input data and the layer thickness value is used as output data. For selected bath components, immersion time, and temperature variables, the layer thicknesses are derived from the mathematical expression. The results of the mathematical expressions are compared to that of experimental data; it is determined that the derived mathematical expression has an accuracy of 89%.

  2. Motivational and evolutionary aspects of a physical exercise training program: a longitudinal study

    PubMed Central

    Rosa, João P. P.; de Souza, Altay A. L.; de Lima, Giscard H. O.; Rodrigues, Dayane F.; de Aquino Lemos, Valdir; da Silva Alves, Eduardo; Tufik, Sergio; de Mello, Marco T.

    2015-01-01

    Several studies have indicated that motivational level and prior expectations influence one’s commitment to physical activity. Moreover, these aspects are not properly described in terms of proximal (SDT, Self Determination Theory) and distal (evolutionary) explanations in the literature. This paper aims to verify if level of motivation (BREQ-2, Behavioral Regulation in Exercise Questionnaire-2) and expectations regarding regular physical exercise (IMPRAF-54) before starting a 1-year exercise program could determine likelihood of completion. Ninety-four volunteers (53 women) included a completed protocol group (CPG; n = 21) and drop-out group (n = 73). The IMPRAF-54 scale was used to assess six different expectations associated with physical activity, and the BREQ-2 inventory was used to assess the level of motivation in five steps (from amotivation to intrinsic motivation). Both questionnaires were assessed before starting a regular exercise program. The CPG group presented higher sociability and lower pleasure scores according to IMPRAF-54 domains. A logistic regression analysis showed that a one-point increment on sociability score increased the chance of completing the program by 10%, and the same one-point increment on pleasure score reduced the chance of completing the protocol by 16%. ROC curves were also calculated to establish IMPRAF-54 cutoffs for adherence (Sociability – 18.5 points – 81% sensibility/50% specificity) and dropout (Pleasure – 25.5 points – 86% sensibility/20% specificity) of the exercise protocol. Our results indicate that an expectation of social interaction was a positive factor in predicting adherence to exercise. Grounded in SDT and its innate needs (competence, autonomy, relatedness), physical exercise is not an end; it is a means to achieve autonomy and self-cohesion. The association of physical activity with social practices, as occurs in hunter-gathering groups, can engage people to be physically active and can provide

  3. A graph-based evolutionary algorithm: Genetic Network Programming (GNP) and its extension using reinforcement learning.

    PubMed

    Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu

    2007-01-01

    This paper proposes a graph-based evolutionary algorithm called Genetic Network Programming (GNP). Our goal is to develop GNP, which can deal with dynamic environments efficiently and effectively, based on the distinguished expression ability of the graph (network) structure. The characteristics of GNP are as follows. 1) GNP programs are composed of a number of nodes which execute simple judgment/processing, and these nodes are connected by directed links to each other. 2) The graph structure enables GNP to re-use nodes, thus the structure can be very compact. 3) The node transition of GNP is executed according to its node connections without any terminal nodes, thus the past history of the node transition affects the current node to be used and this characteristic works as an implicit memory function. These structural characteristics are useful for dealing with dynamic environments. Furthermore, we propose an extended algorithm, "GNP with Reinforcement Learning (GNPRL)" which combines evolution and reinforcement learning in order to create effective graph structures and obtain better results in dynamic environments. In this paper, we applied GNP to the problem of determining agents' behavior to evaluate its effectiveness. Tileworld was used as the simulation environment. The results show some advantages for GNP over conventional methods.

  4. A Heuristic Ranking Approach on Capacity Benefit Margin Determination Using Pareto-Based Evolutionary Programming Technique

    PubMed Central

    Othman, Muhammad Murtadha; Abd Rahman, Nurulazmi; Musirin, Ismail; Fotuhi-Firuzabad, Mahmud; Rajabi-Ghahnavieh, Abbas

    2015-01-01

    This paper introduces a novel multiobjective approach for capacity benefit margin (CBM) assessment taking into account tie-line reliability of interconnected systems. CBM is the imperative information utilized as a reference by the load-serving entities (LSE) to estimate a certain margin of transfer capability so that a reliable access to generation through interconnected system could be attained. A new Pareto-based evolutionary programming (EP) technique is used to perform a simultaneous determination of CBM for all areas of the interconnected system. The selection of CBM at the Pareto optimal front is proposed to be performed by referring to a heuristic ranking index that takes into account system loss of load expectation (LOLE) in various conditions. Eventually, the power transfer based available transfer capability (ATC) is determined by considering the firm and nonfirm transfers of CBM. A comprehensive set of numerical studies are conducted on the modified IEEE-RTS79 and the performance of the proposed method is numerically investigated in detail. The main advantage of the proposed technique is in terms of flexibility offered to an independent system operator in selecting an appropriate solution of CBM simultaneously for all areas. PMID:25879068

  5. A heuristic ranking approach on capacity benefit margin determination using Pareto-based evolutionary programming technique.

    PubMed

    Othman, Muhammad Murtadha; Abd Rahman, Nurulazmi; Musirin, Ismail; Fotuhi-Firuzabad, Mahmud; Rajabi-Ghahnavieh, Abbas

    2015-01-01

    This paper introduces a novel multiobjective approach for capacity benefit margin (CBM) assessment taking into account tie-line reliability of interconnected systems. CBM is the imperative information utilized as a reference by the load-serving entities (LSE) to estimate a certain margin of transfer capability so that a reliable access to generation through interconnected system could be attained. A new Pareto-based evolutionary programming (EP) technique is used to perform a simultaneous determination of CBM for all areas of the interconnected system. The selection of CBM at the Pareto optimal front is proposed to be performed by referring to a heuristic ranking index that takes into account system loss of load expectation (LOLE) in various conditions. Eventually, the power transfer based available transfer capability (ATC) is determined by considering the firm and nonfirm transfers of CBM. A comprehensive set of numerical studies are conducted on the modified IEEE-RTS79 and the performance of the proposed method is numerically investigated in detail. The main advantage of the proposed technique is in terms of flexibility offered to an independent system operator in selecting an appropriate solution of CBM simultaneously for all areas.

  6. Evolutionary neural networks for anomaly detection based on the behavior of a program.

    PubMed

    Han, Sang-Jun; Cho, Sung-Bae

    2006-06-01

    The process of learning the behavior of a given program by using machine-learning techniques (based on system-call audit data) is effective to detect intrusions. Rule learning, neural networks, statistics, and hidden Markov models (HMMs) are some of the kinds of representative methods for intrusion detection. Among them, neural networks are known for good performance in learning system-call sequences. In order to apply this knowledge to real-world problems successfully, it is important to determine the structures and weights of these call sequences. However, finding the appropriate structures requires very long time periods because there are no suitable analytical solutions. In this paper, a novel intrusion-detection technique based on evolutionary neural networks (ENNs) is proposed. One advantage of using ENNs is that it takes less time to obtain superior neural networks than when using conventional approaches. This is because they discover the structures and weights of the neural networks simultaneously. Experimental results with the 1999 Defense Advanced Research Projects Agency (DARPA) Intrusion Detection Evaluation (IDEVAL) data confirm that ENNs are promising tools for intrusion detection.

  7. Evolutionary conservation and modulation of a juvenile growth-regulating genetic program

    PubMed Central

    Delaney, Angela; Padmanabhan, Vasantha; Rezvani, Geoffrey; Chen, Weiping; Forcinito, Patricia; Cheung, Crystal S.F.; Baron, Jeffrey; Lui, Julian C.K.

    2014-01-01

    Body size varies enormously among mammalian species. In small mammals, body growth is typically suppressed rapidly, within weeks, whereas in large mammals, growth is suppressed slowly, over years, allowing for a greater adult size. We recently reported evidence that body growth suppression in rodents is caused in part by a juvenile genetic program that occurs in multiple tissues simultaneously and involves the downregulation of a large set of growth-promoting genes. We hypothesized that this genetic program is conserved in large mammals but that its time course is evolutionarily modulated such that it plays out more slowly, allowing for more prolonged growth. Consistent with this hypothesis, using expression microarray analysis, we identified a set of genes that are downregulated with age in both juvenile sheep kidney and lung. This overlapping gene set was enriched for genes involved in cell proliferation and growth and showed striking similarity to a set of genes downregulated with age in multiple organs of the juvenile mouse and rat, indicating that the multiorgan juvenile genetic program previously described in rodents has been conserved in the 80 million years since sheep and rodents diverged in evolution. Using microarray and real-time PCR, we found that the pace of this program was most rapid in mice, more gradual in rats, and most gradual in sheep. The findings support the hypothesis that a growth-regulating genetic program is conserved among mammalian species but that its pace is modulated to allow more prolonged growth and therefore greater adult body size in larger mammals. PMID:24776848

  8. Evolutionary conservation of microRNA regulatory programs in plant flower development.

    PubMed

    Luo, Yan; Guo, Zhenhua; Li, Lu

    2013-08-15

    MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. Flowering is critical for the reproduction of angiosperms. Flower development entails the transition from vegetative growth to reproductive growth, floral organ initiation, and the development of floral organs. These developmental processes are genetically regulated by miRNAs, which participate in complex genetic networks of flower development. A survey of the literature shows that miRNAs, their specific targets, and the regulatory programs in which they participate are conserved throughout the plant kingdom. This review summarizes the role of miRNAs and their targets in the regulation of gene expression during the floral developmental phase, which includes the floral transition stage, followed by floral patterning, and then the development of floral organs. The conservation patterns observed in each component of the miRNA regulatory system suggest that these miRNAs play important roles in the evolution of flower development.

  9. Programmed translational bypassing elements in mitochondria: structure, mobility, and evolutionary origin.

    PubMed

    Nosek, Jozef; Tomaska, Lubomir; Burger, Gertraud; Lang, B Franz

    2015-04-01

    Programmed translational bypassing enables ribosomes to 'ignore' a precise mRNA interval of several dozen nucleotides. Well-characterized bypassed sequences include hop and byp elements, present in bacteriophage T4 and mitochondria of the yeast Magnusiomyces capitatus, respectively. The bypassing mechanism of byps is probably similar to that of hop, yet the former appears more effective and less constrained as to sequence context. Furthermore, both elements are mobile but hop moves as part of a cassette including a homing endonuclease, whereas byps seem to spread like miniature DNA transposable elements known as GC clusters. Here, we argue that hop and byps arose independently by convergent evolution, and that byps evolved in magnusiomycete mitochondria due to (as yet unknown) alterations of the mitochondrial translation machinery.

  10. Velocity inversion in cross-hole seismic tomography bycounter-propagation neural network, genetic algorithmand evolutionary programming techniques

    NASA Astrophysics Data System (ADS)

    Nath, Sankar Kumar; Chakraborty, Subrata; Singh, Sanjiv Kumar; Ganguly, Nilanjan

    1999-07-01

    The disadvantages of conventional seismic tomographic ray tracing and inversion by calculus-based techniques include the assumption of a single ray path for each source-receiver pair, the non-inclusion of head waves, long computation times, and the difficulty in finding ray paths in a complicated velocity distribution. A ray-tracing algorithm is therefore developed using the reciprocity principle and dynamic programming approach. This robust forward calculation routine is subsequently used for the cross-hole seismic velocity inversion. Seismic transmission tomography can be considered to be a function approximation problem; that is, of mapping the traveltime vector to the velocity vector. This falls under the purview of pattern classification problems, so we propose a forward-only counter-propagation neural network (CPNN) technique for the tomographic imaging of the subsurface. The limitation of neural networks, however, lies in the requirement of exhaustive training for its use in routine interpretation. Since finding the optimal solution, sometimes from poor initial models, is the ultimate goal, global optimization and search techniques such as simulated evolution are also implemented in the cross-well traveltime tomography. Genetic algorithms (GA), evolution strategies and evolutionary programming (EP) are the main avenues of research in simulated evolution. Part of this investigation therefore deals with GA and EP schemes for tomographic applications. In the present work on simulated evolution, a new genetic operator called `region-growing mutation' is introduced to speed up the search process. The potential of the forward-only CPNN, GA and EP methods is demonstrated in three synthetic examples. Velocity tomograms of the first model present plausible images of a diagonally orientated velocity contrast bounding two constant-velocity areas by both the CPNN and GA schemes, but the EP scheme could not image the model completely. In the second case, while GA and EP

  11. An efficient and accurate solution methodology for bilevel multi-objective programming problems using a hybrid evolutionary-local-search algorithm.

    PubMed

    Deb, Kalyanmoy; Sinha, Ankur

    2010-01-01

    Bilevel optimization problems involve two optimization tasks (upper and lower level), in which every feasible upper level solution must correspond to an optimal solution to a lower level optimization problem. These problems commonly appear in many practical problem solving tasks including optimal control, process optimization, game-playing strategy developments, transportation problems, and others. However, they are commonly converted into a single level optimization problem by using an approximate solution procedure to replace the lower level optimization task. Although there exist a number of theoretical, numerical, and evolutionary optimization studies involving single-objective bilevel programming problems, not many studies look at the context of multiple conflicting objectives in each level of a bilevel programming problem. In this paper, we address certain intricate issues related to solving multi-objective bilevel programming problems, present challenging test problems, and propose a viable and hybrid evolutionary-cum-local-search based algorithm as a solution methodology. The hybrid approach performs better than a number of existing methodologies and scales well up to 40-variable difficult test problems used in this study. The population sizing and termination criteria are made self-adaptive, so that no additional parameters need to be supplied by the user. The study indicates a clear niche of evolutionary algorithms in solving such difficult problems of practical importance compared to their usual solution by a computationally expensive nested procedure. The study opens up many issues related to multi-objective bilevel programming and hopefully this study will motivate EMO and other researchers to pay more attention to this important and difficult problem solving activity.

  12. Evolutionary thinking

    PubMed Central

    Hunt, Tam

    2014-01-01

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

  13. The Suitability of Using an Evolutionary Acquisition Strategy in Joint Acquisition Programs for Command and Control Systems

    DTIC Science & Technology

    1989-06-02

    Missouri, 1978 Acceso • For M.S., Air Force Institute of Technology, 1981 rTIS , D•2 TVAB 0 6y I fivColes Fort Leavenworth, Kansas A j, -dlor 1989 .CIdI...external interfaces at multiple organizational levels, some of which may be inter-Service and multinational (15). Evolutionary Acquisition. This is...and intelligence which serve multiple services (30). The group concluded that the services have not made the necessary commitments to execute joint

  14. At the crossroads of evolutionary computation and music: self-programming synthesizers, swarm orchestras and the origins of melody.

    PubMed

    Miranda, Eduardo Reck

    2004-01-01

    This paper introduces three approaches to using Evolutionary Computation (EC) in Music (namely, engineering, creative and musicological approaches) and discusses examples of representative systems that have been developed within the last decade, with emphasis on more recent and innovative works. We begin by reviewing engineering applications of EC in Music Technology such as Genetic Algorithms and Cellular Automata sound synthesis, followed by an introduction to applications where EC has been used to generate musical compositions. Next, we introduce ongoing research into EC models to study the origins of music and detail our own research work on modelling the evolution of melody.

  15. Evolutionary Computing

    SciTech Connect

    Patton, Robert M; Cui, Xiaohui; Jiao, Yu; Potok, Thomas E

    2008-01-01

    The rate at which information overwhelms humans is significantly more than the rate at which humans have learned to process, analyze, and leverage this information. To overcome this challenge, new methods of computing must be formulated, and scientist and engineers have looked to nature for inspiration in developing these new methods. Consequently, evolutionary computing has emerged as new paradigm for computing, and has rapidly demonstrated its ability to solve real-world problems where traditional techniques have failed. This field of work has now become quite broad and encompasses areas ranging from artificial life to neural networks. This chapter focuses specifically on two sub-areas of nature-inspired computing: Evolutionary Algorithms and Swarm Intelligence.

  16. Evolutionary pattern search algorithms

    SciTech Connect

    Hart, W.E.

    1995-09-19

    This paper defines a class of evolutionary algorithms called evolutionary pattern search algorithms (EPSAs) and analyzes their convergence properties. This class of algorithms is closely related to evolutionary programming, evolutionary strategie and real-coded genetic algorithms. EPSAs are self-adapting systems that modify the step size of the mutation operator in response to the success of previous optimization steps. The rule used to adapt the step size can be used to provide a stationary point convergence theory for EPSAs on any continuous function. This convergence theory is based on an extension of the convergence theory for generalized pattern search methods. An experimental analysis of the performance of EPSAs demonstrates that these algorithms can perform a level of global search that is comparable to that of canonical EAs. We also describe a stopping rule for EPSAs, which reliably terminated near stationary points in our experiments. This is the first stopping rule for any class of EAs that can terminate at a given distance from stationary points.

  17. Evolutionary lunar transportation family

    NASA Technical Reports Server (NTRS)

    Capps, Stephen

    1992-01-01

    The development of an evolutionary lunar transportation family (LTF) that can accommodate evolving human exploration goals is discussed. An evolutionary system is aimed at minimizing program costs while preserving programmatic versatility. Technical requirements that affect the design strategy for LTF include aerobraking technology and packaging constraints; mixed, unsymmetrical payload manifests; crew and payload exchange operations; crew and cargo off-loading on the lunar surface; and cryogenic lunar transfer and storage. It is concluded that the LTF is capable of meeting exploration goals, which include the provision for a significant early manned lunar surface science and exploration capability, the avoidance or reduction of some major operational and infrastructure requirements, and the incorporation of common vehicle designs and existing/near-term technology.

  18. Evolutionary theory, psychiatry, and psychopharmacology.

    PubMed

    Stein, Dan J

    2006-07-01

    Darwin's seminal publications in the nineteenth century laid the foundation for an evolutionary approach to psychology and psychiatry. Advances in 20th century evolutionary theory facilitated the development of evolutionary psychology and psychiatry as recognized areas of scientific investigation. In this century, advances in understanding the molecular basis of evolution, of the mind, and of psychopathology, offer the possibility of an integrated approach to understanding the proximal (psychobiological) and distal (evolutionary) mechanisms of interest to psychiatry and psychopharmacology. There is, for example, growing interest in the question of whether specific genetic variants mediate psychobiological processes that have evolutionary value in specific contexts, and of the implications of this for understanding the vulnerability to psychopathology and for considering the advantages and limitations of pharmacotherapy. The evolutionary value, and gene-environmental mediation, of early life programming is potentially a particularly rich area of investigation. Although evolutionary approaches to psychology and to medicine face important conceptual and methodological challenges, current work is increasingly sophisticated, and may prove to be an important foundational discipline for clinicians and researchers in psychiatry and psychopharmacology.

  19. Evolutionary novelties.

    PubMed

    Wagner, Günter P; Lynch, Vincent J

    2010-01-26

    How novel traits arise in organisms has long been a major problem in biology. Indeed, the sharpest critiques of Darwin's theory of evolution by natural selection often centered on explaining how novel body parts arose. In his response to The Origin of Species, St. George J. Mivart challenged Darwin to explain the origin of evolutionary novelties such as the mammary gland, asking if it was "conceivable that the young of any animal was ever saved from destruction by accidentally sucking a drop of scarcely nutritious fluid from an accidentally hypertrophied cutaneous gland of its mother?" It is only now that modern molecular and genomic tools are being brought to bear on this question that we are finally in a position to answer Mivart's challenge and explain one of the most fundamental questions of biology: how does novelty arise in evolution?

  20. From the "Modern Synthesis" to cybernetics: Ivan Ivanovich Schmalhausen (1884-1963) and his research program for a synthesis of evolutionary and developmental biology.

    PubMed

    Levit, Georgy S; Hossfeld, Uwe; Olsson, Lennart

    2006-03-15

    Ivan I. Schmalhausen was one of the central figures in the Russian development of the "Modern Synthesis" in evolutionary biology. He is widely cited internationally even today. Schmalhausen developed the main principles of his theory facing the danger of death in the totalitarian Soviet Union. His great services to evolutionary and theoretical biology are indisputable. However, the received view of Schmalhausen's contributions to evolutionary biology makes an unbiased reading of his texts difficult. Here we show that taking all of his works into consideration (including those only available in Russian) paints a much more dynamic and exciting picture of what he tried to achieve. Schmalhausen pioneered the integration of a developmental perspective into evolutionary thinking. A main tool for achieving this was his approach to living objects as complex multi-level self-regulating systems. Schmalhausen put enormous effort into bringing this idea into fruition during the final stages of his career by combining evolutionary theory with cybernetics. His results and ideas remain thought-provoking, and his texts are of more than just historical interest.

  1. Evolutionary principles and their practical application

    PubMed Central

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

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

  2. Evolutionary Perspective in Child Growth

    PubMed Central

    Hochberg, Ze’ev

    2011-01-01

    Hereditary, environmental, and stochastic factors determine a child’s growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment. PMID:23908815

  3. Evolutionary perspective in child growth.

    PubMed

    Hochberg, Ze'ev

    2011-07-01

    Hereditary, environmental, and stochastic factors determine a child's growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.

  4. Molecular phylogenetics: testing evolutionary hypotheses.

    PubMed

    Walsh, David A; Sharma, Adrian K

    2009-01-01

    A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.

  5. Evolutionary stability on graphs

    PubMed Central

    Ohtsuki, Hisashi; Nowak, Martin A.

    2008-01-01

    Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k > 2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs. PMID:18295801

  6. Exaptation, adaptation, and evolutionary psychology.

    PubMed

    Schulz, Armin

    2013-01-01

    One of the most well known methodological criticisms of evolutionary psychology is Gould's claim that the program pays too much attention to adaptations, and not enough to exaptations. Almost as well known is the standard rebuttal of that criticism: namely, that the study of exaptations in fact depends on the study of adaptations. However, as I try to show in this paper, it is premature to think that this is where this debate ends. First, the notion of exaptation that is commonly used in this debate is different from the one that Gould and Vrba originally defined. Noting this is particularly important, since, second, the standard reply to Gould's criticism only works if the criticism is framed in terms of the former notion of exaptation, and not the latter. However, third, this ultimately does not change the outcome of the debate much, as evolutionary psychologists can respond to the revamped criticism of their program by claiming that the original notion of exaptation is theoretically and empirically uninteresting. By discussing these issues further, I also seek to determine, more generally, which ways of approaching the adaptationism debate in evolutionary biology are useful, and which not.

  7. Remembering the evolutionary Freud.

    PubMed

    Young, Allan

    2006-03-01

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

  8. Polymorphic Evolutionary Games.

    PubMed

    Fishman, Michael A

    2016-06-07

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

  9. Evolutionary Fingerprinting of Genes

    PubMed Central

    Kosakovsky Pond, Sergei L.; Scheffler, Konrad; Gravenor, Michael B.; Poon, Art F.Y.; Frost, Simon D.W.

    2010-01-01

    Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change—an “evolutionary fingerprint” of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast. To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates. PMID:19864470

  10. IonRock: software for solving strain gradients of ion-implanted semiconductors by X-ray diffraction measurements and evolutionary programming

    NASA Astrophysics Data System (ADS)

    Bleicher, Lucas; Sasaki, José Marcos; Orloski, Renata Villela; Cardoso, Lisandro Pavie; Hayashi, Marcelo Assaoka; Swart, Jacobus Willibrordus

    2004-07-01

    We present a program that uses an optimization algorithm to fit rocking curves of ion-implanted semiconductors. This is an inverse problem that cannot be solved by simple methods. However, using recursion formulae for rocking curve calculations and a model of ion distribution after implantation, it is possible to fit experimental data with a general-purpose optimization method. In our case, we use a modified version of the genetic algorithm, which has been shown to be a good technique for this problem. The program also calculates rocking curves for a given ion profile, such as those generated by ion implantation simulation programs. Program summaryTitle of program: IonRock, version 1.0 Catalogue identifier: ADTP Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTP Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: any computer with Windows95 or later version Operating systems: Windows95/98/2000/NT/XP Programming language used: C++ Memory required to execute with typical data: about 4 MB No. of bytes in distributed program, including test data, etc.: 2 742 530 No of lines in distributed program, including test data etc.: 49 988 Distribution format: tar gzip file Nature of physical problem: strain determination on ion implanted zinc-blend structure semiconductors Method of solution: adapted version of the Genetic Algorithm meta-heuristic Restrictions on the complexity of the problem: strain determination is related to the strain generated by interstitial ions, which causes the left-side distortions on the rocking curve Typical running time: on an Athlon PC computer the computing time for solving the strain gradient using 16 layers takes from 10 to 30 minutes

  11. Evolutionary tree reconstruction

    NASA Technical Reports Server (NTRS)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

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

    PubMed

    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.

  13. Evolutionary behavioral genetics

    PubMed Central

    Zietsch, Brendan P.; de Candia, Teresa R; Keller, Matthew C.

    2014-01-01

    We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics—a field that could be termed Evolutionary Behavioral Genetics—and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants. PMID:25587556

  14. Evolutionary Mechanisms for Loneliness

    PubMed Central

    Cacioppo, John T.; Cacioppo, Stephanie; Boomsma, Dorret I.

    2013-01-01

    Robert Weiss (1973) conceptualized loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organization than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale. PMID:24067110

  15. Evolutionary mechanisms for loneliness.

    PubMed

    Cacioppo, John T; Cacioppo, Stephanie; Boomsma, Dorret I

    2014-01-01

    Robert Weiss (1973) conceptualised loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organisation than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale.

  16. Molluscan Evolutionary Genomics

    SciTech Connect

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  17. A theoretical comparison of evolutionary algorithms and simulated annealing

    SciTech Connect

    Hart, W.E.

    1995-08-28

    This paper theoretically compares the performance of simulated annealing and evolutionary algorithms. Our main result is that under mild conditions a wide variety of evolutionary algorithms can be shown to have greater performance than simulated annealing after a sufficiently large number of function evaluations. This class of EAs includes variants of evolutionary strategie and evolutionary programming, the canonical genetic algorithm, as well as a variety of genetic algorithms that have been applied to combinatorial optimization problems. The proof of this result is based on a performance analysis of a very general class of stochastic optimization algorithms, which has implications for the performance of a variety of other optimization algorithm.

  18. Evolutionary Trends of Problem-Based Learning Practices throughout a Two-Year Preclinical Program: A Comparison of Students' and Teachers' Perceptions

    ERIC Educational Resources Information Center

    Baroffio, Anne; Vu, Nu V.; Gerbase, Margaret W.

    2013-01-01

    Implementation of a pedagogical approach is a continuous and evolving process. As an institution with more than 15 years problem-based learning (PBL), we studied how the learning and teaching processes are currently practiced in a 2-year preclinical basic sciences program to assess whether they still match the intended objectives. Using both…

  19. Evolutionary trends of problem-based learning practices throughout a two-year preclinical program: a comparison of students' and teachers' perceptions.

    PubMed

    Baroffio, Anne; Vu, Nu V; Gerbase, Margaret W

    2013-10-01

    Implementation of a pedagogical approach is a continuous and evolving process. As an institution with more than 15 years problem-based learning (PBL), we studied how the learning and teaching processes are currently practiced in a 2-year preclinical basic sciences program to assess whether they still match the intended objectives. Using both students' and tutors' evaluations, we analyzed and compared their perceptions on the program content and its organization, on tutors' functioning and on the duration of PBL sessions throughout 11 instructional units of the second and third-year of a 6 years medical curriculum. Whereas both tutors and students indicated that the content and problems selected for the curriculum were well adapted to the PBL process, they felt the references as well as the self-study time as moderately appropriate. Over the course of the 2-year program, tutorial sessions got linearly shorter, whereas reporting sessions got longer. While tutors knew well the PBL approach and were suitably prepared to their tutorials, they however, became less regular in providing feedback and in evaluating group functioning over the 2 years. Our results suggest that the practice of the PBL process evolves within and throughout a 2-year preclinical program and moves away from the original intentions. Possible underlying reasons and their implications are discussed within the context of tutors' and students' concepts of teaching and learning, the medical schools' learning environment and teaching practices and the difficulty of developing and maintaining in the long term a deep and self-directed learning approach.

  20. Proteomics in evolutionary ecology.

    PubMed

    Baer, B; Millar, A H

    2016-03-01

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

  1. A comparative study of corrugated horn design by evolutionary techniques

    NASA Technical Reports Server (NTRS)

    Hoorfar, A.

    2003-01-01

    Here an evolutionary programming algorithm is used to optimize the pattern of a corrugated circular horn subject to various constraints on return loss, antenna beamwidth, pattern circularity, and low cross polarization.

  2. Applying Evolutionary Anthropology

    PubMed Central

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

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

  3. Paleoanthropology and evolutionary theory.

    PubMed

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  4. Applying evolutionary anthropology.

    PubMed

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

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

  5. Ecological and evolutionary traps

    USGS Publications Warehouse

    Schlaepfer, Martin A.; Runge, M.C.; Sherman, P.W.

    2002-01-01

    Organisms often rely on environmental cues to make behavioral and life-history decisions. However, in environments that have been altered suddenly by humans, formerly reliable cues might no longer be associated with adaptive outcomes. In such cases, organisms can become 'trapped' by their evolutionary responses to the cues and experience reduced survival or reproduction. Ecological traps occur when organisms make poor habitat choices based on cues that correlated formerly with habitat quality. Ecological traps are part of a broader phenomenon, evolutionary traps, involving a dissociation between cues that organisms use to make any behavioral or life-history decision and outcomes normally associated with that decision. A trap can lead to extinction if a population falls below a critical size threshold before adaptation to the novel environment occurs. Conservation and management protocols must be designed in light of, rather than in spite of, the behavioral mechanisms and evolutionary history of populations and species to avoid 'trapping' them.

  6. Human nutrition: evolutionary perspectives.

    PubMed

    Barnicot, N A

    2005-01-01

    In recent decades, much new evidence relating to the ape forerunners of modern humans has come to hand and diet appears to be an important factor. At some stage, there must have been a transition from a largely vegetarian ape diet to a modern human hunting economy providing significant amounts of meat. On an even longer evolutionary time scale the change was more complex. The mechanisms of evolutionary change are now better understood than they were in Darwin's time, thanks largely to great advances in genetics, both experimental and theoretical. It is virtually certain that diet, as a major component of the human environment, must have exerted evolutionary effects, but researchers still have little good evidence.

  7. Evolutionary synthetic biology.

    PubMed

    Peisajovich, Sergio G

    2012-06-15

    Signaling networks process vast amounts of environmental information to generate specific cellular responses. As cellular environments change, signaling networks adapt accordingly. Here, I will discuss how the integration of synthetic biology and directed evolution approaches is shedding light on the molecular mechanisms that guide the evolution of signaling networks. In particular, I will review studies that demonstrate how different types of mutations, from the replacement of individual amino acids to the shuffling of modular domains, lead to markedly different evolutionary trajectories and consequently to diverse network rewiring. Moreover, I will argue that intrinsic evolutionary properties of signaling proteins, such as the robustness of wild type functions, the promiscuous nature of evolutionary intermediates, and the modular decoupling between binding and catalysis, play important roles in the evolution of signaling networks. Finally, I will argue that rapid advances in our ability to synthesize DNA will radically alter how we study signaling network evolution at the genome-wide level.

  8. Evolutionary Debunking Arguments.

    PubMed

    Kahane, Guy

    2011-03-01

    Evolutionary debunking arguments (EDAs) are arguments that appeal to the evolutionary origins of evaluative beliefs to undermine their justification. This paper aims to clarify the premises and presuppositions of EDAs-a form of argument that is increasingly put to use in normative ethics. I argue that such arguments face serious obstacles. It is often overlooked, for example, that they presuppose the truth of metaethical objectivism. More importantly, even if objectivism is assumed, the use of EDAs in normative ethics is incompatible with a parallel and more sweeping global evolutionary debunking argument that has been discussed in recent metaethics. After examining several ways of responding to this global debunking argument, I end by arguing that even if we could resist it, this would still not rehabilitate the current targeted use of EDAs in normative ethics given that, if EDAs work at all, they will in any case lead to a truly radical revision of our evaluative outlook.

  9. Evolutionary Debunking Arguments

    PubMed Central

    Kahane, Guy

    2011-01-01

    Evolutionary debunking arguments (EDAs) are arguments that appeal to the evolutionary origins of evaluative beliefs to undermine their justification. This paper aims to clarify the premises and presuppositions of EDAs—a form of argument that is increasingly put to use in normative ethics. I argue that such arguments face serious obstacles. It is often overlooked, for example, that they presuppose the truth of metaethical objectivism. More importantly, even if objectivism is assumed, the use of EDAs in normative ethics is incompatible with a parallel and more sweeping global evolutionary debunking argument that has been discussed in recent metaethics. After examining several ways of responding to this global debunking argument, I end by arguing that even if we could resist it, this would still not rehabilitate the current targeted use of EDAs in normative ethics given that, if EDAs work at all, they will in any case lead to a truly radical revision of our evaluative outlook. PMID:21949447

  10. Evolutionary software for autonomous path planning

    SciTech Connect

    Couture, S; Hage, M

    1999-02-10

    This research project demonstrated the effectiveness of using evolutionary software techniques in the development of path-planning algorithms and control programs for mobile vehicles in radioactive environments. The goal was to take maximum advantage of the programmer's intelligence by tasking the programmer with encoding the measures of success for a path-planning algorithm, rather than developing the path-planning algorithms themselves. Evolutionary software development techniques could then be used to develop algorithms most suitable to the particular environments of interest. The measures of path-planning success were encoded in the form of a fitness function for an evolutionary software development engine. The task for the evolutionary software development engine was to evaluate the performance of individual algorithms, select the best performers for the population based on the fitness function, and breed them to evolve the next generation of algorithms. The process continued for a set number of generations or until the algorithm converged to an optimal solution. The task environment was the navigation of a rover from an initial location to a goal, then to a processing point, in an environment containing physical and radioactive obstacles. Genetic algorithms were developed for a variety of environmental configurations. Algorithms were simple and non-robust strings of behaviors, but they could be evolved to be nearly optimal for a given environment. In addition, a genetic program was evolved in the form of a control algorithm that operates at every motion of the robot. Programs were more complex than algorithms and less optimal in a given environment. However, after training in a variety of different environments, they were more robust and could perform acceptably in environments they were not trained in. This paper describes the evolutionary software development engine and the performance of algorithms and programs evolved by it for the chosen task.

  11. Investigating human evolutionary history

    PubMed Central

    WOOD, BERNARD

    2000-01-01

    We rely on fossils for the interpretation of more than 95% of our evolutionary history. Fieldwork resulting in the recovery of fresh fossil evidence is an important component of reconstructing human evolutionary history, but advances can also be made by extracting additional evidence for the existing fossil record, and by improving the methods used to interpret the fossil evidence. This review shows how information from imaging and dental microstructure has contributed to improving our understanding of the hominin fossil record. It also surveys recent advances in the use of the fossil record for phylogenetic inference. PMID:10999269

  12. Evolutionary Design in Art

    NASA Astrophysics Data System (ADS)

    McCormack, Jon

    Evolution is one of the most interesting and creative processes we currently understand, so it should come as no surprise that artists and designers are embracing the use of evolution in problems of artistic creativity. The material in this section illustrates the diversity of approaches being used by artists and designers in relation to evolution at the boundary of art and science. While conceptualising human creativity as an evolutionary process in itself may be controversial, what is clear is that evolutionary processes can be used to complement, even enhance human creativity, as the chapters in this section aptly demonstrate.

  13. The fastest evolutionary trajectory

    PubMed Central

    Traulsen, Arne; Iwasa, Yoh; Nowak, Martin A.

    2008-01-01

    Given two mutants, A and B, separated by n mutational steps, what is the evolutionary trajectory which allows a homogeneous population of A to reach B in the shortest time? We show that the optimum evolutionary trajectory (fitness landscape) has the property that the relative fitness increase between any two consecutive steps is constant. Hence, the optimum fitness landscape between A and B is given by an exponential function. Our result is precise for small mutation rates and excluding back mutations. We discuss deviations for large mutation rates and including back mutations. For very large mutation rates, the optimum fitness landscape is flat and has a single peak at type B. PMID:17900629

  14. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    PubMed Central

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

    2015-01-01

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

  15. Scalable computing for evolutionary genomics.

    PubMed

    Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

    2012-01-01

    Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project

  16. Evolutionary Developmental Psychology.

    ERIC Educational Resources Information Center

    Geary, David C.; Bjorklund, David F.

