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Sample records for evolutionary pattern search

  1. Evolutionary pattern search algorithms

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Patterns of Evolutionary Speed: In Search of a Causal Mechanism

    Directory of Open Access Journals (Sweden)

    Len N. Gillman

    2013-12-01

    Full Text Available The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns of diversity and diversification. Here we review the mechanisms that have been proposed to explain these biogeographic patterns in rates of genetic evolution. Tests of several proposed mechanisms have produced equivocal results, whereas others such as those invoking annual metabolic activity, or a “Red Queen” effect, remain unexplored. However, rates of genetic evolution have been associated with both productivity mediated rates of germ cell division and active metabolic rates and these explanations therefore justify further empirical investigation.

  3. A Convergence Analysis of Unconstrained and Bound Constrained Evolutionary Pattern Search

    Energy Technology Data Exchange (ETDEWEB)

    Hart, W.E.

    1999-04-22

    The authors present and analyze a class of evolutionary algorithms for unconstrained and bound constrained optimization on R{sup n}: evolutionary pattern search algorithms (EPSAs). EPSAs adaptively modify the step size of the mutation operator in response to the success of previous optimization steps. The design of EPSAs is inspired by recent analyses of pattern search methods. They show that EPSAs can be cast as stochastic pattern search methods, and they use this observation to prove that EpSAs have a probabilistic weak stationary point convergence theory. This work provides the first convergence analysis for a class of evolutionary algorithms that guarantees convergence almost surely to a stationary point of a nonconvex objective function.

  4. Search Patterns

    CERN Document Server

    Morville, Peter

    2010-01-01

    What people are saying about Search Patterns "Search Patterns is a delight to read -- very thoughtful and thought provoking. It's the most comprehensive survey of designing effective search experiences I've seen." --Irene Au, Director of User Experience, Google "I love this book! Thanks to Peter and Jeffery, I now know that search (yes, boring old yucky who cares search) is one of the coolest ways around of looking at the world." --Dan Roam, author, The Back of the Napkin (Portfolio Hardcover) "Search Patterns is a playful guide to the practical concerns of search interface design. It cont

  5. Evolutionary Minority Game with searching behavior

    Science.gov (United States)

    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.

  6. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...

  7. Evolutionary change - patterns and processes

    Directory of Open Access Journals (Sweden)

    Francisco M. Salzano

    2005-12-01

    Full Text Available The present review considered: (a the factors that conditioned the early transition from non-life to life; (b genome structure and complexity in prokaryotes, eukaryotes, and organelles; (c comparative human chromosome genomics; and (d the Brazilian contribution to some of these studies. Understanding the dialectical conflict between freedom and organization is fundamental to give meaning to the patterns and processes of organic evolution.A presente revisão considerou: (a os fatores que condicionaram a transição inicial entre não-vida e vida; (b a estrutura e complexidade genômica em procariotos, eucariotos e organelas; (c a genômica comparada dos cromossomos humanos; (d a contribuição brasileira a alguns desses estudos. A compreensão do conflito dialético entre liberdade e organização é fundamental para dar significado aos padrões e processos da evolução orgânica.

  8. Learning from evolutionary optimization by retracing search paths

    NARCIS (Netherlands)

    van der Walle, P.; Savolainen, Janne; Kuipers, L.; Herek, Jennifer Lynn

    2009-01-01

    Evolutionary search algorithms are used routinely to find optimal solutions for multi-parameter problems, such as complex pulse shapes in coherent control experiments. The algorithms are based on evolving a set of trial solutions iteratively until an optimum is reached, at which point the experiment

  9. Combined electronic structure and evolutionary search approach to materials design

    DEFF Research Database (Denmark)

    Johannesson, Gisli Holmar; Bligaard, Thomas; Ruban, Andrei

    2002-01-01

    We show that density functional theory calculations have reached an accuracy and speed making it possible to use them in conjunction with an evolutionary algorithm to search for materials with specific properties. The approach is illustrated by finding the most stable four component alloys out of...

  10. Foraging patterns in online searches

    Science.gov (United States)

    Wang, Xiangwen; Pleimling, Michel

    2017-03-01

    Nowadays online searches are undeniably the most common form of information gathering, as witnessed by billions of clicks generated each day on search engines. In this work we describe online searches as foraging processes that take place on the semi-infinite line. Using a variety of quantities like probability distributions and complementary cumulative distribution functions of step length and waiting time as well as mean square displacements and entropies, we analyze three different click-through logs that contain the detailed information of millions of queries submitted to search engines. Notable differences between the different logs reveal an increased efficiency of the search engines. In the language of foraging, the newer logs indicate that online searches overwhelmingly yield local searches (i.e., on one page of links provided by the search engines), whereas for the older logs the foraging processes are a combination of local searches and relocation phases that are power law distributed. Our investigation of click logs of search engines therefore highlights the presence of intermittent search processes (where phases of local explorations are separated by power law distributed relocation jumps) in online searches. It follows that good search engines enable the users to find the information they are looking for through a local exploration of a single page with search results, whereas for poor search engine users are often forced to do a broader exploration of different pages.

  11. Applications of evolutionary computation in image processing and pattern recognition

    CERN Document Server

    Cuevas, Erik; Perez-Cisneros, Marco

    2016-01-01

    This book presents the use of efficient Evolutionary Computation (EC) algorithms for solving diverse real-world image processing and pattern recognition problems. It provides an overview of the different aspects of evolutionary methods in order to enable the reader in reaching a global understanding of the field and, in conducting studies on specific evolutionary techniques that are related to applications in image processing and pattern recognition. It explains the basic ideas of the proposed applications in a way that can also be understood by readers outside of the field. Image processing and pattern recognition practitioners who are not evolutionary computation researchers will appreciate the discussed techniques beyond simple theoretical tools since they have been adapted to solve significant problems that commonly arise on such areas. On the other hand, members of the evolutionary computation community can learn the way in which image processing and pattern recognition problems can be translated into an...

  12. Tree patterns with full text search

    NARCIS (Netherlands)

    Peetz, M.H.; Marx, M.

    2010-01-01

    Tree patterns with full text search form the core of both XQuery Full Text and the NEXI query language. On such queries, users expect a relevance-ranked list of XML elements as an answer. But this requirement may lead to undesirable behavior of XML retrieval systems: two queries which are

  13. Evolutionary rate patterns of the Gibberellin pathway genes

    Directory of Open Access Journals (Sweden)

    Zhang Fu-min

    2009-08-01

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

  14. Asynchronous parallel pattern search for nonlinear optimization

    Energy Technology Data Exchange (ETDEWEB)

    P. D. Hough; T. G. Kolda; V. J. Torczon

    2000-01-01

    Parallel pattern search (PPS) can be quite useful for engineering optimization problems characterized by a small number of variables (say 10--50) and by expensive objective function evaluations such as complex simulations that take from minutes to hours to run. However, PPS, which was originally designed for execution on homogeneous and tightly-coupled parallel machine, is not well suited to the more heterogeneous, loosely-coupled, and even fault-prone parallel systems available today. Specifically, PPS is hindered by synchronization penalties and cannot recover in the event of a failure. The authors introduce a new asynchronous and fault tolerant parallel pattern search (AAPS) method and demonstrate its effectiveness on both simple test problems as well as some engineering optimization problems

  15. Searching social networks for subgraph patterns

    Science.gov (United States)

    Ogaard, Kirk; Kase, Sue; Roy, Heather; Nagi, Rakesh; Sambhoos, Kedar; Sudit, Moises

    2013-06-01

    Software tools for Social Network Analysis (SNA) are being developed which support various types of analysis of social networks extracted from social media websites (e.g., Twitter). Once extracted and stored in a database such social networks are amenable to analysis by SNA software. This data analysis often involves searching for occurrences of various subgraph patterns (i.e., graphical representations of entities and relationships). The authors have developed the Graph Matching Toolkit (GMT) which provides an intuitive Graphical User Interface (GUI) for a heuristic graph matching algorithm called the Truncated Search Tree (TruST) algorithm. GMT is a visual interface for graph matching algorithms processing large social networks. GMT enables an analyst to draw a subgraph pattern by using a mouse to select categories and labels for nodes and links from drop-down menus. GMT then executes the TruST algorithm to find the top five occurrences of the subgraph pattern within the social network stored in the database. GMT was tested using a simulated counter-insurgency dataset consisting of cellular phone communications within a populated area of operations in Iraq. The results indicated GMT (when executing the TruST graph matching algorithm) is a time-efficient approach to searching large social networks. GMT's visual interface to a graph matching algorithm enables intelligence analysts to quickly analyze and summarize the large amounts of data necessary to produce actionable intelligence.

  16. In silico analysis of evolutionary patterns in restriction endonucleases.

    Science.gov (United States)

    Singh, Tiratha Raj; Pardasani, Kamal Raj

    2009-01-01

    Restriction endonucleases represent one of the best studied examples of DNA binding proteins. Type II restriction endonucleases recognize short sequences of foreign DNA and cleave the target on both strands with remarkable sequence specificity. Type II restriction endonucleases are part of restriction modification systems. Restriction modification systems occur ubiquitously among bacteria and archaea. Restriction endonucleases are indispensable tools in molecular biology and biotechnology. They are important model system for specific protein-nucleic acid interactions and also serve as good example for investigating structural, functional and evolutionary relationships among various biomolecules. The interaction between restriction endonucleases and their recognition sequences plays a crucial role in biochemical activities like catalytic site/metal binding, DNA repair and recombination etc. We study various patterns in restriction endonucleases type II and analyzed their structural, functional and evolutionary role. Our studies support X-ray crystallographic studies, arguing for divergence and molecular evolution. Conservation patterns of the nuclease superfamily have also been analyzed by estimating site-specific evolutionary rates for the analyzed structures related to respective chains in this study.

  17. Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

    Directory of Open Access Journals (Sweden)

    Richard W R Wallbank

    2016-01-01

    Full Text Available An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

  18. Speeding up Evolutionary Search by Small Fitness Fluctuations.

    Science.gov (United States)

    Otwinowski, Jakub; Tanase-Nicola, Sorin; Nemenman, Ilya

    2011-07-01

    We consider a fixed size population that undergoes an evolutionary adaptation in the weak mutation rate limit, which we model as a biased Langevin process in the genotype space. We show analytically and numerically that, if the fitness landscape has a small highly epistatic (rough) and time-varying component, then the population genotype exhibits a high effective diffusion in the genotype space and is able to escape local fitness minima with a large probability. We argue that our principal finding that even very small time-dependent fluctuations of fitness can substantially speed up evolution is valid for a wide class of models.

  19. On the Runtime of Randomized Local Search and Simple Evolutionary Algorithms for Dynamic Makespan Scheduling

    DEFF Research Database (Denmark)

    Neumann, Frank; Witt, Carsten

    2015-01-01

    Evolutionary algorithms have been frequently used for dynamic optimization problems. With this paper, we contribute to the theoretical understanding of this research area. We present the first computational complexity analysis of evolutionary algorithms for a dynamic variant of a classical...... combinatorial optimization problem, namely makespan scheduling. We study the model of a strong adversary which is allowed to change one job at regular intervals. Furthermore, we investigate the setting of random changes. Our results show that randomized local search and a simple evolutionary algorithm are very...... effective in dynamically tracking changes made to the problem instance....

  20. The Roles and Evolutionary Patterns of Intronless Genes in Deuterostomes

    Directory of Open Access Journals (Sweden)

    Ming Zou

    2011-01-01

    Full Text Available Genes without introns are a characteristic feature of prokaryotes, but there are still a number of intronless genes in eukaryotes. To study these eukaryotic genes that have prokaryotic architecture could help to understand the evolutionary patterns of related genes and genomes. Our analyses revealed a number of intronless genes that reside in 6 deuterostomes (sea urchin, sea squirt, zebrafish, chicken, platypus, and human. We also determined the conservation for each intronless gene in archaea, bacteria, fungi, plants, metazoans, and other eukaryotes. Proportions of intronless genes that are inherited from the common ancestor of archaea, bacteria, and eukaryotes in these species were consistent with their phylogenetic positions, with more proportions of ancient intronless genes residing in more primitive species. In these species, intronless genes belong to different cellular roles and gene ontology (GO categories, and some of these functions are very basic. Part of intronless genes is derived from other intronless genes or multiexon genes in each species. In conclusion, we showed that a varying number and proportion of intronless genes reside in these 6 deuterostomes, and some of them function importantly. These genes are good candidates for subsequent functional and evolutionary analyses specifically.

  1. Using evolutionary tools to search for novel psychoactive plants

    DEFF Research Database (Denmark)

    Halse-Gramkow, Morten; Ernst, Madeleine; Rønsted, Nina

    2016-01-01

    Bioprospecting is the search for valuable products from natural sources. Given that most species are poorly known, a key question is where to search. Ethnodirected bioprospecting approaches use traditional knowledge in the process of selecting plants to screen for desired properties...... and phylogenetic distribution of psychoactive plants. We compiled a database of 501 psychoactive plant species and their properties from published sources. We mapped these plant attributes on a phylogenetic tree of all land plant genera and showed that psychoactive properties are not randomly distributed...... on the phylogeny of land plants; instead certain plant lineages show overabundance of psychoactive properties. Furthermore, employing a "hot nodes" approach to identify these lineages, we can narrow down our search for novel psychoactive plants to 8.5% of all plant genera for psychoactivity in general and 1...