    2000-01-01

    Describes evolutionary developmental psychology as the study of the genetic and ecological mechanisms that govern the development of social and cognitive competencies common to all human beings and the epigenetic (gene-environment interactions) processes that adapt these competencies to local conditions. Outlines basic assumptions and domains of…

  17. Evolutionary developmental psychology.

    PubMed

    King, Ashley C; Bjorklund, David F

    2010-02-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several aspects of childhood (e.g., play and immature cognition) serve both as deferred adaptations as well as imparting immediate benefits. Intense selection pressure was surely exerted on childhood over human evolutionary history and, as a result, neglecting to consider the early developmental period of children when studying their later adulthood produces an incomplete picture of the evolved adaptations expressed through human behavior and cognition.

  18. Learning: An Evolutionary Analysis

    ERIC Educational Resources Information Center

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  19. Evolutionary Theory under Fire.

    ERIC Educational Resources Information Center

    Lewin, Roger

    1980-01-01

    Summarizes events of a conference on evolutionary biology in Chicago entitled: "Macroevolution." Reviews the theory of modern synthesis, a term used to explain Darwinism in terms of population biology and genetics. Issues presented at the conference are discussed in detail. (CS)

  20. Evolutionary Theories of Detection

    SciTech Connect

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  1. Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions

    PubMed Central

    Ray, Jessica L.; Haramaty, Liti; Thyrhaug, Runar; Fredricks, Helen F.; Van Mooy, Benjamin A. S.; Larsen, Aud; Bidle, Kay D.; Sandaa, Ruth-Anne

    2014-01-01

    The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity. PMID:25013242

  2. Bell-Curve Based Evolutionary Strategies for Structural Optimization

    NASA Technical Reports Server (NTRS)

    Kincaid, Rex K.

    2001-01-01

    Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity. However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold. One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumbersome binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back and Dasgupta and Michalesicz. We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

  3. Bell-Curve Based Evolutionary Strategies for Structural Optimization

    NASA Technical Reports Server (NTRS)

    Kincaid, Rex K.

    2000-01-01

    Evolutionary methods are exceedingly popular with practitioners of many fields; more so than perhaps any optimization tool in existence. Historically Genetic Algorithms (GAs) led the way in practitioner popularity (Reeves 1997). However, in the last ten years Evolutionary Strategies (ESs) and Evolutionary Programs (EPS) have gained a significant foothold (Glover 1998). One partial explanation for this shift is the interest in using GAs to solve continuous optimization problems. The typical GA relies upon a cumber-some binary representation of the design variables. An ES or EP, however, works directly with the real-valued design variables. For detailed references on evolutionary methods in general and ES or EP in specific see Back (1996) and Dasgupta and Michalesicz (1997). We call our evolutionary algorithm BCB (bell curve based) since it is based upon two normal distributions.

  4. Evolutionary Determinants of Cancer

    PubMed Central

    Greaves, Mel

    2015-01-01

    ‘Nothing in biology makes sense except in the light of evolution’ Th. Dobzhansky, 1973 Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as complex, dynamic and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints facilitating increasing complexity and longevity of species. But our own has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. PMID:26193902

  5. Predicting evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Balazsi, Gabor

    We developed an ordinary differential equation-based model to predict the evolutionary dynamics of yeast cells carrying a synthetic gene circuit. The predicted aspects included the speed at which the ancestral genotype disappears from the population; as well as the types of mutant alleles that establish in each environmental condition. We validated these predictions by experimental evolution. The agreement between our predictions and experimental findings suggests that cellular and population fitness landscapes can be useful to predict short-term evolution.

  6. Evolutionary mysteries in meiosis.

    PubMed

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  7. Literary study and evolutionary theory : A review essay.

    PubMed

    Carroll, J

    1998-09-01

    Several recent books have claimed to integrate literary study with evolutionary biology. All of the books here considered, except Robert Storey's, adopt conceptions of evolutionary theory that are in some way marginal to the Darwinian adaptationist program. All the works attempt to connect evolutionary study with various other disciplines or methodologies: for example, with cultural anthropology, cognitive psychology, the psychology of emotion, neurobiology, chaos theory, or structuralist linguistics. No empirical paradigm has yet been established for this field, but important steps have been taken, especially by Storey, in formulating basic principles, identifying appropriate disciplinary connections, and marking out lines of inquiry. Reciprocal efforts are needed from biologists and social scientists.

  8. Evolutionary programming for neutron instrument optimisation

    NASA Astrophysics Data System (ADS)

    Bentley, Phillip M.; Pappas, Catherine; Habicht, Klaus; Lelièvre-Berna, Eddy

    2006-11-01

    Virtual instruments based on Monte-Carlo techniques are now integral part of novel instrumentation development and the existing codes (McSTAS and Vitess) are extensively used to define and optimise novel instrumental concepts. Neutron spectrometers, however, involve a large number of parameters and their optimisation is often a complex and tedious procedure. Artificial intelligence algorithms are proving increasingly useful in such situations. Here, we present an automatic, reliable and scalable numerical optimisation concept based on the canonical genetic algorithm (GA). The algorithm was used to optimise the 3D magnetic field profile of the NSE spectrometer SPAN, at the HMI. We discuss the potential of the GA which combined with the existing Monte-Carlo codes (Vitess, McSTAS, etc.) leads to a very powerful tool for automated global optimisation of a general neutron scattering instrument, avoiding local optimum configurations.

  9. Landscape evolutionary genomics.

    PubMed

    Lowry, David B

    2010-08-23

    Tremendous advances in genetic and genomic techniques have resulted in the capacity to identify genes involved in adaptive evolution across numerous biological systems. One of the next major steps in evolutionary biology will be to determine how landscape-level geographical and environmental features are involved in the distribution of this functional adaptive genetic variation. Here, I outline how an emerging synthesis of multiple disciplines has and will continue to facilitate a deeper understanding of the ways in which heterogeneity of the natural landscapes mould the genomes of organisms.

  10. Evolutionary Design in Biology

    NASA Astrophysics Data System (ADS)

    Wiese, Kay C.

    Much progress has been achieved in recent years in molecular biology and genetics. The sheer volume of data in the form of biological sequences has been enormous and efficient methods for dealing with these huge amounts of data are needed. In addition, the data alone does not provide information on the workings of biological systems; hence much research effort has focused on designing mathematical and computational models to address problems from molecular biology. Often, the terms bioinformatics and computational biology are used to refer to the research fields concerning themselves with designing solutions to molecular problems in biology. However, there is a slight distinction between bioinformatics and computational biology: the former is concerned with managing the enormous amounts of biological data and extracting information from it, while the latter is more concerned with the design and development of new algorithms to address problems such as protein or RNA folding. However, the boundary is blurry, and there is no consistent usage of the terms. We will use the term bioinformatics to encompass both fields. To cover all areas of research in bioinformatics is beyond the scope of this section and we refer the interested reader to [2] for a general introduction. A large part of what bioinformatics is concerned about is evolution and function of biological systems on a molecular level. Evolutionary computation and evolutionary design are concerned with developing computational systems that "mimic" certain aspects of natural evolution (mutation, crossover, selection, fitness). Much of the inner workings of natural evolutionary systems have been copied, sometimes in modified format into evolutionary computation systems. Artificial neural networks mimic the functioning of simple brain cell clusters. Fuzzy systems are concerned with the "fuzzyness" in decision making, similar to a human expert. These three computational paradigms fall into the category of

  11. Evolutionary dynamics of enzymes.

    PubMed

    Demetrius, L

    1995-08-01

    This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute

  12. Thermodynamics and evolutionary genetics

    NASA Astrophysics Data System (ADS)

    Müller, Ingo

    2010-03-01

    Thermodynamics and evolutionary genetics have something in common. Thus, the randomness of mutation of cells may be likened to the random thermal fluctuations in a gas. And the probabilistic nature of entropy in statistical thermodynamics can be carried over to a population of haploid and diploid cells without any conceptual change. The energetic potential wells in which the atoms of a liquid are caught correspond to selective advantages for some phenotype over others. Thus, the eventual stable state in a population comes about as a compromise in the universal competition between entropy and energy.

  13. Practical advantages of evolutionary computation

    NASA Astrophysics Data System (ADS)

    Fogel, David B.

    1997-10-01

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

  14. Space Politics and Policy. An Evolutionary Perspective

    NASA Astrophysics Data System (ADS)

    Sadeh, E.

    2003-01-01

    This book is the first comprehensive source for the Space Politics and Policies of the United States Civil, Military, Intelligence, and Commercial Space Programs. Space Politics and Policy: An Evolutionary Perspective provides a comprehensive survey of Space Policy. This book is organized around two themes. Space Policy is evolutionary in that it has responded to dramatic political events, such as the launching of Sputnik and the Cold War, and has undergone dynamic and evolutionary policy changes over the course of the space age. Space Policy is an integral part of and interacts with public policy processes in the United States and abroad. The book analyzes Space Policy at several levels including historical context, political actors and institutions, political processes and policy outcomes. It examines the symbiotic relationships between policy, technology, and science; provides a review and synthesis of the existing body of knowledge in Space Policy; and identifies Space Policy trends and developments from the beginnings of the space age through the current era of the twenty-first century. The book is intended for those interested in Space Policy, especially Space Policy decision-makers, program and project managers, as well as students and lecturers of Space Policy. Link: http://www.wkap.nl/prod/b/1-4020-0879-1 and http://www.wkap.nl/prod/b/1-4020-0902-X

  15. Evolutionary status of Polaris

    NASA Astrophysics Data System (ADS)

    Fadeyev, Yu. A.

    2015-05-01

    Hydrodynamic models of short-period Cepheids were computed to determine the pulsation period as a function of evolutionary time during the first and third crossings of the instability strip. The equations of radiation hydrodynamics and turbulent convection for radial stellar pulsations were solved with the initial conditions obtained from the evolutionary models of Population I stars (X = 0.7, Z = 0.02) with masses from 5.2 to 6.5 M⊙ and the convective core overshooting parameter 0.1 ≤ αov ≤ 0.3. In Cepheids with period of 4 d the rate of pulsation period change during the first crossing of the instability strip is over 50 times larger than that during the third crossing. Polaris is shown to cross the instability strip for the first time and to be the fundamental mode pulsator. The best agreement between the predicted and observed rates of period change was obtained for the model with mass of 5.4 M⊙ and the overshooting parameter αov = 0.25. The bolometric luminosity and radius are L = 1.26 × 103 L⊙ and R = 37.5 R⊙, respectively. In the HR diagram, Polaris is located at the red edge of the instability strip.

  16. On evolutionary systems.

    PubMed

    Alvarez de Lorenzana, J M; Ward, L M

    1987-01-01

    This paper develops a metatheoretical framework for understanding evolutionary systems (systems that develop in ways that increase their own variety). The framework addresses shortcomings seen in other popular systems theories. It concerns both living and nonliving systems, and proposes a metahierarchy of hierarchical systems. Thus, it potentially addresses systems at all descriptive levels. We restrict our definition of system to that of a core system whose parts have a different ontological status than the system, and characterize the core system in terms of five global properties: minimal length interval, minimal time interval, system cycle, total receptive capacity, and system potential. We propose two principles through the interaction of which evolutionary systems develop. The Principle of Combinatorial Expansion describes how a core system realizes its developmental potential through a process of progressive differentiation of the single primal state up to a limit stage. The Principle of Generative Condensation describes how the components of the last stage of combinatorial expansion condense and become the environment for and components of new, enriched systems. The early evolution of the Universe after the "big bang" is discussed in light of these ideas as an example of the application of the framework.

  17. Turbopump Performance Improved by Evolutionary Algorithms

    NASA Technical Reports Server (NTRS)

    Oyama, Akira; Liou, Meng-Sing

    2002-01-01

    The development of design optimization technology for turbomachinery has been initiated using the multiobjective evolutionary algorithm under NASA's Intelligent Synthesis Environment and Revolutionary Aeropropulsion Concepts programs. As an alternative to the traditional gradient-based methods, evolutionary algorithms (EA's) are emergent design-optimization algorithms modeled after the mechanisms found in natural evolution. EA's search from multiple points, instead of moving from a single point. In addition, they require no derivatives or gradients of the objective function, leading to robustness and simplicity in coupling any evaluation codes. Parallel efficiency also becomes very high by using a simple master-slave concept for function evaluations, since such evaluations often consume the most CPU time, such as computational fluid dynamics. Application of EA's to multiobjective design problems is also straightforward because EA's maintain a population of design candidates in parallel. Because of these advantages, EA's are a unique and attractive approach to real-world design optimization problems.

  18. Synthesis of logic circuits with evolutionary algorithms

    SciTech Connect

    JONES,JAKE S.; DAVIDSON,GEORGE S.

    2000-01-26

    In the last decade there has been interest and research in the area of designing circuits with genetic algorithms, evolutionary algorithms, and genetic programming. However, the ability to design circuits of the size and complexity required by modern engineering design problems, simply by specifying required outputs for given inputs has as yet eluded researchers. This paper describes current research in the area of designing logic circuits using an evolutionary algorithm. The goal of the research is to improve the effectiveness of this method and make it a practical aid for design engineers. A novel method of implementing the algorithm is introduced, and results are presented for various multiprocessing systems. In addition to evolving standard arithmetic circuits, work in the area of evolving circuits that perform digital signal processing tasks is described.

  19. Phylomemetics—Evolutionary Analysis beyond the Gene

    PubMed Central

    Howe, Christopher J.; Windram, Heather F.

    2011-01-01

    Genes are propagated by error-prone copying, and the resulting variation provides the basis for phylogenetic reconstruction of evolutionary relationships. Horizontal gene transfer may be superimposed on a tree-like evolutionary pattern, with some relationships better depicted as networks. The copying of manuscripts by scribes is very similar to the replication of genes, and phylogenetic inference programs can be used directly for reconstructing the copying history of different versions of a manuscript text. Phylogenetic methods have also been used for some time to analyse the evolution of languages and the development of physical cultural artefacts. These studies can help to answer a range of anthropological questions. We propose the adoption of the term “phylomemetics” for phylogenetic analysis of reproducing non-genetic elements. PMID:21655311

  20. Evolutionary complexity for protection of critical assets.

    SciTech Connect

    Battaile, Corbett Chandler; Chandross, Michael Evan

    2005-01-01

    This report summarizes the work performed as part of a one-year LDRD project, 'Evolutionary Complexity for Protection of Critical Assets.' A brief introduction is given to the topics of genetic algorithms and genetic programming, followed by a discussion of relevant results obtained during the project's research, and finally the conclusions drawn from those results. The focus is on using genetic programming to evolve solutions for relatively simple algebraic equations as a prototype application for evolving complexity in computer codes. The results were obtained using the lil-gp genetic program, a C code for evolving solutions to user-defined problems and functions. These results suggest that genetic programs are not well-suited to evolving complexity for critical asset protection because they cannot efficiently evolve solutions to complex problems, and introduce unacceptable performance penalties into solutions for simple ones.

  1. Spore: Spawning Evolutionary Misconceptions?

    NASA Astrophysics Data System (ADS)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  2. Anxiety: an evolutionary approach.

    PubMed

    Bateson, Melissa; Brilot, Ben; Nettle, Daniel

    2011-12-01

    Anxiety disorders are among the most common mental illnesses, with huge attendant suffering. Current treatments are not universally effective, suggesting that a deeper understanding of the causes of anxiety is needed. To understand anxiety disorders better, it is first necessary to understand the normal anxiety response. This entails considering its evolutionary function as well as the mechanisms underlying it. We argue that the function of the human anxiety response, and homologues in other species, is to prepare the individual to detect and deal with threats. We use a signal detection framework to show that the threshold for expressing the anxiety response ought to vary with the probability of threats occurring, and the individual's vulnerability to them if they do occur. These predictions are consistent with major patterns in the epidemiology of anxiety. Implications for research and treatment are discussed.

  3. Open Issues in Evolutionary Robotics.

    PubMed

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

    2016-01-01

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

  4. Observability in dynamic evolutionary models.

    PubMed

    López, I; Gámez, M; Carreño, R

    2004-02-01

    In the paper observability problems are considered in basic dynamic evolutionary models for sexual and asexual populations. Observability means that from the (partial) knowledge of certain phenotypic characteristics the whole evolutionary process can be uniquely recovered. Sufficient conditions are given to guarantee observability for both sexual and asexual populations near an evolutionarily stable state.

  5. Species Concepts and the Evolutionary Paradigm in Modem Nematology

    PubMed Central

    Adams, Byron J.

    1998-01-01

    Given the task of recovering and representing evolutionary history, nematode taxonomists can choose from among several species concepts. All species concepts have theoretical and (or) operational inconsistencies that can result in failure to accurately recover and represent species. This failure not only obfuscates nematode taxonomy but hinders other research programs in hematology that are dependent upon a phylogenetically correct taxonomy, such as biodiversity, biogeography, cospeciation, coevolution, and adaptation. Three types of systematic errors inherent in different species concepts and their potential effects on these research programs are presented. These errors include overestimating and underestimating the number of species (type I and II error, respectively) and misrepresenting their phylogenetic relationships (type III error). For research programs in hematology that utilize recovered evolutionary history, type II and III errors are the most serious. Linnean, biological, evolutionary, and phylogenefic species concepts are evaluated based on their sensitivity to systematic error. Linnean and biological species concepts are more prone to serious systematic error than evolutionary or phylogenetic concepts. As an alternative to the current paradigm, an amalgamation of evolutionary and phylogenetic species concepts is advocated, along with a set of discovery operations designed to minimize the risk of making systematic errors. Examples of these operations are applied to species and isolates of Heterorhabditis. PMID:19274195

  6. RNA based evolutionary optimization

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    1993-12-01

    The notion of an RNA world has been introduced for a prebiotic scenario that is dominated by RNA molecules and their properties, in particular their capabilities to act as templates for reproduction and as catalysts for several cleavage and ligation reactions of polynucleotides and polypeptides. This notion is used here also for simple experimental assays which are well suited to study evolution in the test tube. In molecular evolution experiments fitness is determined in essence by the molecular structures of RNA molecules. Evidence is presented for adaptation to environment in cell-free media. RNA based molecular evolution experiments have led to interesting spin-offs in biotechnology, commonly called ‘applied molecular evolution’, which make use of Darwinian trial-and-error strategies in order to synthesize new pharmacological compounds and other advanced materials on a biological basis. Error-propagation in RNA replication leads to formation of mutant spectra called ‘quasispecies’. An increase in the error rate broadens the mutant spectrum. There exists a sharply defined threshold beyond which heredity breaks down and evolutionary adaptation becomes impossible. Almost all RNA viruses studied so far operate at conditions close to this error threshold. Quasispecies and error thresholds are important for an understanding of RNA virus evolution, and they may help to develop novel antiviral strategies. Evolution of RNA molecules can be studied and interpreted by considering secondary structures. The notion of sequence space introduces a distance between pairs of RNA sequences which is tantamount to counting the minimal number of point mutations required to convert the sequences into each other. The mean sensitivity of RNA secondary structures to mutation depends strongly on the base pairing alphabet: structures from sequences which contain only one base pair (GC or AU are much less stable against mutation than those derived from the natural (AUGC) sequences

  7. Evolutionary and Developmental Modules

    PubMed Central

    Lacquaniti, Francesco; Ivanenko, Yuri P.; d’Avella, Andrea; Zelik, Karl E.; Zago, Myrka

    2013-01-01

    The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates. PMID:23730285

  8. Evolutionary Tracks for Betelgeuse

    NASA Astrophysics Data System (ADS)

    Dolan, Michelle; Mathews, Grant; Dearborn, David

    2008-04-01

    We have constructed a series of quasi-hydrostatic evolutionary models for the M2 Iab supergiant Betelgeuse (Õrionis). Our models are constrained by the observed temperature, luminosity, surface composition and mass loss for this star, along with recent parallax measurements and high resolution imagery which directly determine its radius. The surface convective zone obtained in our model naturally accounts for observed variations in surface luminosity and the size of detected surface bright spots. In our models these result from upflowing convective material from regions of high temperature in a surface convective zone. We also account for the observed periodic variability as the result of the effective equation of state in a simple linear pulsation model. Based upon a comparison between the accumulated mass loss in the observed circumstellar shell, and the lower limit on luminosity we suggest that this star most likely has a mass of either 16 ±2 M if a Reimers lass loss rate applies or 20 ±2 for the de Jager mass loss rate. For any mass loss rate the star must be close to the tip of the first ascent up the giant branch.

  9. Evolutionary cytogenetics in salamanders.

    PubMed

    Sessions, Stanley K

    2008-01-01

    Salamanders (Amphibia: Caudata/Urodela) have been the subject of numerous cytogenetic studies, and data on karyotypes and genome sizes are available for most groups. Salamanders show a more-or-less distinct dichotomy between families with large chromosome numbers and interspecific variation in chromosome number, relative size, and shape (i.e. position of the centromere), and those that exhibit very little variation in these karyological features. This dichotomy is the basis of a major model of karyotype evolution in salamanders involving a kind of 'karyotypic orthoselection'. Salamanders are also characterized by extremely large genomes (in terms of absolute mass of nuclear DNA) and extensive variation in genome size (and overall size of the chromosomes), which transcends variation in chromosome number and shape. The biological significance and evolution of chromosome number and shape within the karyotype is not yet understood, but genome size variation has been found to have strong phenotypic, biogeographic, and phylogenetic correlates that reveal information about the biological significance of this cytogenetic variable. Urodeles also present the advantage of only 10 families and less than 600 species, which facilitates the analysis of patterns within the entire order. The purpose of this review is to present a summary of what is currently known about overall patterns of variation in karyology and genome size in salamanders. These patterns are discussed within an evolutionary context.

  10. Evolutionary financial market models

    NASA Astrophysics Data System (ADS)

    Ponzi, A.; Aizawa, Y.

    2000-12-01

    We study computer simulations of two financial market models, the second a simplified model of the first. The first is a model of the self-organized formation and breakup of crowds of traders, motivated by the dynamics of competitive evolving systems which shows interesting self-organized critical (SOC)-type behaviour without any fine tuning of control parameters. This SOC-type avalanching and stasis appear as realistic volatility clustering in the price returns time series. The market becomes highly ordered at ‘crashes’ but gradually loses this order through randomization during the intervening stasis periods. The second model is a model of stocks interacting through a competitive evolutionary dynamic in a common stock exchange. This model shows a self-organized ‘market-confidence’. When this is high the market is stable but when it gets low the market may become highly volatile. Volatile bursts rapidly increase the market confidence again. This model shows a phase transition as temperature parameter is varied. The price returns time series in the transition region is very realistic power-law truncated Levy distribution with clustered volatility and volatility superdiffusion. This model also shows generally positive stock cross-correlations as is observed in real markets. This model may shed some light on why such phenomena are observed.

  11. Evolutionary rescue beyond the models

    PubMed Central

    Gomulkiewicz, Richard; Shaw, Ruth G.

    2013-01-01

    Laboratory model systems and mathematical models have shed considerable light on the fundamental properties and processes of evolutionary rescue. But it remains to determine the extent to which these model-based findings can help biologists predict when evolution will fail or succeed in rescuing natural populations that are facing novel conditions that threaten their persistence. In this article, we present a prospectus for transferring our basic understanding of evolutionary rescue to wild and other non-laboratory populations. Current experimental and theoretical results emphasize how the interplay between inheritance processes and absolute fitness in changed environments drive population dynamics and determine prospects of extinction. We discuss the challenge of inferring these elements of the evolutionary rescue process in field and natural settings. Addressing this challenge will contribute to a more comprehensive understanding of population persistence that combines processes of evolutionary rescue with developmental and ecological mechanisms. PMID:23209173

  12. Army ants: an evolutionary bestseller?

    PubMed

    Berghoff, Stefanie M

    2003-09-02

    Army ants are characterized by a complex combination of behavioral and morphological traits. Molecular data now indicate that army ant behavior has a unique evolutionary origin and has been conserved for over more than 100 million years.

  13. Transforming Biology Assessment with Machine Learning: Automated Scoring of Written Evolutionary Explanations

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Ha, Minsu; Mayfield, Elijah

    2012-01-01

    This study explored the use of machine learning to automatically evaluate the accuracy of students' written explanations of evolutionary change. Performance of the Summarization Integrated Development Environment (SIDE) program was compared to human expert scoring using a corpus of 2,260 evolutionary explanations written by 565 undergraduate…

  14. Evolutionary constraints or opportunities?

    PubMed Central

    Sharov, Alexei A.

    2014-01-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155

  15. Understanding Evolutionary Change within the Framework of Geological Time

    ERIC Educational Resources Information Center

    Dodick, Jeff

    2007-01-01

    This paper focuses on a learning strategy designed to overcome students' difficulty in understanding evolutionary change within the framework of geological time. Incorporated into the learning program "From Dinosaurs to Darwin: Evolution from the Perspective of Time," this strategy consists of four scaffolded investigations in which…

  16. Active Processor Scheduling Using Evolutionary Algorithms

    DTIC Science & Technology

    2002-12-01

    xiii Active Processor Scheduling Using Evolutionary Algorithms I. Introduction A distributed system offers the ability to run applications across...calculations are made. This model is sometimes referred to as a form of the island model of evolutionary computation because each population is evolved... Evolutionary Algorithms for Solving Multi-Objective Problems. Genetic Algorithms and Evolutionary Computation , New York: Kluwer Academic Publishers, 2002

  17. Empirical verification of evolutionary theories of aging

    PubMed Central

    Glebov, Anastasia; Asbah, Nimara; Bruno, Luigi; Meunier, Carolynne; Iouk, Tatiana; Titorenko, Vladimir I.

    2016-01-01

    We recently selected 3 long-lived mutant strains of Saccharomyces cerevisiae by a lasting exposure to exogenous lithocholic acid. Each mutant strain can maintain the extended chronological lifespan after numerous passages in medium without lithocholic acid. In this study, we used these long-lived yeast mutants for empirical verification of evolutionary theories of aging. We provide evidence that the dominant polygenic trait extending longevity of each of these mutants 1) does not affect such key features of early-life fitness as the exponential growth rate, efficacy of post-exponential growth and fecundity; and 2) enhances such features of early-life fitness as susceptibility to chronic exogenous stresses, and the resistance to apoptotic and liponecrotic forms of programmed cell death. These findings validate evolutionary theories of programmed aging. We also demonstrate that under laboratory conditions that imitate the process of natural selection within an ecosystem, each of these long-lived mutant strains is forced out of the ecosystem by the parental wild-type strain exhibiting shorter lifespan. We therefore concluded that yeast cells have evolved some mechanisms for limiting their lifespan upon reaching a certain chronological age. These mechanisms drive the evolution of yeast longevity towards maintaining a finite yeast chronological lifespan within ecosystems. PMID:27783562

  18. Light water reactor program

    SciTech Connect

    Franks, S.M.

    1994-12-31

    The US Department of Energy`s Light Water Reactor Program is outlined. The scope of the program consists of: design certification of evolutionary plants; design, development, and design certification of simplified passive plants; first-of-a-kind engineering to achieve commercial standardization; plant lifetime improvement; and advanced reactor severe accident program. These program activities of the Office of Nuclear Energy are discussed.

  19. Parallel Evolutionary Optimization for Neuromorphic Network Training

    SciTech Connect

    Schuman, Catherine D; Disney, Adam; Singh, Susheela; Bruer, Grant; Mitchell, John Parker; Klibisz, Aleksander; Plank, James

    2016-01-01

    One of the key impediments to the success of current neuromorphic computing architectures is the issue of how best to program them. Evolutionary optimization (EO) is one promising programming technique; in particular, its wide applicability makes it especially attractive for neuromorphic architectures, which can have many different characteristics. In this paper, we explore different facets of EO on a spiking neuromorphic computing model called DANNA. We focus on the performance of EO in the design of our DANNA simulator, and on how to structure EO on both multicore and massively parallel computing systems. We evaluate how our parallel methods impact the performance of EO on Titan, the U.S.'s largest open science supercomputer, and BOB, a Beowulf-style cluster of Raspberry Pi's. We also focus on how to improve the EO by evaluating commonality in higher performing neural networks, and present the result of a study that evaluates the EO performed by Titan.

  20. Can An Evolutionary Process Create English Text?

    SciTech Connect

    Bailey, David H.

    2008-10-29

    Critics of the conventional theory of biological evolution have asserted that while natural processes might result in some limited diversity, nothing fundamentally new can arise from 'random' evolution. In response, biologists such as Richard Dawkins have demonstrated that a computer program can generate a specific short phrase via evolution-like iterations starting with random gibberish. While such demonstrations are intriguing, they are flawed in that they have a fixed, pre-specified future target, whereas in real biological evolution there is no fixed future target, but only a complicated 'fitness landscape'. In this study, a significantly more sophisticated evolutionary scheme is employed to produce text segments reminiscent of a Charles Dickens novel. The aggregate size of these segments is larger than the computer program and the input Dickens text, even when comparing compressed data (as a measure of information content).

  1. Control of quantum phenomena through evolutionary engineering: let the system do the thinking

    NASA Astrophysics Data System (ADS)

    Rabitz, Herschel H.; Bosacchi, Bruno

    2002-12-01

    We discuss a successful application of evolutionary algorithms and femtosecond pulse-shaping technology to the coherent control of quantum phenomena. After a brief review of the field of quantum control, we show how evolutionary algorithms provide an effective and, so far, the only general solution to the problem of managing the complex interplay of interference effects which characterize quantum phenomena. A representative list of experimental results is presented, and some directions for future developments are discussed. The success of evolutionary algorithms in quantum control is seen as a significant step in the evolution of computational intelligence, from evolutionary algorithms, to evolutionary programming, to evolutionary engineering, whereby a hardware system organizes itself and evolves on line to achieve a desired result.

  2. Supercritical water oxidation - Concept analysis for evolutionary Space Station application

    NASA Technical Reports Server (NTRS)

    Hall, John B., Jr.; Brewer, Dana A.

    1986-01-01

    The ability of a supercritical water oxidation (SCWO) concept to reduce the number of processes needed in an evolutionary Space Station design's Environmental Control and Life Support System (ECLSS), while reducing resupply requirements and enhancing the integration of separate ECLSS functions into a single Supercritical Water Oxidation process, is evaluated. While not feasible for an initial operational capability Space Station, the SCWO's application to the evolutionary Space Station configuration would aid the integration of eight ECLSS functions into a single one, thereby significantly reducing program costs.

  3. Evolutionary foundations for cancer biology

    PubMed Central

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885

  4. Evolutionary foundations for cancer biology.

    PubMed

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  5. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  6. The major synthetic evolutionary transitions

    PubMed Central

    Solé, Ricard

    2016-01-01

    Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431528

  7. Neuronal boost to evolutionary dynamics.

    PubMed

    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.

  8. Neuronal boost to evolutionary dynamics

    PubMed Central

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    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. PMID:26640653

  9. Evolutionary Aspects of Enzyme Dynamics*

    PubMed Central

    Klinman, Judith P.; Kohen, Amnon

    2014-01-01

    The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein. PMID:25210031

  10. Evolutionary engineering for industrial microbiology.

    PubMed

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  11. Evolutionary psychology and intelligence research.

    PubMed

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative variation on a monomorphic design allows us to incorporate heritable individual differences in evolved adaptations. The Savanna-IQ Interaction Hypothesis, which is one consequence of the integration of evolutionary psychology and intelligence research, can potentially explain why less intelligent individuals enjoy TV more, why liberals are more intelligent than conservatives, and why night owls are more intelligent than morning larks, among many other findings. The general approach proposed here will allow us to integrate evolutionary psychology with any other aspect of differential psychology.

  12. Anticipatory Mechanisms in Evolutionary Living Systems

    NASA Astrophysics Data System (ADS)

    Dubois, Daniel M.; Holmberg, Stig C.

    2010-11-01

    This paper deals firstly with a revisiting of Darwin's theory of Natural Selection. Darwin in his book never uses the word "evolution", but shows a clear position about mutability of species. Darwin's Natural Selection was mainly inspired by the anticipatory Artificial Selection by humans in domestication, and the Malthus struggle for existence. Darwin showed that the struggle for existence leads to the preservation of the most divergent offspring of any one species. He cited several times the canon of "Natura non facit saltum". He spoke about the origin of life from some one primordial form, into which life was first breathed. Finally, Darwin made anticipation about the future researches in psychology. This paper cites the work of Ernst Mayr who was the first, after 90 years of an intense scientific debate, to present a new and stable Darwinian paradigm as the "Evolutionary Synthesis" in 1942. To explain what is life, the Living Systems Theory (LST) by J. G. Miller is presented. It is showed that the Autopoietic Systems Theory of Varela et al is also a fundamental component of living systems. In agreement with Darwin, the natural selection is a necessary condition for transformation of biological systems, but is not a sufficient condition. Thus, in this paper we conjecture that an anticipatory evolutionary mechanism exists with the genetic code that is a self-replicating and self-modifying anticipatory program. As demonstrated by Nobel laureate McClintock, evolution in genomes is programmed. The word "program" comes from "pro-gram" meaning to write before, by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes of behavioural responses, that is part of an organism. For example, cell death may be programmed by what is called the apoptosis. This definitively is a great breakthrough in our understanding of biological evolution. Hence

  13. Achieving sustainable plant disease management through evolutionary principles.

    PubMed

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

    2014-09-01

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

  14. Individual-based modeling of ecological and evolutionary processes

    USGS Publications Warehouse

    DeAngelis, Donald L.; Mooij, Wolf M.

    2005-01-01

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

  15. An inquiry into evolutionary inquiry

    NASA Astrophysics Data System (ADS)

    Donovan, Samuel S.

    2005-11-01

    While evolution education has received a great deal of attention within the science education research community it still poses difficult teaching and learning challenges. Understanding evolutionary biology has been given high priority in national science education policy because of its role in coordinating our understanding of the life sciences, its importance in our intellectual history, its role in the perception of humans' position in nature, and its impact on our current medical, agricultural, and conservation practices. The rhetoric used in evolution education policy statements emphasizes familiarity with the nature of scientific inquiry as an important learning outcome associated with understanding evolution but provide little guidance with respect to how one might achieve this goal. This dissertation project explores the nature of evolutionary inquiry and how understanding the details of disciplinary reasoning can inform evolution education. The first analysis involves recasting the existing evolution education research literature to assess educational outcomes related to students ability to reason about data using evolutionary biology methods and models. This is followed in the next chapter by a detailed historical and philosophical characterization of evolutionary biology with the goal of providing a richer context for considering what exactly it is we want students to know about evolution as a discipline. Chapter 4 describes the development and implementation of a high school evolution curriculum that engages students with many aspects of model based reasoning. The final component of this reframing of evolution education involves an empirical study characterizing students' understanding of evolutionary biology as a modeling enterprise. Each chapter addresses a different aspect of evolution education and explores the implications of foregrounding disciplinary reasoning as an educational outcome. The analyses are coordinated with one another in the sense

  16. Deep evolutionary origins of neurobiology

    PubMed Central

    Mancuso, Stefano

    2009-01-01

    It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary ‘recent’ specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes. PMID:19513267

  17. Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

    PubMed Central

    Bryson, David M.; Ofria, Charles

    2013-01-01

    We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a

  18. The extended evolutionary synthesis: its structure, assumptions and predictions

    PubMed Central

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

    2015-01-01

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

  19. Commentary: tempo of evolutionary change in ecological systems.

    PubMed

    Collins, James P

    2015-04-01

    As ecology and evolutionary biology developed during the 20th century one thing that frustrated an integration of research programs in these areas was the assumption that ecological and evolutionary processes operated on very different time scales. In 1961 the ecologist Lawrence Slobodkin reflected this assumption in his distinction between "evolutionary time" and "ecological time." This commentary reflects on the four papers in this Special Section that advance our understanding of the history of research at the intersection of phenotypes, genotypes, ecology, and evolution using plants as study organisms. Early in the 20th century at least some researchers, especially in agricultural systems, were already using observations and experiments to show how natural selection could operate over relatively short time periods and small spatial scales. These four studies offer a more nuanced view of the history of our understanding of the rate of phenotypic change via natural selection and the use of experiments to study evolutionary change. They illuminate the route that has led to the current presumption that in many cases ecological and evolutionary processes may indeed operate on similar, not dissimilar, time scales.