  2. Search pattern of databases by the undergraduate students of ...

    African Journals Online (AJOL)

    The main objective of this study is to assess the awareness and search pattern of databases in order to determine the extent to which user are aware and search for databases by examining the relationship between their Awareness and search patterns of Databases, and their information literacy skills. The methodology ...

  3. Searching for Pulsars Using Image Pattern Recognition

    Science.gov (United States)

    Zhu, W. W.; Berndsen, A.; Madsen, E. C.; Tan, M.; Stairs, I. H.; Brazier, A.; Lazarus, P.; Lynch, R.; Scholz, P.; Stovall, K.; Ransom, S. M.; Banaszak, S.; Biwer, C. M.; Cohen, S.; Dartez, L. P.; Flanigan, J.; Lunsford, G.; Martinez, J. G.; Mata, A.; Rohr, M.; Walker, A.; Allen, B.; Bhat, N. D. R.; Bogdanov, S.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J. S.; Desvignes, G.; Ferdman, R. D.; Freire, P. C. C.; Hessels, J. W. T.; Jenet, F. A.; Kaplan, D. L.; Kaspi, V. M.; Knispel, B.; Lee, K. J.; van Leeuwen, J.; Lyne, A. G.; McLaughlin, M. A.; Siemens, X.; Spitler, L. G.; Venkataraman, A.

    2014-02-01

    In the modern era of big data, many fields of astronomy are generating huge volumes of data, the analysis of which can sometimes be the limiting factor in research. Fortunately, computer scientists have developed powerful data-mining techniques that can be applied to various fields. In this paper, we present a novel artificial intelligence (AI) program that identifies pulsars from recent surveys by using image pattern recognition with deep neural nets—the PICS (Pulsar Image-based Classification System) AI. The AI mimics human experts and distinguishes pulsars from noise and interference by looking for patterns from candidate plots. Different from other pulsar selection programs that search for expected patterns, the PICS AI is taught the salient features of different pulsars from a set of human-labeled candidates through machine learning. The training candidates are collected from the Pulsar Arecibo L-band Feed Array (PALFA) survey. The information from each pulsar candidate is synthesized in four diagnostic plots, which consist of image data with up to thousands of pixels. The AI takes these data from each candidate as its input and uses thousands of such candidates to train its ~9000 neurons. The deep neural networks in this AI system grant it superior ability to recognize various types of pulsars as well as their harmonic signals. The trained AI's performance has been validated with a large set of candidates from a different pulsar survey, the Green Bank North Celestial Cap survey. In this completely independent test, the PICS ranked 264 out of 277 pulsar-related candidates, including all 56 previously known pulsars and 208 of their harmonics, in the top 961 (1%) of 90,008 test candidates, missing only 13 harmonics. The first non-pulsar candidate appears at rank 187, following 45 pulsars and 141 harmonics. In other words, 100% of the pulsars were ranked in the top 1% of all candidates, while 80% were ranked higher than any noise or interference. The

  4. Searching for pulsars using image pattern recognition

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, W. W.; Berndsen, A.; Madsen, E. C.; Tan, M.; Stairs, I. H. [Department of Physics and Astronomy, 6224 Agricultural Road, University of British Columbia, Vancouver, BC, V6T 1Z1 (Canada); Brazier, A. [Astronomy Department, Cornell University, Ithaca, NY 14853 (United States); Lazarus, P. [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Lynch, R.; Scholz, P. [Department of Physics, McGill University, Montreal, QC H3A 2T8 (Canada); Stovall, K.; Cohen, S.; Dartez, L. P.; Lunsford, G.; Martinez, J. G.; Mata, A. [Center for Advanced Radio Astronomy, University of Texas at Brownsville, Brownsville, TX 78520 (United States); Ransom, S. M. [NRAO, Charlottesville, VA 22903 (United States); Banaszak, S.; Biwer, C. M.; Flanigan, J.; Rohr, M., E-mail: zhuww@phas.ubc.ca, E-mail: berndsen@phas.ubc.ca [Center for Gravitation, Cosmology and Astrophysics. University of Wisconsin Milwaukee, Milwaukee, WI 53211 (United States); and others

    2014-02-01

    In the modern era of big data, many fields of astronomy are generating huge volumes of data, the analysis of which can sometimes be the limiting factor in research. Fortunately, computer scientists have developed powerful data-mining techniques that can be applied to various fields. In this paper, we present a novel artificial intelligence (AI) program that identifies pulsars from recent surveys by using image pattern recognition with deep neural nets—the PICS (Pulsar Image-based Classification System) AI. The AI mimics human experts and distinguishes pulsars from noise and interference by looking for patterns from candidate plots. Different from other pulsar selection programs that search for expected patterns, the PICS AI is taught the salient features of different pulsars from a set of human-labeled candidates through machine learning. The training candidates are collected from the Pulsar Arecibo L-band Feed Array (PALFA) survey. The information from each pulsar candidate is synthesized in four diagnostic plots, which consist of image data with up to thousands of pixels. The AI takes these data from each candidate as its input and uses thousands of such candidates to train its ∼9000 neurons. The deep neural networks in this AI system grant it superior ability to recognize various types of pulsars as well as their harmonic signals. The trained AI's performance has been validated with a large set of candidates from a different pulsar survey, the Green Bank North Celestial Cap survey. In this completely independent test, the PICS ranked 264 out of 277 pulsar-related candidates, including all 56 previously known pulsars and 208 of their harmonics, in the top 961 (1%) of 90,008 test candidates, missing only 13 harmonics. The first non-pulsar candidate appears at rank 187, following 45 pulsars and 141 harmonics. In other words, 100% of the pulsars were ranked in the top 1% of all candidates, while 80% were ranked higher than any noise or interference. The

  5. Playing Multi-Action Adversarial Games: Online Evolutionary Planning versus Tree Search

    DEFF Research Database (Denmark)

    Justesen, Niels; Mahlmann, Tobias; Risi, Sebastian

    2017-01-01

    We address the problem of playing turn-based multi-action adversarial games, which include many strategy games with extremely high branching factors as players take multiple actions each turn. This leads to the breakdown of standard tree search methods, including Monte Carlo Tree Search (MCTS......), as they become unable to reach a sufficient depth in the game tree. In this paper, we introduce Online Evolutionary Planning (OEP) to address this challenge, which searches for combinations of actions to perform during a single turn guided by a fitness function that evaluates the quality of a particular state...... of plans more efficiently than any of the tested tree search methods as it has a relative advantage when the number of actions per turn increases....

  6. Can evolutionary principles explain patterns of family violence?

    Science.gov (United States)

    Archer, John

    2013-03-01

    The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated by (a) parents to unrelated children, (b) parents to genetic offspring, and (c) offspring to parents and between (d) siblings and (e) sexual partners. Precise figures for risks have been calculated where possible. The major conclusions are that most of the evidence is consistent with evolutionary predictions derived from kin selection and reproductive value: There were (a) higher rates of violence to stepchildren, (b) a decline in violence with the age of offspring, and (c) an increase in violence with parental age, while (d) violence between siblings was generally at a low level and concerned resource disputes. The issue of distinguishing evolutionary from alternative explanations is addressed throughout and is problematic for predictions derived from reproductive value. The main evolutionary explanation for male partner violence, mate guarding as a result of paternity uncertainty, cannot explain Western studies where sex differences in control and violence between partners were absent, although other aspects of male partner violence are consistent with it, and it may explain sex differences in traditional cultures. Recurrent problems in evaluating the evidence were to control for possible confounds and thus to distinguish evolutionary from alternative explanations. Suggestions are outlined to address this and other issues arising from the review. © 2013 American Psychological Association

  7. Cultural evolutionary modeling of patterns in language change : exercises in evolutionary linguistics

    NARCIS (Netherlands)

    Landsbergen, Frank

    2009-01-01

    This thesis describes the use of an evolutionary linguistic approach in the study of language change in a series of case studies. The main purpose of this exercise is to get a better insight in the mechanisms that have played a role in the respective cases of change. Human language can be

  8. Systematic search for low-enthalpy sp3 carbon allotropes using evolutionary metadynamics

    Science.gov (United States)

    Zhu, Qiang; Zeng, Qingfeng; Oganov, Artem R.

    2012-05-01

    We present a systematic search for low-energy metastable superhard carbon allotropes by using the recently developed evolutionary metadynamics technique. It is known that cold compression of graphite produces an allotrope at 15-20 GPa. Here we look for all low-enthalpy structures accessible from graphite. Starting from 2H- or 3R-graphite and applying a pressure of 20 GPa, a large variety of intermediate sp3 carbon allotropes were observed in evolutionary metadynamics simulation. Our calculation not only found all the previous proposed candidates for “superhard graphite,” but also predicted two allotropes (X-carbon and Y-carbon) showing unusual types of 5+7 and 4+8 topologies. These superhard carbon allotropes can be classified into five families based on 6 (diamond/lonsdaleite), 5+7 (M- and W-carbon), 5+7 (X-carbon), 4+8 (bct-C4), and 4+8 (Y-carbon) topologies. This study shows that evolutionary metadynamics is a powerful approach both to find the global minima and systematically search for low-energy metastable phases reachable from given starting materials.

  9. Patterns of Strong Coupling for LHC Searches

    CERN Document Server

    Liu, Da; Rattazzi, Riccardo; Riva, Francesco

    2016-11-23

    Even though the Standard Model (SM) is weakly coupled at the Fermi scale, a new strong dynamics involving its degrees of freedom may conceivably lurk at slightly higher energies, in the multi TeV range. Approximate symmetries provide a structurally robust context where, within the low energy description, the dimensionless SM couplings are weak, while the new strong dynamics manifests itself exclusively through higher-derivative interactions. We present an exhaustive classification of such scenarios in the form of effective field theories, paying special attention to new classes of models where the strong dynamics involves, along with the Higgs boson, the SM gauge bosons and/or the fermions. The IR softness of the new dynamics suppresses its effects at LEP energies, but deviations are in principle detectable at the LHC, even at energies below the threshold for production of new states. Our construction provides the so far unique structurally robust context where to motivate several searches in Higgs physics, d...

  10. Patterns of strong coupling for LHC searches

    Science.gov (United States)

    Liu, Da; Pomarol, Alex; Rattazzi, Riccardo; Riva, Francesco

    2016-11-01

    Even though the Standard Model (SM) is weakly coupled at the Fermi scale, a new strong dynamics involving its degrees of freedom may conceivably lurk at slightly higher energies, in the multi TeV range. Approximate symmetries provide a structurally robust context where, within the low energy description, the dimensionless SM couplings are weak, while the new strong dynamics manifests itself exclusively through higher-derivative interactions. We present an exhaustive classification of such scenarios in the form of effective field theories, paying special attention to new classes of models where the strong dynamics involves, along with the Higgs boson, the SM gauge bosons and/or the fermions. The IR softness of the new dynamics suppresses its effects at LEP energies, but deviations are in principle detectable at the LHC, even at energies below the threshold for production of new states. We believe our construction provides the so far unique structurally robust context where to motivate several LHC searches in Higgs physics, diboson production, or W W scattering. Perhaps surprisingly, the interplay between weak coupling, strong coupling and derivatives, which is controlled by symmetries, can override the naive expansion in operator dimension, providing instances where dimension-8 dominates dimension-6, well within the domain of validity of the low energy effective theory. This result reveals the limitations of an analysis that is both ambitiously general and restricted to dimension-6 operators.

  11. Genetic evolutionary taboo search for optimal marker placement in infrared patient setup

    Energy Technology Data Exchange (ETDEWEB)

    Riboldi, M [TBMLab, Department of Bioengineering, Politecnico di Milano University, Plaza Leonardo da Vinci 32, 20133 Milan (Italy); Baroni, G [TBMLab, Department of Bioengineering, Politecnico di Milano University, Plaza Leonardo da Vinci 32, 20133 Milan (Italy); Spadea, M F [TBMLab, Department of Bioengineering, Politecnico di Milano University, Plaza Leonardo da Vinci 32, 20133 Milan (Italy); Tagaste, B [Medical Physics Department, European Institute of Oncology, Via Ripamonti 435, 20141 Milan (Italy); Garibaldi, C [Medical Physics Department, European Institute of Oncology, Via Ripamonti 435, 20141 Milan (Italy); Cambria, R [Medical Physics Department, European Institute of Oncology, Via Ripamonti 435, 20141 Milan (Italy); Orecchia, R [Radiotherapy Division, European Institute of Oncology, Via Ripamonti 435, 20141 Milan (Italy); Pedotti, A [TBMLab, Department of Bioengineering, Politecnico di Milano University, Plaza Leonardo da Vinci 32, 20133 Milan (Italy)

    2007-09-21

    In infrared patient setup adequate selection of the external fiducial configuration is required for compensating inner target displacements (target registration error, TRE). Genetic algorithms (GA) and taboo search (TS) were applied in a newly designed approach to optimal marker placement: the genetic evolutionary taboo search (GETS) algorithm. In the GETS paradigm, multiple solutions are simultaneously tested in a stochastic evolutionary scheme, where taboo-based decision making and adaptive memory guide the optimization process. The GETS algorithm was tested on a group of ten prostate patients, to be compared to standard optimization and to randomly selected configurations. The changes in the optimal marker configuration, when TRE is minimized for OARs, were specifically examined. Optimal GETS configurations ensured a 26.5% mean decrease in the TRE value, versus 19.4% for conventional quasi-Newton optimization. Common features in GETS marker configurations were highlighted in the dataset of ten patients, even when multiple runs of the stochastic algorithm were performed. Including OARs in TRE minimization did not considerably affect the spatial distribution of GETS marker configurations. In conclusion, the GETS algorithm proved to be highly effective in solving the optimal marker placement problem. Further work is needed to embed site-specific deformation models in the optimization process.

  12. Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

    Directory of Open Access Journals (Sweden)

    Chira Camelia

    2011-07-01

    Full Text Available Abstract Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods.

  13. Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

    Science.gov (United States)

    2011-01-01

    Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP) model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods. PMID:21801435

  14. Pattern Nulling of Linear Antenna Arrays Using Backtracking Search Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Kerim Guney

    2015-01-01

    Full Text Available An evolutionary method based on backtracking search optimization algorithm (BSA is proposed for linear antenna array pattern synthesis with prescribed nulls at interference directions. Pattern nulling is obtained by controlling only the amplitude, position, and phase of the antenna array elements. BSA is an innovative metaheuristic technique based on an iterative process. Various numerical examples of linear array patterns with the prescribed single, multiple, and wide nulls are given to illustrate the performance and flexibility of BSA. The results obtained by BSA are compared with the results of the following seventeen algorithms: particle swarm optimization (PSO, genetic algorithm (GA, modified touring ant colony algorithm (MTACO, quadratic programming method (QPM, bacterial foraging algorithm (BFA, bees algorithm (BA, clonal selection algorithm (CLONALG, plant growth simulation algorithm (PGSA, tabu search algorithm (TSA, memetic algorithm (MA, nondominated sorting GA-2 (NSGA-2, multiobjective differential evolution (MODE, decomposition with differential evolution (MOEA/D-DE, comprehensive learning PSO (CLPSO, harmony search algorithm (HSA, seeker optimization algorithm (SOA, and mean variance mapping optimization (MVMO. The simulation results show that the linear antenna array synthesis using BSA provides low side-lobe levels and deep null levels.

  15. Evolutionary Policy Transfer and Search Methods for Boosting Behavior Quality: RoboCup Keep-Away Case Study

    Directory of Open Access Journals (Sweden)

    Geoff Nitschke

    2017-11-01

    Full Text Available This study evaluates various evolutionary search methods to direct neural controller evolution in company with policy (behavior transfer across increasingly complex collective robotic (RoboCup keep-away tasks. Robot behaviors are first evolved in a source task and then transferred for further evolution to more complex target tasks. Evolutionary search methods tested include objective-based search (fitness function, behavioral and genotypic diversity maintenance, and hybrids of such diversity maintenance and objective-based search. Evolved behavior quality is evaluated according to effectiveness and efficiency. Effectiveness is the average task performance of transferred and evolved behaviors, where task performance is the average time the ball is controlled by a keeper team. Efficiency is the average number of generations taken for the fittest evolved behaviors to reach a minimum task performance threshold given policy transfer. Results indicate that policy transfer coupled with hybridized evolution (behavioral diversity maintenance and objective-based search addresses the bootstrapping problem for increasingly complex keep-away tasks. That is, this hybrid method (coupled with policy transfer evolves behaviors that could not otherwise be evolved. Also, this hybrid evolutionary search was demonstrated as consistently evolving topologically simple neural controllers that elicited high-quality behaviors.

  16. Optimal search patterns in honeybee orientation flights are robust against emerging infectious diseases.

    Science.gov (United States)

    Wolf, Stephan; Nicholls, Elizabeth; Reynolds, Andrew M; Wells, Patricia; Lim, Ka S; Paxton, Robert J; Osborne, Juliet L

    2016-09-12

    Lévy flights are scale-free (fractal) search patterns found in a wide range of animals. They can be an advantageous strategy promoting high encounter rates with rare cues that may indicate prey items, mating partners or navigational landmarks. The robustness of this behavioural strategy to ubiquitous threats to animal performance, such as pathogens, remains poorly understood. Using honeybees radar-tracked during their orientation flights in a novel landscape, we assess for the first time how two emerging infectious diseases (Nosema sp. and the Varroa-associated Deformed wing virus (DWV)) affect bees' behavioural performance and search strategy. Nosema infection, unlike DWV, affected the spatial scale of orientation flights, causing significantly shorter and more compact flights. However, in stark contrast to disease-dependent temporal fractals, we find the same prevalence of optimal Lévy flight characteristics (μ ≈ 2) in both healthy and infected bees. We discuss the ecological and evolutionary implications of these surprising insights, arguing that Lévy search patterns are an emergent property of fundamental characteristics of neuronal and sensory components of the decision-making process, making them robust against diverse physiological effects of pathogen infection and possibly other stressors.

  17. A Hybrid Evolutionary Algorithm to Quadratic Three-Dimensional Assignment Problem with Local Search for Many-Core Graphics Processors

    Science.gov (United States)

    Lipinski, Piotr

    This paper concerns the quadratic three-dimensional assignment problem (Q3AP), an extension of the quadratic assignment problem (QAP), and proposes an efficient hybrid evolutionary algorithm combining stochastic optimization and local search with a number of crossover operators, a number of mutation operators and an auto-adaptation mechanism. Auto-adaptation manages the pool of evolutionary operators applying different operators in different computation phases to better explore the search space and to avoid premature convergence. Local search additionally optimizes populations of candidate solutions and accelerates evolutionary search. It uses a many-core graphics processor to optimize a number of solutions in parallel, which enables its incorporation into the evolutionary algorithm without excessive increases in the computation time. Experiments performed on benchmark Q3AP instances derived from the classic QAP instances proposed by Nugent et al. confirmed that the proposed algorithm is able to find optimal solutions to Q3AP in a reasonable time and outperforms best known results found in the literature.

  18. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation.

    Directory of Open Access Journals (Sweden)

    Philippe Julien

    Full Text Available As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore the original transcriptional output, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI. However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. Here we trace the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials, whereas we do not detect a global upregulation of this chromosome in placental mammals. However, we find that a subset of autosomal genes interacting with X-linked genes have become downregulated in placentals upon the emergence of sex chromosomes. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have partially homologous sex chromosome systems, partial upregulation of the X (Z in birds evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.

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

    Science.gov (United States)

    Krasny, Darren P; Orin, David E

    2004-08-01

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

  20. SYNTHESIS OF DUAL RADIATION PATTERN OF RECTANGULAR PLANAR ARRAY ANTENNA USING EVOLUTIONARY ALGORITHM

    Directory of Open Access Journals (Sweden)

    Debasis Mandal

    2015-09-01

    Full Text Available A pattern synthesis method based on Evolutionary Algorithm is presented to generate a dual radiation pattern from a planar array of isotropic antennas. The desired patterns are obtained by finding out optimum set of elements excitations. Flat-top and Pencil beams share a common optimum amplitude distribution among the array elements. Flat-top beam is generated by updating the zero phases with the optimum phases among the elements. 4 bit discrete amplitudes and 5 bit discrete phases have been taken to simplify the design of the feed network. Results clearly show the effectiveness of the proposed method.

  1. Plans, Patterns, and Move Categories Guiding a Highly Selective Search

    Science.gov (United States)

    Trippen, Gerhard

    In this paper we present our ideas for an Arimaa-playing program (also called a bot) that uses plans and pattern matching to guide a highly selective search. We restrict move generation to moves in certain move categories to reduce the number of moves considered by the bot significantly. Arimaa is a modern board game that can be played with a standard Chess set. However, the rules of the game are not at all like those of Chess. Furthermore, Arimaa was designed to be as simple and intuitive as possible for humans, yet challenging for computers. While all established Arimaa bots use alpha-beta search with a variety of pruning techniques and other heuristics ending in an extensive positional leaf node evaluation, our new bot, Rat, starts with a positional evaluation of the current position. Based on features found in the current position - supported by pattern matching using a directed position graph - our bot Rat decides which of a given set of plans to follow. The plan then dictates what types of moves can be chosen. This is another major difference from bots that generate "all" possible moves for a particular position. Rat is only allowed to generate moves that belong to certain categories. Leaf nodes are evaluated only by a straightforward material evaluation to help avoid moves that lose material. This highly selective search looks, on average, at only 5 moves out of 5,000 to over 40,000 possible moves in a middle game position.

  2. Optimization of machining processes using pattern search algorithm

    Directory of Open Access Journals (Sweden)

    Miloš Madić

    2014-04-01

    Full Text Available Optimization of machining processes not only increases machining efficiency and economics, but also the end product quality. In recent years, among the traditional optimization methods, stochastic direct search optimization methods such as meta-heuristic algorithms are being increasingly applied for solving machining optimization problems. Their ability to deal with complex, multi-dimensional and ill-behaved optimization problems made them the preferred optimization tool by most researchers and practitioners. This paper introduces the use of pattern search (PS algorithm, as a deterministic direct search optimization method, for solving machining optimization problems. To analyze the applicability and performance of the PS algorithm, six case studies of machining optimization problems, both single and multi-objective, were considered. The PS algorithm was employed to determine optimal combinations of machining parameters for different machining processes such as abrasive waterjet machining, turning, turn-milling, drilling, electrical discharge machining and wire electrical discharge machining. In each case study the optimization solutions obtained by the PS algorithm were compared with the optimization solutions that had been determined by past researchers using meta-heuristic algorithms. Analysis of obtained optimization results indicates that the PS algorithm is very applicable for solving machining optimization problems showing good competitive potential against stochastic direct search methods such as meta-heuristic algorithms. Specific features and merits of the PS algorithm were also discussed.

  3. Drivers’ Visual Search Patterns during Overtaking Maneuvers on Freeway

    Directory of Open Access Journals (Sweden)

    Wenhui Zhang

    2016-11-01

    Full Text Available Drivers gather traffic information primarily by means of their vision. Especially during complicated maneuvers, such as overtaking, they need to perceive a variety of characteristics including the lateral and longitudinal distances with other vehicles, the speed of others vehicles, lane occupancy, and so on, to avoid crashes. The primary object of this study is to examine the appropriate visual search patterns during overtaking maneuvers on freeways. We designed a series of driving simulating experiments in which the type and speed of the leading vehicle were considered as two influential factors. One hundred and forty participants took part in the study. The participants overtook the leading vehicles just like they would usually do so, and their eye movements were collected by use of the Eye Tracker. The results show that participants’ gaze durations and saccade durations followed normal distribution patterns and that saccade angles followed a log-normal distribution pattern. It was observed that the type of leading vehicle significantly impacted the drivers’ gaze duration and gaze frequency. As the speed of a leading vehicle increased, subjects’ saccade durations became longer and saccade angles became larger. In addition, the initial and destination lanes were found to be key areas with the highest visual allocating proportion, accounting for more than 65% of total visual allocation. Subjects tended to more frequently shift their viewpoints between the initial lane and destination lane in order to search for crucial traffic information. However, they seldom directly shifted their viewpoints between the two wing mirrors.

  4. Global Patterns of Evolutionary Distinct and Globally Endangered Amphibians and Mammals

    Science.gov (United States)

    Safi, Kamran; Armour-Marshall, Katrina; Baillie, Jonathan E. M.; Isaac, Nick J. B.

    2013-01-01

    Background Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The “EDGE of Existence” programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Methods and Principal Findings Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Conclusions Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme. PMID:23691071

  5. Graphing evolutionary pattern and process: a history of techniques in archaeology and paleobiology.

    Science.gov (United States)

    Lyman, R Lee

    2009-02-01

    Graphs displaying evolutionary patterns are common in paleontology and in United States archaeology. Both disciplines subscribed to a transformational theory of evolution and graphed evolution as a sequence of archetypes in the late nineteenth and early twentieth centuries. U.S. archaeologists in the second decade of the twentieth century, and paleontologists shortly thereafter, developed distinct graphic styles that reflected the Darwinian variational model of evolution. Paleobiologists adopted the view of a species as a set of phenotypically variant individuals and graphed those variations either as central tendencies or as histograms of frequencies of variants. Archaeologists presumed their artifact types reflected cultural norms of prehistoric artisans and the frequency of specimens in each type reflected human choice and type popularity. They graphed cultural evolution as shifts in frequencies of specimens representing each of several artifact types. Confusion of pattern and process is exemplified by a paleobiologist misinterpreting the process illustrated by an archaeological graph, and an archaeologist misinterpreting the process illustrated by a paleobiological graph. Each style of graph displays particular evolutionary patterns and implies particular evolutionary processes. Graphs of a multistratum collection of prehistoric mammal remains and a multistratum collection of artifacts demonstrate that many graph styles can be used for both kinds of collections.

  6. Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

    Science.gov (United States)

    Safi, Kamran; Armour-Marshall, Katrina; Baillie, Jonathan E M; Isaac, Nick J B

    2013-01-01

    Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

  7. Autonomous change of behavior for environmental context: An intermittent search model with misunderstanding search pattern

    Science.gov (United States)

    Murakami, Hisashi; Gunji, Yukio-Pegio

    2017-07-01

    Although foraging patterns have long been predicted to optimally adapt to environmental conditions, empirical evidence has been found in recent years. This evidence suggests that the search strategy of animals is open to change so that animals can flexibly respond to their environment. In this study, we began with a simple computational model that possesses the principal features of an intermittent strategy, i.e., careful local searches separated by longer steps, as a mechanism for relocation, where an agent in the model follows a rule to switch between two phases, but it could misunderstand this rule, i.e., the agent follows an ambiguous switching rule. Thanks to this ambiguity, the agent's foraging strategy can continuously change. First, we demonstrate that our model can exhibit an optimal change of strategy from Brownian-type to Lévy-type depending on the prey density, and we investigate the distribution of time intervals for switching between the phases. Moreover, we show that the model can display higher search efficiency than a correlated random walk.