  20. The extended evolutionary synthesis: its structure, assumptions and predictions.

    PubMed

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

    2015-08-22

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

  1. Subwavelength Lattice Optics by Evolutionary Design

    PubMed Central

    2015-01-01

    This paper describes a new class of structured optical materials—lattice opto-materials—that can manipulate the flow of visible light into a wide range of three-dimensional profiles using evolutionary design principles. Lattice opto-materials are based on the discretization of a surface into a two-dimensional (2D) subwavelength lattice whose individual lattice sites can be controlled to achieve a programmed optical response. To access a desired optical property, we designed a lattice evolutionary algorithm that includes and optimizes contributions from every element in the lattice. Lattice opto-materials can exhibit simple properties, such as on- and off-axis focusing, and can also concentrate light into multiple, discrete spots. We expanded the unit cell shapes of the lattice to achieve distinct, polarization-dependent optical responses from the same 2D patterned substrate. Finally, these lattice opto-materials can also be combined into architectures that resemble a new type of compound flat lens. PMID:25380062

  2. Stochastic Evolutionary Algorithms for Planning Robot Paths

    NASA Technical Reports Server (NTRS)

    Fink, Wolfgang; Aghazarian, Hrand; Huntsberger, Terrance; Terrile, Richard

    2006-01-01

    A computer program implements stochastic evolutionary algorithms for planning and optimizing collision-free paths for robots and their jointed limbs. Stochastic evolutionary algorithms can be made to produce acceptably close approximations to exact, optimal solutions for path-planning problems while often demanding much less computation than do exhaustive-search and deterministic inverse-kinematics algorithms that have been used previously for this purpose. Hence, the present software is better suited for application aboard robots having limited computing capabilities (see figure). The stochastic aspect lies in the use of simulated annealing to (1) prevent trapping of an optimization algorithm in local minima of an energy-like error measure by which the fitness of a trial solution is evaluated while (2) ensuring that the entire multidimensional configuration and parameter space of the path-planning problem is sampled efficiently with respect to both robot joint angles and computation time. Simulated annealing is an established technique for avoiding local minima in multidimensional optimization problems, but has not, until now, been applied to planning collision-free robot paths by use of low-power computers.

  3. Statistical methods for evolutionary trees.

    PubMed

    Edwards, A W F

    2009-09-01

    In 1963 and 1964, L. L. Cavalli-Sforza and A. W. F. Edwards introduced novel methods for computing evolutionary trees from genetical data, initially for human populations from blood-group gene frequencies. The most important development was their introduction of statistical methods of estimation applied to stochastic models of evolution.

  4. Is evolutionary biology strategic science?

    PubMed

    Meagher, Thomas R

    2007-01-01

    There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field.

  5. Evolutionary Psychology and Intelligence Research

    ERIC Educational Resources Information Center

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  6. Cryptic eco-evolutionary dynamics.

    PubMed

    Kinnison, Michael T; Hairston, Nelson G; Hendry, Andrew P

    2015-12-01

    Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.

  7. Current Issues in Evolutionary Paleontology.

    ERIC Educational Resources Information Center

    Scully, Erik Paul

    1987-01-01

    Describes some of the contributions made by the field of paleontology to theories in geology and biology. Suggests that the two best examples of modern evolutionary paleontology relate to the theory of punctuated equilibria, and the possibility that mass extinctions may be cyclic. (TW)

  8. Euryhalinity in an evolutionary context

    USGS Publications Warehouse

    Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.

    2013-01-01

    This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

  9. Towards a mechanistic foundation of evolutionary theory.

    PubMed

    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.

  10. Evolutionary use of nuclear electric propulsion

    NASA Technical Reports Server (NTRS)

    Hack, K. J.; George, J. A.; Riehl, J. P.; Gilland, J. H.

    1990-01-01

    Evolving new propulsion technologies through a rational and conscious effort to minimize development costs and program risks while maximizing the performance benefits is intuitively practical. A phased approach to the evolution of nuclear electric propulsion from use on planetary probes, to lunar cargo vehicles, and finally to manned Mars missions with a concomitant growth in technology is considered. Technology levels and system component makeup are discussed for nuclear power systems and both ion and magnetoplasmadynamic thrusters. Mission scenarios are described, which include analysis of a probe to Pluto, a lunar cargo mission, Martian split, all-up, and quick-trip mission options. Evolutionary progression of the use of NEP in such missions is discussed.

  11. Ultimate Realities: Deterministic and Evolutionary

    PubMed Central

    Moxley, Roy A

    2007-01-01

    References to ultimate reality commonly turn up in the behavioral literature as references to determinism. However, this determinism is often difficult to interpret. There are different kinds of determinisms as well as different kinds of ultimate realities for a behaviorist to consider. To clarify some of the issues involved, the views of ultimate realities are treated as falling along a continuum, with extreme views of complete indeterminism and complete determinism at either end and various mixes in between. Doing so brings into play evolutionary realities and the movement from indeterminism to determinism, as in Peirce's evolutionary cosmology. In addition, this framework helps to show how the views of determinism by B. F. Skinner and other behaviorists have shifted over time. PMID:22478489

  12. Evolutionary model of stock markets

    NASA Astrophysics Data System (ADS)

    Kaldasch, Joachim

    2014-12-01

    The paper presents an evolutionary economic model for the price evolution of stocks. Treating a stock market as a self-organized system governed by a fast purchase process and slow variations of demand and supply the model suggests that the short term price distribution has the form a logistic (Laplace) distribution. The long term return can be described by Laplace-Gaussian mixture distributions. The long term mean price evolution is governed by a Walrus equation, which can be transformed into a replicator equation. This allows quantifying the evolutionary price competition between stocks. The theory suggests that stock prices scaled by the price over all stocks can be used to investigate long-term trends in a Fisher-Pry plot. The price competition that follows from the model is illustrated by examining the empirical long-term price trends of two stocks.

  13. Evolutionary Models of Irregular Warfare

    DTIC Science & Technology

    2013-03-01

    1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no...PI Prof Dominic Johnson. The project seeks to explore if and how we can derive insights from nature to help tackle problems of international ...evolutionary principles to the level of grand strategy and international politics. This has given rise to some unexpected results: for example, work

  14. Evolutionary dynamics of diploid populations

    NASA Astrophysics Data System (ADS)

    Desimone, Ralph; Newman, Timothy

    2003-10-01

    There has been much recent interest in constructing computer models of evolutionary dynamics. Typically these models focus on asexual population dynamics, which are appropriate for haploid organsims such as bacteria. Using a recently developed ``genome template'' model, we extend the algorithm to a sexual population of diploid organisms. We will present some early results showing the temporal evolution of mean fitness and genetic variation, and compare this to typical results from haploid populations.

  15. Rare mutations in evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Amadori, Anna Lisa; Calzolari, Antonella; Natalini, Roberto; Torti, Barbara

    2015-12-01

    In this paper we study the effect of rare mutations, driven by a marked point process, on the evolutionary behavior of a population. We derive a Kolmogorov equation describing the expected values of the different frequencies and prove some rigorous analytical results about their behavior. Finally, in a simple case of two different quasispecies, we are able to prove that the rarity of mutations increases the survival opportunity of the low fitness species.

  16. What's wrong with evolutionary biology?

    PubMed

    Welch, John J

    2017-01-01

    There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.

  17. Superoxide dismutase: an evolutionary puzzle

    SciTech Connect

    Lee, Y.M.; Friedman, D.J.; Ayala, F.J.

    1985-02-01

    The authors have obtained the complete amino acid sequence of copper/zinc-containing superoxide dismutase (SOD, superoxide:superoxide oxidoreductase, EC 1.15.1.1) from Drosophila melanogaster. The sequence of this enzyme is also known for man, horse, cow, and the yeast Saccharomyces cerevisiae. The rate of evolution of this enzyme is far from constant. The number of amino acid substitutions per 100 residues per 100 million years is 30.9 when the three mammals are compared to each other, 10.6 when Drosophila is compared to the three mammals, and 5.8 when the yeast is compared to the four animals. The first value represents one of the fastest evolutionary rates for any protein, the second is similar to the globin rate, and the third is similar to some cytochromes and other slowly evolving proteins. Hence, SOD is not acceptable evolutionary clock. Another peculiarity of this enzyme is that a two-amino-acid deletion must have occurred independently in the lineages going to the cow and to Drosophila. The authors conclude that using the primary structure of a single gene or protein to time evolutionary events or to reconstruct phylogenetic relationships is potentially fraught with error.

  18. Evolutionary origins of invasive populations

    PubMed Central

    Lee, Carol Eunmi; Gelembiuk, Gregory William

    2008-01-01

    What factors shape the evolution of invasive populations? Recent theoretical and empirical studies suggest that an evolutionary history of disturbance might be an important factor. This perspective presents hypotheses regarding the impact of disturbance on the evolution of invasive populations, based on a synthesis of the existing literature. Disturbance might select for life-history traits that are favorable for colonizing novel habitats, such as rapid population growth and persistence. Theoretical results suggest that disturbance in the form of fluctuating environments might select for organismal flexibility, or alternatively, the evolution of evolvability. Rapidly fluctuating environments might favor organismal flexibility, such as broad tolerance or plasticity. Alternatively, longer fluctuations or environmental stress might lead to the evolution of evolvability by acting on features of the mutation matrix. Once genetic variance is generated via mutations, temporally fluctuating selection across generations might promote the accumulation and maintenance of genetic variation. Deeper insights into how disturbance in native habitats affects evolutionary and physiological responses of populations would give us greater capacity to predict the populations that are most likely to tolerate or adapt to novel environments during habitat invasions. Moreover, we would gain fundamental insights into the evolutionary origins of invasive populations. PMID:25567726

  19. Evolutionary dynamics in finite populations

    NASA Astrophysics Data System (ADS)

    Hauert, Christoph

    2013-03-01

    Traditionally, evolutionary dynamics has been studied based on infinite populations and deterministic frameworks such as the replicator equation. Only more recently the focus has shifted to the stochastic dynamics arising in finite populations. Over the past years new concepts have been developed to describe such dynamics and has lead to interesting results that arise from the stochastic, microscopic updates, which drive the evolutionary process. Here we discuss a transparent link between the dynamics in finite and infinite populations. The focus on microscopic processes reveals interesting insights into (sometimes implicit) assumptions in terms of biological interactions that provide the basis for deterministic frameworks and the replicator equation in particular. More specifically, we demonstrate that stochastic differential equations can provide an efficient approach to model evolutionary dynamics in finite populations and we use the rock-scissors-paper game with mutations as an example. For sufficiently large populations the agreement with individual based simulations is excellent, with the interesting caveat that mutation events may not be too rare. In the absence of mutations, the excellent agreement extends to small population sizes.

  20. Evolutionary branching under slow directional evolution.

    PubMed

    Ito, Hiroshi C; Dieckmann, Ulf

    2014-11-07

    Evolutionary branching is the process by which ecological interactions induce evolutionary diversification. In asexual populations with sufficiently rare mutations, evolutionary branching occurs through trait-substitution sequences caused by the sequential invasion of successful mutants. A necessary and sufficient condition for evolutionary branching of univariate traits is the existence of a convergence stable trait value at which selection is locally disruptive. Real populations, however, undergo simultaneous evolution in multiple traits. Here we extend conditions for evolutionary branching to bivariate trait spaces in which the response to disruptive selection on one trait can be suppressed by directional selection on another trait. To obtain analytical results, we study trait-substitution sequences formed by invasions that possess maximum likelihood. By deriving a sufficient condition for evolutionary branching of bivariate traits along such maximum-likelihood-invasion paths (MLIPs), we demonstrate the existence of a threshold ratio specifying how much disruptive selection in one trait direction is needed to overcome the obstruction of evolutionary branching caused by directional selection in the other trait direction. Generalizing this finding, we show that evolutionary branching of bivariate traits can occur along evolutionary-branching lines on which residual directional selection is sufficiently weak. We then present numerical analyses showing that our generalized condition for evolutionary branching is a good indicator of branching likelihood even when trait-substitution sequences do not follow MLIPs and when mutations are not rare. Finally, we extend the derived conditions for evolutionary branching to multivariate trait spaces.

  1. Clustering Genes of Common Evolutionary History.

    PubMed

    Gori, Kevin; Suchan, Tomasz; Alvarez, Nadir; Goldman, Nick; Dessimoz, Christophe

    2016-06-01

    Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl).

  2. Evolutionary plasticity of insect immunity.

    PubMed

    Vilcinskas, Andreas

    2013-02-01

    Many insect genomes have been sequenced and the innate immune responses of several species have been studied by transcriptomics, inviting the comparative analysis of immunity-related genes. Such studies have demonstrated significant evolutionary plasticity, with the emergence of novel proteins and protein domains correlated with insects adapting to both abiotic and biotic environmental stresses. This review article focuses on effector molecules such as antimicrobial peptides (AMPs) and proteinase inhibitors, which display greater evolutionary dynamism than conserved components such as immunity-related signaling molecules. There is increasing evidence to support an extended role for insect AMPs beyond defense against pathogens, including the management of beneficial endosymbionts. The total number of AMPs varies among insects with completed genome sequences, providing intriguing examples of immunity gene expansion and loss. This plasticity is discussed in the context of recent developments in evolutionary ecology suggesting that the maintenance and deployment of immune responses reallocates resources from other fitness-related traits thus requiring fitness trade-offs. Based on our recent studies using both model and non-model insects, I propose that insect immunity genes can be lost when alternative defense strategies with a lower fitness penalty have evolved, such as the so-called social immunity in bees, the chemical sanitation of the microenvironment by some beetles, and the release of antimicrobial secondary metabolites in the hemolymph. Conversely, recent studies provide evidence for the expansion and functional diversification of insect AMPs and proteinase inhibitors to reflect coevolution with a changing pathosphere and/or adaptations to habitats or food associated with microbial contamination.

  3. Introduced species as evolutionary traps

    USGS Publications Warehouse

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  4. Evolutionary processes in finite populations

    NASA Astrophysics Data System (ADS)

    Lorenz, Dirk M.; Park, Jeong-Man; Deem, Michael W.

    2013-02-01

    We consider the evolution of large but finite populations on arbitrary fitness landscapes. We describe the evolutionary process by a Markov-Moran process. We show that to O(1/N), the time-averaged fitness is lower for the finite population than it is for the infinite population. We also show that fluctuations in the number of individuals for a given genotype can be proportional to a power of the inverse of the mutation rate. Finally, we show that the probability for the system to take a given path through the fitness landscape can be nonmonotonic in system size.

  5. Policy folklists and evolutionary theory

    PubMed Central

    O’Neill, Barry

    2014-01-01

    Policy folklists present a set of alleged historical facts seen as relevant to some social issue. Although the validity of these folklists is dubious, leaders and writers circulate them in the media, variants arise, and the lists continue on, sometimes for decades. Folklists are repeated because their messages are appealing and their users are credible. Because folklists are on the record, we can examine their origins and changes. This report draws an analogy with evolutionary theory and suggests that biological mechanisms of self-repair, boundary maintenance, plasticity, speciation, and predation have significant interpretations for folklists, and clarify how the lists win the credence of otherwise skeptical people. PMID:25024210

  6. Evolutionary shaping of demographic schedules

    PubMed Central

    Wachter, Kenneth W.; Steinsaltz, David; Evans, Steven N.

    2014-01-01

    Evolutionary processes of natural selection may be expected to leave their mark on age patterns of survival and reproduction. Demographic theory includes three main strands—mutation accumulation, stochastic vitality, and optimal life histories. This paper reviews the three strands and, concentrating on mutation accumulation, extends a mathematical result with broad implications concerning the effect of interactions between small age-specific effects of deleterious mutant alleles. Empirical data from genomic sequencing along with prospects for combining strands of theory hold hope for future progress. PMID:25024186

  7. Metabolism at Evolutionary Optimal States

    PubMed Central

    Rabbers, Iraes; van Heerden, Johan H.; Nordholt, Niclas; Bachmann, Herwig; Teusink, Bas; Bruggeman, Frank J.

    2015-01-01

    Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization. PMID:26042723

  8. Historical change and evolutionary theory.

    PubMed

    Masters, Roger D

    2007-09-01

    Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological

  9. The structure of microbial evolutionary theory.

    PubMed

    Sapp, J

    2007-12-01

    The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life's history over billions of years, but also in transcending the structure of thought that has shaped evolutionary theory since the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists.

  10. Evolutionary developmental biology its roots and characteristics.

    PubMed

    Morange, Michel

    2011-09-01

    The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology.

  11. Conceptual Barriers to Progress Within Evolutionary Biology

    PubMed Central

    Laland, Kevin N.; Odling-Smee, John; Feldman, Marcus W.; Kendal, Jeremy

    2011-01-01

    In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, “niche construction”. This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory. PMID:21572912

  12. Evolutionary objections to "alien design" models.

    NASA Astrophysics Data System (ADS)

    Coffey, E. J.

    A previous paper demonstrated that the principal supporters of SETI have ignored the biological and evolutionary consequences of a creature's body form. In fact, the supporting evidence they provide actually contradicts their view. The approach they employ is that of the engineer: the process of "designing" a hypothetical creature to a specification irrespective of biological or evolutionary considerations. The principal types of "alien designs" which have been employed shall be discussed, and the evolutionary objections to them given.

  13. An introduction to evolutionary developmental psychology.

    PubMed

    Machluf, Karin; Liddle, James R; Bjorklund, David F

    2014-04-29

    Evolutionary developmental psychology represents a synthesis of modern evolutionary theory and developmental psychology. Here we introduce the special issue on evolutionary developmental psychology by briefly discussing the history of this field and then summarizing the variety of topics that are covered. In this special issue, leading researchers provide a collection of theoretical and empirical articles that highlight recent findings and propose promising areas for future research.

  14. The Council of Ontario Universities' Research Program

    ERIC Educational Resources Information Center

    Hansen, Bertrand L.

    1976-01-01

    The Council's history and the development of its research program provide insights into the evolutionary nature of its interinstitutional research activities. A case study of the program, which has both consortial and coordinating characteristics, is described. (Author/LBH)

  15. The ABCs of an evolutionary education science: The academic, behavioral, and cultural implications of an evolutionary approach to education theory and practice

    NASA Astrophysics Data System (ADS)

    Kauffman, Rick, Jr.

    Calls for improving research-informed policy in education are everywhere. Yet, while there is an increasing trend towards science-based practice, there remains little agreement over which of the sciences to consult and how to organize a collective effort between them. What Education lacks is a general theoretical framework through which policies can be constructed, implemented, and assessed. This dissertation submits that evolutionary theory can provide a suitable framework for coordinating educational policies and practice, and can provide the entire field of education with a clearer sense of how to better manage the learning environment. This dissertation explores two broad paths that outline the conceptual foundations for an Evolutionary Education Science: "Teaching Evolution" and "Using Evolution to Teach." Chapter 1 introduces both of these themes. After describing why evolutionary science is best suited for organizing education research and practice, Chapter 1 proceeds to "teach" an overview of the "evolutionary toolkit"---the mechanisms and principles that underlie the modern evolutionary perspective. The chapter then employs the "toolkit" in examining education from an evolutionary perspective, outlining the evolutionary precepts that can guide theorizing and research in education, describing how educators can "use evolution to teach.". Chapters 2-4 expand on this second theme. Chapters 2 and 3 describe an education program for at-risk 9th and 10th grade students, the Regents Academy, designed entirely with evolutionary principles in mind. The program was rigorously assessed in a randomized control design and has demonstrated success at improving students' academic performance (Chapter 2) and social & behavioral development (Chapter 3). Chapter 4 examines current teaching strategies that underlie effective curriculum-instruction-assessment practices and proposes a framework for organizing successful, evidence-based strategies for neural

  16. Evolutionary Models for Simple Biosystems

    NASA Astrophysics Data System (ADS)

    Bagnoli, Franco

    The concept of evolutionary development of structures constituted a real revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.

  17. The evolutionary puzzle of suicide.

    PubMed

    Aubin, Henri-Jean; Berlin, Ivan; Kornreich, Charles

    2013-12-09

    Mechanisms of self-destruction are difficult to reconcile with evolution's first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent-Toxoplasma gondii host-parasite model, in which the parasite induces a "suicidal" feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory.

  18. The Evolutionary Puzzle of Suicide

    PubMed Central

    Aubin, Henri-Jean; Berlin, Ivan; Kornreich, Charles

    2013-01-01

    Mechanisms of self-destruction are difficult to reconcile with evolution’s first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent—Toxoplasma gondii host-parasite model, in which the parasite induces a “suicidal” feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory. PMID:24351787

  19. [Evolutionary endocrinology: a pending matter].

    PubMed

    Zafón, Carles

    2012-01-01

    Twenty years have passed since the foundational article of what is now known as evolutionary medicine (EM) was published. This young medical discipline examines, following Darwinian principles, susceptibility to certain diseases and how we react to them. In short, EM analyzes the final cause of the disease from a historical perspective. Over the years, EM has been introduced in various medical areas in very different ways. While it has found a role in some fields such as infectious diseases and oncology, its contribution in other areas has been quite limited. In endocrinology, EM has only gained prominence as a basis for the so-called "diseases of civilization", including diabetes mellitus and obesity. However, many experts suggest that it may have a much higher potential. The aim of this paper is to provide a view about what evolutionary medicine is. Some examples of how EM may contribute to progress of our specialty are also given. There is no doubt that evolution enriches medicine, but medicine also offers knowledge to evolution.

  20. Evolutionary potential games on lattices

    NASA Astrophysics Data System (ADS)

    Szabó, György; Borsos, István

    2016-04-01

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

  1. Unifying evolutionary and network dynamics

    NASA Astrophysics Data System (ADS)

    Swarup, Samarth; Gasser, Les

    2007-06-01

    Many important real-world networks manifest small-world properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is preferential attachment, where nodes acquire new links with probability proportional to the number of links they already have. We show that preferential attachment is a special case of the process of molecular evolution. We present a single-parameter model of network growth that unifies varieties of preferential attachment with the quasispecies equation (which models molecular evolution), and also with the Erdős-Rényi random graph model. We suggest some properties of evolutionary models that might be applied to the study of networks. We also derive the form of the degree distribution resulting from our algorithm, and we show through simulations that the process also models aspects of network growth. The unification allows mathematical machinery developed for evolutionary dynamics to be applied in the study of network dynamics, and vice versa.

  2. Major evolutionary transitions in individuality

    PubMed Central

    West, Stuart A.; Fisher, Roberta M.; Gardner, Andy; Kiers, E. Toby

    2015-01-01

    The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. PMID:25964342

  3. An introduction to comparative evolutionary psychology.

    PubMed

    Vonk, Jennifer; Shackelford, Todd K

    2013-07-18

    Previously we (Vonk and Shackelford, 2012, in press) proposed an integration of comparative psychology and evolutionary psychology into a new field of "comparative evolutionary psychology." This integrative discipline incorporates principles from ethology, ecology, biology, anthropology, and psychology, broadly defined. We present in this special issue a collection of original empirical and theoretical review articles in which leading researchers propose ways to successfully integrate comparative and evolutionary approaches within their particular areas of study. We showcase the key contributions of these articles and highlight several empirical and theoretical challenges, as well as key future directions, for comparative evolutionary psychology.

  4. Child murder by parents and evolutionary psychology.

    PubMed

    Friedman, Susan Hatters; Cavney, James; Resnick, Phillip J

    2012-12-01

    This article explores the contribution of evolutionary theory to the understanding of causation and motive in filicide cases and also reviews special issues in the forensic evaluation of alleged perpetrators of filicide. Evolutionary social psychology seeks to understand the context in which our brains evolved, to understand human behaviors. The authors propose evolutionary theory as a framework theory to meaningfully appreciate research about filicide. Using evolutionary psychology as a theoretical lens, this article reviews the research on filicide over the past 40 years, and describes epidemiologic and typologic studies of filicide, and theoretical analyses from a range of disciplines.

  5. Soft Selective Sweeps in Evolutionary Rescue

    PubMed Central

    Wilson, Benjamin A.; Pennings, Pleuni S.; Petrov, Dmitri A.

    2017-01-01

    Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population-genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens. PMID:28213477

  6. Evolutionary games in wireless networks.

    PubMed

    Tembine, Hamidou; Altman, Eitan; El-Azouzi, Rachid; Hayel, Yezekael

    2010-06-01

    We consider a noncooperative interaction among a large population of mobiles that interfere with each other through many local interactions. The first objective of this paper is to extend the evolutionary game framework to allow an arbitrary number of mobiles that are involved in a local interaction. We allow for interactions between mobiles that are not necessarily reciprocal. We study 1) multiple-access control in a slotted Aloha-based wireless network and 2) power control in wideband code-division multiple-access wireless networks. We define and characterize the equilibrium (called evolutionarily stable strategy) for these games and study the influence of wireless channels and pricing on the evolution of dynamics and the equilibrium.

  7. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

  8. Bacterial Actins? An Evolutionary Perspective

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.; York, Amanda L.

    2003-01-01

    According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

  9. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  10. Evolutionary Industrial Physical Model Generation

    NASA Astrophysics Data System (ADS)

    Carrascal, Alberto; Alberdi, Amaia

    Both complexity and lack of knowledge associated to physical processes makes physical models design an arduous task. Frequently, the only available information about the physical processes are the heuristic data obtained from experiments or at best a rough idea on what are the physical principles and laws that underlie considered physical processes. Then the problem is converted to find a mathematical expression which fits data. There exist traditional approaches to tackle the inductive model search process from data, such as regression, interpolation, finite element method, etc. Nevertheless, these methods either are only able to solve a reduced number of simple model typologies, or the given black-box solution does not contribute to clarify the analyzed physical process. In this paper a hybrid evolutionary approach to search complex physical models is proposed. Tests carried out on a real-world industrial physical process (abrasive water jet machining) demonstrate the validity of this approach.

  11. Genomic clocks and evolutionary timescales

    NASA Technical Reports Server (NTRS)

    Blair Hedges, S.; Kumar, Sudhir

    2003-01-01

    For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a 'supergene') and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.

  12. Evolutionary primacy of sodium bioenergetics

    PubMed Central

    Mulkidjanian, Armen Y; Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

    2008-01-01

    Background The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and V-type (found in archaea, some bacteria, and eukaryotic vacuoles) ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments. Results We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree. Conclusion Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions. Reviewers This article was reviewed by J. Peter Gogarten, Martijn A. Huynen, and Igor B. Zhulin. For the full reviews, please go to the Reviewers' comments section. PMID:18380897

  13. Evolutionary History of the Hymenoptera.

    PubMed

    Peters, Ralph S; Krogmann, Lars; Mayer, Christoph; Donath, Alexander; Gunkel, Simon; Meusemann, Karen; Kozlov, Alexey; Podsiadlowski, Lars; Petersen, Malte; Lanfear, Robert; Diez, Patricia A; Heraty, John; Kjer, Karl M; Klopfstein, Seraina; Meier, Rudolf; Polidori, Carlo; Schmitt, Thomas; Liu, Shanlin; Zhou, Xin; Wappler, Torsten; Rust, Jes; Misof, Bernhard; Niehuis, Oliver

    2017-04-03

    Hymenoptera (sawflies, wasps, ants, and bees) are one of four mega-diverse insect orders, comprising more than 153,000 described and possibly up to one million undescribed extant species [1, 2]. As parasitoids, predators, and pollinators, Hymenoptera play a fundamental role in virtually all terrestrial ecosystems and are of substantial economic importance [1, 3]. To understand the diversification and key evolutionary transitions of Hymenoptera, most notably from phytophagy to parasitoidism and predation (and vice versa) and from solitary to eusocial life, we inferred the phylogeny and divergence times of all major lineages of Hymenoptera by analyzing 3,256 protein-coding genes in 173 insect species. Our analyses suggest that extant Hymenoptera started to diversify around 281 million years ago (mya). The primarily ectophytophagous sawflies are found to be monophyletic. The species-rich lineages of parasitoid wasps constitute a monophyletic group as well. The little-known, species-poor Trigonaloidea are identified as the sister group of the stinging wasps (Aculeata). Finally, we located the evolutionary root of bees within the apoid wasp family "Crabronidae." Our results reveal that the extant sawfly diversity is largely the result of a previously unrecognized major radiation of phytophagous Hymenoptera that did not lead to wood-dwelling and parasitoidism. They also confirm that all primarily parasitoid wasps are descendants of a single endophytic parasitoid ancestor that lived around 247 mya. Our findings provide the basis for a natural classification of Hymenoptera and allow for future comparative analyses of Hymenoptera, including their genomes, morphology, venoms, and parasitoid and eusocial life styles.

  14. Algorithmic Mechanism Design of Evolutionary Computation

    PubMed Central

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

  15. Evolutionary Biology in the Medical School Curriculum.

    ERIC Educational Resources Information Center

    Neese, Randolph M.; Schiffman, Joshua D.

    2003-01-01

    Presents a study in which a questionnaire was given to deans at North American medical schools to determine which aspects of evolutionary biology are included in the curricula and the factors that influence this. Suggests that most future physicians should learn evolutionary biology as undergraduates if they are to learn it at all. (Author/NB)

  16. Towards a mechanistic foundation of evolutionary theory

    PubMed Central

    Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

    2017-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.23804.001 PMID:28198700

  17. Oversimplifying Evolutionary Psychology Leads to Explanatory Gaps

    ERIC Educational Resources Information Center

    Tate, Chuck; Ledbetter, Jay N.

    2010-01-01

    Comments on Evolutionary psychology: Controversies, questions, prospects, and limitations by Confer et al. They argued that SST cannot explain the existence of either homosexuality or suicide within the human species. We contend that a sufficiently nuanced evolutionary position has no difficulties explaining either phenomenon. Also in this…

  18. Toward a unifying framework for evolutionary processes

    PubMed Central

    Paixão, Tiago; Badkobeh, Golnaz; Barton, Nick; Çörüş, Doğan; Dang, Duc-Cuong; Friedrich, Tobias; Lehre, Per Kristian; Sudholt, Dirk; Sutton, Andrew M.; Trubenová, Barbora

    2015-01-01

    The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. PMID:26215686

  19. Utopianism in the British evolutionary synthesis.

    PubMed

    Esposito, Maurizio

    2011-03-01

    In this paper I propose a new interpretation of the British evolutionary synthesis. The synthetic work of J. B. S. Haldane, R. A. Fisher and J. S. Huxley was characterized by both an integration of Mendelism and Darwinism and the unification of different biological subdisciplines within a coherent framework. But it must also be seen as a bold and synthetic Darwinian program in which the biosciences served as a utopian blueprint for the progress of civilization. Describing the futuristic visions of these three scientists in their synthetic heydays, I show that, despite a number of important divergences, their biopolitical ideals could be biased toward a controlled and regimented utopian society. Their common ideals entailed a social order where liberal and democratic principles were partially or totally suspended in favor of bioscientific control and planning for the future. Finally, I will argue that the original redefinition of Darwinism that modern synthesizers proposed is a significant historical example of how Darwinism has been used and adapted in different contexts. The lesson I draw from this account is a venerable one: that, whenever we wish to define Darwinism, we need to recognize not only its scientific content and achievements but expose the other traditions and ideologies it may have supported.

  20. Evolutionary theory in letters to the editor.

    PubMed

    Silva, Eric Orion; Lowe, Clayton Cory

    2015-05-01

    This research note presents the results of a content analysis of 234 letters to the editors that discuss evolutionary theory and were published in American newspapers. We find that letters to the editor both support and hinder the cause of teaching evolutionary theory in American secondary schools. On the one hand, anti-evolutionary theory messages are marginalized in the letters section. This marginalization signals a low level of legitimacy for creationism. It might also contribute to the sense of tension that sustains creationist identities. On the other hand, relatively few letters explicitly note the fact that scientists or the scientific community accept evolution. Interestingly, the obscuration of the scientific community's support for evolutionary theory occurs both in letters supporting and opposing evolutionary theory.

  1. Application of an evolutionary algorithm in the optimal design of micro-sensor.

    PubMed

    Lu, Qibing; Wang, Pan; Guo, Sihai; Sheng, Buyun; Liu, Xingxing; Fan, Zhun

    2015-01-01

    This paper introduces an automatic bond graph design method based on genetic programming for the evolutionary design of micro-resonator. First, the system-level behavioral model is discussed, which based on genetic programming and bond graph. Then, the geometry parameters of components are automatically optimized, by using the genetic algorithm with constraints. To illustrate this approach, a typical device micro-resonator is designed as an example in biomedicine. This paper provides a new idea for the automatic optimization design of biomedical sensors by evolutionary calculation.

  2. Physcomitrella patens activates reinforcement of the cell wall, programmed cell death and accumulation of evolutionary conserved defence signals, such as salicylic acid and 12-oxo-phytodienoic acid, but not jasmonic acid, upon Botrytis cinerea infection.

    PubMed

    Ponce De León, Inés; Schmelz, Eric A; Gaggero, Carina; Castro, Alexandra; Álvarez, Alfonso; Montesano, Marcos

    2012-10-01

    The moss Physcomitrella patens is an evolutionarily basal model system suitable for the analysis of plant defence responses activated after pathogen assault. Upon infection with the necrotroph Botrytis cinerea, several defence mechanisms are induced in P. patens, including the fortification of the plant cell wall by the incorporation of phenolic compounds and the induced expression of related genes. Botrytis cinerea infection also activates the accumulation of reactive oxygen species and cell death with hallmarks of programmed cell death in moss tissues. Salicylic acid (SA) levels also increase after fungal infection, and treatment with SA enhances transcript accumulation of the defence gene phenylalanine ammonia-lyase (PAL) in P. patens colonies. The expression levels of the genes involved in 12-oxo-phytodienoic acid (OPDA) synthesis, including lipoxygenase (LOX) and allene oxide synthase (AOS), increase in P. patens gametophytes after pathogen assault, together with a rise in free linolenic acid and OPDA concentrations. However, jasmonic acid (JA) could not be detected in healthy or infected tissues of this plant. Our results suggest that, although conserved defence signals, such as SA and OPDA, are synthesized and are probably involved in the defence response of P. patens against B. cinerea infection, JA production appears to be missing. Interestingly, P. patens responds to OPDA and methyl jasmonate by reducing moss colony growth and rhizoid length, suggesting that jasmonate perception is present in mosses. Thus, P. patens can provide clues with regard to the evolution of different defence pathways in plants, including signalling and perception of OPDA and jasmonates in nonflowering and flowering plants.

  3. Mapping an expanding territory: computer simulations in evolutionary biology.

    PubMed

    Huneman, Philippe

    2014-08-01

    The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as explanations, the nature of validation processes and the relation between simulations and true experiments or mathematical models. After making distinctions, especially between a weak use where simulations test hypotheses about the world, and a strong use where they allow one to explore sets of evolutionary dynamics not necessarily extant in our world, I argue in Sect. 2 that (weak) simulations are likely to represent in virtue of the fact that they instantiate specific features of causal processes that may be isomorphic to features of some causal processes in the world, though the latter are always intertwined with a myriad of different processes and hence unlikely to be directly manipulated and studied. I therefore argue that these simulations are merely able to provide candidate explanations for real patterns. Section 3 ends up by placing strong and weak simulations in Levins' triangle, that conceives of simulations as devices trying to fulfil one or two among three incompatible epistemic values (precision, realism, genericity).

  4. Evolutionary Design and Simulation of a Tube Crawling Inspection Robot

    NASA Technical Reports Server (NTRS)

    Craft, Michael; Howsman, Tom; ONeil, Daniel; Howell, Joe T. (Technical Monitor)

    2002-01-01

    The Space Robotics Assembly Team Simulation (SpaceRATS) is an expansive concept that will hopefully lead to a space flight demonstration of a robotic team cooperatively assembling a system from its constitutive parts. A primary objective of the SpaceRATS project is to develop a generalized evolutionary design approach for multiple classes of robots. The portion of the overall SpaceRats program associated with the evolutionary design and simulation of an inspection robot's morphology is the subject of this paper. The vast majority of this effort has concentrated on the use and modification of Darwin2K, a robotic design and simulation software package, to analyze the design of a tube crawling robot. This robot is designed for carrying out inspection duties in relatively inaccessible locations within a liquid rocket engine similar to the SSME. A preliminary design of the tube crawler robot was completed, and the mechanical dynamics of the system were simulated. An evolutionary approach to optimizing a few parameters of the system was utilized, resulting in a more optimum design.

  5. Evolutionary Algorithms for Boolean Functions in Diverse Domains of Cryptography.

    PubMed

    Picek, Stjepan; Carlet, Claude; Guilley, Sylvain; Miller, Julian F; Jakobovic, Domagoj

    2016-01-01

    The role of Boolean functions is prominent in several areas including cryptography, sequences, and coding theory. Therefore, various methods for the construction of Boolean functions with desired properties are of direct interest. New motivations on the role of Boolean functions in cryptography with attendant new properties have emerged over the years. There are still many combinations of design criteria left unexplored and in this matter evolutionary computation can play a distinct role. This article concentrates on two scenarios for the use of Boolean functions in cryptography. The first uses Boolean functions as the source of the nonlinearity in filter and combiner generators. Although relatively well explored using evolutionary algorithms, it still presents an interesting goal in terms of the practical sizes of Boolean functions. The second scenario appeared rather recently where the objective is to find Boolean functions that have various orders of the correlation immunity and minimal Hamming weight. In both these scenarios we see that evolutionary algorithms are able to find high-quality solutions where genetic programming performs the best.