  8. Synthesis of Steered Flat-top Beam Pattern Using Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    D. Mandal

    2016-12-01

    Full Text Available In this paper a pattern synthesis method based on Evolutionary Algorithm is presented. A Flat-top beam pattern has been generated from a concentric ring array of isotropic elements by finding out the optimum set of elements amplitudes and phases using Differential Evolution algorithm. The said pattern is generated in three predefined azimuth planes instate of a single phi plane and also verified for a range of azimuth plane for the same optimum excitations. The main beam is steered to an elevation angle of 30 degree with lower peak SLL and ripple. Dynamic range ratio (DRR is also being improved by eliminating the weakly excited array elements, which simplify the design complexity of feed networks.

  9. Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd

    2010-01-01

    Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underly......Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins...... higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective...

  10. Biogeography predicts macro-evolutionary patterning of gestural display complexity in a passerine family.

    Science.gov (United States)

    Miles, Meredith C; Cheng, Samantha; Fuxjager, Matthew J

    2017-05-01

    Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species' geographical distribution and social mating system predict macro-evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  11. Biogeography predicts macro‐evolutionary patterning of gestural display complexity in a passerine family

    Science.gov (United States)

    Miles, Meredith C.; Cheng, Samantha; Fuxjager, Matthew J.

    2017-01-01

    Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species’ geographical distribution and social mating system predict macro‐evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. PMID:28240772

  12. Evolutionary insights into global patterns of human cranial diversity: population history, climatic and dietary effects.

    Science.gov (United States)

    von Cramon-Taubadel, Noreen

    2014-01-01

    The study of cranial variation has a long, and somewhat difficult, history within anthropology. Much of this difficulty is rooted in the historical use of craniometric data to justify essentialist typological racial classification schemes. In the post-war era of the "New Physical Anthropology" (sensu Washburn, 1951), anthropologists began to analyse human variation in an explicitly populationist and evolutionary philosophical and analytical framework. However, even within recent decades, substantially different approaches have been employed; some advocate a focus on the analysis of individual traits or clines, while others are explicitly adaptationist, with a focus on natural selection as the preeminent force of phenotypic diversification. In recent years, a series of studies have analysed craniometric data in an explicitly quantitative genetic framework, which emphasises the importance of neutral forces such as migration, gene flow and genetic drift in creating global patterns of phenotypic diversity. This approach has revealed that global patterns of cranial variation can largely be explained on the basis of neutral theory. Therefore, human cranial data can be productively employed as a proxy for neutral genetic data in archaeological contexts. Moreover, there is a growing recognition that regions of the cranium differ in the extent to which they fit a neutral model of microevolutionary expectation, allowing for a more detailed assessment of patterns of adaptation and phenotypic plasticity within the human skull. Taking an historical perspective, the current state of knowledge regarding patterns of cranial adaptation in response to climatic and dietary effects is reviewed. Further insights will be gained by better incorporating the study of cranial and postcranial variation, as well as understanding the impact of neutral versus non-neutral evolution in creating among-species diversity patterns in primates more generally. However, this will most effectively be

  13. Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

    Science.gov (United States)

    Cotten, Matthew; Petrova, Velislava; Phan, My V. T.; Rabaa, Maia A.; Watson, Simon J.; Ong, Swee Hoe; Baker, Stephen

    2014-01-01

    ABSTRACT Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure. IMPORTANCE The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance. PMID

  14. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys

    Science.gov (United States)

    Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M. V.; Drosten, Christian; Lemey, Philippe

    2016-01-01

    ABSTRACT The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. IMPORTANCE The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses

  15. Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

    National Research Council Canada - National Science Library

    Meyer, Fernando; Kurtz, Stefan; Beckstette, Michael

    2013-01-01

    .... However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence data...

  16. Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

  17. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members.

    Science.gov (United States)

    Zhou, Tianyu; Yan, Xiping; Wang, Guosong; Liu, Hehe; Gan, Xiang; Zhang, Tao; Wang, Jiwen; Li, Liang

    2015-01-01

    Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3' UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3' UTR are essential for PPARs evolution and diversity functions acquired.

  18. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

    Directory of Open Access Journals (Sweden)

    Tianyu Zhou

    2015-01-01

    Full Text Available Peroxisome proliferators-activated receptor (PPAR gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

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

    Directory of Open Access Journals (Sweden)

    McDonald John F

    2008-05-01

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

  20. Searching for a major locus for male pattern baldness (MPB)

    Energy Technology Data Exchange (ETDEWEB)

    Anker, R.; Eisen, A.Z.; Donis-Keller, H. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-09-01

    Male pattern baldness (MPB) is a common trait in post-pubertal males. Approximately 50% of adult males present some degree of MPB by age 50. According to the classification provided by Hamilton in 1951 and modified by Norwood in 1975, the trait itself is a continuum that ranges from mild (Type I) to severe (Type VII) cases. In addition, there is extensive variability for the age of onset. The role of androgens in allowing the expression of this trait in males has been well established. This phenotype is uncommonly expressed in females. The high prevalence of the trait, the distribution of MPB as a continuous trait, and several non-allelic mutations identified in the mouse capable of affecting hair pattern, suggest that MPB is genetically heterogeneous. In order to reduce the probability of multiple non-allelic MPB genes within a pedigree, we selected 9 families in which MPB appears to segregate exclusively through the paternal lineage as compared to bilineal pedigrees. There are 32 males expressing this phenotype and females are treated as phenotype unknown. In general, affected individuals expressed the trait before 30 years of age with a severity of at least Type III or IV. We assumed an autosomal dominant model, with a gene frequency of 1/20 for the affected allele, and 90% penetrance. Simulation studies using the SLINK program with these pedigrees showed that these families would be sufficient to detect linkage under the assumption of a single major locus. If heterogeneity is present, the current resource does not have sufficient power to detect linkage at a statistically significant level, although candidate regions of the genome could be identified for further studies with additional pedigrees. Using 53 highly informative microsatellite markers, and a subset of 7 families, we have screened 30% of the genome. This search included several regions where candidate genes for MPB are located.

  1. Molecular evolutionary patterns of NAD+/Sirtuin aging signaling pathway across taxa.

    Directory of Open Access Journals (Sweden)

    Uma Gaur

    Full Text Available A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD+/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that MRPS5 and PPARGC1A were under significant constraints because of their functional significance. FOXO3a also displayed strong purifying selection. All three sirtuins, which were SIRT1, SIRT2 and SIRT6, displayed a great degree of conservation between taxa, which is consistent with the previous report. A significant evolutionary constraint is seen on the anti-oxidant gene, SOD3. As expected, TP53 gene was under significant selection pressure in mammals, owing to its major role in tumor progression. Poly-ADP-ribose polymerase (PARP genes displayed the most sites under positive selection. Further 3D structural analysis of PARP1 and PARP2 protein revealed that some of these positively selected sites caused a change in the electrostatic potential of the protein structure, which may allow a change in its interaction with other proteins and molecules ultimately leading to difference in the function. Although the functional significance of the positively selected sites could not be established in the variants databases, yet it will be interesting to see if these sites actually affect the function of PARP1 and PARP2.

  2. Searching for truth: internet search patterns as a method of investigating online responses to a Russian illicit drug policy debate.

    Science.gov (United States)

    Zheluk, Andrey; Gillespie, James A; Quinn, Casey

    2012-12-13

    This is a methodological study investigating the online responses to a national debate over an important health and social problem in Russia. Russia is the largest Internet market in Europe, exceeding Germany in the absolute number of users. However, Russia is unusual in that the main search provider is not Google, but Yandex. This study had two main objectives. First, to validate Yandex search patterns against those provided by Google, and second, to test this method's adequacy for investigating online interest in a 2010 national debate over Russian illicit drug policy. We hoped to learn what search patterns and specific search terms could reveal about the relative importance and geographic distribution of interest in this debate. A national drug debate, centering on the anti-drug campaigner Egor Bychkov, was one of the main Russian domestic news events of 2010. Public interest in this episode was accompanied by increased Internet search. First, we measured the search patterns for 13 search terms related to the Bychkov episode and concurrent domestic events by extracting data from Google Insights for Search (GIFS) and Yandex WordStat (YaW). We conducted Spearman Rank Correlation of GIFS and YaW search data series. Second, we coded all 420 primary posts from Bychkov's personal blog between March 2010 and March 2012 to identify the main themes. Third, we compared GIFS and Yandex policies concerning the public release of search volume data. Finally, we established the relationship between salient drug issues and the Bychkov episode. We found a consistent pattern of strong to moderate positive correlations between Google and Yandex for the terms "Egor Bychkov" (r(s) = 0.88, P Internet on politics and policy, using low cost methods resilient against potential increases in censorship.

  3. Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns.

    Science.gov (United States)

    Qiao, Qin; Xue, Li; Wang, Qia; Sun, Hang; Zhong, Yang; Huang, Jinling; Lei, Jiajun; Zhang, Ticao

    2016-01-01

    Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557-82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai-Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

  4. Comparative transcriptomics of strawberries (Fragaria spp. provides insights into evolutionary patterns

    Directory of Open Access Journals (Sweden)

    Qin Qiao

    2016-12-01

    Full Text Available Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades.East Asian species appeared in every subclade, suggesting that the genus originated in this area at ~7.99 Mya. Four species found in mountains of Southwest China originated at ~3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

  5. Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus

    Science.gov (United States)

    Labudde, Dirk

    2015-01-01

    The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations. PMID:26180540

  6. Hybrid pattern recognition method using evolutionary computing techniques applied to the exploitation of hyperspectral imagery and medical spectral data

    Science.gov (United States)

    Burman, Jerry A.

    1999-12-01

    Hyperspectral image sets are three dimensional data volumes that are difficult to exploit by manual means because they are comprised of multiple bands of image data that are not easily visualized or assessed. GTE Government Systems Corporation has developed a system that utilizes Evolutionary Computing techniques to automatically identify materials in terrain hyperspectral imagery. The system employs sophisticated signature preprocessing and a unique combination of non- parametric search algorithms guided by a model based cost function to achieve rapid convergence and pattern recognition. The system is scaleable and is capable of discriminating and identifying pertinent materials that comprise a specific object of interest in the terrain and estimating the percentage of materials present within a pixel of interest (spectral unmixing). The method has been applied and evaluated against real hyperspectral imagery data from the AVIRIS sensor. In addition, the process has been applied to remotely sensed infrared spectra collected at the microscopic level to assess the amounts of DNA, RNA and protein present in human tissue samples as an aid to the early detection of cancer.

  7. Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.

    Science.gov (United States)

    Ahn, Insung; Son, Hyeon Seok

    2012-02-01

    In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series codon substitution patterns resulted dramatic changes of BLAST results in influenza A/H1N1, providing a possibility of developing a method for predicting the viral evolution in silico. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Large-Scale Evolutionary Patterns of Host Plant Associations in the Lepidoptera

    DEFF Research Database (Denmark)

    Menken, S.B.J.; Boomsma, J.J.; van Nieukerken, E.J.

    2010-01-01

    significant radiations. Exposed feeding became associated with radiations in the lower Ditrysia and Apoditrysia and remained correlated with more polyphagy, fewer woody host plants, and increasing use of other Angiosperm superorders. The macrolepidopteran radiation has frequent reversals to monophagy on woody......We characterized evolutionary patterns of host plant use across about 2500 species of British Lepidoptera, using character optimization and independent phylogenetic contrasts among 95 operational taxa, and evaluated the extent to which caterpillars are monophagous, use woody host plants, and feed...... categorizations for Britain are accurate predictors for the global fauna. The first (lower glossatan) radiation of the Lepidoptera started with monophagous, internal feeding on woody Eurosids I. Polyphagy on nonwoody Eurosids I evolved together with the ability to feed externally, but did initially not produce...

  9. Evolutionary Patterns of Renewable Energy Technology Development in East Asia (1990–2010

    Directory of Open Access Journals (Sweden)

    Yoonhwan Oh

    2016-07-01

    Full Text Available This study investigates the evolutionary patterns of renewable energy technology in East Asian countries—Japan, Korea, and China—as an emerging technology where the catch-up strategy is actively taking place. To reflect the quality of technology development activities, we assess each country’s research and development (R&D activities using patent citation analysis. The goal of this study is to overcome the limitations of prior research that uses quantitative information, such as R&D expenditures and number of patents. This study observes the process of technological catch-up and leapfrogging in the East Asian renewable energy sector. Furthermore, we find that each nation’s technology development portfolio differs depending on the composition share of technologies. Policymakers in emerging economies can use the findings to shape R&D strategies to develop the renewable energy sector and provide an alternative method of evaluating the qualitative development of technology.

  10. Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

    Directory of Open Access Journals (Sweden)

    Anitha Sundararajan

    2016-09-01

    Full Text Available Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx to instances of a variable GC-rich motif that underlies double strand break (DSB hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.

  11. Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns.

    Science.gov (United States)

    Hutter, Carl R; Guayasamin, Juan M; Wiens, John J

    2013-09-01

    The Tropical Andes are an important global biodiversity hotspot, harbouring extraordinarily high richness and endemism. Although elevational richness and speciation have been studied independently in some Andean groups, the evolutionary and ecological processes that explain elevational richness patterns in the Andes have not been analysed together. Herein, we elucidate the processes underlying Andean richness patterns using glassfrogs (Centrolenidae) as a model system. Glassfrogs show the widespread mid-elevation diversity peak for both local and regional richness. Remarkably, these patterns are explained by greater time (montane museum) rather than faster speciation at mid-elevations (montane species pump), despite the recency of the major Andean uplift. We also show for the first time that rates of climatic-niche evolution and elevational change are related, supporting the hypothesis that climatic-niche conservatism decelerates species' shifts in elevational distributions and underlies the mid-elevation richness peak. These results may be relevant to other Andean clades and montane systems globally. © 2013 John Wiley & Sons Ltd/CNRS.