  6. Structural technology challenges for evolutionary growth of Space Station Freedom

    NASA Technical Reports Server (NTRS)

    Doiron, Harold H.

    1990-01-01

    A proposed evolutionary growth scenario for Space Station Freedom was defined recently by a NASA task force created to study requirements for a Human Exploration Initiative. The study was an initial response to President Bush's July 20, 1989 proposal to begin a long range program of human exploration of space including a permanently manned lunar base and a manned mission to Mars. This growth scenario evolves Freedom into a critical transportation node to support lunar and Mars missions. The growth scenario begins with the Assembly Complete configuration and adds structure, power, and facilities to support a Lunar Transfer Vehicle (LTV) verification flight. Evolutionary growth continues to support expendable, then reusable LTV operations, and finally, LTV and Mars Transfer Vehicle (MTV) operations. The significant structural growth and additional operations creating new loading conditions will present new technological and structural design challenges in addition to the considerable technology requirements of the baseline Space Station Freedom program. Several structural design and technology issues of the baseline program are reviewed and related technology development required by the growth scenario is identified.

  7. Evolutionary assembly patterns of prokaryotic genomes

    PubMed Central

    Press, Maximilian O.; Queitsch, Christine; Borenstein, Elhanan

    2016-01-01

    Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8228 directional dependencies between genes and demonstrated that many such dependencies reflect known functional relationships, including for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes. PMID:27197212

  8. Evolutionary indirect effects of biological invasions.

    PubMed

    Lau, Jennifer A

    2012-09-01

    Just as ecological indirect effects can have a wide range of consequences for community structure and ecosystem function, theory suggests that evolutionary indirect effects can also influence community dynamics and the outcome of species interactions. There is little empirical evidence documenting such effects, however. Here, I use a multi-generation selection experiment in the field to investigate: (1) how the exotic plant Medicago polymorpha and the exotic insect herbivore Hypera brunneipennis affect the evolution of anti-herbivore resistance traits in the native plant Lotus wrangelianus and (2) how observed Lotus evolutionary responses to Hypera alter interactions between Lotus and other members of the herbivore community. In one of two study populations, I document rapid evolutionary changes in Lotus resistance to Hypera in response to insecticide treatments that experimentally reduced Hypera abundance, and in response to Medicago-removal treatments that also reduced Hypera abundance. These evolutionary changes in response to Hypera result in reduced attack by aphids. Thus, an evolutionary change caused by one herbivore species alters interactions with other herbivore taxa, an example of an eco-evolutionary feedback. Given that many traits mediate interactions with multiple species, the effects of evolutionary changes in response to one key biotic selective agent may often cascade through interaction webs to influence additional community members.

  9. Evolutionary psychology. Controversies, questions, prospects, and limitations.

    PubMed

    Confer, Jaime C; Easton, Judith A; Fleischman, Diana S; Goetz, Cari D; Lewis, David M G; Perilloux, Carin; Buss, David M

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from hypotheses that go against traditional psychological theories; some from empirical findings that may have disturbing implications; some from misunderstandings about the logic of evolutionary psychology; and some from reasonable scientific concerns about its underlying framework. This article identifies some of the most common concerns and attempts to elucidate evolutionary psychology's stance pertaining to them. These include issues of testability and falsifiability; the domain specificity versus domain generality of psychological mechanisms; the role of novel environments as they interact with evolved psychological circuits; the role of genes in the conceptual structure of evolutionary psychology; the roles of learning, socialization, and culture in evolutionary psychology; and the practical value of applied evolutionary psychology. The article concludes with a discussion of the limitations of current evolutionary psychology.

  10. Evolutionary Development of the Simulation by Logical Modeling System (SIBYL)

    NASA Technical Reports Server (NTRS)

    Wu, Helen

    1995-01-01

    Through the evolutionary development of the Simulation by Logical Modeling System (SIBYL) we have re-engineered the expensive and complex IBM mainframe based Long-term Hardware Projection Model (LHPM) to a robust cost-effective computer based mode that is easy to use. We achieved significant cost reductions and improved productivity in preparing long-term forecasts of Space Shuttle Main Engine (SSME) hardware. The LHPM for the SSME is a stochastic simulation model that projects the hardware requirements over 10 years. SIBYL is now the primary modeling tool for developing SSME logistics proposals and Program Operating Plan (POP) for NASA and divisional marketing studies.

  11. Measuring the Evolutionary Rate of Cooling of ZZ Ceti

    NASA Astrophysics Data System (ADS)

    Mukadam, Anjum S.; Bischoff-Kim, Agnes; Fraser, Oliver; Córsico, A. H.; Montgomery, M. H.; Kepler, S. O.; Romero, A. D.; Winget, D. E.; Hermes, J. J.; Riecken, T. S.; Kronberg, M. E.; Winget, K. I.; Falcon, Ross E.; Chandler, D. W.; Kuehne, J. W.; Sullivan, D. J.; Reaves, D.; von Hippel, T.; Mullally, F.; Shipman, H.; Thompson, S. E.; Silvestri, N. M.; Hynes, R. I.

    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) × 10-15 s s-1 employing the O - C method and (5.45 ± 0.79) × 10-15 s s-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) × 10-15 s s-1. After correcting for proper motion, the evolutionary rate of cooling of ZZ Ceti is computed to be (3.3 ± 1.1) × 10-15 s s-1. This value is consistent within uncertainties with the measurement of (4.19 ± 0.73) × 10-15 s s-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.

  12. Human adoption in evolutionary perspective.

    PubMed

    Silk, J B

    1990-03-01

    Exploitation is a fundamental element of the parental strategies of many species of birds. Cuckoos, for example, lay their eggs in the nest of other birds, who often unwittingly rear the alien nestlings as their own. Nest parasitism is an efficient reproductive strategy for cuckoos, who do not have to worry about building a nest, incubating their eggs, or feeding their nestlings. But not all hosts respond passively to such intrusions. In response to parasitic cowbirds, for example, robins have evolved the ability to detect and selectively eject alien young from their nests. Human parenting strategies differ sharply from the strategies of cuckoos and robins. Unlike cuckoos, we are reluctant to allow our children to be raised by others. Unlike robins, we knowingly rear strange young. What makes human behavior toward children so different from that of cuckoos and robins? Humans seem to share a number of predispositions that facilitate successful adoptive relationships, and the desire to raise children seems to be pervasive among modern humans. Despite these commonalities, patterns of adoption transactions vary greatly among contemporary human societies. This paper considers the origins and causes of cross-cultural variation in human adoptive behavior from an evolutionary perspective.

  13. Evolutionary Optimization of Protein Folding

    PubMed Central

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, 3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last 1.5 billion years that began during the “big bang” of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  14. Natural pedagogy as evolutionary adaptation.

    PubMed

    Csibra, Gergely; Gergely, György

    2011-04-12

    We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of 'natural pedagogy' in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species.

  15. Evolutionary advantages of adaptive rewarding

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2012-09-01

    Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment.

  16. Evolutionary genomics of animal personality.

    PubMed

    van Oers, Kees; Mueller, Jakob C

    2010-12-27

    Research on animal personality can be approached from both a phenotypic and a genetic perspective. While using a phenotypic approach one can measure present selection on personality traits and their combinations. However, this approach cannot reconstruct the historical trajectory that was taken by evolution. Therefore, it is essential for our understanding of the causes and consequences of personality diversity to link phenotypic variation in personality traits with polymorphisms in genomic regions that code for this trait variation. Identifying genes or genome regions that underlie personality traits will open exciting possibilities to study natural selection at the molecular level, gene-gene and gene-environment interactions, pleiotropic effects and how gene expression shapes personality phenotypes. In this paper, we will discuss how genome information revealed by already established approaches and some more recent techniques such as high-throughput sequencing of genomic regions in a large number of individuals can be used to infer micro-evolutionary processes, historical selection and finally the maintenance of personality trait variation. We will do this by reviewing recent advances in molecular genetics of animal personality, but will also use advanced human personality studies as case studies of how molecular information may be used in animal personality research in the near future.

  17. Evolutionary games in the multiverse.

    PubMed

    Gokhale, Chaitanya S; Traulsen, Arne

    2010-03-23

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

  18. Democratizing evolutionary biology, lessons from insects.

    PubMed

    Dunn, Robert R; Beasley, DeAnna E

    2016-12-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This review highlights how insect-based citizen science has led to the expansion of specimen collections and reframed research questions in light of new observations and unexpected discoveries. Given the rapid expansion of human-modified (and inhabited) environments, the degree to which the public can participate in insect-based citizen science will allow us to track and monitor evolutionary trends at a global scale.

  19. Scheduling Earth Observing Satellites with Evolutionary Algorithms

    NASA Technical Reports Server (NTRS)

    Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

    2003-01-01

    We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

  20. Evolutionary Phylogenetic Networks: Models and Issues

    NASA Astrophysics Data System (ADS)

    Nakhleh, Luay

    Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapte focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks.

  1. Evolutionary fire ecology: lessons learned from pines.

    PubMed

    Pausas, Juli G

    2015-05-01

    Macroevolutionary studies of the genus Pinus provide the oldest current evidence of fire as an evolutionary pressure on plants and date back to ca. 125 million years ago (Ma). Microevolutionary studies show that fire traits are variable within and among populations, especially among those subject to different fire regimes. In addition, there is increasing evidence of an inherited genetic basis to variability in fire traits. Added together, pines provide compelling evidence that fire can exert an evolutionary pressure on plants and, thus, shape biodiversity. In addition, evolutionary fire ecology is providing insights to improve the management of pine forests under changing conditions. The lessons learned from pines may guide research on the evolutionary ecology of other taxa.

  2. A Philosophical Perspective on Evolutionary Systems Biology.

    PubMed

    O'Malley, Maureen A; Soyer, Orkun S; Siegal, Mark L

    2015-03-01

    Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.

  3. Evolutionary medicine: its scope, interest and potential

    PubMed Central

    Stearns, Stephen C.

    2012-01-01

    This review is aimed at readers seeking an introductory overview, teaching courses and interested in visionary ideas. It first describes the range of topics covered by evolutionary medicine, which include human genetic variation, mismatches to modernity, reproductive medicine, degenerative disease, host–pathogen interactions and insights from comparisons with other species. It then discusses priorities for translational research, basic research and health management. Its conclusions are that evolutionary thinking should not displace other approaches to medical science, such as molecular medicine and cell and developmental biology, but that evolutionary insights can combine with and complement established approaches to reduce suffering and save lives. Because we are on the cusp of so much new research and innovative insights, it is hard to estimate how much impact evolutionary thinking will have on medicine, but it is already clear that its potential is enormous. PMID:22933370

  4. How Evolutionary Biologists Reconstruct History: Patterns & Processes

    ERIC Educational Resources Information Center

    Cooper, Robert A.

    2004-01-01

    Focusing on specific modes of evolutionally inquiry is important for students to achieve a mature understanding about evolutionary biology. Presenting evolution as rhetoric of conclusions would only confuse the minds of students.

  5. Evolutionary origins of leadership and followership.

    PubMed

    Van Vugt, Mark

    2006-01-01

    Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

  6. Evolutionary contingency and SETI revisited

    NASA Astrophysics Data System (ADS)

    Cirkovic, Milan M.

    2014-07-01

    The well-known argument against the Search for ExtraTerrestrial Intelligence (SETI) due to George Gaylord Simpson is re-analyzed almost half a century later, in the light of our improved understanding of preconditions for the emergence of life and intelligence brought about by the ongoing "astrobiological revolution". Simpson's argument has been enormously influential, in particular in biological circles, and it arguably fueled the most serious opposition to SETI programmes and their funding. I argue that both proponents and opponents of Simpson's argument have occasionally mispresented its core content. Proponents often oversimplify it as just another consequence of biological contingency, thus leaving their position open to general arguments limiting the scope of contingency in evolution (such as the recent argument of Geerat Vermeij based on selection effects in the fossil record). They also tend to neglect that the argument has been presented as essentially atemporal, while referring to entities and processes that are likely to change over time; this has become even less justifiable as our astrobiological knowledge increased in recent years. Opponents have failed to see that the weaknesses in Simpson's position could be removed by restructuring of the argument; I suggest one way of such restructuring, envisioned long ago in the fictional context by Stanislaw Lem. While no firm consensus has emerged on the validity of Simpson's argument so far, I suggest that, contrary to the original motivation, today it is less an anti-SETI argument, and more an astrobiological research programme. In this research programme, SETI could be generalized into a platform for testing some of the deepest assumptions about evolutionary continuity and the relative role of contingency versus convergence on unprecedented spatial and temporal scales.

  7. Evolutionary Design of Controlled Structures

    NASA Technical Reports Server (NTRS)

    Masters, Brett P.; Crawley, Edward F.

    1997-01-01

    Basic physical concepts of structural delay and transmissibility are provided for simple rod and beam structures. Investigations show the sensitivity of these concepts to differing controlled-structures variables, and to rational system modeling effects. An evolutionary controls/structures design method is developed. The basis of the method is an accurate model formulation for dynamic compensator optimization and Genetic Algorithm based updating of sensor/actuator placement and structural attributes. One and three dimensional examples from the literature are used to validate the method. Frequency domain interpretation of these controlled structure systems provide physical insight as to how the objective is optimized and consequently what is important in the objective. Several disturbance rejection type controls-structures systems are optimized for a stellar interferometer spacecraft application. The interferometric designs include closed loop tracking optics. Designs are generated for differing structural aspect ratios, differing disturbance attributes, and differing sensor selections. Physical limitations in achieving performance are given in terms of average system transfer function gains and system phase loss. A spacecraft-like optical interferometry system is investigated experimentally over several different optimized controlled structures configurations. Configurations represent common and not-so-common approaches to mitigating pathlength errors induced by disturbances of two different spectra. Results show that an optimized controlled structure for low frequency broadband disturbances achieves modest performance gains over a mass equivalent regular structure, while an optimized structure for high frequency narrow band disturbances is four times better in terms of root-mean-square pathlength. These results are predictable given the nature of the physical system and the optimization design variables. Fundamental limits on controlled performance are discussed

  8. Ecological aspects of the evolutionary processes.

    PubMed

    Bock, Walter J

    2003-03-01

    Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with

  9. Evolutionary Game Theory Analysis of Tumor Progression

    NASA Astrophysics Data System (ADS)

    Wu, Amy; Liao, David; Sturm, James; Austin, Robert

    2014-03-01

    Evolutionary game theory applied to two interacting cell populations can yield quantitative prediction of the future densities of the two cell populations based on the initial interaction terms. We will discuss how in a complex ecology that evolutionary game theory successfully predicts the future densities of strains of stromal and cancer cells (multiple myeloma), and discuss the possible clinical use of such analysis for predicting cancer progression. Supported by the National Science Foundation and the National Cancer Institute.

  10. Properties of Artifact Representations for Evolutionary Design

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2004-01-01

    To achieve evolutionary design systems that scale to the levels achieved by man-made artifacts we can look to their characteristics of modularity, hierarchy and regularity to guide us. For this we focus on design representations, since they strongly determine the ability of evolutionary design systems to evolve artifacts with these characteristics. We identify three properties of design representations - combination, control-flow and abstraction - and discuss how they relate to hierarchy, modularity and regularity.

  11. Humanism and multiculturalism: an evolutionary alliance.

    PubMed

    Comas-Diaz, Lillian

    2012-12-01

    Humanism and multiculturalism are partners in an evolutionary alliance. Humanistic and multicultural psychotherapies have historically influenced each other. Humanism represents the third force in psychotherapy, while multiculturalism embodies the fourth developmental stage. Multiculturalism embraces humanistic values grounded in collective and social justice contexts. Examples of multicultural humanistic constructs include contextualism, holism, and liberation. Certainly, the multicultural-humanistic connection is a necessary shift in the evolution of psychotherapy. Humanism and multiculturalism participate in the development of an inclusive and evolutionary psychotherapy.

  12. Avoiding Local Optima with Interactive Evolutionary Robotics

    DTIC Science & Technology

    2012-07-09

    that together produce the desired behavior. Here we introduce a software framework that allows a user to conduct evolutionary robotics experiments...without having to write any software themselves: the user defines the robot 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13-09-2012 13...Here we introduce a software framework that allows a user to conduct evolutionary robotics experiments without having to write any software

  13. Evolutionary cell biology: Two origins, one objective

    PubMed Central

    Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

    2014-01-01

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

  14. Evolutionary cell biology: two origins, one objective.

    PubMed

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-02

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  15. Extinction as the loss of evolutionary history

    PubMed Central

    Erwin, Douglas H.

    2008-01-01

    Current plant and animal diversity preserves at most 1–2% of the species that have existed over the past 600 million years. But understanding the evolutionary impact of these extinctions requires a variety of metrics. The traditional measurement is loss of taxa (species or a higher category) but in the absence of phylogenetic information it is difficult to distinguish the evolutionary depth of different patterns of extinction: the same species loss can encompass very different losses of evolutionary history. Furthermore, both taxic and phylogenetic measures are poor metrics of morphologic disparity. Other measures of lost diversity include: functional diversity, architectural components, behavioral and social repertoires, and developmental strategies. The canonical five mass extinctions of the Phanerozoic reveals the loss of different, albeit sometimes overlapping, aspects of loss of evolutionary history. The end-Permian mass extinction (252 Ma) reduced all measures of diversity. The same was not true of other episodes, differences that may reflect their duration and structure. The construction of biodiversity reflects similarly uneven contributions to each of these metrics. Unraveling these contributions requires greater attention to feedbacks on biodiversity and the temporal variability in their contribution to evolutionary history. Taxic diversity increases after mass extinctions, but the response by other aspects of evolutionary history is less well studied. Earlier views of postextinction biotic recovery as the refilling of empty ecospace fail to capture the dynamics of this diversity increase. PMID:18695248

  16. Evolutionary Biology Instruction: What Students Gain from Learning through Inquiry.

    ERIC Educational Resources Information Center

    Dremock, Fae, Ed.

    2002-01-01

    This bulletin features articles on real world evolutionary biology, revolutionary classroom science, a review of new curricula in evolutionary biology, and the use of case studies to illustrate points in evolutionary biology. The articles are: (1) "'Real World' Evolutionary Biology: A Pragmatic Quest. Interview with BioQUEST's John Jungck" (Harvey…

  17. A Hybrid Evolutionary Algorithm for Wheat Blending Problem

    PubMed Central

    Bonyadi, Mohammad Reza; Michalewicz, Zbigniew; Barone, Luigi

    2014-01-01

    This paper presents a hybrid evolutionary algorithm to deal with the wheat blending problem. The unique constraints of this problem make many existing algorithms fail: either they do not generate acceptable results or they are not able to complete optimization within the required time. The proposed algorithm starts with a filtering process that follows predefined rules to reduce the search space. Then the linear-relaxed version of the problem is solved using a standard linear programming algorithm. The result is used in conjunction with a solution generated by a heuristic method to generate an initial solution. After that, a hybrid of an evolutionary algorithm, a heuristic method, and a linear programming solver is used to improve the quality of the solution. A local search based posttuning method is also incorporated into the algorithm. The proposed algorithm has been tested on artificial test cases and also real data from past years. Results show that the algorithm is able to find quality results in all cases and outperforms the existing method in terms of both quality and speed. PMID:24707222

  18. Evolutionary plasticity determination by orthologous groups distribution

    PubMed Central

    2011-01-01

    Background Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is. Here, we analyze the abundance and diversity of all Eukaryotic Clusters of Orthologous Groups (KOG) present in STRING database, resulting in a total of 4,850 KOGs. This dataset comprises 481,421 proteins distributed among 55 eukaryotes. Results We propose an index to evaluate the evolutionary plasticity and conservation of an orthologous group based on its abundance and diversity across eukaryotes. To further KOG plasticity analysis, we estimate the evolutionary distance average among all proteins which take part in the same orthologous group. As a result, we found a strong correlation between the evolutionary distance average and the proposed evolutionary plasticity index. Additionally, we found low evolutionary plasticity in Saccharomyces cerevisiae genes associated with inviability and Mus musculus genes associated with early lethality. At last, we plot the evolutionary plasticity value in different gene networks from yeast and humans. As a result, it was possible to discriminate among higher and lower plastic areas of the gene networks analyzed. Conclusions The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes. Reviewers This article was reviewed by Prof Manyuan Long, Hiroyuki Toh, and Sebastien Halary. PMID:21586164

  19. Integrating evolutionary and molecular genetics of aging.

    PubMed

    Flatt, Thomas; Schmidt, Paul S

    2009-10-01

    Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940s and 1950s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980s and 1990s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging.

  20. Evolutionary heritage influences Amazon tree ecology.

    PubMed

    Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

    2016-12-14

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.

  1. The evolutionary ecology of molecular replicators.

    PubMed

    Nee, Sean

    2016-08-01

    By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

  2. Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

    PubMed

    Gupta, Abhishek; Ong, Yew-Soon; Feng, Liang; Tan, Kay Chen

    2016-05-03

    In recent decades, the field of multiobjective optimization has attracted considerable interest among evolutionary computation researchers. One of the main features that makes evolutionary methods particularly appealing for multiobjective problems is the implicit parallelism offered by a population, which enables simultaneous convergence toward the entire Pareto front. While a plethora of related algorithms have been proposed till date, a common attribute among them is that they focus on efficiently solving only a single optimization problem at a time. Despite the known power of implicit parallelism, seldom has an attempt been made to multitask, i.e., to solve multiple optimization problems simultaneously. It is contended that the notion of evolutionary multitasking leads to the possibility of automated transfer of information across different optimization exercises that may share underlying similarities, thereby facilitating improved convergence characteristics. In particular, the potential for automated transfer is deemed invaluable from the standpoint of engineering design exercises where manual knowledge adaptation and reuse are routine. Accordingly, in this paper, we present a realization of the evolutionary multitasking paradigm within the domain of multiobjective optimization. The efficacy of the associated evolutionary algorithm is demonstrated on some benchmark test functions as well as on a real-world manufacturing process design problem from the composites industry.

  3. Three Laws in Darwinian Evolutionary Theory

    NASA Astrophysics Data System (ADS)

    Ao, Ping

    2006-03-01

    Recent works to formulate laws in Darwinian evolutionary dynamics will be discussed. Specifically, three laws which form a consistent mathematical framework for the evolutionary dynamics in biology will be spelt out. The second law is most quantitative and is explicitly expressed in the unique form of a stochastic differential equation. Salient features of Darwinian evolutionary dynamics are captured by this law: the probabilistic nature of evolution, ascendancy, and the adaptive landscape. Four dynamical elements are introduced in this formulation: the ascendant matrix, the transverse matrix, the Wright evolutionary potential, and the stochastic drive. The first law may be regarded as a special case of the second law. It gives the reference point to discuss the evolutionary dynamics. The third law describes the relationship between the focused level of description to its lower and higher ones, and defines the dichotomy of deterministic and stochastic drives. It is an acknowledgement of the hierarchical structure in biology. A new interpretation of Fisher's fundamental theorem of natural selection is provided in terms of the F-Theorem. Ref. P. Ao, Physics of Life Reviews 2 (2005) 117-156.

  4. Evolutionary mechanisms acting on proteinase inhibitor variability.

    PubMed

    Christeller, John T

    2005-11-01

    The interaction of proteinase inhibitors produced, in most cases, by host organisms and the invasive proteinases of pathogens or parasites or the dietary proteinases of predators, results in an evolutionary 'arms race' of rapid and ongoing change in both interacting proteins. The importance of these interactions in pathogenicity and predation is indicated by the high level and diversity of observable evolutionary activity that has been found. At the initial level of evolutionary change, recruitment of other functional protein-folding families has occurred, with the more recent evolution of one class of proteinase inhibitor from another, using the same mechanism and proteinase contact residues. The combination of different inhibitor domains into a single molecule is also observed. The basis from which variation is possible is shown by the high rate of retention of gene duplication events and by the associated process of inhibitory domain multiplication. At this level of reorganization, mutually exclusive splicing is also observed. Finally, the major mechanism by which variation is achieved rapidly is hypervariation of contact residues, an almost ubiquitous feature of proteinase inhibitors. The diversity of evolutionary mechanisms in a single class of proteins is unlikely to be common, because few systems are under similar pressure to create variation. Proteinase inhibitors are therefore a potential model system in which to study basic evolutionary process such as functional diversification.

  5. Evolutionary heritage influences Amazon tree ecology

    PubMed Central

    Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

    2016-01-01

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

  6. Evolutionary accounts of human behavioural diversity

    PubMed Central

    Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.

    2011-01-01

    Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

  7. The evolutionary ecology of molecular replicators

    PubMed Central

    2016-01-01

    By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology. PMID:27853598

  8. Evolutionary orbital period change in BH Virginis

    NASA Astrophysics Data System (ADS)

    Gebrehiwot, Y. M.; Tessema, S. B.; Berdnikov, L. N.

    2017-04-01

    The study of orbital period change of close binaries, such as BH Virginis (BH Vir), using very long time baseline is vital to understand evolutionary processes of the system. In this paper, we use photometric data to analyze the evolutionary orbital period change of the short period RS CVn-type binary system, BH Vir, with a time baseline spanning 123 years. We used the software version of the Hertzsprung method to describe the O-C curve of the system, and we found that the orbital period secularly decreases at a rate of dp/dt=-(0.0013000 ± 0.0000863) s yr^{-1}. Because BH Vir is a typical detached binary system and both components are late type (G0 V + G2 V) stars, the evolutionary period change could be caused by the angular momentum loss due to tides coupled with magnetic breaking.

  9. Evolutionary Multiobjective Optimization: Principles, Procedures, and Practices

    NASA Astrophysics Data System (ADS)

    Deb, Kalyanmoy

    2010-10-01

    Multi-objective optimization problems deal with multiple conflicting objectives. In principle, they give rise to a set of trade-off Pareto-optimal solutions. Over the past one-and-half decade, evolutionary multi-objective optimization (EMO) has established itself as a mature field of research and application with an extensive literature, commercial softwares, numerous freely downloadable codes, a dedicated biannual conference running successfully five times so far since 2001, special sessions and workshops held at all major evolutionary computing conferences, and full-time researchers from universities and industries from all around the globe. This is because evolutionary algorithms (EAs) work with a population of solutions and in solving multi-objective optimization problems, EAs can be modified to find and capture multiple solutions in a single simulation run. In this article, we make a brief outline of EMO principles, discuss one specific EMO algorithm, and present some current research issues of EMO.

  10. Towards a postmodern synthesis of evolutionary biology

    PubMed Central

    Koonin, Eugene V.

    2012-01-01

    In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology—and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin’s legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas. PMID:19242109

  11. The evolutionary impact of invasive species

    PubMed Central

    Mooney, H. A.; Cleland, E. E.

    2001-01-01

    Since the Age of Exploration began, there has been a drastic breaching of biogeographic barriers that previously had isolated the continental biotas for millions of years. We explore the nature of these recent biotic exchanges and their consequences on evolutionary processes. The direct evidence of evolutionary consequences of the biotic rearrangements is of variable quality, but the results of trajectories are becoming clear as the number of studies increases. There are examples of invasive species altering the evolutionary pathway of native species by competitive exclusion, niche displacement, hybridization, introgression, predation, and ultimately extinction. Invaders themselves evolve in response to their interactions with natives, as well as in response to the new abiotic environment. Flexibility in behavior, and mutualistic interactions, can aid in the success of invaders in their new environment. PMID:11344292

  12. Chance, explanation, and causation in evolutionary theory.

    PubMed

    Gayon, Jean

    2005-01-01

    Chance comes into plays at many levels of the explanation of the evolutionary process; but the unity of sense of this category is problematic. The purpose of this talk is to clarify the meaning of chance at various levels in evolutionary theory: mutations, genetic drift, genetic revolutions, ecosystems, macroevolution. Three main concepts of chance are found at these various levels: luck (popular concept), randomness (probabilistic concept), and contingency relative to a given theoretical system (epistemological concept). After identifying which concept(s) of chance fit(s) with these levels, the question is raised whether these concepts can be reduced to a smaller number, and whether chance in evolutionary theory has a subjective or an objective sense.

  13. Towards a postmodern synthesis of evolutionary biology.

    PubMed

    Koonin, Eugene V

    2009-03-15

    In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology-and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin's legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas.

  14. Drug use and addiction: evolutionary perspective.

    PubMed

    Durrant, Russil; Adamson, Simon; Todd, Fraser; Sellman, Doug

    2009-11-01

    Drug use creates a significant amount of harm in modern societies. From an evolutionary perspective, the pervasive use of drugs and the ongoing risk of drug addiction can be explained in terms of the action of drugs on evolved motivational-emotional systems. Addiction arises through interaction of these evolutionarily ancient systems, designed to promote the pursuit of natural rewards, and contemporary environments where purified and potent forms of drugs are readily available. This evolutionary analysis is extended to account for developmental patterns in problem drug use, and to explain the existence of behavioural addictions, such as problem gambling. The paper concludes by considering some of the clinical and public policy implications of the evolutionary perspective presented.

  15. Comparative evolutionary psychology of sperm competition.

    PubMed

    Shackelford, Todd K; Goetz, Aaron T

    2006-05-01

    A comparative evolutionary psychological perspective predicts that species that recurrently faced similar adaptive problems may have evolved similar psychological mechanisms to solve these problems. Sperm competition provides an arena in which to assess the heuristic value of such a comparative evolutionary perspective. The sperm competition that results from female infidelity and polyandry presents a similar class of adaptive problems for individuals across many species. The authors first describe mechanisms of sperm competition in insects and in birds. They suggest that the adaptive problems and evolved solutions in these species provide insight into human anatomy, physiology, psychology, and behavior. The authors then review recent theoretical and empirical arguments for the existence of sperm competition in humans and discuss proposed adaptations in humans that have analogs in insects or birds. The authors conclude by highlighting the heuristic value of a comparative evolutionary psychological approach in this field.

  16. Incorporating evolutionary processes into population viability models.

    PubMed

    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.

  17. Aerodynamic Shape Optimization using an Evolutionary Algorithm

    NASA Technical Reports Server (NTRS)

    Hoist, Terry L.; Pulliam, Thomas H.

    2003-01-01

    A method for aerodynamic shape optimization based on an evolutionary algorithm approach is presented and demonstrated. Results are presented for a number of model problems to access the effect of algorithm parameters on convergence efficiency and reliability. A transonic viscous airfoil optimization problem-both single and two-objective variations is used as the basis for a preliminary comparison with an adjoint-gradient optimizer. The evolutionary algorithm is coupled with a transonic full potential flow solver and is used to optimize the inviscid flow about transonic wings including multi-objective and multi-discipline solutions that lead to the generation of pareto fronts. The results indicate that the evolutionary algorithm approach is easy to implement, flexible in application and extremely reliable.

  18. Aerodynamic Shape Optimization using an Evolutionary Algorithm

    NASA Technical Reports Server (NTRS)

    Holst, Terry L.; Pulliam, Thomas H.; Kwak, Dochan (Technical Monitor)

    2003-01-01

    A method for aerodynamic shape optimization based on an evolutionary algorithm approach is presented and demonstrated. Results are presented for a number of model problems to access the effect of algorithm parameters on convergence efficiency and reliability. A transonic viscous airfoil optimization problem, both single and two-objective variations, is used as the basis for a preliminary comparison with an adjoint-gradient optimizer. The evolutionary algorithm is coupled with a transonic full potential flow solver and is used to optimize the inviscid flow about transonic wings including multi-objective and multi-discipline solutions that lead to the generation of pareto fronts. The results indicate that the evolutionary algorithm approach is easy to implement, flexible in application and extremely reliable.

  19. Fuzzy evolutionary algorithm to solve chromosomes conflict and its application to lecture schedule problems

    NASA Astrophysics Data System (ADS)

    Marwati, Rini; Yulianti, Kartika; Pangestu, Herny Wulandari

    2016-02-01

    A fuzzy evolutionary algorithm is an integration of an evolutionary algorithm and a fuzzy system. In this paper, we present an application of a genetic algorithm to a fuzzy evolutionary algorithm to detect and to solve chromosomes conflict. A chromosome conflict is identified by existence of any two genes in a chromosome that has the same values as two genes in another chromosome. Based on this approach, we construct an algorithm to solve a lecture scheduling problem. Time codes, lecture codes, lecturer codes, and room codes are defined as genes. They are collected to become chromosomes. As a result, the conflicted schedule turns into chromosomes conflict. Built in the Delphi program, results show that the conflicted lecture schedule problem is solvable by this algorithm.

  20. Evolutionary and functional significance of hominoid tooth enamel.

    PubMed

    Gantt, D G; Rafter, J A

    1998-01-01

    The purpose of this investigation is to evaluate enamel thickness in extant and extinct hominoids. The material used in this study spans the evolutionary history of this group, from 20 million years ago to the present. The objectives of this investigation are to test three hypotheses: (1) the Loading Hypothesis: loading areas of the crown have thicker enamel than non-loading areas; (2) the Phyletic Hypothesis: differences in enamel thickness provide a basis for determining evolutionary relationships; and (3) the Functional Hypothesis: differences among hominoids result from adaptations to differing dietary and ecological habitats, that is from folivory to frugivory to hard object feeding and from tropical to forest to savanna habitats. Thin sections were prepared and polished to approximately 100 microm in thickness. Each section was then enlarged and digitally captured to the computer. Image processing and analysis software, SigmaImage (was used to measure the sections. Subsequent statistical analysis was conducted with SigmaStat and SPSS statistical software programs. The data provides statistical support for all hypotheses. In particular, the data support the proposal that "thick" enamel is the ancestral condition for the great apes and human clade. Therefore, Pongo would have retained its enamel thickness from the common ancestor of the great apes and Gorilla and Pan would have secondarily reduced enamel thickness to "thin." The common ancestor of the hominids, the australopithecines, would have "thick" enamel. The "hyper-thick" enamel of the australopithecines would be a derived character for this clade due to increased crushing and grinding and adaptation to savanna habitat. Homo would have secondarily reduced enamel thickness to "thick." Evolutionary biology of enamel differs markedly in hominids from that found in other hominoids and primates. Increased enamel thickness involved both increases in absolute thickness of enamel and crown size in response to

  1. An evolutionary framework for cultural change: Selectionism versus communal exchange

    NASA Astrophysics Data System (ADS)

    Gabora, Liane

    2013-06-01

    Dawkins' replicator-based conception of evolution has led to widespread mis-application of selectionism across the social sciences because it does not address the paradox that necessitated the theory of natural selection in the first place: how do organisms accumulate change when traits acquired over their lifetime are obliterated? This is addressed by von Neumann's concept of a self-replicating automaton (SRA). A SRA consists of a self-assembly code that is used in two distinct ways: (1) actively deciphered during development to construct a self-similar replicant, and (2) passively copied to the replicant to ensure that it can reproduce. Information that is acquired over a lifetime is not transmitted to offspring, whereas information that is inherited during copying is transmitted. In cultural evolution there is no mechanism for discarding acquired change. Acquired change can accumulate orders of magnitude faster than, and quickly overwhelm, inherited change due to differential replication of variants in response to selection. This prohibits a selectionist but not an evolutionary framework for culture and the creative processes that fuel it. The importance non-Darwinian processes in biological evolution is increasingly recognized. Recent work on the origin of life suggests that early life evolved through a non-Darwinian process referred to as communal exchange that does not involve a self-assembly code, and that natural selection emerged from this more haphazard, ancestral evolutionary process. It is proposed that communal exchange provides an evolutionary framework for culture that enables specification of cognitive features necessary for a (real or artificial) societies to evolve culture. This is supported by a computational model of cultural evolution and a conceptual network based program for documenting material cultural history, and it is consistent with high levels of human cooperation.

  2. The Exercise–Affect–Adherence Pathway: An Evolutionary Perspective

    PubMed Central

    Lee, Harold H.; Emerson, Jessica A.; Williams, David M.

    2016-01-01

    The low rates of regular exercise and overall physical activity (PA) in the general population represent a significant public health challenge. Previous research suggests that, for many people, exercise leads to a negative affective response and, in turn, reduced likelihood of future exercise. The purpose of this paper is to examine this exercise–affect–adherence relationship from an evolutionary perspective. Specifically, we argue that low rates of physical exercise in the general population are a function of the evolved human tendency to avoid unnecessary physical exertion. This innate tendency evolved because it allowed our evolutionary ancestors to conserve energy for physical activities that had immediate adaptive utility such as pursuing prey, escaping predators, and engaging in social and reproductive behaviors. The commonly observed negative affective response to exercise is an evolved proximate psychological mechanism through which humans avoid unnecessary energy expenditure. The fact that the human tendencies toward negative affective response to and avoidance of unnecessary physical activities are innate does not mean that they are unchangeable. Indeed, it is only because of human-engineered changes in our environmental conditions (i.e., it is no longer necessary for us to work for our food) that our predisposition to avoid unnecessary physical exertion has become a liability. Thus, it is well within our capabilities to reengineer our environments to once again make PA necessary or, at least, to serve an immediate functional purpose. We propose a two-pronged approach to PA promotion based on this evolutionary functional perspective: first, to promote exercise and other physical activities that are perceived to have an immediate purpose, and second, to instill greater perceived purpose for a wider range of physical activities. We posit that these strategies are more likely to result in more positive (or less negative) affective responses to exercise

  3. A framework for evolutionary systems biology

    PubMed Central

    Loewe, Laurence

    2009-01-01

    Background Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Results Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. Conclusion EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications. PMID:19239699

  4. The evolutionary outcome of sexual conflict

    PubMed Central

    Lessells, C(Kate). M

    2006-01-01

    Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits—those related to parental investment (PI) and to mating—over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation–counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to

  5. The evolutionary outcome of sexual conflict.

    PubMed

    Lessells, C M

    2006-02-28

    Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits-those related to parental investment (PI) and to mating-over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation-counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to

  6. ECOD: an evolutionary classification of protein domains.

    PubMed

    Cheng, Hua; Schaeffer, R Dustin; Liao, Yuxing; Kinch, Lisa N; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V

    2014-12-01

    Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or "fold"). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.

  7. From computers to cultivation: reconceptualizing evolutionary psychology

    PubMed Central

    Barrett, Louise; Pollet, Thomas V.; Stulp, Gert

    2014-01-01

    Does evolutionary theorizing have a role in psychology? This is a more contentious issue than one might imagine, given that, as evolved creatures, the answer must surely be yes. The contested nature of evolutionary psychology lies not in our status as evolved beings, but in the extent to which evolutionary ideas add value to studies of human behavior, and the rigor with which these ideas are tested. This, in turn, is linked to the framework in which particular evolutionary ideas are situated. While the framing of the current research topic places the brain-as-computer metaphor in opposition to evolutionary psychology, the most prominent school of thought in this field (born out of cognitive psychology, and often known as the Santa Barbara school) is entirely wedded to the computational theory of mind as an explanatory framework. Its unique aspect is to argue that the mind consists of a large number of functionally specialized (i.e., domain-specific) computational mechanisms, or modules (the massive modularity hypothesis). Far from offering an alternative to, or an improvement on, the current perspective, we argue that evolutionary psychology is a mainstream computational theory, and that its arguments for domain-specificity often rest on shaky premises. We then go on to suggest that the various forms of e-cognition (i.e., embodied, embedded, enactive) represent a true alternative to standard computational approaches, with an emphasis on “cognitive integration” or the “extended mind hypothesis” in particular. We feel this offers the most promise for human psychology because it incorporates the social and historical processes that are crucial to human “mind-making” within an evolutionarily informed framework. In addition to linking to other research areas in psychology, this approach is more likely to form productive links to other disciplines within the social sciences, not least by encouraging a healthy pluralism in approach. PMID:25161633

  8. Langley's CSI evolutionary model: Phase O

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  9. Evolutionary genetics of insect innate immunity

    PubMed Central

    2015-01-01

    Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. PMID:25750410

  10. Evolutionary explosions and the phylogenetic fuse.

    PubMed

    Cooper, A; Fortey, R

    1998-04-01

    A literal reading of the fossil record indicates that the early Cambrian (c. 545 million years ago) and early Tertiary (c. 65 million years ago) were characterized by enormously accelerated periods of morphological evolution marking the appearance of the animal phyla, and modern bird and placental mammal orders, respectively. Recently, the evidence for these evolutionary `explosions' has been questioned by cladistic and biogeographic studies which reveal that periods of diversification before these events are missing from the fossil record. Furthermore, molecular evidence indicates that prolonged periods of evolutionary innovation and cladogenesis lit the fuse long before the `explosions' apparent in the fossil record.

  11. Genomes, Phylogeny, and Evolutionary Systems Biology

    SciTech Connect

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  12. Reframing developmental biology and building evolutionary theory's new synthesis.

    PubMed

    Tauber, Alfred I

    2010-01-01

    Gilbert and Epel present a new approach to developmental biology: embryogenesis must be understood within the full context of the organism's environment. Instead of an insular embryo following a genetic blueprint, this revised program maintains that embryogenesis is subject to inputs from the environment that generate novel genetic variation with dynamic consequences for development. Beyond allelic variation of structural genes and of regulatory loci, plasticity-derived epigenetic variation completes the triad of the major types of variation required for evolution. Developmental biology and ecology, disciplines that have previously been regarded as distinct, are presented here as fully integrated under the rubric of "eco-devo," and from this perspective, which highlights how the environment not only selects variation, it helps construct it, another synthesis with evolutionary biology must also be made, "eco-evo-devo." This second integration has enormous implications for expanding evolution theory, inasmuch as the Modern Synthesis (Provine 1971), which combined classical genetics and Darwinism in the mid-20th century, did not account for the role of development in evolution. The eco-evo-devo synthesis thus portends a major theoretical inflection in evolutionary biology. Following a description of these scientific developments, comment is offered as to how this new integrated approach might be understood within the larger shifts in contemporary biology.

  13. Evolutionary ecotoxicology of pesticide resistance: a case study in Daphnia.

    PubMed

    Jansen, Mieke; Coors, Anja; Stoks, Robby; De Meester, Luc

    2011-05-01

    Natural populations that are exposed to pesticides in their environment may at the same time be exposed to natural stressors like parasites and predators, which may interact with pesticide exposure. This may not only impact target pest species but also a wide variety of non-target species. This review reports on a joint research program in the water flea Daphnia magna, a non-target species often used as model organism in ecology and ecotoxicology. The focus is on different aspects that are of key importance to understand the evolutionary ecology of pesticide exposure: (1) the capacity of natural populations to genetically adapt to pesticide exposure (2) the added complexity of synergistic effects caused by simultaneous exposure to natural stressors, and (3) the potential interference of evolutionary costs of adaptation to pesticide exposure. Our results showed that natural populations were able to rapidly evolve resistance to the pesticide carbaryl but at the expense of fitness costs. Individuals selected for carbaryl resistance had higher survival rates when exposed to the pesticide but also a greater susceptibility to the challenge imposed by the bacterial endoparasite Pasteuria ramosa. The evolved resistance to carbaryl was in some cases only expressed in the absence of fish kairomones. Further, it became clear that the responses to both exposure to single and combined stressors was for several life history variables strongly dependent upon past exposure to carbaryl. This indicates that past exposures to pesticides are important and can not be neglected when evaluating responses to current stressors.

  14. A search for evolutionary changes in planetary nuclei: A continuation

    NASA Technical Reports Server (NTRS)

    Altner, Bruce

    1995-01-01

    This report summarizes the final results of an IUE investigation to search for signs of evolutionary changes in high-mass central stars of planetary nuclei, as evidenced by UV-optical fading over the lifetime of the satellite. The program is a continuation of an earlier investigation, expanding the target list to include more types of hot central stars and to obtain more spectra of previously observed stars. In order to compare the IUE fluxes of a central star obtained over a more-than-ten-year timespan, several steps were necessary, including reprocessing of very early spectra and correction for the sensitivity degradation of the SWP camera over time. The results indicate that while a few stars appear to have diminished UV fluxes compared to earlier IUE observations, the evidence for this is less than overwhelming due to the sparseness of the data. Those stars which emerge from this study as viable candidates for having faded are the cooler Of-type stars (O6f-O7f), i.e., those for which the change in spectral energy with increasing temperature is greatest. The report describes the data analysis steps and discusses the uncertainties in both the data and in the resulting fading rates. Estimates of stellar mass based on theoretical evolutionary rates are also provided.

  15. Phylogeography and evolutionary history of rodent-borne hantaviruses.

    PubMed

    Souza, W M; Bello, G; Amarilla, A A; Alfonso, H L; Aquino, V H; Figueiredo, L T M

    2014-01-01

    Hantavirus (Family Bunyaviridae) are mostly associated to rodents and transmitted to man by inhalation of aerosolized infected excreta of these animals. The human infection by hantaviruses can lead to severe diseases such as hemorrhagic fever with renal syndrome (HFRS) in Asia and Europe, and pulmonary syndrome (HPS) in the Americas. To determine the origin, spreading and evolutionary dynamics of rodent-borne hantaviruses, 190 sequences of nucleoprotein (N) of hantaviruses identified in 30 countries, from 1985 to 2010, were retrieved from the GenBank and analyzed using the BEAST program. Our evolutionary analysis indicates that current genetic diversity of N gene of rodent-borne hantaviruses probably was originated around 2000 years ago. Hantavirus harbored by Murinae and Arvicolinae subfamilies, probably, were originated in Asia 500-700 years ago and later spread toward Siberia, Europe, Africa and North America. Hantavirus carried by Neotominae subfamily, probably, emerged 500-600 years ago in Central America and spread toward North America. Finally, hantaviruses associated to Sigmodontinae occurred in Brazil 400 years ago and were, probably, originated from Neotominae-associated virus from northern South America. These data offer subsidies to understand the time-scale and worldwide dissemination dynamics of rodent-borne hantaviruses.

  16. Evolutionary origin of gastrulation: insights from sponge development

    PubMed Central

    2014-01-01

    Background The evolutionary origin of gastrulation—defined as a morphogenetic event that leads to the establishment of germ layers—remains a vexing question. Central to this debate is the evolutionary relationship between the cell layers of sponges (poriferans) and eumetazoan germ layers. Despite considerable attention, it remains unclear whether sponge cell layers undergo progressive fate determination akin to eumetazoan primary germ layer formation during gastrulation. Results Here we show by cell-labelling experiments in the demosponge Amphimedon queenslandica that the cell layers established during embryogenesis have no relationship to the cell layers of the juvenile. In addition, juvenile epithelial cells can transdifferentiate into a range of cell types and move between cell layers. Despite the apparent lack of cell layer and fate determination and stability in this sponge, the transcription factor GATA, a highly conserved eumetazoan endomesodermal marker, is expressed consistently in the inner layer of A. queenslandica larvae and juveniles. Conclusions Our results are compatible with sponge cell layers not undergoing progressive fate determination and thus not being homologous to eumetazoan germ layers. Nonetheless, the expression of GATA in the sponge inner cell layer suggests a shared ancestry with the eumetazoan endomesoderm, and that the ancestral role of GATA in specifying internalised cells may antedate the origin of germ layers. Together, these results support germ layers and gastrulation evolving early in eumetazoan evolution from pre-existing developmental programs used for the simple patterning of cells in the first multicellular animals. PMID:24678663

  17. MEASURING THE EVOLUTIONARY RATE OF COOLING OF ZZ Ceti

    SciTech Connect

    Mukadam, Anjum S.; Fraser, Oliver; Riecken, T. S.; Kronberg, M. E.; Bischoff-Kim, Agnes; Corsico, A. H.; Montgomery, M. H.; Winget, D. E.; Hermes, J. J.; Winget, K. I.; Falcon, Ross E.; Reaves, D.; Kepler, S. O.; Romero, A. D.; Chandler, D. W.; Kuehne, J. W.; Sullivan, D. J.; Von Hippel, T.; Mullally, F.; Shipman, H.; 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.

  18. Reconstructing the evolutionary history of natural languages

    SciTech Connect

    Warnow, T.; Ringe, D.; Taylor, A.

    1996-12-31

    In this paper we present a new methodology for determining the evolutionary history of related languages. Our methodology uses linguistic information encoded as qualitative characters, and provides much greater precision than previous methods. Our analysis of Indo-European (IE) languages resolves questions that have troubled scholars for over a century.

  19. Indoor Thermal Comfort, an Evolutionary Biology Perspective

    SciTech Connect

    Stoops, John L.

    2006-04-15

    As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?

  20. Evolutionary Ecology of the Marine Roseobacter Clade

    PubMed Central

    Luo, Haiwei

    2014-01-01

    SUMMARY Members of the Roseobacter clade are equipped with a tremendous diversity of metabolic capabilities, which in part explains their success in so many different marine habitats. Ideas on how this diversity evolved and is maintained are reviewed, focusing on recent evolutionary studies exploring the timing and mechanisms of Roseobacter ecological diversification. PMID:25428935

  1. Molecular selection in a unified evolutionary sequence

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

  2. Evolutionary Stability in the Traveler's Dilemma

    ERIC Educational Resources Information Center

    Barker, Andrew T.

    2009-01-01

    The traveler's dilemma is a generalization of the prisoner's dilemma which shows clearly a paradox of game theory. In the traveler's dilemma, the strategy chosen by analysis and theory seems obviously wrong intuitively. Here we develop a measure of evolutionary stability and show that the evolutionarily stable equilibrium is in some sense not very…

  3. TARGETED CAPTURE IN EVOLUTIONARY AND ECOLOGICAL GENOMICS

    PubMed Central

    Jones, Matthew R.; Good, Jeffrey M.

    2016-01-01

    The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing. PMID:26137993

  4. The Finches' Beaks: Introducing Evolutionary Concepts

    ERIC Educational Resources Information Center

    Kampourakis, Kostas

    2006-01-01

    Many secondary students hold misconceptions about evolution, even after instruction, that are often inconsistent with what is accepted by evolutionary biologists. Understanding evolution is difficult due to major conceptual difficulties concerning variation, differential survival, adaptation, and natural selection. In this article, the author…

  5. Using Human Evolution to Teach Evolutionary Theory

    ERIC Educational Resources Information Center

    Besterman, Hugo; La Velle, Linda Baggott

    2007-01-01

    This paper discusses some traditional approaches to the teaching of evolutionary theory at pre-university level, criticising in particular some of the more commonly used models and exemplars. Curricular demands are described and an alternative approach is suggested, using the emerging story of human evolution. Recent discoveries help to illustrate…

  6. The evolutionary biology of child health.

    PubMed

    Crespi, Bernard

    2011-05-22

    I apply evolutionary perspectives and conceptual tools to analyse central issues underlying child health, with emphases on the roles of human-specific adaptations and genomic conflicts in physical growth and development. Evidence from comparative primatology, anthropology, physiology and human disorders indicates that child health risks have evolved in the context of evolutionary changes, along the human lineage, affecting the timing, growth-differentiation phenotypes and adaptive significance of prenatal stages, infancy, childhood, juvenility and adolescence. The most striking evolutionary changes in humans are earlier weaning and prolonged subsequent pre-adult stages, which have structured and potentiated maladaptations related to growth and development. Data from human genetic and epigenetic studies, and mouse models, indicate that growth, development and behaviour during pre-adult stages are mediated to a notable degree by effects from genomic conflicts and imprinted genes. The incidence of cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes that control aspects of growth. Understanding the adaptive significance of child growth and development phenotypes, in the context of human-evolutionary changes and genomic conflicts, provides novel insights into the causes of disease in childhood.

  7. College Students' Misconceptions about Evolutionary Trees

    ERIC Educational Resources Information Center

    Meir, Eli; Perry, Judy; Herron, Jon C.; Kingsolver, Joel

    2007-01-01

    Evolution is at the center of the biological sciences and is therefore a required topic for virtually every college biology student. Over the past year, the authors have been building a new simulation software package called EvoBeaker to teach college-level evolutionary biology through simulated experiments. They have built both micro and…

  8. Evolutionary Psychology: Controversies, Questions, Prospects, and Limitations

    ERIC Educational Resources Information Center

    Confer, Jaime C.; Easton, Judith A.; Fleischman, Diana S.; Goetz, Cari D.; Lewis, David M. G.; Perilloux, Carin; Buss, David M.

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from…

  9. Evolutionary Drift Models for Moving Target Defense

    SciTech Connect

    Oehmen, Christopher S.; Peterson, Elena S.; Teuton, Jeremy R.

    2012-10-31

    One of the biggest challenges faced by cyber defenders is that attacks evolve more rapidly than our ability to recognize them. We propose a moving target defense concept in which the means of detection is set in motion. This is done by moving away from static signature-based detection and instead adopting biological modeling techniques that describe families of related sequences. We present here one example for how to apply evolutionary models to cyber sequences, and demonstrate the feasibility of this technique on analysis of a complex, evolving software project. Specifically, we applied sequence-based and profile-based evolutionary models and report the ability of these models to recognize highly volatile code regions. We found that different drift models reliably identify different types of evolutionarily related code regions. The impact is that these (and possibly other) evolutionary models could be used in a moving target defense in which the "signature" being used to detect sequence-based behaviors is not a fixed signature but one that can recognize new variants of a known family based on multiple evolutionary models.

  10. Teaching about Adaptation: Why Evolutionary History Matters

    ERIC Educational Resources Information Center

    Kampourakis, Kostas

    2013-01-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

  11. The emergence of communication in evolutionary robots.

    PubMed

    Marocco, Davide; Cangelosi, Angelo; Nolfi, Stefano

    2003-10-15

    Evolutionary robotics is a biologically inspired approach to robotics that is advantageous to studying the evolution of communication. A new model for the emergence of communication is developed and tested through various simulation experiments. In the first simulation, the emergence of simple signalling behaviour is studied. This is used to investigate the inter-relationships between communication abilities, namely linguistic production and comprehension, and other behavioural skills. The model supports the hypothesis that the ability to form categories from direct interaction with an environment constitutes the grounds for subsequent evolution of communication and language. In the second simulation, evolutionary robots are used to study the emergence of simple syntactic categories, e.g. action names (verbs). Comparisons between the two simulations indicate that the signalling lexicon emerged in the first simulation follows the evolutionary pattern of nouns, as observed in related models on the evolution of syntactic categories. Results also support the language-origin hypothesis on the fact that nouns precede verbs in both phylogenesis and ontogenesis. Further extensions of this new evolutionary robotic model for testing hypotheses on language origins are also discussed.

  12. Conceptualizing evolutionary novelty: moving beyond definitional debates.

    PubMed

    Brigandt, Ingo; Love, Alan C

    2012-09-01

    According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light of a different epistemic role played by the concept of evolutionary novelty-the structuring of a problem space or setting of an explanatory agenda-rather than the concept's capacity to categorize traits as novel. This distinctive role is consistent with the definitional diversity and shows that the concept of novelty benefits ongoing investigation by focusing attention on answering different questions related to comprehending the origins of novelty. A review of recent theoretical and empirical work on evolutionary novelty confirms this interpretation.

  13. Evolutionary Biology: Its Value to Society

    ERIC Educational Resources Information Center

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  14. Compassion: An Evolutionary Analysis and Empirical Review

    ERIC Educational Resources Information Center

    Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

    2010-01-01

    What is compassion? And how did it evolve? In this review, we integrate 3 evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct…

  15. Intervals in evolutionary algorithms for global optimization

    SciTech Connect

    Patil, R.B.

    1995-05-01

    Optimization is of central concern to a number of disciplines. Interval Arithmetic methods for global optimization provide us with (guaranteed) verified results. These methods are mainly restricted to the classes of objective functions that are twice differentiable and use a simple strategy of eliminating a splitting larger regions of search space in the global optimization process. An efficient approach that combines the efficient strategy from Interval Global Optimization Methods and robustness of the Evolutionary Algorithms is proposed. In the proposed approach, search begins with randomly created interval vectors with interval widths equal to the whole domain. Before the beginning of the evolutionary process, fitness of these interval parameter vectors is defined by evaluating the objective function at the center of the initial interval vectors. In the subsequent evolutionary process the local optimization process returns an estimate of the bounds of the objective function over the interval vectors. Though these bounds may not be correct at the beginning due to large interval widths and complicated function properties, the process of reducing interval widths over time and a selection approach similar to simulated annealing helps in estimating reasonably correct bounds as the population evolves. The interval parameter vectors at these estimated bounds (local optima) are then subjected to crossover and mutation operators. This evolutionary process continues for predetermined number of generations in the search of the global optimum.

  16. Analysis of Students' Arguments on Evolutionary Theory

    ERIC Educational Resources Information Center

    Basel, Nicolai; Harms, Ute; Prechtl, Helmut

    2013-01-01

    A qualitative exploratory study was conducted to reveal students' argumentation skills in the context of the topic of evolution. Transcripts from problem-centred interviews on secondary students' beliefs about evolutionary processes of adaptation were analysed using a content analysis approach. For this purpose two categorical systems were…

  17. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  18. An Interdisciplinary Model for Teaching Evolutionary Ecology.

    ERIC Educational Resources Information Center

    Coletta, John

    1992-01-01

    Describes a general systems evolutionary model and demonstrates how a previously established ecological model is a function of its past development based on the evolution of the rock, nutrient, and water cycles. Discusses the applications of the model in environmental education. (MDH)

  19. On the Evolutionary Bases of Consumer Reinforcement

    ERIC Educational Resources Information Center

    Nicholson, Michael; Xiao, Sarah Hong

    2010-01-01

    This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…

  20. Telling Tales at Work: An Evolutionary Explanation

    ERIC Educational Resources Information Center

    Yang, Chulguen

    2013-01-01

    This article explores the adaptive functions of storytelling in the workplace from an evolutionary perspective. Based on the analysis of ethnographic studies on hunter-gatherer and modern work organizations, this article claims that storytelling, as an adapted cognitive device, was selectively retained by natural and sexual selection, because of…

  1. Knowledge Guided Evolutionary Algorithms in Financial Investing

    ERIC Educational Resources Information Center

    Wimmer, Hayden

    2013-01-01

    A large body of literature exists on evolutionary computing, genetic algorithms, decision trees, codified knowledge, and knowledge management systems; however, the intersection of these computing topics has not been widely researched. Moving through the set of all possible solutions--or traversing the search space--at random exhibits no control…

  2. When population and evolutionary genetics met behaviour.

    PubMed

    Costa, Rodolfo; Stanewsky, Ralf

    2013-01-01

    In this review, we analyse the impact of a population and evolutionary genetics approach on the study of insect behaviour. Our attention is focused on the model organism Drosophila melanogaster and several other insect species. In particular, we explore the relationship between rhythmic behaviours and the molecular evolution of clock and ion channel genes.

  3. Haplogroups as Evolutionary Markers of Cognitive Ability

    ERIC Educational Resources Information Center

    Rindermann, Heiner; Woodley, Michael A.; Stratford, James

    2012-01-01

    Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal…

  4. An evolutionary advantage for extravagant honesty.

    PubMed

    Bullock, Seth

    2012-01-07

    A game-theoretic model of handicap signalling over a pair of signalling channels is introduced in order to determine when one channel has an evolutionary advantage over the other. The stability conditions for honest handicap signalling are presented for a single channel and are shown to conform with the results of prior handicap signalling models. Evolutionary simulations are then used to show that, for a two-channel system in which honest signalling is possible on both channels, the channel featuring larger advertisements at equilibrium is favoured by evolution. This result helps to address a significant tension in the handicap principle literature. While the original theory was motivated by the prevalence of extravagant natural signalling, contemporary models have demonstrated that it is the cost associated with deception that stabilises honesty, and that the honest signals exhibited at equilibrium need not be extravagant at all. The current model suggests that while extravagant and wasteful signals are not required to ensure a signalling system's evolutionary stability, extravagant signalling systems may enjoy an advantage in terms of evolutionary attainability.

  5. Evolutionary Dynamics of Digitized Organizational Routines

    ERIC Educational Resources Information Center

    Liu, Peng

    2013-01-01

    This dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of…

  6. Constraints in Genetic Programming

    NASA Technical Reports Server (NTRS)

    Janikow, Cezary Z.

    1996-01-01

    Genetic programming refers to a class of genetic algorithms utilizing generic representation in the form of program trees. For a particular application, one needs to provide the set of functions, whose compositions determine the space of program structures being evolved, and the set of terminals, which determine the space of specific instances of those programs. The algorithm searches the space for the best program for a given problem, applying evolutionary mechanisms borrowed from nature. Genetic algorithms have shown great capabilities in approximately solving optimization problems which could not be approximated or solved with other methods. Genetic programming extends their capabilities to deal with a broader variety of problems. However, it also extends the size of the search space, which often becomes too large to be effectively searched even by evolutionary methods. Therefore, our objective is to utilize problem constraints, if such can be identified, to restrict this space. In this publication, we propose a generic constraint specification language, powerful enough for a broad class of problem constraints. This language has two elements -- one reduces only the number of program instances, the other reduces both the space of program structures as well as their instances. With this language, we define the minimal set of complete constraints, and a set of operators guaranteeing offspring validity from valid parents. We also show that these operators are not less efficient than the standard genetic programming operators if one preprocesses the constraints - the necessary mechanisms are identified.

  7. Shaping communicative colour signals over evolutionary time

    PubMed Central

    Oyola Morales, José R.; Vital-García, Cuauhcihuatl; Hews, Diana K.; Martins, Emília P.

    2016-01-01

    Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus) represents an ancient loss of the belly patch by S. siniferus, and the second evolutionary shift, bounded by S. undulatus and S. virgatus, represents a more recent loss of blue belly patch by S. virgatus. Conspicuousness measurements suggest that the species with the recent loss (S. virgatus) is the least conspicuous. Results for two other species (S. siniferus and S. merriami) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch (S. siniferus) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours. PMID:28018661

  8. Evolutionary Optimization of a Quadrifilar Helical Antenna

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Kraus, William F.; Linden, Derek S.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.

  9. EVO—Evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

    We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running EVO with different numbers of carbon atoms per unit cell yields graphite as the lowest energy structure as well as a diamond-like structure, both in one run. Our implementation also supports the search for 2D structures and was able to find a boron sheet with structural features so far not considered in literature. Program summaryProgram title: EVO Catalogue identifier: AEOZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 23488 No. of bytes in distributed program, including test data, etc.: 1830122 Distribution format: tar.gz Programming language: Python. Computer: No limitations known. Operating system: Linux. RAM: Negligible compared to the requirements of the electronic structure programs used Classification: 7.8. External routines: Quantum ESPRESSO (http://www.quantum-espresso.org/), GULP (https://projects.ivec.org/gulp/) Nature of problem: Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Solution method: Evolutionary algorithms transfer the main features of biological evolution to use them in global searches. The combination of the "survival of the fittest" (deterministic) and the

  10. Automated Antenna Design with Evolutionary Algorithms

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.; Globus, Al; Linden, Derek S.; Lohn, Jason D.

    2006-01-01

    Current methods of designing and optimizing antennas by hand are time and labor intensive, and limit complexity. Evolutionary design techniques can overcome these limitations by searching the design space and automatically finding effective solutions. In recent years, evolutionary algorithms have shown great promise in finding practical solutions in large, poorly understood design spaces. In particular, spacecraft antenna design has proven tractable to evolutionary design techniques. Researchers have been investigating evolutionary antenna design and optimization since the early 1990s, and the field has grown in recent years as computer speed has increased and electromagnetic simulators have improved. Two requirements-compliant antennas, one for ST5 and another for TDRS-C, have been automatically designed by evolutionary algorithms. The ST5 antenna is slated to fly this year, and a TDRS-C phased array element has been fabricated and tested. Such automated evolutionary design is enabled by medium-to-high quality simulators and fast modern computers to evaluate computer-generated designs. Evolutionary algorithms automate cut-and-try engineering, substituting automated search though millions of potential designs for intelligent search by engineers through a much smaller number of designs. For evolutionary design, the engineer chooses the evolutionary technique, parameters and the basic form of the antenna, e.g., single wire for ST5 and crossed-element Yagi for TDRS-C. Evolutionary algorithms then search for optimal configurations in the space defined by the engineer. NASA's Space Technology 5 (ST5) mission will launch three small spacecraft to test innovative concepts and technologies. Advanced evolutionary algorithms were used to automatically design antennas for ST5. The combination of wide beamwidth for a circularly-polarized wave and wide impedance bandwidth made for a challenging antenna design problem. From past experience in designing wire antennas, we chose to

  11. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    PubMed

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

  12. Evolutionary Rate Covariation in Meiotic Proteins Results from Fluctuating Evolutionary Pressure in Yeasts and Mammals

    PubMed Central

    Clark, Nathan L.; Alani, Eric; Aquadro, Charles F.

    2013-01-01

    Evolutionary rates of functionally related proteins tend to change in parallel over evolutionary time. Such evolutionary rate covariation (ERC) is a sequence-based signature of coevolution and a potentially useful signature to infer functional relationships between proteins. One major hypothesis to explain ERC is that fluctuations in evolutionary pressure acting on entire pathways cause parallel rate changes for functionally related proteins. To explore this hypothesis we analyzed ERC within DNA mismatch repair (MMR) and meiosis proteins over phylogenies of 18 yeast species and 22 mammalian species. We identified a strong signature of ERC between eight yeast proteins involved in meiotic crossing over, which seems to have resulted from relaxation of constraint specifically in Candida glabrata. These and other meiotic proteins in C. glabrata showed marked rate acceleration, likely due to its apparently clonal reproductive strategy and the resulting infrequent use of meiotic proteins. This correlation between change of reproductive mode and change in constraint supports an evolutionary pressure origin for ERC. Moreover, we present evidence for similar relaxations of constraint in additional pathogenic yeast species. Mammalian MMR and meiosis proteins also showed statistically significant ERC; however, there was not strong ERC between crossover proteins, as observed in yeasts. Rather, mammals exhibited ERC in different pathways, such as piRNA-mediated defense against transposable elements. Overall, if fluctuation in evolutionary pressure is responsible for ERC, it could reveal functional relationships within entire protein pathways, regardless of whether they physically interact or not, so long as there was variation in constraint on that pathway. PMID:23183665

  13. Hybrid Tuning of an Evolutionary Algorithm for Sensor Allocation

    DTIC Science & Technology

    2011-06-01

    13. SUPPLEMENTARY NOTES 2011 IEEE Conference on Evolutionary Computation , 5-8 June, New Orleans, LA. 14. ABSTRACT The application of evolutionary ...i.e. metrics) through multi-objective optimization and its capability to address non-linear classes of optimization problem. Evolutionary computation ...Yilmaz, B. N. Mcquay, H. Yu, A. S. Wu, and J. C. Sciortino, “Evolving sensor suites for enemy radar detection,” in Genetic and Evolutionary Computation

  14. Evolutionary psychiatry: a new College special interest group

    PubMed Central

    Abed, Riadh; St John-Smith, Paul

    2016-01-01

    Evolutionary science remains an overlooked area in psychiatry and medicine. The newly established Royal College of Psychiatrists' Evolutionary Psychiatry Special Interest Group aims to reverse this trend by raising the profile of evolutionary thinking among College members and others further afield. Here we provide a brief outline of the importance of the evolutionary approach to both the theory and practice of psychiatry and for future research. PMID:27752339

  15. Interpreting Evolutionary Diagrams: When Topology and Process Conflict

    ERIC Educational Resources Information Center

    Catley, Kefyn M.; Novick, Laura R.; Shade, Courtney K.

    2010-01-01

    The authors argue that some diagrams in biology textbooks and the popular press presented as depicting evolutionary relationships suggest an inappropriate (anagenic) conception of evolutionary history. The goal of this research was to provide baseline data that begin to document how college students conceptualize the evolutionary relationships…

  16. Gender Inequality in Interaction--An Evolutionary Account

    ERIC Educational Resources Information Center

    Hopcroft, Rosemary L.

    2009-01-01

    In this article I argue that evolutionary theorizing can help sociologists and feminists better understand gender inequality. Evolutionary theory explains why control of the sexuality of young women is a priority across most human societies both past and present. Evolutionary psychology has extended our understanding of male violence against…

  17. A Note on Evolutionary Algorithms and Its Applications

    ERIC Educational Resources Information Center

    Bhargava, Shifali

    2013-01-01

    This paper introduces evolutionary algorithms with its applications in multi-objective optimization. Here elitist and non-elitist multiobjective evolutionary algorithms are discussed with their advantages and disadvantages. We also discuss constrained multiobjective evolutionary algorithms and their applications in various areas.

  18. Parameterized runtime analyses of evolutionary algorithms for the planar euclidean traveling salesperson problem.

    PubMed

    Sutton, Andrew M; Neumann, Frank; Nallaperuma, Samadhi

    2014-01-01

    Parameterized runtime analysis seeks to understand the influence of problem structure on algorithmic runtime. In this paper, we contribute to the theoretical understanding of evolutionary algorithms and carry out a parameterized analysis of evolutionary algorithms for the Euclidean traveling salesperson problem (Euclidean TSP). We investigate the structural properties in TSP instances that influence the optimization process of evolutionary algorithms and use this information to bound their runtime. We analyze the runtime in dependence of the number of inner points k. In the first part of the paper, we study a [Formula: see text] EA in a strictly black box setting and show that it can solve the Euclidean TSP in expected time [Formula: see text] where A is a function of the minimum angle [Formula: see text] between any three points. Based on insights provided by the analysis, we improve this upper bound by introducing a mixed mutation strategy that incorporates both 2-opt moves and permutation jumps. This strategy improves the upper bound to [Formula: see text]. In the second part of the paper, we use the information gained in the analysis to incorporate domain knowledge to design two fixed-parameter tractable (FPT) evolutionary algorithms for the planar Euclidean TSP. We first develop a [Formula: see text] EA based on an analysis by M. Theile, 2009, "Exact solutions to the traveling salesperson problem by a population-based evolutionary algorithm," Lecture notes in computer science, Vol. 5482 (pp. 145-155), that solves the TSP with k inner points in [Formula: see text] generations with probability [Formula: see text]. We then design a [Formula: see text] EA that incorporates a dynamic programming step into the fitness evaluation. We prove that a variant of this evolutionary algorithm using 2-opt mutation solves the problem after [Formula: see text] steps in expectation with a cost of [Formula: see text] for each fitness evaluation.

  19. Toward an evolutionary definition of cheating.

    PubMed

    Ghoul, Melanie; Griffin, Ashleigh S; West, Stuart A

    2014-02-01

    The term "cheating" is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term "cheat" from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.

  20. Applying evolutionary biology to address global challenges.

    PubMed

    Carroll, Scott P; Jørgensen, Peter Søgaard; Kinnison, Michael T; Bergstrom, Carl T; Denison, R Ford; Gluckman, Peter; Smith, Thomas B; Strauss, Sharon Y; Tabashnik, Bruce E

    2014-10-17

    Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

  1. The Ancient Evolutionary History of Polyomaviruses.

    PubMed

    Buck, Christopher B; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M; Tisza, Michael J; An, Ping; Katz, Joshua P; Pipas, James M; McBride, Alison A; Camus, Alvin C; McDermott, Alexa J; Dill, Jennifer A; Delwart, Eric; Ng, Terry F F; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V; Varsani, Arvind

    2016-04-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

  2. Human nature, cultural diversity and evolutionary theory.

    PubMed

    Plotkin, Henry

    2011-02-12

    Incorporating culture into an expanded theory of evolution will provide the foundation for a universal account of human diversity. Two requirements must be met. The first is to see learning as an extension of the processes of evolution. The second is to understand that there are specific components of human culture, viz. higher order knowledge structures and social constructions, which give rise to culture as invented knowledge. These components, which are products of psychological processes and mechanisms, make human culture different from the forms of shared knowledge observed in other species. One serious difficulty for such an expanded theory is that social constructions may not add to the fitness of all humans exposed to them. This may be because human culture has existed for only a relatively short time in evolutionary terms. Or it may be that, as some maintain, adaptation is a limited, even a flawed, aspect of evolutionary theory.

  3. Evolutionary biology of harvestmen (Arachnida, Opiliones).

    PubMed

    Giribet, Gonzalo; Sharma, Prashant P

    2015-01-07

    Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.

  4. The Ancient Evolutionary History of Polyomaviruses

    PubMed Central

    Buck, Christopher B.; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M.; Tisza, Michael J.; An, Ping; Katz, Joshua P.; Pipas, James M.; McBride, Alison A.; Camus, Alvin C.; McDermott, Alexa J.; Dill, Jennifer A.; Delwart, Eric; Ng, Terry F. F.; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V.; Varsani, Arvind

    2016-01-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

  5. Applying evolutionary biology to address global challenges

    PubMed Central

    Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.