  12. Revisiting our Evolutionary Path: The Search for Holistic Education in a Fragmented World

    OpenAIRE

    Gerald Gutenschwager

    2017-01-01

    When the World Academy of Art & Science (WAAS) was founded, it sought to address the gap between science and society, or rather the apparent unwillingness or inability of scientists to address their responsibilities as important members of society. This problem is related to the growing disparity between tool making and symbol making, those ancient skills that brought humans to the highest stage in the evolutionary process (at least until now?). Symbols—language, mathematics, graphics and oth...

  13. The use of a multiobjective evolutionary algorithm to increase flexibility in the search for better IMRT plans.

    Science.gov (United States)

    Holdsworth, Clay; Kim, Minsun; Liao, Jay; Phillips, Mark

    2012-04-01

    To evaluate how a more flexible and thorough multiobjective search of feasible IMRT plans affects performance in IMRT optimization. A multiobjective evolutionary algorithm (MOEA) was used as a tool to investigate how expanding the search space to include a wider range of penalty functions affects the quality of the set of IMRT plans produced. The MOEA uses a population of IMRT plans to generate new IMRT plans through deterministic minimization of recombined penalty functions that are weighted sums of multiple, tissue-specific objective functions. The quality of the generated plans are judged by an independent set of nonconvex, clinically relevant decision criteria, and all dominated plans are eliminated. As this process repeats itself, better plans are produced so that the population of IMRT plans will approach the Pareto front. Three different approaches were used to explore the effects of expanding the search space. First, the evolutionary algorithm used genetic optimization principles to search by simultaneously optimizing both the weights and tissue-specific dose parameters in penalty functions. Second, penalty function parameters were individually optimized for each voxel in all organs at risk (OARs) in the MOEA. Finally, a heuristic voxel-specific improvement (VSI) algorithm that can be used on any IMRT plan was developed that incrementally improves voxel-specific penalty function parameters for all structures (OARs and targets). Different approaches were compared using the concept of domination comparison applied to the sets of plans obtained by multiobjective optimization. MOEA optimizations that simultaneously searched both importance weights and dose parameters generated sets of IMRT plans that were superior to sets of plans produced when either type of parameter was fixed for four example prostate plans. The amount of improvement increased with greater overlap between OARs and targets. Allowing the MOEA to search for voxel-specific penalty functions

  14. New Maximally Entangled States for Pattern-Association Through Evolutionary Processes in a Two-Qubit System

    Science.gov (United States)

    Singh, Manu Pratap; Rajput, Balwant S.

    2017-04-01

    New set of maximally entangled states (Singh-Rajput MES), constituting orthonormal eigen bases, has been revisited and its superiority and suitability in pattern-association (Quantum Associative Memory, QuAM) have been demonstrated. Using these MES as memory states in the evolutionary process of pattern storage in a two-qubit system, it has been shown that the first two states of Singh-Rajput MES are useful for storing the pattern |11> and the last two of these MES are useful in storing the pattern |10> Recall operations of quantum associate memory (QuAM) have been conducted through evolutionary process in terms of unitary operators by separately choosing Singh-Rajput MES and Bell's MES as memory states and it has been shown that Singh-Rajput MES as valid memory states for recalling the patterns in a two-qubit system are much more suitable than Bell's MES.

  15. Is There a Weekly Pattern for Health Searches on Wikipedia and Is the Pattern Unique to Health Topics?

    Science.gov (United States)

    Gabarron, Elia; Lau, Annie Y S; Wynn, Rolf

    2015-12-22

    Online health information-seeking behaviors have been reported to be more common at the beginning of the workweek. This behavior pattern has been interpreted as a kind of "healthy new start" or "fresh start" due to regrets or attempts to compensate for unhealthy behavior or poor choices made during the weekend. However, the observations regarding the most common health information-seeking day were based only on the analyses of users' behaviors with websites on health or on online health-related searches. We wanted to confirm if this pattern could be found in searches of Wikipedia on health-related topics and also if this search pattern was unique to health-related topics or if it could represent a more general pattern of online information searching--which could be of relevance even beyond the health sector. The aim was to examine the degree to which the search pattern described previously was specific to health-related information seeking or whether similar patterns could be found in other types of information-seeking behavior. We extracted the number of searches performed on Wikipedia in the Norwegian language for 911 days for the most common sexually transmitted diseases (chlamydia, gonorrhea, herpes, human immunodeficiency virus [HIV], and acquired immune deficiency syndrome [AIDS]), other health-related topics (influenza, diabetes, and menopause), and 2 nonhealth-related topics (footballer Lionel Messi and pop singer Justin Bieber). The search dates were classified according to the day of the week and ANOVA tests were used to compare the average number of hits per day of the week. The ANOVA tests showed that the sexually transmitted disease queries had their highest peaks on Tuesdays (P<.001) and the fewest searches on Saturdays. The other health topics also showed a weekly pattern, with the highest peaks early in the week and lower numbers on Saturdays (P<.001). Footballer Lionel Messi had the highest mean number of hits on Tuesdays and Wednesdays, whereas

  16. Searching for Truth: Internet Search Patterns as a Method of Investigating Online Responses to a Russian Illicit Drug Policy Debate

    OpenAIRE

    Zheluk, Andrey; Gillespie, James A.; Quinn, Casey

    2012-01-01

    Background This is a methodological study investigating the online responses to a national debate over an important health and social problem in Russia. Russia is the largest Internet market in Europe, exceeding Germany in the absolute number of users. However, Russia is unusual in that the main search provider is not Google, but Yandex. Objective This study had two main objectives. First, to validate Yandex search patterns against those provided by Google, and second, to test this method's a...

  17. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Directory of Open Access Journals (Sweden)

    Diane I Schroeder

    2015-08-01

    Full Text Available Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs and highly methylated domains (HMDs with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  18. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Science.gov (United States)

    Schroeder, Diane I; Jayashankar, Kartika; Douglas, Kory C; Thirkill, Twanda L; York, Daniel; Dickinson, Pete J; Williams, Lawrence E; Samollow, Paul B; Ross, Pablo J; Bannasch, Danika L; Douglas, Gordon C; LaSalle, Janine M

    2015-08-01

    Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  19. Evolutionary patterning of hemagglutinin gene sequence of 2009 H1N1 pandemic.

    Science.gov (United States)

    Banerjee, Rachana; Roy, Ayan; Ahmad, Fayaz; Das, Santasabuj; Basak, Surajit

    2012-01-01

    The 2009 H1N1 swine flu is the first pandemic in decades. Infectivity of the influenza virus for human host depends largely on its ability to evade antibodies specific for viral protein called hemagglutinin (HA) that mediates attachment to the host. In the present study we analysed large number of HA gene sequences available in Flu Database maintained at NCBI. Our sequence based analysis clearly demonstrates that the amino acid usage pattern may dramatically change during the course of evolution, and there exists a clear link between a particular pattern of amino acid usage of HA genes and its potential to become infectious. Structural studies revealed how binding efficiency between the HA and sialic acid may alter the pandemic potential of infection. Our work highlights the evolutionary significance and biochemical basis of the selective advantage of certain amino acids of HA in 2009 and provides a link between the characteristics changes in HA protein and their potential to pronounce a global menace to public health.

  20. Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies

    Directory of Open Access Journals (Sweden)

    R. Shyama Prasad Rao

    2010-02-01

    Full Text Available Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline which are the potential sites of asparagine (N linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.

  1. Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

    KAUST Repository

    Choat, John. H.

    2012-09-05

    Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well-supported clades with mid Pliocene/Pleistocene diversification. Twenty-two reciprocally monophyletic sister-species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London.

  2. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (pinaceae): range-wide evolutionary history and implications for conservation

    Science.gov (United States)

    Kevin M. Potter; Valerie D. Hipkins; Mary F. Mahalovich; Robert E. Means

    2013-01-01

    Premise of the study: Ponderosa pine ( Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic...

  3. Evolutionary Search for Globally Optimal Stable Multicycles in Complex Systems with Inventory Couplings

    Directory of Open Access Journals (Sweden)

    M. Skowron

    2009-01-01

    Full Text Available This note is devoted to multiperiodically operated complex system with inventory couplings transferring waste products from some subsystems as useful components to other subsystems. The flexibility of the inventory couplings is used to force each of the subsystems with its own period and to exploit its particular dynamic properties. This enhances the performance of the complex system endowed with many recycling loops, which reduce the amount of waste products endangering the natural environment. The subsystems are characterized by generalized populations composed of the individuals (the cycles, each of them encompasses its period, its initial state, its local control, and its inventory interaction. An evolutionary optimization algorithm employing such generalized populations coordinated on the basis of the inventory interaction constraints is developed. It includes the stability requirements imposed on the cyclic control processes connected with particular subsystems. The algorithm proposed is applied to the global multiperiodic optimization of some interconnected chemical production processes.

  4. In Search Of The Consensus Among Musical Pattern Discovery Algorithms

    NARCIS (Netherlands)

    Ren, Iris Yuping; Koops, Vincent; Volk, Anja|info:eu-repo/dai/nl/304842117; Swierstra, Wouter|info:eu-repo/dai/nl/377565326

    2017-01-01

    Patterns are an essential part of music and there are many different algorithms that aim to discover them. Based on the improvements brought by using data fusion methods to find the consensus of algorithms on other MIR tasks, we hypothesize that fusing the output from musical pattern discovery

  5. Patterns of semantic relations to improve image content search

    NARCIS (Netherlands)

    Hollink, L.; Schreiber, A.T.; Wielinga, B.J.

    2007-01-01

    This paper reports on a study to explore how semantic relations can be used to expand a query for objects in an image. The study is part of a project with the overall objective to provide semantic annotation and search facilities for a virtual collection of art resources. In this study we used

  6. High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China.

    Science.gov (United States)

    Du, Xi-Hui; Zhao, Qi; Xu, Jianping; Yang, Zhu L

    2016-03-01

    As highly prized, popular mushrooms, morels are widely distributed in the northern hemisphere, with China as a modern centre of speciation and diversity. Overharvesting of morels has caused concern over how to effectively preserve their biological and genetic diversity. However, little is known about their population biology and life cycle. In this study, we selected two sympatric phylogenetic species, Mel-13 (124 collections from 11 geographical locations) and Morchella eohespera (156 collections from 14 geographical locations), using fragments of 4 DNA sequences, to analyse their genetic structure. Our results indicated significant differentiation among geographic locations in both species, whereas no obvious correlation between genetic and geographic distance was identified in either species. M. eohespera exhibited a predominantly clonal population structure with limited recombination detected in only 1 of the 14 geographic locations. In contrast, relatively frequent recombination was identified in 6 of the 11 geographic locations of Mel-13. Our analysis indicated that the sympatric species Mel-13 and M. eohespera might have divergent evolutionary patterns, with the former showing signatures of recent population expansion and the latter being relatively stable. Interestingly, we found no heterozygosity but strong evidence for genealogical incongruence, indicating a high level of inbreeding and hybridisation among morel species.

  7. Evolutionary fields can explain patterns of high-dimensional complexity in ecology.

    Science.gov (United States)

    Wilsenach, James; Landi, Pietro; Hui, Cang

    2017-04-01

    One of the properties that make ecological systems so unique is the range of complex behavioral patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to stochastic factors that have very high-degrees of freedom. Orthodox study of the evolution of these simple networks has generally been limited in its ability to explain complexity, since it restricts evolutionary adaptation to an inertia-free process with few degrees of freedom in which only gradual, moderately complex behaviors are possible. We propose a model inspired by particle-mediated field phenomena in classical physics in combination with fundamental concepts in adaptation, which suggests that small but high-dimensional chaotic dynamics near to the adaptive trait optimum could help explain complex properties shared by most ecological datasets, such as aperiodicity and pink, fractal noise spectra. By examining a simple predator-prey model and appealing to real ecological data, we show that this type of complexity could be easily confused for or confounded by stochasticity, especially when spurred on or amplified by stochastic factors that share variational and spectral properties with the underlying dynamics.

  8. Evolutionary fields can explain patterns of high-dimensional complexity in ecology

    Science.gov (United States)

    Wilsenach, James; Landi, Pietro; Hui, Cang

    2017-04-01

    One of the properties that make ecological systems so unique is the range of complex behavioral patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to stochastic factors that have very high-degrees of freedom. Orthodox study of the evolution of these simple networks has generally been limited in its ability to explain complexity, since it restricts evolutionary adaptation to an inertia-free process with few degrees of freedom in which only gradual, moderately complex behaviors are possible. We propose a model inspired by particle-mediated field phenomena in classical physics in combination with fundamental concepts in adaptation, which suggests that small but high-dimensional chaotic dynamics near to the adaptive trait optimum could help explain complex properties shared by most ecological datasets, such as aperiodicity and pink, fractal noise spectra. By examining a simple predator-prey model and appealing to real ecological data, we show that this type of complexity could be easily confused for or confounded by stochasticity, especially when spurred on or amplified by stochastic factors that share variational and spectral properties with the underlying dynamics.

  9. Patterns of evolutionary conservation of essential genes correlate with their compensability.

    Directory of Open Access Journals (Sweden)

    Tobias Bergmiller

    2012-06-01

    Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

  10. Ecological and evolutionary patterns of freshwater maturation in Pacific and Atlantic salmonines

    Science.gov (United States)

    Sloat, Matthew R.; Fraser, Dylan J.; Dunham, Jason B.; Falke, Jeffery A.; Jordan, Chris E.; McMillan, John R.; Ohms, Haley A.