    2014-01-01

    Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376

  6. Were there evolutionary advantages to premenstrual syndrome?

    PubMed Central

    Gillings, Michael R

    2014-01-01

    Premenstrual syndrome (PMS) affects up to 80% of women, often leading to significant personal, social and economic costs. When apparently maladaptive states are widespread, they sometimes confer a hidden advantage, or did so in our evolutionary past. We suggest that PMS had a selective advantage because it increased the chance that infertile pair bonds would dissolve, thus improving the reproductive outcomes of women in such partnerships. We confirm predictions arising from the hypothesis: PMS has high heritability; gene variants associated with PMS can be identified; animosity exhibited during PMS is preferentially directed at current partners; and behaviours exhibited during PMS may increase the chance of finding a new partner. Under this view, the prevalence of PMS might result from genes and behaviours that are adaptive in some societies, but are potentially less appropriate in modern cultures. Understanding this evolutionary mismatch might help depathologize PMS, and suggests solutions, including the choice to use cycle-stopping contraception. PMID:25469168

  7. Evolutionary ethics from Darwin to Moore.

    PubMed

    Allhoff, Fritz

    2003-01-01

    Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded

  8. Chromosomal polymorphism in mammals: an evolutionary perspective.

    PubMed

    Dobigny, Gauthier; Britton-Davidian, Janice; Robinson, Terence J

    2017-02-01

    Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.

  9. Mixing Times in Evolutionary Game Dynamics

    NASA Astrophysics Data System (ADS)

    Black, Andrew J.; Traulsen, Arne; Galla, Tobias

    2012-07-01

    Without mutation and migration, evolutionary dynamics ultimately leads to the extinction of all but one species. Such fixation processes are well understood and can be characterized analytically with methods from statistical physics. However, many biological arguments focus on stationary distributions in a mutation-selection equilibrium. Here, we address the mixing time required to reach stationarity in the presence of mutation. We show that mixing times in evolutionary games have the opposite behavior from fixation times when the intensity of selection increases: in coordination games with bistabilities, the fixation time decreases, but the mixing time increases. In coexistence games with metastable states, the fixation time increases, but the mixing time decreases. Our results are based on simulations and the Wentzel-Kramers-Brillouin approximation of the master equation.

  10. Product Mix Selection Using AN Evolutionary Technique

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Vasant, Pandian

    2009-08-01

    This paper proposes an evolutionary technique for the solution of a real—life industrial problem and particular for the product mix selection problem. The evolutionary technique is a combination of a genetic algorithm that preserves the feasibility of the trial solutions with penalties and some local optimization method. The goal of this paper has been achieved in finding the best near optimal solution for the profit fitness function respect to vagueness factor and level of satisfaction. The findings of the profit values will be very useful for the decision makers in the industrial engineering sector for the implementation purpose. It's possible to improve the solutions obtained in this study by employing other meta-heuristic methods such as simulated annealing, tabu Search, ant colony optimization, particle swarm optimization and artificial immune systems.

  11. Breaking records in the evolutionary race

    NASA Astrophysics Data System (ADS)

    Krug, Joachim; Jain, Kavita

    2005-12-01

    We explore some aspects of the relationship between biological evolution processes and the mathematical theory of records. For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories traced out by a population initially localized at a randomly chosen point in sequence space can be described in close analogy to record dynamics, with two complications. First, the increasing number of genotypes that become available with increasing distance from the starting point implies that fitness records are more frequent than for the standard case of independent, identically distributed random variables. Second, fitness records can be bypassed, which strongly reduces the number of genotypes that take part in an evolutionary trajectory. For exponential and Gaussian fitness distributions, this number scales with sequence length N as √{N}, and it is of order unity for distributions with a power law tail. This is in strong contrast to the number of records, which is of order N for any fitness distribution.

  12. Evolutionary algorithms and multi-agent systems

    NASA Astrophysics Data System (ADS)

    Oh, Jae C.

    2006-05-01

    This paper discusses how evolutionary algorithms are related to multi-agent systems and the possibility of military applications using the two disciplines. In particular, we present a game theoretic model for multi-agent resource distribution and allocation where agents in the environment must help each other to survive. Each agent maintains a set of variables representing actual friendship and perceived friendship. The model directly addresses problems in reputation management schemes in multi-agent systems and Peer-to-Peer distributed systems. We present algorithms based on evolutionary game process for maintaining the friendship values as well as a utility equation used in each agent's decision making. For an application problem, we adapted our formal model to the military coalition support problem in peace-keeping missions. Simulation results show that efficient resource allocation and sharing with minimum communication cost is achieved without centralized control.

  13. Evolutionary Games with Randomly Changing Payoff Matrices

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  14. Human nature, cultural diversity and evolutionary theory

    PubMed Central

    Plotkin, Henry

    2011-01-01

    Incorporating culture into an expanded theory of evolution will provide the foundation for a universal account of human diversity. Two requirements must be met. The first is to see learning as an extension of the processes of evolution. The second is to understand that there are specific components of human culture, viz. higher order knowledge structures and social constructions, which give rise to culture as invented knowledge. These components, which are products of psychological processes and mechanisms, make human culture different from the forms of shared knowledge observed in other species. One serious difficulty for such an expanded theory is that social constructions may not add to the fitness of all humans exposed to them. This may be because human culture has existed for only a relatively short time in evolutionary terms. Or it may be that, as some maintain, adaptation is a limited, even a flawed, aspect of evolutionary theory. PMID:21199849

  15. Evolutionary Algorithm for Calculating Available Transfer Capability

    NASA Astrophysics Data System (ADS)

    Šošić, Darko; Škokljev, Ivan

    2013-09-01

    The paper presents an evolutionary algorithm for calculating available transfer capability (ATC). ATC is a measure of the transfer capability remaining in the physical transmission network for further commercial activity over and above already committed uses. In this paper, MATLAB software is used to determine the ATC between any bus in deregulated power systems without violating system constraints such as thermal, voltage, and stability constraints. The algorithm is applied on IEEE 5 bus system and on IEEE 30 bus system.

  16. Conservatism of ecological niches in evolutionary time

    PubMed

    Peterson; Sober n J; Sanchez-Cordero

    1999-08-20

    Theory predicts low niche differentiation between species over evolutionary time scales, but little empirical evidence is available. Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism over several million years of independent evolution (between putative sister taxon pairs) but little conservatism at the level of families. Niche conservatism over such time scales indicates that speciation takes place in geographic, not ecological, dimensions and that ecological differences evolve later.

  17. A Simple General Model of Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Thurner, Stefan

    Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense

  18. High evolutionary potential of marine zooplankton

    PubMed Central

    Peijnenburg, Katja T C A; Goetze, Erica

    2013-01-01

    Abstract Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean. Recent attention has focused on the ecological responses of open ocean zooplankton to current global change, including range shifts and changing phenology. Here, we argue that marine zooplankton also are well poised for evolutionary responses to global change. PMID:24567838

  19. Evolutionary design of corrugated horn antennas

    NASA Technical Reports Server (NTRS)

    Hoorfar, F.; Manshadi, V.; Jamnejad, A.

    2002-01-01

    An evolutionary progranirnitzg (EP) algorithm is used to optimize pattern of a corrugated circularhorn subject to various constraints on return loss and antenna beamwidth and pattern circularity and low crosspolarization. The EP algorithm uses a Gaussian mutation operator. Examples on design synthesis of a 45 section corrugated horn, with a total of 90 optimization parameters, are presented. The results show excellent and efficient optimization of the desired horn parameters.

  20. Breaking evolutionary constraint with a tradeoff ratchet

    PubMed Central

    de Vos, Marjon G. J.; Dawid, Alexandre; Sunderlikova, Vanda; Tans, Sander J.

    2015-01-01

    Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype–environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor–operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that cross-environmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance. PMID:26567153

  1. Evolutionary transitions during RNA virus experimental evolution.

    PubMed

    Elena, Santiago F

    2016-08-19

    In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'.

  2. Endosymbiosis and its implications for evolutionary theory

    PubMed Central

    O’Malley, Maureen A.

    2015-01-01

    Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics “follows” genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation. PMID:25883268

  3. Investigating intertemporal choice through experimental evolutionary robotics.

    PubMed

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

    2015-06-01

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

  4. Evolutionary quantitative genetics of nonlinear developmental systems.

    PubMed

    Morrissey, Michael B

    2015-08-01

    In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium-term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time-steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances.

  5. Cryptic Genetic Variation in Evolutionary Developmental Genetics.

    PubMed

    Paaby, Annalise B; Gibson, Greg

    2016-06-13

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

  6. The evolutionary ecology of C4 plants.

    PubMed

    Christin, Pascal-Antoine; Osborne, Colin P

    2014-12-01

    C4 photosynthesis is a physiological syndrome resulting from multiple anatomical and biochemical components, which function together to increase the CO2 concentration around Rubisco and reduce photorespiration. It evolved independently multiple times and C4 plants now dominate many biomes, especially in the tropics and subtropics. The C4 syndrome comes in many flavours, with numerous phenotypic realizations of C4 physiology and diverse ecological strategies. In this work, we analyse the events that happened in a C3 context and enabled C4 physiology in the descendants, those that generated the C4 physiology, and those that happened in a C4 background and opened novel ecological niches. Throughout the manuscript, we evaluate the biochemical and physiological evidence in a phylogenetic context, which demonstrates the importance of contingency in evolutionary trajectories and shows how these constrained the realized phenotype. We then discuss the physiological innovations that allowed C4 plants to escape these constraints for two important dimensions of the ecological niche--growth rates and distribution along climatic gradients. This review shows that a comprehensive understanding of C4 plant ecology can be achieved by accounting for evolutionary processes spread over millions of years, including the ancestral condition, functional convergence via independent evolutionary trajectories, and physiological diversification.

  7. The evolutionary ecology of the Lygaeidae

    PubMed Central

    Burdfield-Steel, Emily R; Shuker, David M

    2014-01-01

    The Lygaeidae (sensu lato) are a highly successful family of true bugs found worldwide, yet many aspects of their ecology and evolution remain obscure or unknown. While a few species have attracted considerable attention as model species for the study of insect physiology, it is only relatively recently that biologists have begun to explore aspects of their behavior, life history evolution, and patterns of intra- and interspecific ecological interactions across more species. As a result though, a range of new phenotypes and opportunities for addressing current questions in evolutionary ecology has been uncovered. For example, researchers have revealed hitherto unexpectedly rich patterns of bacterial symbiosis, begun to explore the evolutionary function of the family's complex genitalia, and also found evidence of parthenogenesis. Here we review our current understanding of the biology and ecology of the group as a whole, focusing on several of the best-studied characteristics of the group, including aposematism (i.e., the evolution of warning coloration), chemical communication, sexual selection (especially, postcopulatory sexual selection), sexual conflict, and patterns of host-endosymbiont coevolution. Importantly, many of these aspects of lygaeid biology are likely to interact, offering new avenues for research, for instance into how the evolution of aposematism influences sexual selection. With the growing availability of genomic tools for previously “non-model” organisms, combined with the relative ease of keeping many of the polyphagous species in the laboratory, we argue that these bugs offer many opportunities for behavioral and evolutionary ecologists. PMID:25360267

  8. Evolutionary hotspots in the Mojave Desert

    USGS Publications Warehouse

    Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

    2013-01-01

    Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  9. Evolutionary games on multilayer networks: a colloquium

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Wang, Lin; Szolnoki, Attila; Perc, Matjaž

    2015-05-01

    Networks form the backbone of many complex systems, ranging from the Internet to human societies. Accordingly, not only is the range of our interactions limited and thus best described and modeled by networks, it is also a fact that the networks that are an integral part of such models are often interdependent or even interconnected. Networks of networks or multilayer networks are therefore a more apt description of social systems. This colloquium is devoted to evolutionary games on multilayer networks, and in particular to the evolution of cooperation as one of the main pillars of modern human societies. We first give an overview of the most significant conceptual differences between single-layer and multilayer networks, and we provide basic definitions and a classification of the most commonly used terms. Subsequently, we review fascinating and counterintuitive evolutionary outcomes that emerge due to different types of interdependencies between otherwise independent populations. The focus is on coupling through the utilities of players, through the flow of information, as well as through the popularity of different strategies on different network layers. The colloquium highlights the importance of pattern formation and collective behavior for the promotion of cooperation under adverse conditions, as well as the synergies between network science and evolutionary game theory.

  10. Promoter Motifs in NCLDVs: An Evolutionary Perspective.

    PubMed

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia Dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen Dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-20

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses' evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters' evolutionary scenarios and propose the term "MEGA-box" to designate an ancestor promoter motif ('TATATAAAATTGA') that could be evolved gradually by nucleotides' gain and loss and point mutations.

  11. Evolutionary game theory: cells as players.

    PubMed

    Hummert, Sabine; Bohl, Katrin; Basanta, David; Deutsch, Andreas; Werner, Sarah; Theissen, Günter; Schroeter, Anja; Schuster, Stefan

    2014-12-01

    In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.

  12. On the evolutionary origins of equity

    PubMed Central

    2017-01-01

    Equity, defined as reward according to contribution, is considered a central aspect of human fairness in both philosophical debates and scientific research. Despite large amounts of research on the evolutionary origins of fairness, the evolutionary rationale behind equity is still unknown. Here, we investigate how equity can be understood in the context of the cooperative environment in which humans evolved. We model a population of individuals who cooperate to produce and divide a resource, and choose their cooperative partners based on how they are willing to divide the resource. Agent-based simulations, an analytical model, and extended simulations using neural networks provide converging evidence that equity is the best evolutionary strategy in such an environment: individuals maximize their fitness by dividing benefits in proportion to their own and their partners’ relative contribution. The need to be chosen as a cooperative partner thus creates a selection pressure strong enough to explain the evolution of preferences for equity. We discuss the limitations of our model, the discrepancies between its predictions and empirical data, and how interindividual and intercultural variability fit within this framework. PMID:28323830

  13. Endosymbiosis and its implications for evolutionary theory.

    PubMed

    O'Malley, Maureen A

    2015-08-18

    Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.

  14. On the evolutionary origins of equity.

    PubMed

    Debove, Stéphane; Baumard, Nicolas; André, Jean-Baptiste

    2017-01-01

    Equity, defined as reward according to contribution, is considered a central aspect of human fairness in both philosophical debates and scientific research. Despite large amounts of research on the evolutionary origins of fairness, the evolutionary rationale behind equity is still unknown. Here, we investigate how equity can be understood in the context of the cooperative environment in which humans evolved. We model a population of individuals who cooperate to produce and divide a resource, and choose their cooperative partners based on how they are willing to divide the resource. Agent-based simulations, an analytical model, and extended simulations using neural networks provide converging evidence that equity is the best evolutionary strategy in such an environment: individuals maximize their fitness by dividing benefits in proportion to their own and their partners' relative contribution. The need to be chosen as a cooperative partner thus creates a selection pressure strong enough to explain the evolution of preferences for equity. We discuss the limitations of our model, the discrepancies between its predictions and empirical data, and how interindividual and intercultural variability fit within this framework.

  15. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  16. Ecological interactions drive evolutionary loss of traits.

    PubMed

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

    2012-10-01

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

  17. Convex recoloring as an evolutionary marker.

    PubMed

    Frenkel, Zeev; Kiat, Yosef; Izhaki, Ido; Snir, Sagi

    2017-02-01

    With the availability of enormous quantities of genetic data it has become common to construct very accurate trees describing the evolutionary history of the species under study, as well as every single gene of these species. These trees allow us to examine the evolutionary compliance of given markers (characters). A marker compliant with the history of the species investigated, has undergone mutations along the species tree branches, such that every subtree of that tree exhibits a different state. Convex recoloring (CR) uses combinatorial representation to measure the adequacy of a taxonomic classifier to a given tree. Despite its biological origins, research on CR has been almost exclusively dedicated to mathematical properties of the problem, or variants of it with little, if any, relationship to taxonomy. In this work we return to the origins of CR. We put CR in a statistical framework and introduce and learn the notion of the statistical significance of a character. We apply this measure to two data sets - Passerine birds and prokaryotes, and four examples. These examples demonstrate various applications of CR, from evolutionary relatedness, through lateral evolution, to supertree construction. The above study was done with a new software that we provide, containing algorithmic improvement with a graphical output of a (optimally) recolored tree.

  18. Evolutionary tracks of massive stars during formation

    NASA Astrophysics Data System (ADS)

    Smith, Michael D.

    2014-02-01

    A model for massive stars is constructed by piecing together evolutionary algorithms for the protostellar structure, the environment, the inflow and the radiation feedback. We investigate specified accretion histories of constant, decelerating and accelerating forms and consider both hot and cold accretion, identified with spherical free-fall and disc accretion, respectively. Diagnostic tools for the interpretation of the phases of massive star formation and testing the evolutionary models are then developed. Evolutionary tracks able to fit Herschel Space Telescope data require the generated stars to be three to four times less massive than in previous interpretations, thus being consistent with clump star formation efficiencies of 10-15 per cent. However, for these cold Herschel clumps, the bolometric temperature is not a good diagnostic to differentiate between accretion models. We also find that neither spherical nor disc accretion can explain the high radio luminosities of many protostars. Nevertheless, we discover a solution in which the extreme ultraviolet flux needed to explain the radio emission is produced if the accretion flow is via free-fall on to hotspots covering less than 10 per cent of the surface area. Moreover, the protostar must be compact, and so has formed through cold accretion. We show that these conclusions are independent of the imposed accretion history. This suggests that massive stars form via gas accretion through discs which, in the phase before the star bloats, download their mass via magnetic flux tubes on to the protostar.

  19. An evolutionary ecology of individual differences

    PubMed Central

    Dall, Sasha R. X.; Bell, Alison M.; Bolnick, Daniel I.; Ratnieks, Francis L. W.

    2014-01-01

    Individuals often differ in what they do. This has been recognised since antiquity. Nevertheless, the ecological and evolutionary significance of such variation is attracting widespread interest, which is burgeoning to an extent that is fragmenting the literature. As a first attempt at synthesis, we focus on individual differences in behaviour within populations that exceed the day-to-day variation in individual behaviour (i.e. behavioural specialisation). Indeed, the factors promoting ecologically relevant behavioural specialisation within natural populations are likely to have far-reaching ecological and evolutionary consequences. We discuss such individual differences from three distinct perspectives: individual niche specialisations, the division of labour within insect societies and animal personality variation. In the process, while recognising that each area has its own unique motivations, we identify a number of opportunities for productive ‘crossfertilisation’ among the (largely independent) bodies of work. We conclude that a complete understanding of evolutionarily and ecologically relevant individual differences must specify how ecological interactions impact the basic biological process (e.g. Darwinian selection, development and information processing) that underpin the organismal features determining behavioural specialisations. Moreover, there is likely to be covariation amongst behavioural specialisations. Thus, we sketch the key elements of a general framework for studying the evolutionary ecology of individual differences. PMID:22897772

  20. An extended synthesis for evolutionary biology.

    PubMed

    Pigliucci, Massimo

    2009-06-01

    Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo-devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that--like its predecessor--will probably take decades to complete.

  1. Evolutionary perspectives into placental biology and disease.

    PubMed

    Chuong, Edward B; Hannibal, Roberta L; Green, Sherril L; Baker, Julie C

    2013-12-01

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

  2. Evolutionary problems in centrosome and centriole biology.

    PubMed

    Ross, L; Normark, B B

    2015-05-01

    Centrosomes have been an enigma to evolutionary biologists. Either they have been the subject of ill-founded speculation or they have been ignored. Here, we highlight evolutionary paradoxes and problems of centrosome and centriole evolution and seek to understand them in the light of recent advances in centrosome biology. Most evolutionary accounts of centrosome evolution have been based on the hypothesis that centrosomes are replicators, independent of the nucleus and cytoplasm. It is now clear, however, that this hypothesis is not tenable. Instead, centrosomes are formed de novo each cell division, with the presence of an old centrosome regulating, but not essential for, the assembly of a new one. Centrosomes are the microtubule-organizing centres of cells. They can potentially affect sensory and motor characters (as the basal body of cilia), as well as the movements of chromosomes during cell division. This latter role does not seem essential, however, except in male meiosis, and the reasons for this remain unclear. Although the centrosome is absent in some taxa, when it is present, its structure is extraordinarily conserved: in most taxa across eukaryotes, it does not appear to evolve at all. And yet a few insect groups display spectacular hypertrophy of the centrioles. We discuss how this might relate to the unusual reproductive system found in these insects. Finally, we discuss why the fate of centrosomes in sperm and early embryos might differ between different groups of animals.

  3. Evolutionary Conserved Positions Define Protein Conformational Diversity

    PubMed Central

    Saldaño, Tadeo E.; Monzon, Alexander M.; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-01-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  4. Evolutionary games on cycles with strong selection.

    PubMed

    Altrock, P M; Traulsen, A; Nowak, M A

    2017-02-01

    Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. The intuition is that fixation of a beneficial mutant happens fast in a dominance game, that fixation takes very long in a coexistence game, and that strong selection eliminates demographic noise. Here we show that these intuitions can be misleading in structured populations. We analyze mean fixation times on the cycle graph under strong frequency-dependent selection for two different microscopic evolutionary update rules (death-birth and birth-death). We establish exact analytical results for fixation times under strong selection and show that there are coexistence games in which fixation occurs in time polynomial in population size. Depending on the underlying game, we observe inherence of demographic noise even under strong selection if the process is driven by random death before selection for birth of an offspring (death-birth update). In contrast, if selection for an offspring occurs before random removal (birth-death update), then strong selection can remove demographic noise almost entirely.

  5. Evolutionary Dynamics and Diversity in Microbial Populations

    NASA Astrophysics Data System (ADS)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  6. Virulence in malaria: an evolutionary viewpoint.

    PubMed Central

    Mackinnon, Margaret J; Read, Andrew F

    2004-01-01

    Malaria parasites cause much morbidity and mortality to their human hosts. From our evolutionary perspective, this is because virulence is positively associated with parasite transmission rate. Natural selection therefore drives virulence upwards, but only to the point where the cost to transmission caused by host death begins to outweigh the transmission benefits. In this review, we summarize data from the laboratory rodent malaria model, Plasmodium chabaudi, and field data on the human malaria parasite, P. falciparum, in relation to this virulence trade-off hypothesis. The data from both species show strong positive correlations between asexual multiplication, transmission rate, infection length, morbidity and mortality, and therefore support the underlying assumptions of the hypothesis. Moreover, the P. falciparum data show that expected total lifetime transmission of the parasite is maximized in young children in whom the fitness cost of host mortality balances the fitness benefits of higher transmission rates and slower clearance rates, thus exhibiting the hypothesized virulence trade-off. This evolutionary explanation of virulence appears to accord well with the clinical and molecular explanations of pathogenesis that involve cytoadherence, red cell invasion and immune evasion, although direct evidence of the fitness advantages of these mechanisms is scarce. One implication of this evolutionary view of virulence is that parasite populations are expected to evolve new levels of virulence in response to medical interventions such as vaccines and drugs. PMID:15306410

  7. Bell-Curve Based Evolutionary Optimization Algorithm

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Laba, K.; Kincaid, R.

    1998-01-01

    The paper presents an optimization algorithm that falls in the category of genetic, or evolutionary algorithms. While the bit exchange is the basis of most of the Genetic Algorithms (GA) in research and applications in America, some alternatives, also in the category of evolutionary algorithms, but use a direct, geometrical approach have gained popularity in Europe and Asia. The Bell-Curve Based Evolutionary Algorithm (BCB) is in this alternative category and is distinguished by the use of a combination of n-dimensional geometry and the normal distribution, the bell-curve, in the generation of the offspring. The tool for creating a child is a geometrical construct comprising a line connecting two parents and a weighted point on that line. The point that defines the child deviates from the weighted point in two directions: parallel and orthogonal to the connecting line, the deviation in each direction obeying a probabilistic distribution. Tests showed satisfactory performance of BCB. The principal advantage of BCB is its controllability via the normal distribution parameters and the geometrical construct variables.

  8. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    PubMed Central

    Paaby, Annalise B.; Gibson, Greg

    2016-01-01

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits. PMID:27304973

  9. Evolutionary Dynamics of Abundant Stop Codon Readthrough

    PubMed Central

    Jungreis, Irwin; Kellis, Manolis

    2016-01-01

    Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede. PMID:27604222

  10. Evolutionary games on cycles with strong selection

    NASA Astrophysics Data System (ADS)

    Altrock, P. M.; Traulsen, A.; Nowak, M. A.

    2017-02-01

    Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. The intuition is that fixation of a beneficial mutant happens fast in a dominance game, that fixation takes very long in a coexistence game, and that strong selection eliminates demographic noise. Here we show that these intuitions can be misleading in structured populations. We analyze mean fixation times on the cycle graph under strong frequency-dependent selection for two different microscopic evolutionary update rules (death-birth and birth-death). We establish exact analytical results for fixation times under strong selection and show that there are coexistence games in which fixation occurs in time polynomial in population size. Depending on the underlying game, we observe inherence of demographic noise even under strong selection if the process is driven by random death before selection for birth of an offspring (death-birth update). In contrast, if selection for an offspring occurs before random removal (birth-death update), then strong selection can remove demographic noise almost entirely.

  11. The evolutionary language game: an orthogonal approach.

    PubMed

    Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

    2005-08-21

    Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning.

  12. Evolutionary plant physiology: Charles Darwin's forgotten synthesis

    NASA Astrophysics Data System (ADS)

    Kutschera, Ulrich; Niklas, Karl J.

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  13. Automated Hardware Design via Evolutionary Search

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Colombano, Silvano P.

    2000-01-01

    The goal of this research is to investigate the application of evolutionary search to the process of automated engineering design. Evolutionary search techniques involve the simulation of Darwinian mechanisms by computer algorithms. In recent years, such techniques have attracted much attention because they are able to tackle a wide variety of difficult problems and frequently produce acceptable solutions. The results obtained are usually functional, often surprising, and typically "messy" because the algorithms are told to concentrate on the overriding objective and not elegance or simplicity. advantages. First, faster design cycles translate into time and, hence, cost savings. Second, automated design techniques can be made to scale well and hence better deal with increasing amounts of design complexity. Third, design quality can increase because design properties can be specified a priori. For example, size and weight specifications of a device, smaller and lighter than the best known design, might be optimized by the automated design technique. The domain of electronic circuit design is an advantageous platform in which to study automated design techniques because it is a rich design space that is well understood, permitting human-created designs to be compared to machine- generated designs. developed for circuit design was to automatically produce high-level integrated electronic circuit designs whose properties permit physical implementation in silicon. This process entailed designing an effective evolutionary algorithm and solving a difficult multiobjective optimization problem. FY 99 saw many accomplishments in this effort.

  14. Evolutionary Cost-Sensitive Extreme Learning Machine.

    PubMed

    Zhang, Lei; Zhang, David

    2016-10-11

    Conventional extreme learning machines (ELMs) solve a Moore-Penrose generalized inverse of hidden layer activated matrix and analytically determine the output weights to achieve generalized performance, by assuming the same loss from different types of misclassification. The assumption may not hold in cost-sensitive recognition tasks, such as face recognition-based access control system, where misclassifying a stranger as a family member may result in more serious disaster than misclassifying a family member as a stranger. Though recent cost-sensitive learning can reduce the total loss with a given cost matrix that quantifies how severe one type of mistake against another, in many realistic cases, the cost matrix is unknown to users. Motivated by these concerns, this paper proposes an evolutionary cost-sensitive ELM, with the following merits: 1) to the best of our knowledge, it is the first proposal of ELM in evolutionary cost-sensitive classification scenario; 2) it well addresses the open issue of how to define the cost matrix in cost-sensitive learning tasks; and 3) an evolutionary backtracking search algorithm is induced for adaptive cost matrix optimization. Experiments in a variety of cost-sensitive tasks well demonstrate the effectiveness of the proposed approaches, with about 5%-10% improvements.

  15. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    PubMed Central

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  16. An evolutionary behaviorist perspective on orgasm

    PubMed Central

    Fleischman, Diana S.

    2016-01-01

    Evolutionary explanations for sexual behavior and orgasm most often posit facilitating reproduction as the primary function (i.e. greater rate of fertilization). Other reproductive benefits of sexual pleasure and orgasm such as improved bonding of parents have also been discussed but not thoroughly. Although sex is known to be highly reinforcing, behaviorist principles are rarely invoked alongside evolutionary psychology in order to account for human sexual and social behavior. In this paper, I will argue that intense sexual pleasure, especially orgasm, can be understood as a primary reinforcer shaped by evolution to reinforce behavior that facilitates reproductive success (i.e. conception through copulation). Next, I will describe an evolutionary account of social shaping. In particular, I will focus on how humans evolved to use orgasm and sexual arousal to shape the social behavior and emotional states of others through both classical and operant conditioning and through both reproductive and non-reproductive forms of sexual behavior. Finally, I will describe how orgasm is a signal of sensitivity to reinforcement that is itself reinforcing. PMID:27799083

  17. Complex Cooperative Networks from Evolutionary Preferential Attachment

    PubMed Central

    Poncela, Julia; Gómez-Gardeñes, Jesús; Floría, Luis M.; Sánchez, Angel; Moreno, Yamir

    2008-01-01

    In spite of its relevance to the origin of complex networks, the interplay between form and function and its role during network formation remains largely unexplored. While recent studies introduce dynamics by considering rewiring processes of a pre-existent network, we study network growth and formation by proposing an evolutionary preferential attachment model, its main feature being that the capacity of a node to attract new links depends on a dynamical variable governed in turn by the node interactions. As a specific example, we focus on the problem of the emergence of cooperation by analyzing the formation of a social network with interactions given by the Prisoner's Dilemma. The resulting networks show many features of real systems, such as scale-free degree distributions, cooperative behavior and hierarchical clustering. Interestingly, results such as the cooperators being located mostly on nodes of intermediate degree are very different from the observations of cooperative behavior on static networks. The evolutionary preferential attachment mechanism points to an evolutionary origin of scale-free networks and may help understand similar feedback problems in the dynamics of complex networks by appropriately choosing the game describing the interaction of nodes. PMID:18560601

  18. On the programmed/non-programmed aging controversy.

    PubMed

    Goldsmith, T C

    2012-07-01

    The programmed vs. non-programmed aging controversy has now existed in some form for at least 150 years. For much of the XX century, it was almost universally believed that evolution theory prohibited programmed (adaptive) aging in mammals and there was little direct experimental or observational evidence favoring it. More recently, multiple new evolutionary mechanics concepts that support programmed aging and steadily increasing direct evidence favoring it overwhelmingly support the existence of programmed aging in humans and other organisms. This issue is important because the different theories suggest very different mechanisms for the aging process that in turn suggest very different paths toward treating and preventing age-related diseases.

  19. Incorporating evolutionary principles into environmental management and policy

    PubMed Central

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J; Sih, Andrew

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary changes. Such evolution-based management has potential to be a highly efficient and consistent way to create greater ecological resilience to widespread, rapid, and multifaceted environmental change. PMID:25567975

  20. Eco-evolutionary dynamics in an urbanizing planet.

    PubMed

    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.

  1. Toward an integration of evolutionary biology and ecosystem science.

    PubMed

    Matthews, Blake; Narwani, Anita; Hausch, Stephen; Nonaka, Etsuko; Peter, Hannes; Yamamichi, Masato; Sullam, Karen E; Bird, Kali C; Thomas, Mridul K; Hanley, Torrance C; Turner, Caroline B

    2011-07-01

    At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.

  2. The transition from evolutionary stability to branching: A catastrophic evolutionary shift

    PubMed Central

    Dercole, Fabio; Della Rossa, Fabio; Landi, Pietro

    2016-01-01

    Evolutionary branching—resident-mutant coexistence under disruptive selection—is one of the main contributions of Adaptive Dynamics (AD), the mathematical framework introduced by S.A.H. Geritz, J.A.J. Metz, and coauthors to model the long-term evolution of coevolving multi-species communities. It has been shown to be the basic mechanism for sympatric and parapatric speciation, despite the essential asexual nature of AD. After 20 years from its introduction, we unfold the transition from evolutionary stability (ESS) to branching, along with gradual change in environmental, control, or exploitation parameters. The transition is a catastrophic evolutionary shift, the branching dynamics driving the system to a nonlocal evolutionary attractor that is viable before the transition, but unreachable from the ESS. Weak evolutionary stability hence qualifies as an early-warning signal for branching and a testable measure of the community’s resilience against biodiversity. We clarify a controversial theoretical question about the smoothness of the mutant invasion fitness at incipient branching. While a supposed nonsmoothness at third order long prevented the analysis of the ESS-branching transition, we argue that smoothness is generally expected and derive a local canonical model in terms of the geometry of the invasion fitness before branching. Any generic AD model undergoing the transition qualitatively behaves like our canonical model. PMID:27215588

  3. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

    PubMed

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-03-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

  4. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

    PubMed Central

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-01-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries. PMID:26430388

  5. Scalable Evolutionary Computation for Efficient Information Extraction from Remote Sensed Imagery

    NASA Astrophysics Data System (ADS)

    Almutairi, L. M.; Shetty, S.; Momm, H. G.

    2014-11-01

    Evolutionary computation, in the form of genetic programming, is used to aid information extraction process from high-resolution satellite imagery in a semi-automatic fashion. Distributing and parallelizing the task of evaluating all candidate solutions during the evolutionary process could significantly reduce the inherent computational cost of evolving solutions that are composed of multichannel large images. In this study, we present the design and implementation of a system that leverages cloud-computing technology to expedite supervised solution development in a centralized evolutionary framework. The system uses the MapReduce programming model to implement a distributed version of the existing framework in a cloud-computing platform. The proposed system has two major subsystems; (i) data preparation: the generation of random spectral indices; and (ii) distributed processing: the distributed implementation of genetic programming, which is used to spectrally distinguish the features of interest from the remaining image background in the cloud computing environment in order to improve scalability. The proposed system reduces response time by leveraging the vast computational and storage resources in a cloud computing environment. The results demonstrate that distributing the candidate solutions reduces the execution time by 91.58%. These findings indicate that such technology could be applied to more complex problems that involve a larger population size and number of generations.

  6. Evolutionary autonomous agents and the nature of apraxia

    PubMed Central

    Borrett, Donald S; Jin, Frank; Kwan, Hon C

    2005-01-01

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

  7. Evolutionary psychology and evolutionary developmental psychology: understanding the evolution of human behavior and development.

    PubMed

    Hernández Blasi, Carlos; Causey, Kayla

    2010-02-01

    This is an introduction to this special issue on evolutionary psychology (EP) and evolutionary developmental psychology (EDP). We suggest here that, contrary to some common assumptions, mainstream psychology continues to be essentially non Darwinian and that EP and EDP are new approaches that can potentially help us to change this situation. We then present the organization of the special issue (composed of six papers). We conclude that evolution is certainly not the final consideration in psychology, but emphasize its importance as the basis upon which all modern behaviors and development are built.

  8. Making evolutionary biology a basic science for medicine

    PubMed Central

    Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

    2010-01-01

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

  9. Evolutionary Computing Methods for Spectral Retrieval

    NASA Technical Reports Server (NTRS)

    Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

    2009-01-01

    A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

  10. The evolutionary origin and diversification of feathers.

    PubMed

    Prum, Richard O; Brush, Alan H

    2002-09-01

    Progress on the evolutionary origin and diversification of feathers has been hampered by conceptual problems and by the lack of plesiomorphic feather fossils. Recently, both of these limitations have been overcome by the proposal of the developmental theory of the origin of feathers, and the discovery of primitive feather fossils on nonavian theropod dinosaurs. The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critique and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.

  11. Evolutionary genomics of fast evolving tunicates.

    PubMed

    Berná, Luisa; Alvarez-Valin, Fernando

    2014-07-08

    Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed.

  12. Evolutionary Genomics of Fast Evolving Tunicates

    PubMed Central

    Berná, Luisa; Alvarez-Valin, Fernando

    2014-01-01

    Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed. PMID:25008364

  13. Extrapolating Weak Selection in Evolutionary Games

    PubMed Central

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

    2013-01-01

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

  14. Life Beyond Earth and the Evolutionary Synthesis

    NASA Astrophysics Data System (ADS)

    Vakoch, Douglas A.

    For many astronomers, the progressive development of life has been seen as a natural occurrence given proper environmental conditions on a planet: even though such beings would not be identical to humans, there would be significant parallels. A striking contrast is seen in writings of nonphysical scientists, who have held more widely differing views. But within this diversity, reasons for differences become more apparent when we see how views about extraterrestrials can be related to the differential emphasis placed on modern evolutionary theory by scientists of various disciplines. One clue to understanding the differences between the biologists, paleontologists, and anthropologists who speculated on extraterrestrials is suggested by noting who wrote on the subject. Given the relatively small number of commentators on the topic, it seems more than coincidental that four of the major contributors to the evolutionary synthesis in the 1930s and 1940s are among them. Upon closer examination it is evident that the exobiological arguments of Theodosius Dobzhansky and George Gaylord Simpson and, less directly, of H. J. Muller and Ernst Mayr are all related to their earlier work in formulating synthetic evolution. By examining the variety of views held by nonphysical scientists, we can see that there were significant disagreements between them about evolution into the 1960s. By the mid-1980s, many believed that "higher" life, particularly intelligent life, probably occurs quite infrequently in the universe; nevertheless, some held out the possibility that convergence of intelligence could occur across worlds. Regardless of the final conclusions these scientists reached about the likely prevalence of extraterrestrial intelligence, the use of evolutionary arguments to support their positions became increasingly common.

  15. Using diagnostic radiology in human evolutionary studies

    PubMed Central

    SPOOR, FRED; JEFFERY, NATHAN; ZONNEVELD, FRANS

    2000-01-01

    This paper reviews the application of medical imaging and associated computer graphics techniques to the study of human evolutionary history, with an emphasis on basic concepts and on the advantages and limitations of each method. Following a short discussion of plain film radiography and pluridirectional tomography, the principles of computed tomography (CT) and magnetic resonance imaging (MRI) and their role in the investigation of extant and fossil morphology are considered in more detail. The second half of the paper deals with techniques of 3-dimensional visualisation based on CT and MRI and with quantitative analysis of digital images. PMID:10999271

  16. On the evolutionary constraint surface of hydra

    NASA Technical Reports Server (NTRS)

    Slobodkin, L. B.; Dunn, K.

    1983-01-01

    Food consumption, body size, and budding rate were measured simultaneously in isolated individual hydra of six strains. For each individual hydra the three measurements define a point in the three dimensional space with axes: food consumption, budding rate, and body size. These points lie on a single surface, regardless of species. Floating rate and incidence of sexuality map onto this surface. It is suggested that this surface is an example of a general class of evolutionary constraint surfaces derived from the conjunction of evolutinary theory and the theory of ecological resource budgets. These constraint surfaces correspond to microevolutionary domains.

  17. Inferring Evolutionary Scenarios for Protein Domain Compositions

    NASA Astrophysics Data System (ADS)

    Wiedenhoeft, John; Krause, Roland; Eulenstein, Oliver

    Essential cellular processes are controlled by functional interactions of protein domains, which can be inferred from their evolutionary histories. Methods to reconstruct these histories are challenged by the complexity of reconstructing macroevolutionary events. In this work we model these events using a novel network-like structure that represents the evolution of domain combinations, called plexus. We describe an algorithm to find a plexus that represents the evolution of a given collection of domain histories as phylogenetic trees with the minimum number of macroevolutionary events, and demonstrate its effectiveness in practice.

  18. Evolutionary Minority Game with searching behavior

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Sun, Yuxin; Feng, Xu; Xiong, Xiong

    2015-10-01

    In this paper, we determine the impact of searching behavior on the evolutionary minority game (EMG). We introduce searching behavior in two ways: optimal neighbor searching and global searching. Our study investigates the distribution equilibriums of probabilities that agents follow a given strategy and on system performance of the game. The results indicate that the distribution equilibriums of the probabilities are different with searching behavior, as opposed to without searching behavior. The system performance becomes worse after adding the searching behavior. Additionally, we test other variables in a standard EMG with and without searching behavior.

  19. Evolutionary models of in-group favoritism

    PubMed Central

    Fu, Feng

    2015-01-01

    In-group favoritism is the tendency for individuals to cooperate with in-group members more strongly than with out-group members. Similar concepts have been described across different domains, including in-group bias, tag-based cooperation, parochial altruism, and ethnocentrism. Both humans and other animals show this behavior. Here, we review evolutionary mechanisms for explaining this phenomenon by covering recently developed mathematical models. In fact, in-group favoritism is not easily realized on its own in theory, although it can evolve under some conditions. We also discuss the implications of these modeling results in future empirical and theoretical research. PMID:25926978

  20. Informations in Models of Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Rivoire, Olivier

    2016-03-01

    Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.

  1. Quantumness To Survive In An Evolutionary Environment

    SciTech Connect

    Baladron, Carlos

    2011-03-28

    An outlined subquantum theory that might be considered a possible extension of Bohmian mechanics is further discussed. In this theory a fundamental physical system is modelled as a particle endowed with a methodological probabilistic classical Turing machine, which characterizes systems as data processing devices, making of information a crucial physical concept in the determination of the system dynamics. The main idea of this theory resides in proposing a Darwinian evolutionary mechanism - therefore based on natural selection - as the central element that would determine the emergence of quantum mechanics from an evolutionarily stable strategy (ESS) whose essentials are supposedly captured in three regulating principles. The Darwinian character of these regulating principles is explored.

  2. Colour spaces in ecology and evolutionary biology.

    PubMed

    Renoult, Julien P; Kelber, Almut; Schaefer, H Martin

    2017-02-01

    The recognition that animals sense the world in a different way than we do has unlocked important lines of research in ecology and evolutionary biology. In practice, the subjective study of natural stimuli has been permitted by perceptual spaces, which are graphical models of how stimuli are perceived by a given animal. Because colour vision is arguably the best-known sensory modality in most animals, a diversity of colour spaces are now available to visual ecologists, ranging from generalist and basic models allowing rough but robust predictions on colour perception, to species-specific, more complex models giving accurate but context-dependent predictions. Selecting among these models is most often influenced by historical contingencies that have associated models to specific questions and organisms; however, these associations are not always optimal. The aim of this review is to provide visual ecologists with a critical perspective on how models of colour space are built, how well they perform and where their main limitations are with regard to their most frequent uses in ecology and evolutionary biology. We propose a classification of models based on their complexity, defined as whether and how they model the mechanisms of chromatic adaptation and receptor opponency, the nonlinear association between the stimulus and its perception, and whether or not models have been fitted to experimental data. Then, we review the effect of modelling these mechanisms on predictions of colour detection and discrimination, colour conspicuousness, colour diversity and diversification, and for comparing the perception of colour traits between distinct perceivers. While a few rules emerge (e.g. opponent log-linear models should be preferred when analysing very distinct colours), in general model parameters still have poorly known effects. Colour spaces have nonetheless permitted significant advances in ecology and evolutionary biology, and more progress is expected if ecologists

  3. Genomic basis of evolutionary change: evolving immunity

    PubMed Central

    Wertheim, Bregje

    2015-01-01

    Complex traits are manifestations of intricate gene interaction networks. Evolution of complex traits revolves around the genetic variation in such networks. Genomics has increased our ability to investigate the complex gene interaction networks, and characterize the extent of genetic variation in these networks. Immunity is a complex trait, for which the ecological drivers and molecular networks are fairly well understood in Drosophila. By characterizing the natural variation in immunity, and mapping how the genome changes during the evolution of immunity in Drosophila, we can integrate our knowledge on the complex genetic architecture of traits and the molecular basis of evolutionary processes. PMID:26150830

  4. Canonical transformations and Hamiltonian evolutionary systems

    SciTech Connect

    Al-Ashhab, Samer

    2012-06-15

    In many Lagrangian field theories, one has a Poisson bracket defined on the space of local functionals. We find necessary and sufficient conditions for a transformation on the space of local functionals to be canonical in three different cases. These three cases depend on the specific dimensions of the vector bundle of the theory and the associated Hamiltonian differential operator. We also show how a canonical transformation transforms a Hamiltonian evolutionary system and its conservation laws. Finally, we illustrate these ideas with three examples.

  5. Darwinism and the Expansion of Evolutionary Theory

    NASA Astrophysics Data System (ADS)

    Gould, Stephen Jay

    1982-04-01

    The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level ``individuals'' as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, as strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level.

  6. Evolutionary conservation of alternative splicing in chicken

    PubMed Central

    Katyal, S.; Gao, Z.; Liu, R.-Z.; Godbout, R.

    2013-01-01

    Alternative splicing represents a source of great diversity for regulating protein expression and function. It has been estimated that one-third to two-thirds of mammalian genes are alternatively spliced. With the sequencing of the chicken genome and analysis of transcripts expressed in chicken tissues, we are now in a position to address evolutionary conservation of alternative splicing events in chicken and mammals. Here, we compare chicken and mammalian transcript sequences of 41 alternatively-spliced genes and 50 frequently accessed genes. Our results support a high frequency of splicing events in chicken, similar to that observed in mammals. PMID:17675855

  7. Servicing Capability for the Evolutionary Space Station

    NASA Technical Reports Server (NTRS)

    Alcorn, George; Corbo, Jim; Martin, Deborah; Levin, Lenny

    1990-01-01

    User servicing for Space Station Freedom (SSF) will span an evolutionary period paralleling that of the station's growth plan. This will include a baseline servicing configuration followed by a final growth phase in which all user servicing requirements are satisfied. Although the basic requirements for user servicing are not station configuration dependent, the emphasis placed on different aspects of servicing may change with the eventual SSF growth objectives. This paper will discuss the servicing requirements and how they will be satisfied by Freedom baseline and growth capabilities. The accomodation of the growth servicing elements will be addressed, including the required hooks and scars to implement these growth servicing capabilities.

  8. The evolutionary sequence: origin and emergences.

    PubMed

    Fox, S W

    1986-03-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  9. The evolutionary sequence: origin and emergences

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  10. Expansion of biological pathways based on evolutionary inference

    PubMed Central

    Li, Yang; Calvo, Sarah E.; Gutman, Roee

    2014-01-01

    Summary Availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history, but rather, consist of distinct “evolutionary modules.” We introduce a computational algorithm, CLIME (clustering by inferred models of evolution), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1000 annotated human pathways, organelles and proteomes of yeast, red algae, and malaria, reveals unanticipated evolutionary modularity and novel, co-evolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. PMID:24995987

  11. The descent of words: evolutionary thinking 1780-1880.

    PubMed

    van Wyhe, John

    2005-09-01

    Histories of evolutionary thought are dominated by organic evolution. The colossus in our midst that is evolutionary biology casts its shadow over history, making it appear that what is so widespread and important today was always the primary subject of evolutionary speculation. Thus many histories assume that the core meaning of evolution is the change of organic life and that other forms of evolutionary thinking, such as linguistic, social or cultural evolution, are only analogies or offshoots of the main biological evolutionary trunk. Ironically this is an ahistorical understanding. Long before the work of Charles Darwin, scholars were independently developing evolutionary concepts such as descent with modification and divergence from a common stock in order to understand cultural change.

  12. Evolutionary conservation—evaluating the adaptive potential of species

    PubMed Central

    Eizaguirre, Christophe; Baltazar-Soares, Miguel

    2014-01-01

    Despite intense efforts, biodiversity around the globe continues to decrease. To cease this phenomenon, we urgently need a better knowledge not only of the true extent of biodiversity, but also of the evolutionary potential of species to respond to environmental change. These aims are the heart of the developing field of Evolutionary conservation. Here, after describing problems associated with implementing evolutionary perspectives into management, we outline how evolutionary principles can contribute to efficient conservation programmes. We then introduce articles from this special issue on Evolutionary conservation, outlining how each study or review provides tools and concepts to contribute to efficient management of species or populations. Ultimately, we highlight what we believe can be future research avenues for evolutionary conservation.

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

    PubMed

    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.

  14. Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

    NASA Astrophysics Data System (ADS)

    von der Heyden, Sophie

    2017-03-01

    Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning for protection and conservation in marine systems is complex, but usually focuses on maintaining levels of biodiversity and protecting special and unique landscape features while avoiding negative impacts to socio-economic benefits. Conversely, the integration of evolutionary processes that have shaped extant species assemblages is rarely taken into account. However, it is as important to protect processes as it is to protect patterns for maintaining the evolutionary trajectories of populations and species. This review focuses on different approaches for integrating genetic analyses, such as phylogenetic diversity, phylogeography and the delineation of management units, temporal and spatial monitoring of genetic diversity and quantification of adaptive variation for protecting evolutionary resilience, into marine spatial planning, specifically for coral reef fishes. Many of these concepts are not yet readily applied to coral reef fish studies, but this synthesis highlights their potential and the importance of including historical processes into systematic biodiversity planning for conserving not only extant, but also future, biodiversity and its evolutionary potential.

  15. Classifying nucleic acid sub-sequences as introns or exons using genetic programming

    SciTech Connect

    Handley, S.

    1995-12-31

    An evolutionary computation technique, genetic programming, created programs that classify messenger RNA sequences into one of two classes: (1) the sequence is expressed as (part of) a protein (an exon), or (2) not expressed as protein (an intron).

  16. Evolutionary Medicine: The Ongoing Evolution of Human Physiology and Metabolism.

    PubMed

    Rühli, Frank; van Schaik, Katherine; Henneberg, Maciej

    2016-11-01

    The field of evolutionary medicine uses evolutionary principles to understand changes in human anatomy and physiology that have occurred over time in response to environmental changes. Through this evolutionary-based approach, we can understand disease as a consequence of anatomical and physiological "trade-offs" that develop to facilitate survival and reproduction. We demonstrate how diachronic study of human anatomy and physiology is fundamental for an increased understanding of human health and disease.

  17. Application of proteomics in phylogenetic and evolutionary studies.

    PubMed

    Navas, Alfonso; Albar, Juan Pablo

    2004-02-01

    There are few papers that deal specifically with evolutionary studies and proteomics. However, applying proteomics to these studies promises to open new perspectives apropos the construction of phylogenetic trees and the detection of evolutionary changes. Principles and methods of phylogenetic systematics could be used to compare and evaluate proteomes. This would permit the detection and characterization of specific proteins that have evolutionary value in defining monophyly, paraphyly, and polyphyly.

  18. Cognitive evolutionary therapy for depression: a case study

    PubMed Central

    Giosan, Cezar; Muresan, Vlad; Moldovan, Ramona

    2014-01-01

    Key Clinical Message We present an evolutionary-driven cognitive–behavioral intervention for a moderately depressed patient. Standard cognitive and behavioral therapy techniques focused on the patient's perfectionistic and self-downing beliefs, while novel, evolutionary-informed techniques were used to guide behavioral activation and conceptualize secondary emotional problems related to anger. The treatment reduced depressive symptomatology and increased evolutionary fitness. PMID:25614817

  19. An evolutionary cascade model for sauropod dinosaur gigantism--overview, update and tests.

    PubMed

    Sander, P Martin

    2013-01-01

    Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades ("Reproduction", "Feeding", "Head and neck", "Avian-style lung", and "Metabolism"). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait "Very high body mass". Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size.

  20. Identifying Evolutionary Patterns of SMBHS Using Characteristic Variables of the Quasar AGNs of eBOSS

    NASA Astrophysics Data System (ADS)

    Martens, Sarah Katherine; Wilcots, Eric M.

    2017-01-01

    We investigate the redshift distribution and environmental conditions of quasar AGNs. The importance of studying these relationships is to use the evolutionary patterns of QSOs (features with many quantifiable characteristics) to gain insight into the evolutionary paths and environmental dependencies of their host super massive black holes (SMBHs), which are more difficult to study directly. We employ specific redshift bins within Data Release 13 of the Sloan Digital Sky Survey's (SDSS) Extended Baryonic Oscillation Spectroscopic Survey (eBOSS) and begin with a sample of 595,025 QSOs. We then incorporate overlapping data sets: The Very Large Array Faint Images of the Radio Sky at Twenty-Centimeters (FIRST) which provides the HI detected QSOs in our sample, along with the galaxy group and cluster sample from Tempel, Tago, Liivamägi 2012 which we cross referenced with our QSO sample to see which of them exist in group environments. The addition of these data sets allows us to create a more holistic view of the processes at work within our sample of QSOs. Understanding the HI presence in different evolutionary phases will allow us to draw conclusions on potential star formation rates or quenching, and by understanding the populations of QSOs in galaxy groups we can determine if QSOs exist overwhelmingly in one particular environment and how environmental conditions effect the other characteristics of QSOs. Overall we provide a multi-faceted analysis of some of the evolutionary patterns and cycles of the eBOSS Data Release 13 QSOs and their implications on the evolutionary paths of SMBHs. This work was supported by the SDSS Research Experience for Undergraduates program, which is funded by a grant from Sloan Foundation to the Astrophysical Research Consortium.

  1. An Evolutionary Cascade Model for Sauropod Dinosaur Gigantism - Overview, Update and Tests

    PubMed Central

    Sander, P. Martin

    2013-01-01

    Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades (“Reproduction”, “Feeding”, “Head and neck”, “Avian-style lung”, and “Metabolism”). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait “Very high body mass”. Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size. PMID:24205267

  2. The evolutionary position of turtles revised

    NASA Astrophysics Data System (ADS)

    Zardoya, Rafael; Meyer, Axel

    2001-05-01

    Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved partly because turtles have such a unique morphology that only few characters can be used to link them with any other group of amniotes. Among the many alternative hypotheses that have been postulated to explain the origin and phylogenetic relationships of turtles, a general agreement among paleontologists emerged in favoring the placement of turtles as the only living survivors of the anapsid reptiles (those that lack temporal fenestrae in the skull). However, recent morphological and molecular studies have radically changed our view of amniote phylogenetic relationships, and evidence is accumulating that supports the diapsid affinities of turtles. Molecular studies favor archosaurs (crocodiles and birds) as the living sister group of turtles, whereas morphological studies support lepidosaurs (tuatara, lizards, and snakes) as the closest living relatives of turtles. Accepting these hypotheses implies that turtles cannot be viewed any longer as primitive reptiles, and that they might have lost the temporal holes in the skull secondarily rather than never having had them.

  3. Estimation of evolutionary distances between nucleotide sequences.

    PubMed

    Zharkikh, A

    1994-09-01

    A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.

  4. Optimizing a reconfigurable material via evolutionary computation

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  5. Mitochondria and the evolutionary roots of cancer

    NASA Astrophysics Data System (ADS)

    Davila, Alfonso F.; Zamorano, Pedro

    2013-04-01

    Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.

  6. The evolutionary psychology of women's aggression

    PubMed Central

    Campbell, Anne

    2013-01-01

    Evolutionary researchers have identified age, operational sex ratio and high variance in male resources as factors that intensify female competition. These are discussed in relation to escalated intrasexual competition for men and their resources between young women in deprived neighbourhoods. For these women, fighting is not seen as antithetical to cultural conceptions of femininity, and female weakness is disparaged. Nonetheless, even where competitive pressures are high, young women's aggression is less injurious and frequent than young men's. From an evolutionary perspective, I argue that the intensity of female aggression is constrained by the greater centrality of mothers, rather than fathers, to offspring survival. This selection pressure is realized psychologically through a lower threshold for fear among women. Neuropsychological evidence is not yet conclusive but suggests that women show heightened amygdala reactivity to threatening stimuli, may be better able to exert prefrontal cortical control over emotional behaviour and may consciously register fear more strongly via anterior cingulate activity. The impact of testosterone and oxytocin on the neural circuitry of emotion is also considered. PMID:24167308

  7. Cognition and Culture in Evolutionary Context.

    PubMed

    Colmenares, Fernando; Hernández-Lloreda, María Victoria

    2017-01-09

    In humans and other animals, the individuals' ability to adapt efficiently and effectively to the niches they have actively contributed to construct relies heavily on an evolved psychology which has been shaped by biological, social, and cultural processes over evolutionary time. As expected, although many of the behavioral and cognitive components of this evolved psychology are widely shared across species, many others are species-unique. Although many animal species are known to acquire group-specific traditions (or cultures) via social learning, human culture is unique in terms of its contents and characteristics (observable and unobservable products, cumulative effects, norm conformity, and norm enforcement) and of its cognitive underpinnings (imitation, instructed teaching, and language). Here we provide a brief overview of some of the issues that are currently tackled in the field. We also highlight some of the strengths of a biological, comparative, non-anthropocentric and evolutionarily grounded approach to the study of culture. The main contributions of this approach to the science of culture are its emphasis (a) on the integration of information on mechanisms, function, and evolution, and on mechanistic factors located at different levels of the biological hierarchy, and (b) on the search for general principles that account for commonalities and differences between species, both in the cultural products and in the processes of innovation, dissemination, and accumulation involved that operate during developmental and evolutionary timespans.

  8. Mitochondria and the evolutionary roots of cancer.

    PubMed

    Davila, Alfonso F; Zamorano, Pedro

    2013-04-01

    Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.

  9. Collective influence in evolutionary social dilemmas

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2016-03-01

    When evolutionary games are contested in structured populations, the degree of each player in the network plays an important role. If they exist, hubs often determine the fate of the population in remarkable ways. Recent research based on optimal percolation in random networks has shown, however, that the degree is neither the sole nor the best predictor of influence in complex networks. Low-degree nodes may also be optimal influencers if they are hierarchically linked to hubs. Taking this into account leads to the formalism of collective influence in complex networks, which as we show here, has far-reaching implications for the favorable resolution of social dilemmas. In particular, there exists an optimal hierarchical depth for the determination of collective influence that we use to describe the potency of players for passing their strategies, which depends on the strength of the social dilemma. Interestingly, the degree, which corresponds to the baseline depth zero, is optimal only when the temptation to defect is small. Our research reveals that evolutionary success stories are related to spreading processes which are rooted in favorable hierarchical structures that extend beyond local neighborhoods.

  10. Evolutionary inference via the Poisson Indel Process.

    PubMed

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

  11. Evolutionary Stability in the Asymmetric Volunteer's Dilemma

    PubMed Central

    Li, Yao-Tang

    2014-01-01

    It is often assumed that in public goods games, contributors are either strong or weak players and each individual has an equal probability of exhibiting cooperation. It is difficult to explain why the public good is produced by strong individuals in some cooperation systems, and by weak individuals in others. Viewing the asymmetric volunteer's dilemma game as an evolutionary game, we find that whether the strong or the weak players produce the public good depends on the initial condition (i.e., phenotype or initial strategy of individuals). These different evolutionarily stable strategies (ESS) associated with different initial conditions, can be interpreted as the production modes of public goods of different cooperation systems. A further analysis revealed that the strong player adopts a pure strategy but mixed strategies for the weak players to produce the public good, and that the probability of volunteering by weak players decreases with increasing group size or decreasing cost-benefit ratio. Our model shows that the defection probability of a “strong” player is greater than the “weak” players in the model of Diekmann (1993). This contradicts Selten's (1980) model that public goods can only be produced by a strong player, is not an evolutionarily stable strategy, and will therefore disappear over evolutionary time. Our public good model with ESS has thus extended previous interpretations that the public good can only be produced by strong players in an asymmetric game. PMID:25111781

  12. Religion's evolutionary landscape: counterintuition, commitment, compassion, communion.

    PubMed

    Atran, Scott; Norenzayan, Ara

    2004-12-01

    Religion is not an evolutionary adaptation per se, but a recurring cultural by-product of the complex evolutionary landscape that sets cognitive, emotional, and material conditions for ordinary human interactions. Religion exploits only ordinary cognitive processes to passionately display costly devotion to counterintuitive worlds governed by supernatural agents. The conceptual foundations of religion are intuitively given by task-specific panhuman cognitive domains, including folkmechanics, folkbiology, and folkpsychology. Core religious beliefs minimally violate ordinary notions about how the world is, with all of its inescapable problems, thus enabling people to imagine minimally impossible supernatural worlds that solve existential problems, including death and deception. Here the focus is on folkpsychology and agency. A key feature of the supernatural agent concepts common to all religions is the triggering of an "Innate Releasing Mechanism," or "agency detector," whose proper (naturally selected) domain encompasses animate objects relevant to hominid survival--such as predators, protectors, and prey--but which actually extends to moving dots on computer screens, voices in wind, and faces on clouds. Folkpsychology also crucially involves metarepresentation, which makes deception possible and threatens any social order. However, these same metacognitive capacities provide the hope and promise of open-ended solutions through representations of counterfactual supernatural worlds that cannot be logically or empirically verified or falsified. Because religious beliefs cannot be deductively or inductively validated, validation occurs only by ritually addressing the very emotions motivating religion. Cross-cultural experimental evidence encourages these claims.

  13. Cyclic dominance in evolutionary games: a review

    PubMed Central

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

    2014-01-01

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

  14. Evolutionary history of African mongoose rabies.

    PubMed

    Van Zyl, N; Markotter, W; Nel, L H

    2010-06-01

    Two biotypes or variants of rabies virus (RABV) occur in southern Africa. These variants are respectively adapted to hosts belonging to the Canidae family (the canid variant) and hosts belonging to the Herpestidae family (the mongoose variant). Due to the distinct host adaptation and differences in epidemiology and pathogenesis, it has been hypothesized that the two variants were introduced into Africa at different times. The objective of this study was to investigate the molecular phylogeny of representative RABV isolates of the mongoose variant towards a better understanding of the origins of this group. The study was based on an analysis of the full nucleoprotein and glycoprotein gene sequences of a panel of 27 viruses. Phylogenetic analysis of this dataset confirmed extended evolutionary adaptation of isolates in specific geographic areas. The evolutionary dynamics of this virus variant was investigated using Bayesian methodology, allowing for rate variation among viral lineages. Molecular clock analysis estimated the age of the African mongoose RABV to be approximately 200 years old, which is in concurrence with literature describing rabies in mongooses since the early 1800 s.

  15. Specialization and evolutionary branching within migratory populations.

    PubMed

    Torney, Colin J; Levin, Simon A; Couzin, Iain D

    2010-11-23

    Understanding the mechanisms that drive specialization and speciation within initially homogeneous populations is a fundamental challenge for evolutionary theory. It is an issue of relevance for significant open questions in biology concerning the generation and maintenance of biodiversity, the origins of reciprocal cooperation, and the efficient division of labor in social or colonial organisms. Several mathematical frameworks have been developed to address this question and models based on evolutionary game theory or the adaptive dynamics of phenotypic mutation have demonstrated the emergence of polymorphic, specialized populations. Here we focus on a ubiquitous biological phenomenon, migration. Individuals in our model may evolve the capacity to detect and follow an environmental cue that indicates a preferred migration route. The strategy space is defined by the level of investment in acquiring personal information about this route or the alternative tendency to follow the direction choice of others. The result is a relation between the migratory process and a game theoretic dynamic that is generally applicable to situations where information may be considered a public good. Through the use of an approximation of social interactions, we demonstrate the emergence of a stable, polymorphic population consisting of an uninformed subpopulation that is dependent upon a specialized group of leaders. The branching process is classified using the techniques of adaptive dynamics.

  16. The evolutionary origin of flatfish asymmetry.

    PubMed

    Friedman, Matt

    2008-07-10

    All adult flatfishes (Pleuronectiformes), including the gastronomically familiar plaice, sole, turbot and halibut, have highly asymmetrical skulls, with both eyes placed on one side of the head. This arrangement, one of the most extraordinary anatomical specializations among vertebrates, arises through migration of one eye during late larval development. Although the transformation of symmetrical larvae into asymmetrical juveniles is well documented, the evolutionary origins of flatfish asymmetry are uncertain because there are no transitional forms linking flatfishes with their symmetrical relatives. The supposed inviability of such intermediates gave pleuronectiforms a prominent role in evolutionary debates, leading to attacks on natural selection and arguments for saltatory change. Here I show that Amphistium and the new genus Heteronectes, both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals. This condition is intermediate between that in living pleuronectiforms and the arrangement found in other fishes. Amphistium and Heteronectes indicate that the evolution of the profound cranial asymmetry of extant flatfishes was gradual in nature.

  17. Before senescence: the evolutionary demography of ontogenesis

    PubMed Central

    Levitis, Daniel A.

    2011-01-01

    The age-specific mortality curve for many species, including humans, is U-shaped: mortality declines with age in the developing cohort (ontogenescence) before increasing with age (senescence). The field of evolutionary demography has long focused on understanding the evolution of senescence while largely failing to address the evolution of ontogenescence. The current review is the first to gather the few available hypotheses addressing the evolution of ontogenescence, examine the basis and assumptions of each and ask what the phylogenetic extent of ontogenescence may be. Ontogenescence is among the most widespread of life-history traits, occurring in every population for which I have found sufficiently detailed data, in major groups throughout the eukaryotes, across many causes of death and many life-history types. Hypotheses seeking to explain ontogenescence include those based on kin selection, the acquisition of robustness, heterogeneous frailties and life-history optimization. I propose a further hypothesis, arguing that mortality drops with age because most transitions that could trigger the risks caused by genetic and developmental malfunctions are concentrated in early life. Of these hypotheses, only those that frame ontogenescence as an evolutionary by-product rather than an adaptation can explain the tremendous diversity of organisms and environments in which it occurs. PMID:21123273

  18. Evolutionary Games of Multiplayer Cooperation on Graphs

    PubMed Central

    Arranz, Jordi; Traulsen, Arne

    2016-01-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  19. Evolutionary lessons from California plant phylogeography

    PubMed Central

    Sork, Victoria L.; Chen, Jin-Ming

    2016-01-01

    Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change. PMID:27432984

  20. Evolutionary Dynamics of Homophily and Heterophily

    PubMed Central

    Ramazi, Pouria; Cao, Ming; Weissing, Franz J.

    2016-01-01

    Most social interactions do not take place at random. In many situations, individuals choose their interaction partners on the basis of phenotypic cues. When this happens, individuals are often homophilic, that is, they tend to interact with individuals that are similar to them. Here we investigate the joint evolution of phenotypic cues and cue-dependent interaction strategies. By a combination of individual-based simulations and analytical arguments, we show that homophily evolves less easily than earlier studies suggest. The evolutionary interplay of cues and cue-based behaviour is intricate and has many interesting facets. For example, an interaction strategy like heterophily may stably persist in the population even if it is selected against in association with any particular cue. Homophily persisted for extensive periods of time just in those simulations where homophilic interactions provide a lower (rather than a higher) payoff than heterophilic interactions. Our results indicate that even the simplest cue-based social interactions can have rich dynamics and a surprising diversity of evolutionary outcomes. PMID:26951038

  1. Evolutionary diversification in stickleback affects ecosystem functioning.

    PubMed

    Harmon, Luke J; Matthews, Blake; Des Roches, Simone; Chase, Jonathan M; Shurin, Jonathan B; Schluter, Dolph

    2009-04-30

    Explaining the ecological causes of evolutionary diversification is a major focus of biology, but surprisingly little has been said about the effects of evolutionary diversification on ecosystems. The number of species in an ecosystem and their traits are key predictors of many ecosystem-level processes, such as rates of productivity, biomass sequestration and decomposition. Here we demonstrate short-term ecosystem-level effects of adaptive radiation in the threespine stickleback (Gasterosteus aculeatus) over the past 10,000 years. These fish have undergone recent parallel diversification in several lakes in coastal British Columbia, resulting in the formation of two specialized species (benthic and limnetic) from a generalist ancestor. Using a mesocosm experiment, we demonstrate that this diversification has strong effects on ecosystems, affecting prey community structure, total primary production, and the nature of dissolved organic materials that regulate the spectral properties of light transmission in the system. However, these ecosystem effects do not simply increase in their relative strength with increasing specialization and species richness; instead, they reflect the complex and indirect consequences of ecosystem engineering by sticklebacks. It is well known that ecological factors influence adaptive radiation. We demonstrate that adaptive radiation, even over short timescales, can have profound effects on ecosystems.

  2. Evolutionary origin of rhizobium Nod factor signaling

    PubMed Central

    Streng, Arend; op den Camp, Rik; Bisseling, Ton

    2011-01-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor.1 Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes.2 As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the vast majority of land plants, it is most probable that this signaling cascade is wide spread in the plant kingdom.3 However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of rhizobium Nod factor signaling demonstrate that this is not the case.4,5 The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling. PMID:21904113

  3. Evolutionary Computing for Low-thrust Navigation

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; Fink, Wolfgang; vonAllmed, Paul; Petropoulos, Anastassios E.; Russell, Ryan P.; Terrile, Richard J.

    2005-01-01

    The development of new mission concepts requires efficient methodologies to analyze, design and simulate the concepts before implementation. New mission concepts are increasingly considering the use of ion thrusters for fuel-efficient navigation in deep space. This paper presents parallel, evolutionary computing methods to design trajectories of spacecraft propelled by ion thrusters and to assess the trade-off between delivered payload mass and required flight time. The developed methods utilize a distributed computing environment in order to speed up computation, and use evolutionary algorithms to find globally Pareto-optimal solutions. The methods are coupled with two main traditional trajectory design approaches, which are called direct and indirect. In the direct approach, thrust control is discretized in either arc time or arc length, and the resulting discrete thrust vectors are optimized. In the indirect approach, a thrust control problem is transformed into a costate control problem, and the initial values of the costate vector are optimized. The developed methods are applied to two problems: 1) an orbit transfer around the Earth and 2) a transfer between two distance retrograde orbits around Europa, the closest to Jupiter of the icy Galilean moons. The optimal solutions found with the present methods are comparable to other state-of-the-art trajectory optimizers and to analytical approximations for optimal transfers, while the required computational time is several orders of magnitude shorter than other optimizers thanks to an intelligent design of control vector discretization, advanced algorithmic parameterization, and parallel computing.

  4. Evolutionary Optimization of a Geometrically Refined Truss

    NASA Technical Reports Server (NTRS)

    Hull, P. V.; Tinker, M. L.; Dozier, G. V.

    2007-01-01

    Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection, and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This Technical Publication (TP) presents a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: genetic algorithms and differential evolution to successfully optimize a benchmark structural optimization problem. A nontraditional solution to the benchmark problem is presented in this TP, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.

  5. Evolutionary ecology of the wild cereals

    SciTech Connect

    Blumler, M.A.

    1995-12-31

    The evolutionary ecology of the Near Eastern wild cereal grasses sheds light on the environmental conditions under which the Neolithic Revolution took place. Globally, as well as in the Near East, the annual habit, large seed size, and seasonal drought are associated with each other and with agricultural origins. The connection with agricultural appears to involve ease of cultivation and necessity for seasonal storage rather than hunter-gatherer preference for large seeds. The Near Eastern wild cereal species separate ecologically according to seasonality of precipitation, primarily, though there may also be minor differences in temperature and edaphic tolerances. This reflects the evolution, over the course of the Quaternary, of species with increased seed size in response to increasingly pronounced seasonal drought. Wild emmer and wild barley, the progenitors of perhaps the very first domesticates, are evolutionary monstrosities that represent the culmination of this trend. The possibly complex changes in seasonality, aridity, and atmospheric CO2 during the millenia leading up to the Neolithic should have produced equally complex, but to some extent predictable, changes in the abundance and distribution of the different wild cereal species.

  6. Application of evolutionary principles to cancer therapy

    PubMed Central

    Enriquez-Navas, Pedro M.; Wojtkowiak, Jonathan W.; Gatenby, Robert A.

    2015-01-01

    The dynamic cancer ecosystem, with its rich temporal and spatial diversity in environmental conditions and heritable cell phenotypes, is remarkably robust to therapeutic perturbations. Even when response to therapy is clinically complete, adaptive tumor strategies almost inevitably emerge and the tumor returns. Although evolution of resistance remains the proximate cause of death in most cancer patients, a recent analysis (1) found that evolutionary terms were included in less than 1% of manuscripts on the cancer treatment outcomes and this has not changed in 30 years. Here we review treatment methods that attempt to understand and exploit intratumoral evolution to prolong response to therapy. In general, we find that treating metastatic (i.e. non-curable) cancers using the traditional strategy aimed at killing the maximum number of tumor cells is evolutionarily unsound because, by eliminating all treatment-sensitive cells, it enables rapid proliferation of resistant populations – a well-known evolutionary phenomenon termed “competitive release (2, 3).” Alternative strategies such as adaptive therapy (4, 5), “ersatzdroges (6),” and double bind treatments (7) shift focus from eliminating tumor cells to evolution-based methods that suppress growth of resistant populations to maintain long term control. PMID:26527288

  7. The Best and the Worst of Times for Evolutionary Biology.

    ERIC Educational Resources Information Center

    Avise, John C.

    2003-01-01

    Discusses opportunities and challenges for the field of evolutionary biology, particularly in areas related to molecular genetic technologies, the environment, biodiversity, and public education. (Author/KHR)

  8. The genomic basis of eco-evolutionary dynamics.

    PubMed

    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.

  9. Optimal satellite formation reconfiguration using co-evolutionary particle swarm optimization in deep space

    NASA Astrophysics Data System (ADS)

    Huang, Haibin; Zhuang, Yufei

    2015-08-01

    This paper proposes a method that plans energy-optimal trajectories for multi-satellite formation reconfiguration in deep space environment. A novel co-evolutionary particle swarm optimization algorithm is stated to solve the nonlinear programming problem, so that the computational complexity of calculating the gradient information could be avoided. One swarm represents one satellite, and through communication with other swarms during the evolution, collisions between satellites can be avoided. In addition, a dynamic depth first search algorithm is proposed to solve the redundant search problem of a co-evolutionary particle swarm optimization method, with which the computation time can be shorten a lot. In order to make the actual trajectories optimal and collision-free with disturbance, a re-planning strategy is deduced for formation reconfiguration maneuver.