    2014-01-01

    Reproductive tactics and migratory strategies in Pacific and Atlantic salmonines are inextricably linked through the effects of migration (or lack thereof) on age and size at maturity. In this review, we focus on the ecological and evolutionary patterns of freshwater maturation in salmonines, a key process resulting in the diversification of their life histories. We demonstrate that the energetics of maturation and reproduction provides a unifying theme for understanding both the proximate and ultimate causes of variation in reproductive schedules among species, populations, and the sexes. We use probabilistic maturation reaction norms to illustrate how variation in individual condition, in terms of body size, growth rate, and lipid storage, influences the timing of maturation. This useful framework integrates both genetic and environmental contributions to conditional strategies for maturation and, in doing so, demonstrates how flexible life histories can be both heritable and subject to strong environmental influences. We review evidence that the propensity for freshwater maturation in partially anadromous species is predictable across environmental gradients at geographic and local spatial scales. We note that growth is commonly associated with the propensity for freshwater maturation, but that life-history responses to changes in growth caused by temperature may be strikingly different than changes caused by differences in food availability. We conclude by exploring how contemporary management actions can constrain or promote the diversity of maturation phenotypes in Pacific and Atlantic salmonines and caution against underestimating the role of freshwater maturing forms in maintaining the resiliency of these iconic species.

  11. Molecular phylogeny of echiuran worms (Phylum: Annelida reveals evolutionary pattern of feeding mode and sexual dimorphism.

    Directory of Open Access Journals (Sweden)

    Ryutaro Goto

    Full Text Available The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs. Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms.

  12. Molecular phylogeny of echiuran worms (Phylum: Annelida) reveals evolutionary pattern of feeding mode and sexual dimorphism.

    Science.gov (United States)

    Goto, Ryutaro; Okamoto, Tomoko; Ishikawa, Hiroshi; Hamamura, Yoichi; Kato, Makoto

    2013-01-01

    The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms.

  13. Molecular Phylogeny of Echiuran Worms (Phylum: Annelida) Reveals Evolutionary Pattern of Feeding Mode and Sexual Dimorphism

    Science.gov (United States)

    Goto, Ryutaro; Okamoto, Tomoko; Ishikawa, Hiroshi; Hamamura, Yoichi; Kato, Makoto

    2013-01-01

    The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms. PMID:23457618

  14. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae.

    Directory of Open Access Journals (Sweden)

    Carlos Pedraza-Lara

    Full Text Available The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group and into Central México (Mexican Group, has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047, resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric

  15. The pachytene checkpoint and its relationship to evolutionary patterns of polyploidization and hybrid sterility.

    Science.gov (United States)

    Li, X C; Barringer, B C; Barbash, D A

    2009-01-01

    Sterility is a commonly observed phenotype in interspecific hybrids. Sterility may result from chromosomal or genic incompatibilities, and much progress has been made toward understanding the genetic basis of hybrid sterility in various taxa. The underlying mechanisms causing hybrid sterility, however, are less well known. The pachytene checkpoint is a meiotic surveillance system that many organisms use to detect aberrant meiotic products, in order to prevent the production of defective gametes. We suggest that activation of the pachytene checkpoint may be an important mechanism contributing to two types of hybrid sterility. First, the pachytene checkpoint may form the mechanistic basis of some gene-based hybrid sterility phenotypes. Second, the pachytene checkpoint may be an important mechanism that mediates chromosomal-based hybrid sterility phenotypes involving gametes with non-haploid (either non-reduced or aneuploid) chromosome sets. Studies in several species suggest that the strength of the pachytene checkpoint is sexually dimorphic, observations that warrant future investigation into whether such variation may contribute to differences in patterns of sterility between male and female interspecific hybrids. In addition, plants seem to lack the pachytene checkpoint, which correlates with increased production of unreduced gametes and a higher incidence of polyploid species in plants versus animals. Although the pachytene checkpoint occurs in many animals and in fungi, at least some of the genes that execute the pachytene checkpoint are different among organisms. This finding suggests that the penetrance of the pachytene checkpoint, and even its presence or absence can evolve rapidly. The surprising degree of evolutionary flexibility in this meiotic surveillance system may contribute to the observed variation in patterns of hybrid sterility and in rates of polyploidization.

  16. Revisiting our Evolutionary Path: The Search for Holistic Education in a Fragmented World

    Directory of Open Access Journals (Sweden)

    Gerald Gutenschwager

    2017-10-01

    Full Text Available When the World Academy of Art & Science (WAAS was founded, it sought to address the gap between science and society, or rather the apparent unwillingness or inability of scientists to address their responsibilities as important members of society. This problem is related to the growing disparity between tool making and symbol making, those ancient skills that brought humans to the highest stage in the evolutionary process (at least until now?. Symbols—language, mathematics, graphics and other pictorial and linguistic representations, as well as clothing, hairstyles, etc.—when used to establish social rank, may serve to give legitimacy to the current social order or may serve to criticize and change it. Reincorporating science into society would require that scientists, as well as every member of society, recognize this. This would require an educational system that would give equal emphasis to tool making and symbol making, and this would help students to understand how society is a product of both of these processes.

  17. Hybrid local search algorithm via evolutionary avalanches for spin glass based portfolio selection

    Directory of Open Access Journals (Sweden)

    Majid Vafaei Jahan

    2012-07-01

    As shown in this paper, this strategy can lead to faster rate of convergence and improved performance than conventional SA and EO algorithm. The resulting are then used to solve the portfolio selection multi-objective problem that is a non-deterministic polynomial complete (NPC problem. This is confirmed by test results of five of the world’s major stock markets, reliability test and phase transition diagram; and finally, the convergence speed is compared to other heuristic methods such as Neural Network (NN, Tabu Search (TS, and Genetic Algorithm (GA.

  18. Micro-evolutionary divergence patterns of mandible shapes in wild house mouse (Mus musculus populations

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2011-10-01

    Full Text Available Abstract Background Insights into the micro-evolutionary patterns of morphological traits require an assessment of the natural variation of the trait within and between populations and closely related species. The mouse mandible is a particularly suitable morphological trait for such an analysis, since it has long been used as a model to study the quantitative genetics of shape. In addition, many distinct populations, sub-species and closely related species are known for the house mouse. However, morphological comparisons among wild caught animals require an assessment in how far environmental and technical factors could interfere with the shape change measurements. Results Using geometric morphometrics, we have surveyed mandible shapes in 15 natural populations of the genus Mus, with a focus on the subspecies Mus musculus domesticus. In parallel we have carefully assessed possibly confounding technical and biological factors. We find that there are distinct differences on average between populations, subspecies and species, but these differences are smaller than differences between individuals within populations. Populations from summer-dry regions, although more ancestral, are less distinct from each other than are populations from the more recently colonized northern areas. Populations with especially distinct shapes occur in an area of sympatry of M. m. domesticus and M. spretus and on recently colonized sub-antarctic islands. We have also studied a number of inbred strains to assess in how far their mandible shapes resemble those from the wild. We find that they fall indeed into the shape space of natural variation between individuals in populations. Conclusions Although mandible shapes in natural populations can be influenced by environmental variables, these influences are insufficient to explain the average extent of shape differences between populations, such that evolutionary processes must be invoked to explain this level of diversity

  19. Real view radiology-impact on search patterns and confidence in radiology education.

    Science.gov (United States)

    Bailey, Jared H; Roth, Trenton D; Kohli, Mark D; Heitkamp, Darel E

    2014-07-01

    Search patterns are important for radiologists because they enable systematic case review. Because radiology residents are exposed to so many imaging modalities and anatomic regions, and they rotate on-and-off service so frequently, they may have difficulty establishing effective search patterns. We developed Real View Radiology (RVR), an educational system founded on guided magnetic resonance imaging (MRI) case review and evaluated its impact on search patterns and interpretative confidence of junior radiology residents. RVR guides learners through unknown examinations by sequentially prompting learners to certain aspects of a case via a comprehensive question set and then providing immediate feedback. Junior residents first completed a brief evaluation regarding their level of confidence when interpreting certain joint MRI cases and frequency of search pattern use. They spent four half-days interpreting cases using RVR. Once finished, they repeated the evaluations. The junior resident results were compared to third-year residents who had not used RVR. The data were analyzed for change in confidence, use of search patterns, and number of cases completed. Twelve first-year and thirteen second-year residents (trained cohort) were enrolled in the study. During their 4-week musculoskeletal rotations, they completed on average 29.3 MRI knee (standard deviation [SD], 1.6) and 17.4 shoulder (SD, 1.2) cases using RVR. Overall search pattern scores of the trained cohort increased significantly both from pretraining to posttraining (knee P confidence scores also increased significantly from pre to post for all joints (knee P confidence and improve the consistency of search pattern use by training with a question-based sequential reveal educational program. RVR could be used to supplement training and assist with search pattern creation in areas in which residents often do not acquire adequate clinical exposure. Copyright © 2014 AUR. Published by Elsevier Inc. All rights

  20. Searching the Evolutionary Origin of Epithelial Mucus Protein Components—Mucins and FCGBP

    Science.gov (United States)

    Lang, Tiange; Klasson, Sofia; Larsson, Erik; Johansson, Malin E. V.; Hansson, Gunnar C.; Samuelsson, Tore

    2016-01-01

    The gel-forming mucins are large glycosylated proteins that are essential components of the mucus layers covering epithelial cells. Using novel methods of identifying mucins based on profile hidden Markov models, we have found a large number of such proteins in Metazoa, aiding in their classification and allowing evolutionary studies. Most vertebrates have 5–6 gel-forming mucin genes and the genomic arrangement of these genes is well conserved throughout vertebrates. An exception is the frog Xenopus tropicalis with an expanded repertoire of at least 26 mucins of this type. Furthermore, we found that the ovomucin protein, originally identified in chicken, is characteristic of reptiles, birds, and amphibians. Muc6 is absent in teleost fish, but we now show that it is present in animals such as ghost sharks, demonstrating an early origin in vertebrate evolution. Public RNA-Seq data were analyzed with respect to mucins in zebrafish, frog, and chicken, thus allowing comparison in regard of tissue and developmental specificity. Analyses of invertebrate proteins reveal that gel-forming-mucin type of proteins is widely distributed also in this group. Their presence in Cnidaria, Porifera, and in Ctenophora (comb jellies) shows that these proteins were present early in metazoan evolution. Finally, we examined the evolution of the FCGBP protein, abundant in mucus and related to gel-forming mucins in terms of structure and localization. We demonstrate that FCGBP, ubiquitous in vertebrates, has a conserved N-terminal domain. Interestingly, this domain is also present as an N-terminal sequence in a number of bacterial proteins. PMID:27189557

  1. Homo Digitalis – in Search of a Patterned Usage Identity

    Directory of Open Access Journals (Sweden)

    Adrian STOICESCU

    2015-01-01

    Full Text Available There is a great debate around the ways identity is shaped online, mainly as a result of understanding the online as networked individuals. The present papers tries to open the discussion on whether the quasi-synonym words constantly used to talk about the online communication cyber, virtual and digital define the same reality or whether they can be associated with particular aspects of the identity forged within the computer mediated communication. The search for the differentiating aspects is carried out against the backdrop of technological development which inevitably alters with every new aspect unveiled a new side of each individual’s identity.

  2. Tight-binding and evolutionary search approach for nanoscale CoRh alloys

    Energy Technology Data Exchange (ETDEWEB)

    Diaz-Ortiz, A. [Texas Materials Institute, The University of Texas at Austin, 78712 Austin, TX (United States)]. E-mail: ado@mail.utexas.edu; Aguilera-Granja, F. [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, 78000 San Luis Potosi, S.L.P. (Mexico); Michaelian, K. [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, 20-364, 01000 Mexico, D.F. (Mexico); Berlanga-Ramirez, E.O. [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, 78000 San Luis Potosi, S.L.P. (Mexico); Montejano-Carrizales, J.M. [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, 78000 San Luis Potosi, S.L.P. (Mexico); Vega, A. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, E-47005 Valladolid (Spain)

    2005-12-15

    The dependence of the structural and magnetic properties of Co-Rh alloys at the nanoscale was investigated by exhaustively searching the minimum energy via a symbiotic algorithm on a Gupta potential for particle sizes of 13, 19, and 23 atoms. An unrestricted spd tight-binding Hamiltonian was then used to model the electronic properties. Our results underscore the importance of determining both the geometrical and the chemical configuration. A central result points toward a surface segregation that qualitatively and quantitatively depends on system size, with size effects dominating the surface segregation for small Co-Rh clusters (Rh atoms preferentially occupy surface sites), whereas surface energy dictates the segregation for large Co-Rh nanoparticles (Co segregates to the surface). This might have important consequences for heterogeneous catalysis, where the catalytic activity strongly depends on surface composition.

  3. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

    Directory of Open Access Journals (Sweden)

    Sun Qi

    2009-11-01

    Full Text Available Abstract Background The bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species. Some Salmonella serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium, two host restricted serotypes (Typhi [two genomes] and Paratyphi and one host adapted serotype (Choleraesuis were used to identify core genome genes that show evidence for recombination and positive selection. Results Overall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] ompC, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns. Conclusion Our data show that, among the four serotypes analyzed, (i less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii branch specific positive selection contributes to the evolution of host restricted Salmonella serotypes.