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

    PubMed

    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.

  11. Minimum of Information Distance Criterion for Optimal Control of Mutation Rate in Evolutionary Systems

    NASA Astrophysics Data System (ADS)

    Belavkin, Roman V.

    2013-01-01

    Evolutionary dynamics studies changes in populations of species, which occur due to various processes such as replication and mutation. Here we consider this dynamics as an example of Markov evolution on a simplex of probability measures describing the populations, and then define optimality of this evolution with respect to constraints on information distance between these measures. We show how this convex programming problem is related to a variational problem of optimizing Markov transition kernel subject to a constraint on Shannon's mutual information. This relation is represented by the Pythagorean theorem in information geometry considered on the simplex of joint probability measures. We discuss the application of this variational approach to optimization of a stochastic search in metric spaces, and in particular to optimization of mutation rate parameter during the search for optimal DNA sequences in evolutionary systems.

  12. Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment

    PubMed Central

    2014-01-01

    Background To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. Results This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Conclusions Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel

  13. Hybrid Architectures for Evolutionary Computing Algorithms

    DTIC Science & Technology

    2006-01-01

    SIMBIOSYS program we managed. We developed prototype optimization software tools in three programming environments, Labview, Matlab, and compiled C, and...Optimization Toolbox from North Carolina State University, integrated MatLab bio-models from Purdue University SIMBIOSYS PI and also with C version...That work was done actually done as a part of the in-house component of our involvement in the DARPA SIMBIOSYS and BIOCOMP programs. Under those

  14. Attachment, mating, and parenting : An evolutionary interpretation.

    PubMed

    Belsky, J

    1997-12-01

    A modern evolutionary perspective emphasizing life history theory and behavioral ecology is brought to bear on the three core patterns of attachment that are identified in studies of infants and young children in the Strange Situation and adults using the Adult Attachment Interview. Mating and parenting correlates of secure/autonomous, avoidant/dismissing, and resistant/preoccupied attachment patterns are reviewed, and the argument is advanced that security evolved to promote mutually beneficial interpersonal relations and high investment parenting; that avoidant/dismissing attachment evolved to promote opportunistic interpersonal relations and low-investment parenting; and that resistant/preoccupied attachment evolved to foster "helper-at-the-nest" behavior and indirect reproduction.

  15. EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY

    PubMed Central

    Davidson, Eric H.

    2011-01-01

    At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved. Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, so causal explanation of evolutionary change in developmental process must be considered at a system level. Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network. PMID:21320483

  16. On evolutionary explanations of cognitive biases.

    PubMed

    Marshall, James A R; Trimmer, Pete C; Houston, Alasdair I; McNamara, John M

    2013-08-01

    Apparently irrational biases such as overconfidence, optimism, and pessimism are increasingly studied by biologists, psychologists, and neuroscientists. Functional explanations of such phenomena are essential; we argue that recent proposals, focused on benefits from overestimating the probability of success in conflicts or practising self-deception to better deceive others, are still lacking in crucial regards. Attention must be paid to the difference between cognitive and outcome biases; outcome biases are suboptimal, yet cognitive biases can be optimal. However, given that cognitive biases are subjectively experienced by affected individuals, developing theory and collecting evidence on them poses challenges. An evolutionary theory of cognitive bias might require closer integration of function and mechanism, analysing the evolution of constraints imposed by the mechanisms that determine behaviour.

  17. Cenozoic climate change influences mammalian evolutionary dynamics

    PubMed Central

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

    2012-01-01

    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. 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 (δ18O) 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. PMID:22203974

  18. Reassessing the evolutionary importance of inflammasomes

    PubMed Central

    Maltez, Vivien I.; Miao, Edward A.

    2015-01-01

    Inflammasomes monitor the cytosol for microbial contamination or perturbation, and are thus predicted to provide potent defense against infection. However, the compendium of data from murine infection models suggests that inflammasomes merely delay the course of disease, allowing the host time to mount an adaptive response. Interpretations of such results are confounded by inflammasome evasion strategies of vertebrate-adapted pathogens. Conversely, environmental opportunistic pathogens have not evolved in the context of inflammasomes, and are therefore less likely to evade them. Indeed, opportunistic pathogens do not normally cause disease in wild type animals. Accordantly, the extreme virulence of two opportunistic bacterial pathogens, Burkholderia thailandensis and Chromobacterium violaceum, is fully counteracted by inflammasomes in murine models. This leads us to propose a new hypothesis: perhaps animals maintain inflammasomes over evolutionary time not to defend against vertebrate-adapted pathogens, but instead to counteract infection by a plethora of undiscovered opportunistic pathogens residing in the environment. PMID:26802061

  19. Epigenetic origin of evolutionary novel centromeres

    PubMed Central

    Tolomeo, Doron; Capozzi, Oronzo; Stanyon, Roscoe R.; Archidiacono, Nicoletta; D’Addabbo, Pietro; Catacchio, Claudia R.; Purgato, Stefania; Perini, Giovanni; Schempp, Werner; Huddleston, John; Malig, Maika; Eichler, Evan E.; Rocchi, Mariano

    2017-01-01

    Most evolutionary new centromeres (ENC) are composed of large arrays of satellite DNA and surrounded by segmental duplications. However, the hypothesis is that ENCs are seeded in an anonymous sequence and only over time have acquired the complexity of “normal” centromeres. Up to now evidence to test this hypothesis was lacking. We recently discovered that the well-known polymorphism of orangutan chromosome 12 was due to the presence of an ENC. We sequenced the genome of an orangutan homozygous for the ENC, and we focused our analysis on the comparison of the ENC domain with respect to its wild type counterpart. No significant variations were found. This finding is the first clear evidence that ENC seedings are epigenetic in nature. The compaction of the ENC domain was found significantly higher than the corresponding WT region and, interestingly, the expression of the only gene embedded in the region was significantly repressed. PMID:28155877

  20. Friends reunited? Evolutionary robotics and representational explanation.

    PubMed

    Wheeler, Michael

    2005-01-01

    Robotics as practiced within the artificial life community is no longer the bitter enemy of representational explanation in the way that it sometimes seemed to be in the heady, revolutionary days of the 1990s. This rapprochement is, however, fragile, because the field of evolutionary robotics continues to pose two important challenges to the idea that real-time intelligent action must or should be explained by appeal to inner representations. The first of these challenges, the threat from nontrivial causal spread, occurs when extra-neural factors account for the kind of adaptive richness and flexibility normally associated with representation-based control. The second, the threat from continuous reciprocal causation, occurs when the causal contributions made by the systemic components collectively responsible for behavior generation are massively context-sensitive and variable over time. I argue that while the threat from nontrivial causal spread can be resisted, the threat from continuous reciprocal causation provides a stern test for our representational intuitions.

  1. Compassion: An Evolutionary Analysis and Empirical Review

    PubMed Central

    Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

    2010-01-01

    What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization, and a phenomenological experience and physiological response that orients the individual to social approach. This response profile of compassion differs from those of distress, sadness, and love, suggesting that compassion is indeed a distinct emotion. We conclude by considering how compassion shapes moral judgment and action, how it varies across different cultures, and how it may engage specific patterns of neural activation, as well as emerging directions of research. PMID:20438142

  2. An evolutionary theory of human motivation.

    PubMed

    Bernard, Larry C; Mills, Michael; Swenson, Leland; Walsh, R Patricia

    2005-05-01

    The authors review psychology's historical, competing perspectives on human motivation and propose a new comprehensive theory. The new theory is based on evolutionary principles as proposed by C. Darwin (1859) and modified by W. D. Hamilton (1964, 1996), R. L. Trivers (1971, 1972), and R. Dawkins (1989). The theory unifies biological, behavioral, and cognitive approaches to motivation. The theory is neuropsychological and addresses conscious and nonconscious processes that underlie motivation, emotion, and self-control. The theory predicts a hierarchical structure of motives that are measurable as individual differences in human behavior. These motives are related to social problem domains (D. B. Bugental, 2000; D. T. Kenrick, N. P. Li, & J. Butner, 2003), and each is hypothesized to solve a particular problem of human inclusive fitness.

  3. Evolutionary dynamics of Newcastle disease virus

    SciTech Connect

    Miller, Patti J.; Kim, L. Mia; Ip, Hon S.; Afonso, Claudio L.

    2009-08-15

    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.

  4. Evolutionary history and biotechnological future of carboxylases.

    PubMed

    Schada von Borzyskowski, Lennart; Rosenthal, Raoul G; Erb, Tobias J

    2013-11-01

    Carbon dioxide (CO2) is a potent greenhouse gas whose presence in the atmosphere is a critical factor for global warming. At the same time atmospheric CO2 is also a cheap and readily available carbon source that can in principle be used to synthesize value-added products. However, as uncatalyzed chemical CO2-fixation reactions usually require quite harsh conditions to functionalize the CO2 molecule, not many processes have been developed that make use of CO2. In contrast to synthetical chemistry, Nature provides a multitude of different carboxylating enzymes whose carboxylating principle(s) might be exploited in biotechnology. This review focuses on the biochemical features of carboxylases, highlights possible evolutionary scenarios for the emergence of their reactivity, and discusses current, as well as potential future applications of carboxylases in organic synthesis, biotechnology and synthetic biology.

  5. Evolutionary Optimization of Yagi-Uda Antennas

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Kraus, William F.; Linden, Derek S.; Colombano, Silvano P.

    2001-01-01

    Yagi-Uda antennas are known to be difficult to design and optimize due to their sensitivity at high gain, and the inclusion of numerous parasitic elements. We present a genetic algorithm-based automated antenna optimization system that uses a fixed Yagi-Uda topology and a byte-encoded antenna representation. The fitness calculation allows the implicit relationship between power gain and sidelobe/backlobe loss to emerge naturally, a technique that is less complex than previous approaches. The genetic operators used are also simpler. Our results include Yagi-Uda antennas that have excellent bandwidth and gain properties with very good impedance characteristics. Results exceeded previous Yagi-Uda antennas produced via evolutionary algorithms by at least 7.8% in mainlobe gain. We also present encouraging preliminary results where a coevolutionary genetic algorithm is used.

  6. Evolutionary algorithm for metabolic pathways synthesis.

    PubMed

    Gerard, Matias F; Stegmayer, Georgina; Milone, Diego H

    2016-06-01

    Metabolic pathway building is an active field of research, necessary to understand and manipulate the metabolism of organisms. There are different approaches, mainly based on classical search methods, to find linear sequences of reactions linking two compounds. However, an important limitation of these methods is the exponential increase of search trees when a large number of compounds and reactions is considered. Besides, such models do not take into account all substrates for each reaction during the search, leading to solutions that lack biological feasibility in many cases. This work proposes a new evolutionary algorithm that allows searching not only linear, but also branched metabolic pathways, formed by feasible reactions that relate multiple compounds simultaneously. Tests performed using several sets of reactions show that this algorithm is able to find feasible linear and branched metabolic pathways.

  7. Evolutionary history of the genus Trisopterus.

    PubMed

    Gonzalez, Elena G; Cunha, Regina L; Sevilla, Rafael G; Ghanavi, Hamid R; Krey, Grigorios; Bautista, José M

    2012-03-01

    The group of small poor cods and pouts from the genus Trisopterus, belonging to the Gadidae family, comprises four described benthopelagic species that occur across the North-eastern Atlantic, from the Baltic Sea to the coast of Morocco, and the Mediterranean. Here, we combined molecular data from mitochondrial (cytochrome b) and nuclear (rhodopsin) genes to confirm the taxonomic status of the described species and to disentangle the evolutionary history of the genus. Our analyses supported the monophyly of the genus Trisopterus and confirmed the recently described species Trisopterus capelanus. A relaxed molecular clock analysis estimated an Oligocene origin for the group (~30 million years ago; mya) indicating this genus as one of the most ancestral within the Gadidae family. The closure and re-opening of the Strait of Gibraltar after the Messinian Salinity Crisis (MSC) probably triggered the speciation process that resulted in the recently described T. capelanus.

  8. Evolutionary vaccination dilemma in complex networks.

    PubMed

    Cardillo, Alessio; Reyes-Suárez, Catalina; Naranjo, Fernando; Gómez-Gardeñes, Jesús

    2013-09-01

    In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so that individuals take or do not take the vaccine upon their previous experience. Our framework thus puts in competition two well-known dynamical properties of scale-free networks: the fast propagation of diseases and the promotion of cooperative behaviors. Our results show that when vaccine is perfect, scale-free networks enhance the vaccination behavior with respect to random graphs with homogeneous connectivity patterns. However, when imperfection appears we find a crossover effect so that the number of infected (vaccinated) individuals increases (decreases) with respect to homogeneous networks, thus showing the competition between the aforementioned properties of scale-free graphs.

  9. Evolutionary approaches to cultural and linguistic diversity.

    PubMed

    Steele, James; Jordan, Peter; Cochrane, Ethan

    2010-12-12

    Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a 'grand synthesis' is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely 'cultural' fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.

  10. Epigenetic origin of evolutionary novel centromeres.

    PubMed

    Tolomeo, Doron; Capozzi, Oronzo; Stanyon, Roscoe R; Archidiacono, Nicoletta; D'Addabbo, Pietro; Catacchio, Claudia R; Purgato, Stefania; Perini, Giovanni; Schempp, Werner; Huddleston, John; Malig, Maika; Eichler, Evan E; Rocchi, Mariano

    2017-02-03

    Most evolutionary new centromeres (ENC) are composed of large arrays of satellite DNA and surrounded by segmental duplications. However, the hypothesis is that ENCs are seeded in an anonymous sequence and only over time have acquired the complexity of "normal" centromeres. Up to now evidence to test this hypothesis was lacking. We recently discovered that the well-known polymorphism of orangutan chromosome 12 was due to the presence of an ENC. We sequenced the genome of an orangutan homozygous for the ENC, and we focused our analysis on the comparison of the ENC domain with respect to its wild type counterpart. No significant variations were found. This finding is the first clear evidence that ENC seedings are epigenetic in nature. The compaction of the ENC domain was found significantly higher than the corresponding WT region and, interestingly, the expression of the only gene embedded in the region was significantly repressed.

  11. Evolutionary Divergence of Arabidopsis thaliana Classical Peroxidases.

    PubMed

    Kupriyanova, E V; Mamoshina, P O; Ezhova, T A

    2015-10-01

    Polymorphisms of 62 peroxidase genes derived from Arabidopsis thaliana were investigated to evaluate evolutionary dynamics and divergence of peroxidase proteins. By comparing divergence of duplicated genes AtPrx53-AtPrx54 and AtPrx36-AtPrx72 and their products, nucleotide and amino acid substitutions were identified that were apparently targets of positive selection. These substitutions were detected among paralogs of 461 ecotypes from Arabidopsis thaliana. Some of these substitutions are conservative and matched paralogous peroxidases in other Brassicaceae species. These results suggest that after duplication, peroxidase genes evolved under the pressure of positive selection, and amino acid substitutions identified during our study provided divergence of properties and physiological functions in peroxidases. Our predictions regarding functional significance for amino acid residues identified in variable sites of peroxidases may allow further experimental assessment of evolution of peroxidases after gene duplication.

  12. Evolutionary optimization of rotational population transfer

    SciTech Connect

    Rouzee, Arnaud; Vrakking, Marc J. J.; Ghafur, Omair; Gijsbertsen, Arjan; Vidma, Konstantin; Meijer, Afric; Zande, Wim J. van der; Parker, David; Shir, Ofer M.; Baeck, Thomas

    2011-09-15

    We present experimental and numerical studies on control of rotational population transfer of NO(J=1/2) molecules to higher rotational states. We are able to transfer 57% of the population to the J=5/2 state and 46% to J=9/2, in good agreement with quantum mechanical simulations. The optimal pulse shapes are composed of pulse sequences with delays corresponding to the beat frequencies of states on the rotational ladder. The evolutionary algorithm is limited by experimental constraints such as volume averaging and the finite laser intensity used, the latter to circumvent ionization. Without these constraints, near-perfect control (>98%) is possible. In addition, we show that downward control, moving molecules from high to low rotational states, is also possible.

  13. Testing evolutionary theories of discriminative grandparental investment.

    PubMed

    Kaptijn, Ralf; Thomese, Fleur; Liefbroer, Aart C; Silverstein, Merril

    2013-05-01

    This study tests two evolutionary hypotheses on grandparental investments differentiated by the child's sex: the paternity uncertainty hypothesis and the Trivers-Willard hypothesis. Data are from two culturally different countries: the Dutch Longitudinal Aging Study Amsterdam (n=2375) and the Chinese Anhui Survey (n=4026). In the Netherlands, grandparental investments are biased towards daughters' children, which is in accordance with the paternity uncertainty hypothesis. But in China, grandparental investments are biased towards sons' children, which is in conflict with the paternity uncertainty hypothesis. This study found no support for the Trivers-Willard hypothesis. These results raise doubts over the relevance of paternity uncertainty as an explanation of a grandparental investment bias towards daughters' children that is often found in Western populations. The results suggest that discriminative grandparental investments are better understood as the outcome of cultural prescriptions and economic motives.

  14. The Evolutionary Basis of Honor Cultures.

    PubMed

    Nowak, Andrzej; Gelfand, Michele J; Borkowski, Wojciech; Cohen, Dov; Hernandez, Ivan

    2016-01-01

    Around the globe, people fight for their honor, even if it means sacrificing their lives. This is puzzling from an evolutionary perspective, and little is known about the conditions under which honor cultures evolve. We implemented an agent-based model of honor, and our simulations showed that the reliability of institutions and toughness of the environment are crucial conditions for the evolution of honor cultures. Honor cultures survive when the effectiveness of the authorities is low, even in very tough environments. Moreover, the results show that honor cultures and aggressive cultures are mutually dependent in what resembles a predator-prey relationship described in the renowned Lotka-Volterra model. Both cultures are eliminated when institutions are reliable. These results have implications for understanding conflict throughout the world, where Western-based strategies are exported, often unsuccessfully, to contexts of weak institutional authority wherein honor-based strategies have been critical for survival.

  15. Evolutionary prisoner's dilemma on evolving random networks.

    PubMed

    Xu, Zhaojin; Le, Yun; Zhang, Lianzhong

    2014-04-01

    In this paper, we investigate the evolution of cooperation in the spatial prisoner's dilemma game by incorporating partner choice into the framework of evolutionary game theory. Our research shows that the introduction of partner choice can notably promote the cooperative behavior in the prisoner's dilemma game. All the players are more likely to play the game with cooperators, which makes it easier for cooperators to form alliances. In particular, the system will be dominated completely by cooperators in a comfortable environment (i.e., with lower survival cost) because the cooperators can get more benefits than the defectors in this case due to their good reputation. In addition, we have found that the sustenance of cooperators improves notably as well in the snowdrift game and the stag-hunt game due to this introduction.

  16. Cenozoic climate change influences mammalian evolutionary dynamics.

    PubMed

    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.

  17. Evolutionary Technique for Designing Optimized Arrays

    NASA Astrophysics Data System (ADS)

    Villazón, J.; Ibañez, A.

    2011-06-01

    Many ultrasonic inspection applications in the industry could benefit from the use of phased array distributions specifically designed for them. Some common design requirements are: to adapt the shape of the array to that of the part to be inspected, to use large apertures for increasing lateral resolution, to find a layout of elements that avoids artifacts produced by lateral and/or grating lobes, to maintain the total number of independent elements (and the number of control channels) as low as possible to reduce complexity and cost of the inspection system. Recent advances in transducer technology have made possible to design and build arrays whit non-regular layout of elements. In this paper we propose to use Evolutionary Algorithms to find layouts of ultrasonic arrays (whether 1D or 2D array) that approach a set of specified beampattern characteristics using a low number of elements.

  18. Host shifts and evolutionary radiations of butterflies.

    PubMed

    Fordyce, James A

    2010-12-22

    Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today.

  19. Transitions, transversions, and the molecular evolutionary clock.

    PubMed

    Jukes, T H

    1987-01-01

    Nucleotide substitutions in the form of transitions (purine-purine or pyrimidine-pyrimidine interchanges) and transversions (purine-pyrimidine interchanges) occur during evolution and may be compiled by aligning the sequences of homologous genes. Referring to the genetic code tables, silent transitions take place in third positions of codons in family boxes and two-codon sets. Silent transversions in third positions occur only in family boxes, except for A = C transversions between AGR and CGR arginine codons (R = A or G). Comparisons of several protein genes have been made, and various subclasses of transitional and transversional nucleotide substitutions have been compiled. Considerable variations occur among the relative proportions of transitions and transversions. Such variations could possibly be caused by mutator genes, favoring either transitions or, conversely, transversions, during DNA replication. At earlier stages of evolutionary divergence, transitions are usually more frequent, but there are exceptions. No indication was found that transversions usually originate from multiple substitutions in transitions.

  20. Dynamic Ising model: reconstruction of evolutionary trees

    NASA Astrophysics Data System (ADS)

    de Oliveira, P. M. C.

    2013-09-01

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

  1. Evolutionary bioscience as regulatory systems biology.

    PubMed

    Davidson, Eric H

    2011-09-01

    At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved. Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, causal explanation of evolutionary change in developmental process must be considered at a system level. Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network.

  2. Evolutionary vaccination dilemma in complex networks

    NASA Astrophysics Data System (ADS)

    Cardillo, Alessio; Reyes-Suárez, Catalina; Naranjo, Fernando; Gómez-Gardeñes, Jesús

    2013-09-01

    In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so that individuals take or do not take the vaccine upon their previous experience. Our framework thus puts in competition two well-known dynamical properties of scale-free networks: the fast propagation of diseases and the promotion of cooperative behaviors. Our results show that when vaccine is perfect, scale-free networks enhance the vaccination behavior with respect to random graphs with homogeneous connectivity patterns. However, when imperfection appears we find a crossover effect so that the number of infected (vaccinated) individuals increases (decreases) with respect to homogeneous networks, thus showing the competition between the aforementioned properties of scale-free graphs.

  3. Evolutionary rewiring of bacterial regulatory networks

    PubMed Central

    Taylor, Tiffany B.; Mulley, Geraldine; McGuffin, Liam J.; Johnson, Louise J.; Brockhurst, Michael A.; Arseneault, Tanya; Silby, Mark W.; Jackson, Robert W.

    2015-01-01

    Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks - homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015), 347(6225)] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs. PMID:28357301

  4. Evolutionary epistemology and dynamical virtual learning networks.

    PubMed

    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.

  5. Exploring the evolutionary history of centrosomes

    PubMed Central

    Azimzadeh, Juliette

    2014-01-01

    The centrosome is the main organizer of the microtubule cytoskeleton in animals, higher fungi and several other eukaryotic lineages. Centrosomes are usually located at the centre of cell in tight association with the nuclear envelope and duplicate at each cell cycle. Despite a great structural diversity between the different types of centrosomes, they are functionally equivalent and share at least some of their molecular components. In this paper, we explore the evolutionary origin of the different centrosomes, in an attempt to understand whether they are derived from an ancestral centrosome or evolved independently from the motile apparatus of distinct flagellated ancestors. We then discuss the evolution of centrosome structure and function within the animal lineage. PMID:25047607

  6. Choroid plexus in developmental and evolutionary perspective

    PubMed Central

    Bill, Brent Roy; Korzh, Vladimir

    2014-01-01

    The blood-cerebrospinal fluid boundary is present at the level of epithelial cells of the choroid plexus. As one of the sources of the cerebrospinal fluid (CSF), the choroid plexus (CP) plays an important role during brain development and function. Its formation has been studied largely in mammalian species. Lately, progress in other model animals, in particular the zebrafish, has brought a deeper understanding of CP formation, due in part to the ability to observe CP development in vivo. At the same time, advances in comparative genomics began providing information, which opens a possibility to understand further the molecular mechanisms involved in evolution of the CP and the blood-cerebrospinal fluid boundary formation. Hence this review focuses on analysis of the CP from developmental and evolutionary perspectives. PMID:25452709

  7. Transition matrix model for evolutionary game dynamics

    NASA Astrophysics Data System (ADS)

    Ermentrout, G. Bard; Griffin, Christopher; Belmonte, Andrew

    2016-03-01

    We study an evolutionary game model based on a transition matrix approach, in which the total change in the proportion of a population playing a given strategy is summed directly over contributions from all other strategies. This general approach combines aspects of the traditional replicator model, such as preserving unpopulated strategies, with mutation-type dynamics, which allow for nonzero switching to unpopulated strategies, in terms of a single transition function. Under certain conditions, this model yields an endemic population playing non-Nash-equilibrium strategies. In addition, a Hopf bifurcation with a limit cycle may occur in the generalized rock-scissors-paper game, unlike the replicator equation. Nonetheless, many of the Folk Theorem results are shown to hold for this model.

  8. The evolutionary journey of Argonaute proteins

    PubMed Central

    Swarts, Daan C; Makarova, Kira; Wang, Yanli; Nakanishi, Kotaro; Ketting, René F; Koonin, Eugene V; Patel, Dinshaw J; van der Oost, John

    2015-01-01

    Argonaute proteins are conserved throughout all domains of life. Recently characterized prokaryotic Argonaute proteins (pAgos) participate in host defense by DNA interference, whereas eukaryotic Argonaute proteins (eAgos) control a wide range of processes by RNA interference. Here we review molecular mechanisms of guide and target binding by Argonaute proteins, and describe how the conformational changes induced by target binding lead to target cleavage. On the basis of structural comparisons and phylogenetic analyses of pAgos and eAgos, we reconstruct the evolutionary journey of the Argonaute proteins through the three domains of life and discuss how different structural features of pAgos and eAgos relate to their distinct physiological roles. PMID:25192263

  9. Using Evolutionary Computation on GPS Position Correction

    PubMed Central

    2014-01-01

    More and more devices are equipped with global positioning system (GPS). However, those handheld devices with consumer-grade GPS receivers usually have low accuracy in positioning. A position correction algorithm is therefore useful in this case. In this paper, we proposed an evolutionary computation based technique to generate a correction function by two GPS receivers and a known reference location. Locating one GPS receiver on the known location and combining its longitude and latitude information and exact poisoning information, the proposed technique is capable of evolving a correction function by such. The proposed technique can be implemented and executed on handheld devices without hardware reconfiguration. Experiments are conducted to demonstrate performance of the proposed technique. Positioning error could be significantly reduced from the order of 10 m to the order of 1 m. PMID:24578657

  10. XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2011-02-01

    The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely

  11. Evolutionary mechanism unifies the hallmarks of cancer.

    PubMed

    Horne, Steven D; Pollick, Sarah A; Heng, Henry H Q

    2015-05-01

    The basis for the gene mutation theory of cancer that dominates current molecular cancer research consists of: the belief that gene-level aberrations such as mutations are the main cause of cancers, the concept that stepwise gene mutation accumulation drives cancer progression, and the hallmarks of cancer. The research community swiftly embraced the hallmarks of cancer, as such synthesis has supported the notions that common cancer genes are responsible for the majority of cancers and the complexity of cancer can be dissected into simplified molecular principles. The gene/pathway classification based on individual hallmarks provides explanation for the large number of diverse gene mutations, which is in contrast to the original estimation that only a handful of gene mutations would be discovered. Further, these hallmarks have been highly influential as they also provide the rationale and research direction for continued gene-based cancer research. While the molecular knowledge of these hallmarks is drastically increasing, the clinical implication remains limited, as cancer dynamics cannot be summarized by a few isolated/fixed molecular principles. Furthermore, the highly heterogeneous genetic signature of cancers, including massive stochastic genome alterations, challenges the utility of continuously studying each individual gene mutation under the framework of these hallmarks. It is therefore necessary to re-evaluate the concept of cancer hallmarks through the lens of cancer evolution. In this analysis, the evolutionary basis for the hallmarks of cancer will be discussed and the evolutionary mechanism of cancer suggested by the genome theory will be employed to unify the diverse molecular mechanisms of cancer.

  12. Papillomaviruses: Viral evolution, cancer and evolutionary medicine.

    PubMed

    Bravo, Ignacio G; Félez-Sánchez, Marta

    2015-01-28

    Papillomaviruses (PVs) are a numerous family of small dsDNA viruses infecting virtually all mammals. PVs cause infections without triggering a strong immune response, and natural infection provides only limited protection against reinfection. Most PVs are part and parcel of the skin microbiota. In some cases, infections by certain PVs take diverse clinical presentations from highly productive self-limited warts to invasive cancers. We propose PVs as an excellent model system to study the evolutionary interactions between the immune system and pathogens causing chronic infections: genotypically, PVs are very diverse, with hundreds of different genotypes infecting skin and mucosa; phenotypically, they display extremely broad gradients and trade-offs between key phenotypic traits, namely productivity, immunogenicity, prevalence, oncogenicity and clinical presentation. Public health interventions have been launched to decrease the burden of PV-associated cancers, including massive vaccination against the most oncogenic human PVs, as well as systematic screening for PV chronic anogenital infections. Anti-PVs vaccines elicit protection against infection, induce cross-protection against closely related viruses and result in herd immunity. However, our knowledge on the ecological and intrapatient dynamics of PV infections remains fragmentary. We still need to understand how the novel anthropogenic selection pressures posed by vaccination and screening will affect viral circulation and epidemiology. We present here an overview of PV evolution and the connection between PV genotypes and the phenotypic, clinical manifestations of the diseases they cause. This differential link between viral evolution and the gradient cancer-warts-asymptomatic infections makes PVs a privileged playground for evolutionary medicine research.

  13. Plant grafting: new mechanisms, evolutionary implications

    PubMed Central

    Goldschmidt, Eliezer E.

    2014-01-01

    Grafting, an old plant propagation practice, is still widely used with fruit trees and in recent decades also with vegetables. Taxonomic proximity is a general prerequisite for successful graft-take and long-term survival of the grafted, composite plant. However, the mechanisms underlying interspecific graft incompatibility are as yet insufficiently understood. Hormonal signals, auxin in particular, are believed to play an important role in the wound healing and vascular regeneration within the graft union zone. Incomplete and convoluted vascular connections impede the vital upward and downward whole plant transfer routes. Long-distance protein, mRNA and small RNA graft-transmissible signals currently emerge as novel mechanisms which regulate nutritional and developmental root/top relations and may play a pivotal role in grafting physiology. Grafting also has significant pathogenic projections. On one hand, stock to scion mechanical contact enables the spread of diseases, even without a complete graft union. But, on the other hand, grafting onto resistant rootstocks serves as a principal tool in the management of fruit tree plagues and vegetable soil-borne diseases. The ‘graft hybrid’ historic controversy has not yet been resolved. Recent evidence suggests that epigenetic modification of DNA-methylation patterns may account for certain graft-transformation phenomena. Root grafting is a wide spread natural phenomenon; both intraspecific and interspecific root grafts have been recorded. Root grafts have an evolutionary role in the survival of storm-hit forest stands as well as in the spread of devastating diseases. A more fundamental evolutionary role is hinted by recent findings that demonstrate plastid and nuclear genome transfer between distinct Nicotiana species in the graft union zone, within a tissue culture system. This has led to the formation of alloploid cells that, under laboratory conditions, gave rise to a novel, alloploid Nicotiana species

  14. The evolutionary advantage of limited network knowledge.

    PubMed

    Larson, Jennifer M

    2016-06-07

    Groups of individuals have social networks that structure interactions within the groups; evolutionary theory increasingly uses this fact to explain the emergence of cooperation (Eshel and Cavalli-Sforza, 1982; Boyd and Richerson, 1988, 1989; Ohtsuki et al., 2006; Nowak et al., 2010; Van Veelen et al., 2012). This approach has resulted in a number of important insights for the evolution of cooperation in the biological and social sciences, but omits a key function of social networks that has persisted throughout recent evolutionary history (Apicella et al., 2012): their role in transmitting gossip about behavior within a group. Accounting for this well-established role of social networks among rational agents in a setting of indirect reciprocity not only shows a new mechanism by which the structure of networks is fitness-relevant, but also reveals that knowledge of social networks can be fitness-relevant as well. When groups enforce cooperation by sanctioning peers whom gossip reveals to have deviated, individuals in certain peripheral network positions are tempting targets of uncooperative behavior because gossip they share about misbehavior spreads slowly through the network. The ability to identify these individuals creates incentives to behave uncooperatively. Consequently, groups comprised of individuals who knew precise information about their social networks would be at a fitness disadvantage relative to groups of individuals with a coarser knowledge of their networks. Empirical work has consistently shown that modern humans know little about the structure of their own social networks and perform poorly when tasked with learning new ones. This robust empirical regularity may be the product of natural selection in an environment of strong selective pressure at the group level. Imprecise views of networks make enforcing cooperation easier.

  15. The evolutionary phylogeny of the oomycete "fungi".

    PubMed

    Beakes, Gordon W; Glockling, Sally L; Sekimoto, Satoshi

    2012-01-01

    Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate "superkingdom" clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum "Pseudofungi", which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main "saprolegnian" and "peronosporalean" lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host-pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic "saprolegnian line" is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.

  16. Evolutionary Genomics of Salmonella enterica Subspecies

    PubMed Central

    Desai, Prerak T.; Porwollik, Steffen; Long, Fred; Cheng, Pui; Wollam, Aye; Clifton, Sandra W.; Weinstock, George M.; McClelland, Michael

    2013-01-01

    ABSTRACT Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies enterica) is responsible for nearly all infections in humans and warm-blooded animals, while five other subspecies are isolated principally from cold-blooded animals. We sequenced 21 phylogenetically diverse strains, including two representatives from each of the previously unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica, to put this species into an evolutionary perspective. The phylogeny of the subspecies was partly obscured by abundant recombination events between lineages and a relatively short period of time within which subspeciation took place. Nevertheless, a variety of different tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total of 285 gene families were identified that were recruited into subspecies enterica, and most of these are of unknown function. At least 2,807 gene families were identified in one or more of the other subspecies that are not found in subspecies I or Salmonella bongori. Among these gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third complete type III secretion system not present in subspecies enterica (I) isolates was found in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as the type VI secretion systems, which were recruited from four different lineages in five of six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the more-recently acquired regions in S. enterica are undergoing faster fixation rates than the rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions, are under ongoing selection to maintain their high AT content. PMID:23462113

  17. Evolutionary origin of the turtle skull.

    PubMed

    Bever, G S; Lyson, Tyler R; Field, Daniel J; Bhullar, Bhart-Anjan S

    2015-09-10

    Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology. Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus, a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles. Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land. Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics, and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development.

  18. Selective evolutionary generation systems: Theory and applications

    NASA Astrophysics Data System (ADS)

    Menezes, Amor A.

    This dissertation is devoted to the problem of behavior design, which is a generalization of the standard global optimization problem: instead of generating the optimizer, the generalization produces, on the space of candidate optimizers, a probability density function referred to as the behavior. The generalization depends on a parameter, the level of selectivity, such that as this parameter tends to infinity, the behavior becomes a delta function at the location of the global optimizer. The motivation for this generalization is that traditional off-line global optimization is non-resilient and non-opportunistic. That is, traditional global optimization is unresponsive to perturbations of the objective function. On-line optimization methods that are more resilient and opportunistic than their off-line counterparts typically consist of the computationally expensive sequential repetition of off-line techniques. A novel approach to inexpensive resilience and opportunism is to utilize the theory of Selective Evolutionary Generation Systems (SECS), which sequentially and probabilistically selects a candidate optimizer based on the ratio of the fitness values of two candidates and the level of selectivity. Using time-homogeneous, irreducible, ergodic Markov chains to model a sequence of local, and hence inexpensive, dynamic transitions, this dissertation proves that such transitions result in behavior that is called rational; such behavior is desirable because it can lead to both efficient search for an optimizer as well as resilient and opportunistic behavior. The dissertation also identifies system-theoretic properties of the proposed scheme, including equilibria, their stability and their optimality. Moreover, this dissertation demonstrates that the canonical genetic algorithm with fitness proportional selection and the (1+1) evolutionary strategy are particular cases of the scheme. Applications in three areas illustrate the versatility of the SECS theory: flight

  19. Evolutionary Perspectives on the Development of Social Exchanges.

    ERIC Educational Resources Information Center

    Sheese, Brad E.; Graziano, William G.

    2002-01-01

    Argues that apparent incompatibilities between social exchange and developmental perspectives can be resolved by using evolutionary theories to extend the logic of social exchange. Discusses the implications of an expanded evolutionary perspective on social exchange and development, proposing that developmental context and genetic relatedness may…

  20. Regulatory Evolution and Theoretical Arguments in Evolutionary Biology

    ERIC Educational Resources Information Center

    Ioannidis, Stavros

    2013-01-01

    The "cis"-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for "cis"-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current…