  4. Knowledge-discovery incorporated evolutionary search for microcalcification detection in breast cancer diagnosis.

    Science.gov (United States)

    Peng, Yonghong; Yao, Bin; Jiang, Jianmin

    2006-05-01

    The presence of microcalcifications (MCs), clusters of tiny calcium deposits that appear as small bright spots in a mammogram, has been considered as a very important indicator for breast cancer diagnosis. Much research has been performed for developing computer-aided systems for the accurate identification of MCs, however, the computer-based automatic detection of MCs has been shown difficult because of the complicated nature of surrounding of breast tissue, the variation of MCs in shape, orientation, brightness and size. This paper presents a new approach for the effective detection of MCs by incorporating a knowledge-discovery mechanism in the genetic algorithm (GA). In the proposed approach, called knowledge-discovery incorporated genetic algorithm (KD-GA), the genetic algorithm is used to search for the bright spots in mammogram and a knowledge-discovery mechanism is integrated to improve the performance of the GA. The function of the knowledge-discovery mechanism includes evaluating the possibility of a bright spot being a true MC, and adaptively adjusting the associated fitness values. The adjustment of fitness is to indirectly guide the GA to extract the true MCs and eliminate the false MCs (FMCs) accordingly. The experimental results demonstrate that the incorporation of knowledge-discovery mechanism into the genetic algorithm is able to eliminate the FMCs and produce improved performance comparing with the conventional GA methods. Furthermore, the experimental results show that the proposed KD-GA method provides a promising and generic approach for the development of computer-aided diagnosis for breast cancer.

  5. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

    Science.gov (United States)

    Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A; Janke, Axel

    2015-05-27

    The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Beam angle optimization for intensity-modulated radiation therapy using a guided pattern search method

    Science.gov (United States)

    Rocha, Humberto; Dias, Joana M.; Ferreira, Brígida C.; Lopes, Maria C.

    2013-05-01

    Generally, the inverse planning of radiation therapy consists mainly of the fluence optimization. The beam angle optimization (BAO) in intensity-modulated radiation therapy (IMRT) consists of selecting appropriate radiation incidence directions and may influence the quality of the IMRT plans, both to enhance better organ sparing and to improve tumor coverage. However, in clinical practice, most of the time, beam directions continue to be manually selected by the treatment planner without objective and rigorous criteria. The goal of this paper is to introduce a novel approach that uses beam’s-eye-view dose ray tracing metrics within a pattern search method framework in the optimization of the highly non-convex BAO problem. Pattern search methods are derivative-free optimization methods that require a few function evaluations to progress and converge and have the ability to better avoid local entrapment. The pattern search method framework is composed of a search step and a poll step at each iteration. The poll step performs a local search in a mesh neighborhood and ensures the convergence to a local minimizer or stationary point. The search step provides the flexibility for a global search since it allows searches away from the neighborhood of the current iterate. Beam’s-eye-view dose metrics assign a score to each radiation beam direction and can be used within the pattern search framework furnishing a priori knowledge of the problem so that directions with larger dosimetric scores are tested first. A set of clinical cases of head-and-neck tumors treated at the Portuguese Institute of Oncology of Coimbra is used to discuss the potential of this approach in the optimization of the BAO problem.

  7. Spatial pattern of invasion and the evolutionary responses of native plant species.

    Science.gov (United States)

    Stotz, Gisela C; Gianoli, Ernesto; Cahill, James F

    2016-09-01

    Invasive plant species can have a strong negative impact on the resident native species, likely imposing new selective pressures on them. Altered selective pressures may result in evolutionary changes in some native species, reducing competitive exclusion and allowing for coexistence with the invader. Native genotypes that are able to coexist with strong invaders may represent a valuable resource for management efforts. A better understanding of the conditions under which native species are more, or less, likely to adapt to an invader is necessary to incorporate these eco-evolutionary dynamics into management strategies. We propose that the spatial structure of invasion, in particular the size and isolation of invaded patches, is one factor which can influence the evolutionary responses of native species through modifying gene flow and the strength of selection. We present a conceptual model in which large, dense, and well-connected patches result in a greater likelihood of native species adaptation. We also identify characteristics of the interacting species that may influence the evolutionary response of native species to invasion and outline potential management implications. Identifying areas of rapid evolutionary change may offer one additional tool to managers in their effort to conserve biodiversity in the face of invasion.

  8. Analysis of C3 suggests three periods of positive selection events and different evolutionary patterns between fish and mammals.

    Directory of Open Access Journals (Sweden)

    Fanxing Meng

    Full Text Available BACKGROUND: The third complement component (C3 is a central protein of the complement system conserved from fish to mammals. It also showed distinct characteristics in different animal groups. Striking features of the fish complement system were unveiled, including prominent levels of extrahepatic expression and isotypic diversity of the complement components. The evidences of the involvement of complement system in the enhancement of B and T cell responses found in mammals indicated that the complement system also serves as a bridge between the innate and adaptive responses. For the reasons mentioned above, it is interesting to explore the evolutionary process of C3 genes and to investigate whether the huge differences between aquatic and terrestrial environments affected the C3 evolution between fish and mammals. METHODOLOGY/PRINCIPAL FINDINGS: Analysis revealed that these two groups of animals had experienced different evolution patterns. The mammalian C3 genes were under purifying selection pressure while the positive selection pressure was detected in fish C3 genes. Three periods of positive selection events of C3 genes were also detected. Two happened on the ancestral lineages to all vertebrates and mammals, respectively, one happened on early period of fish evolutionary history. CONCLUSIONS/SIGNIFICANCE: Three periods of positive selection events had happened on C3 genes during history and the fish and mammals C3 genes experience different evolutionary patterns for their distinct living environments.

  9. Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

    Science.gov (United States)

    Saarinen, Juha J.; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Evans, Alistair R.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Sibly, Richard M.; Stephens, Patrick R.; Theodor, Jessica; Uhen, Mark D.; Smith, Felisa A.

    2014-01-01

    There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing. PMID:24741007

  10. Egg clutch patterning in Lestes virens (Odonata, Lestidae) with evolutionary emphasis on endophytic oviposition in lestid dragonflies.

    Science.gov (United States)

    Matushkina, Natalia A; Buy, Denis; Lambret, Philippe

    2016-12-01

    Egg deposition within plants is one of the most widely distributed and ancient behaviors in Odonata. The resulting clutch consists of eggs placed in peculiar pattern that can be a characteristic for certain groups of Odonata. Despite their importance for paleontological and evolutionary research, data on egg-clutch positioning are missing or insufficient for most species. Here, patterning of egg clutches in Lestes virens was measured and described in detail for the first time. The female usually produces a linear row of single eggs directed at an angle rightward or leftward to the longitudinal axis of plant substrate. Less often eggs are arranged in egg-sets consisting of up to 4 eggs. Apparently, the female insect follows the rigid behavior stereotypes during oviposition and is unable to easily switch to the alternate stereotypical behavior of single egg deposition or production of multiegg sets. Based on a literature review and original data, egg clutch patterning of European Lestidae is overlaid on preexisting phylogenies. The resulting evolutionary scenario of egg-clutch patterning can be considered in the framework of egg-laying behavior in Lestidae. © 2015 Institute of Zoology, Chinese Academy of Sciences.

  11. On the expected duration of a search for a fixed pattern in random data

    DEFF Research Database (Denmark)

    Nielsen, Peter Tolstrup

    1973-01-01

    An expression is obtained for the expected duration of a search to find a givenL-ary sequence in a semi-infinite stream of randomL-ary data. The search time is found to be an increasing function of the lengths of the "bifices" of the pattern, where the term bifix denotes a sequence which is both ...... a prefix and a suffix....

  12. Optimal Point-to-Point Trajectory Tracking of Redundant Manipulators using Generalized Pattern Search

    Directory of Open Access Journals (Sweden)

    Thi Rein Myo

    2008-11-01

    Full Text Available Optimal point-to-point trajectory planning for planar redundant manipulator is considered in this study. The main objective is to minimize the sum of the position error of the end-effector at each intermediate point along the trajectory so that the end-effector can track the prescribed trajectory accurately. An algorithm combining Genetic Algorithm and Pattern Search as a Generalized Pattern Search GPS is introduced to design the optimal trajectory. To verify the proposed algorithm, simulations for a 3-D-O-F planar manipulator with different end-effector trajectories have been carried out. A comparison between the Genetic Algorithm and the Generalized Pattern Search shows that The GPS gives excellent tracking performance.

  13. Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species.

    Science.gov (United States)

    Qian, Lan-Hua; Zhou, Guang-Can; Sun, Xiao-Qin; Lei, Zhao; Zhang, Yan-Mei; Xue, Jia-Yu; Hang, Yue-Yu

    2017-05-05

    Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a "consistent expansion" pattern, tomato exhibits a pattern of "first expansion and then contraction," and pepper presents a "shrinking" pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions. Copyright © 2017 Qian et al.

  14. Stable Walking of Humanoid Robots Using Vertical Center of Mass and Foot Motions by an Evolutionary Optimized Central Pattern Generator

    Directory of Open Access Journals (Sweden)

    Young-Dae Hong

    2016-02-01

    Full Text Available This paper proposes a method to produce the stable walking of humanoid robots by incorporating the vertical center of mass (COM and foot motions, which are generated by the evolutionary optimized central pattern generator (CPG, into the modifiable walking pattern generator (MWPG. The MWPG extends the conventional 3-D linear inverted pendulum model (3-D LIPM by allowing a zero moment point (ZMP variation. The disturbance caused by the vertical COM motion is compensated in real time by the sensory feedback in the CPG. In this paper, the vertical foot trajectory of the swinging leg, as well as the vertical COM trajectory of the 3-D LIPM, are generated by the CPG for the effective compensation of the disturbance. Consequently, using the proposed method, the humanoid robot is able to walk with a vertical COM and the foot motions generated by the CPG, while modifying its walking patterns by using the MWPG in real time. The CPG with the sensory feedback is optimized to obtain the desired output signals. The optimization of the CPG is formulated as a constrained optimization problem with equality constraints and is solved by two-phase evolutionary programming (TPEP. The validity of the proposed method is verified through walking experiments for the small-sized humanoid robot, HanSaRam-IX (HSR-IX.

  15. Macroevolutionary patterns in the evolutionary radiation of archosaurs (Tetrapoda:Diapsida)

    OpenAIRE

    Brusatte, S.L.; Benton, M.J.; Ruta, M.; Lloyd, G.T.; Wang, Steve C.

    2010-01-01

    The rise of archosaurs during the Triassic and Early Jurassic has been treated as a classic example of an evolutionary radiation in the fossil record. This paper reviews published studies and provides new data on archosaur lineage origination, diversity and lineage evolution, morphological disparity, rates of morphological character change, and faunal abundance during the Triassic-Early Jurassic. The fundamental archosaur lineages originated early in the Triassic, in concert with the highest ...

  16. Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis.

    Science.gov (United States)

    He, Peng; Huang, Sheng; Xiao, Guanghui; Zhang, Yuzhou; Yu, Jianing

    2016-12-01

    RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance. In this paper, we investigated 82 protein-coding genes in the chloroplast genome of G. biloba and identified 255 editing sites, which is the highest number of RNA editing events reported in a gymnosperm. All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. RNA editing could change the secondary structures of 82 proteins, and create or eliminate a transmembrane region in five proteins as determined in silico. Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode. The G. biloba chloroplast genome possesses the highest number of RNA editing events reported so far in a seed plant. Most of the RNA editing sites can restore amino acid conservation, increase hydrophobicity, and even influence protein structures. Similar purifying selections constitute the dominant evolutionary force at the editing sites of essential genes, such as the psa, some psb and pet groups, and a positive selection occurred in the editing sites of nonessential genes, such as most ndh and a few psb genes.

  17. Evolutionary potential of upper thermal tolerance: biogeographic patterns and expectations under climate change.

    Science.gov (United States)

    Diamond, Sarah E

    2017-02-01

    How will organisms respond to climate change? The rapid changes in global climate are expected to impose strong directional selection on fitness-related traits. A major open question then is the potential for adaptive evolutionary change under these shifting climates. At the most basic level, evolutionary change requires the presence of heritable variation and natural selection. Because organismal tolerances of high temperature place an upper bound on responding to temperature change, there has been a surge of research effort on the evolutionary potential of upper thermal tolerance traits. Here, I review the available evidence on heritable variation in upper thermal tolerance traits, adopting a biogeographic perspective to understand how heritability of tolerance varies across space. Specifically, I use meta-analytical models to explore the relationship between upper thermal tolerance heritability and environmental variability in temperature. I also explore how variation in the methods used to obtain these thermal tolerance heritabilities influences the estimation of heritable variation in tolerance. I conclude by discussing the implications of a positive relationship between thermal tolerance heritability and environmental variability in temperature and how this might influence responses to future changes in climate. © 2016 New York Academy of Sciences.

  18. Selective Search, Sectoral Patterns, and the Impact on Product Innovation Performance

    DEFF Research Database (Denmark)

    Köhler, Christian; Sofka, Wolfgang; Grimpe, Christoph

    2012-01-01

    . We hypothesize that search strategies driven by science, suppliers and the product market will contribute differently to innovation success with new-to-market versus imitated products. Moreover, we explore the effect of these types of knowledge search within different sectoral patterns of innovation......The shift toward more open and interconnected innovation activities has been a major topic in recent academic and practitioner discussions. Firms must connect their in-house R&D activities with external partners, such as leading customers or universities, to increase the effectiveness...... of their innovation activities. Hence, management needs to define where to search for valuable knowledge in its environment. In this paper we argue that knowledge search has to reflect the heterogeneity of various knowledge sources with regard to the knowledge they can provide and how these sources can be activated...

  19. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

    Science.gov (United States)

    Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

    2013-08-01

    Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

  20. Evolutionary Patterns among Living and Fossil Kogiid Sperm Whales: Evidence from the Neogene of Central America.

    Science.gov (United States)

    Velez-Juarbe, Jorge; Wood, Aaron R; De Gracia, Carlos; Hendy, Austin J W

    2015-01-01

    Kogiids are known by two living species, the pygmy and dwarf sperm whale (Kogia breviceps and K. sima). Both are relatively rare, and as their names suggest, they are closely related to the sperm whale, all being characterized by the presence of a spermaceti organ. However, this organ is much reduced in kogiids and may have become functionally different. Here we describe a fossil kogiid from the late Miocene of Panama and we explore the evolutionary history of the group with special attention to this evolutionary reduction. The fossil consists of cranial material from the late Tortonian (~7.5 Ma) Piña facies of the Chagres Formation in Panama. Detailed comparison with other fossil and extant kogiids and the results of a phylogenetic analysis place the Panamanian kogiid, herein named Nanokogia isthmia gen. et sp. nov., as a taxon most closely related to Praekogia cedrosensis from the Messinian (~6 Ma) of Baja California and to Kogia spp. Furthermore our results show that reduction of the spermaceti organ has occurred iteratively in kogiids, once in Thalassocetus antwerpiensis in the early-middle Miocene, and more recently in Kogia spp. Additionally, we estimate the divergence between extant species of Kogia at around the late Pliocene, later than previously predicted by molecular estimates. Finally, comparison of Nanokogia with the coeval Scaphokogia cochlearis from Peru shows that these two species display a greater morphological disparity between them than that observed between the extant members of the group. We hypothesize that this reflects differences in feeding ecologies of the two species, with Nanokogia being more similar to extant Kogia. Nanokogia shows that kogiids have been part of the Neotropical marine mammal communities at least since the late Miocene, and gives us insight into the evolutionary history and origins of one of the rarest groups of living whales.

  1. Evolutionary Patterns among Living and Fossil Kogiid Sperm Whales: Evidence from the Neogene of Central America.

    Directory of Open Access Journals (Sweden)

    Jorge Velez-Juarbe

    Full Text Available Kogiids are known by two living species, the pygmy and dwarf sperm whale (Kogia breviceps and K. sima. Both are relatively rare, and as their names suggest, they are closely related to the sperm whale, all being characterized by the presence of a spermaceti organ. However, this organ is much reduced in kogiids and may have become functionally different. Here we describe a fossil kogiid from the late Miocene of Panama and we explore the evolutionary history of the group with special attention to this evolutionary reduction. The fossil consists of cranial material from the late Tortonian (~7.5 Ma Piña facies of the Chagres Formation in Panama. Detailed comparison with other fossil and extant kogiids and the results of a phylogenetic analysis place the Panamanian kogiid, herein named Nanokogia isthmia gen. et sp. nov., as a taxon most closely related to Praekogia cedrosensis from the Messinian (~6 Ma of Baja California and to Kogia spp. Furthermore our results show that reduction of the spermaceti organ has occurred iteratively in kogiids, once in Thalassocetus antwerpiensis in the early-middle Miocene, and more recently in Kogia spp. Additionally, we estimate the divergence between extant species of Kogia at around the late Pliocene, later than previously predicted by molecular estimates. Finally, comparison of Nanokogia with the coeval Scaphokogia cochlearis from Peru shows that these two species display a greater morphological disparity between them than that observed between the extant members of the group. We hypothesize that this reflects differences in feeding ecologies of the two species, with Nanokogia being more similar to extant Kogia. Nanokogia shows that kogiids have been part of the Neotropical marine mammal communities at least since the late Miocene, and gives us insight into the evolutionary history and origins of one of the rarest groups of living whales.

  2. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

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

  3. The role of pattern recognition in creative problem solving: a case study in search of new mathematics for biology.

    Science.gov (United States)

    Hong, Felix T

    2013-09-01

    is in line with Campbell's evolutionary epistemology. Instead of treating science as immutable Natural Laws, which already existed and which were just waiting to be discovered, scientific theories are regarded as humans' mental constructs, which must be invented to reconcile with observed natural phenomena. In this way, the pursuit of science is shifted from diligent and systematic (or random) searching for existing Natural Laws to firing up humans' imagination to comprehend Nature's behavioral pattern. The insights gained in understanding human creativity indicated that new mathematics that is capable of handling effectively parallel processing and human subjectivity is sorely needed. The past classification of formalizability vs. non-formalizability was made in reference to contemporary mathematics. Rosen's conclusion did not preclude future inventions of new biology-friendly mathematics. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Insights into performance of pattern search algorithms for high-frequency surface wave analysis

    Science.gov (United States)

    Song, Xianhai; Li, Duanyou; Gu, Hanming; Liao, Yonglong; Ren, Dachun

    2009-08-01

    Inversion of high-frequency surface wave dispersion curves is challenging for most local-search methods due to its high nonlinearity and to its multimodality. In this paper, we implemented an investigation to fully exploit and utilize the potentiality of pattern search algorithms and to further enhance their performance for surface wave analysis. We first investigate effects of different inversion strategies, initial mesh size and final mesh size, expansion factor, and contraction factor, as well as inclusion of noise in surface wave data on the performance of the approaches, by three synthetic earth models. Then, a comparative analysis with genetic algorithms is made to further highlight the advantages of the proposed inverse procedure. Finally, the insights issued from this analysis are verified by a real-world example from Henan, China. Results from both synthetic and field data demonstrate: (a) generalized pattern search (GPS) algorithm with the maximal positive basis set 2 N vectors works better than GPS algorithm with the minimal positive basis set N+1 vectors; (b) if one gets a suitable initial mesh size by taking some experimentation, then setting expansion factor Λ=1 (i.e., not allow expansions) and contraction factor θ=1/2 can greatly enhance the performance of pattern search algorithms. This is particularly true as the algorithm converges and final mesh size should go to zero; and (c) pattern search algorithms possess stronger immunity with respect to noise and should be considered good not only in terms of accuracy but also in terms of computation effort, especially when compared to the application of genetic algorithms to Rayleigh wave inversion.

  5. Interspecific tests of allelism reveal the evolutionary timing and pattern of accumulation of reproductive isolation mutations.

    Science.gov (United States)

    Sherman, Natasha A; Victorine, Anna; Wang, Richard J; Moyle, Leonie C

    2014-09-01

    Despite extensive theory, little is known about the empirical accumulation and evolutionary timing of mutations that contribute to speciation. Here we combined QTL (Quantitative Trait Loci) analyses of reproductive isolation, with information on species evolutionary relationships, to reconstruct the order and timing of mutations contributing to reproductive isolation between three plant (Solanum) species. To evaluate whether reproductive isolation QTL that appear to coincide in more than one species pair are homologous, we used cross-specific tests of allelism and found evidence for both homologous and lineage-specific (non-homologous) alleles at these co-localized loci. These data, along with isolation QTL unique to single species pairs, indicate that >85% of isolation-causing mutations arose later in the history of divergence between species. Phylogenetically explicit analyses of these data support non-linear models of accumulation of hybrid incompatibility, although the specific best-fit model differs between seed (pairwise interactions) and pollen (multi-locus interactions) sterility traits. Our findings corroborate theory that predicts an acceleration ('snowballing') in the accumulation of isolation loci as lineages progressively diverge, and suggest different underlying genetic bases for pollen versus seed sterility. Pollen sterility in particular appears to be due to complex genetic interactions, and we show this is consistent with a snowball model where later arising mutations are more likely to be involved in pairwise or multi-locus interactions that specifically involve ancestral alleles, compared to earlier arising mutations.

  6. Phylogenetics of Australasian gall flies (Diptera: Fergusoninidae): Evolutionary patterns of host-shifting and gall morphology.

    Science.gov (United States)

    Scheffer, S J; Davies, K A; Taylor, G S; Thornhill, A H; Lewis, M L; Winkler, I S; Yeates, D K; Purcell, M F; Makinson, J; Giblin-Davis, R M

    2017-10-01

    This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72.5%) were strictly monophagous, and 11 (27.5%) were reared from multiple closely related hosts. COI variation within species was not correlated with either sample size or geographic distance. However variation was greater within oligophagous species, consistent with expectations of the initial stages of host-associated divergence during speciation. Phylogenetic analysis using both nuclear and mitochondrial genes revealed host genus-restricted clades but also clear evidence of multiple colonizations of both host plant genus and host species. With the exception of unilocular peagalls, evolution of gall type was somewhat constrained, but to a lesser degree than host plant association. Unilocular peagalls arose more often than any other gall type, were primarily located at the tips of the phylogeny, and did not form clades comprising more than a few species. For ecological reasons, species of this gall type are predicted to harbor substantially less genetic variation than others, possibly reducing evolutionary flexibility resulting in reduced diversification in unilocular gallers. Published by Elsevier Inc.

  7. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

    Science.gov (United States)

    Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

    2011-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

  8. Interspecific Tests of Allelism Reveal the Evolutionary Timing and Pattern of Accumulation of Reproductive Isolation Mutations

    Science.gov (United States)

    Sherman, Natasha A.; Victorine, Anna; Wang, Richard J.; Moyle, Leonie C.

    2014-01-01

    Despite extensive theory, little is known about the empirical accumulation and evolutionary timing of mutations that contribute to speciation. Here we combined QTL (Quantitative Trait Loci) analyses of reproductive isolation, with information on species evolutionary relationships, to reconstruct the order and timing of mutations contributing to reproductive isolation between three plant (Solanum) species. To evaluate whether reproductive isolation QTL that appear to coincide in more than one species pair are homologous, we used cross-specific tests of allelism and found evidence for both homologous and lineage-specific (non-homologous) alleles at these co-localized loci. These data, along with isolation QTL unique to single species pairs, indicate that >85% of isolation-causing mutations arose later in the history of divergence between species. Phylogenetically explicit analyses of these data support non-linear models of accumulation of hybrid incompatibility, although the specific best-fit model differs between seed (pairwise interactions) and pollen (multi-locus interactions) sterility traits. Our findings corroborate theory that predicts an acceleration (‘snowballing’) in the accumulation of isolation loci as lineages progressively diverge, and suggest different underlying genetic bases for pollen versus seed sterility. Pollen sterility in particular appears to be due to complex genetic interactions, and we show this is consistent with a snowball model where later arising mutations are more likely to be involved in pairwise or multi-locus interactions that specifically involve ancestral alleles, compared to earlier arising mutations. PMID:25211473

  9. Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae).

    Science.gov (United States)

    McCord, Charlene L; Westneat, Mark W

    2016-06-01

    The robust skull and highly subdivided adductor mandibulae muscles of triggerfishes provide an excellent system within which to analyze the evolutionary processes underlying phenotypic diversification. We surveyed the anatomical diversity of balistid jaws using Procrustes-based geometric morphometric analyses and a phylomorphospace approach to quantifying morphological transformation through evolution. We hypothesized that metrics of interspecific cranial shape would reveal patterns of phylogenetic diversification that are congruent with functional and ecological transformation. Morphological landmarks outlining skull and adductor mandibulae muscle shape were collected from 27 triggerfish species. Procrustes-transformed skull shape configurations revealed significant phylogenetic and size-influenced structure. Phylomorphospace plots of cranial shape diversity reveal groupings of shape between different species of triggerfish that are mostly consistent with phylogenetic relatedness. Repeated instances of convergence upon similar cranial shape by genetically disparate taxa are likely due to the functional demands of shared specialized dietary habits. This study shows that the diversification of triggerfish skulls occurs via modifications of cranial silhouette and the positioning of subdivided jaw adductor muscles. Using the morphometric data collected here as input to a biomechanical model of triggerfish jaw function, we find that subdivided jaw adductors, in conjunction with a unique cranial skeleton, have direct biomechanical consequences that are not always congruent with phylomorphospace patterns in the triggerfish lineage. The integration of geometric morphometrics with biomechanical modeling in a phylogenetic context provides novel insight into the evolutionary patterns and ecological role of muscle subdivisions in triggerfishes. J. Morphol. 277:737-752, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.

    Directory of Open Access Journals (Sweden)

    Jonathan L Klassen

    Full Text Available BACKGROUND: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. METHODOLOGY/PRINCIPAL FINDINGS: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i Proteobacteria; (ii Firmicutes; (iii Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i horizontal gene transfer; (ii gene acquisition followed by differential gene loss; (iii co-evolution with other biochemical structures such as proteorhodopsins; and (iv positive selection. CONCLUSIONS/SIGNIFICANCE: Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident

  11. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.

    Science.gov (United States)

    Klassen, Jonathan L

    2010-06-22

    Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of

  12. A hybrid firefly algorithm and pattern search technique for SSSC based power oscillation damping controller design

    Directory of Open Access Journals (Sweden)

    Srikanta Mahapatra

    2014-12-01

    Full Text Available In this paper, a novel hybrid Firefly Algorithm and Pattern Search (h-FAPS technique is proposed for a Static Synchronous Series Compensator (SSSC-based power oscillation damping controller design. The proposed h-FAPS technique takes the advantage of global search capability of FA and local search facility of PS. In order to tackle the drawback of using the remote signal that may impact reliability of the controller, a modified signal equivalent to the remote speed deviation signal is constructed from the local measurements. The performances of the proposed controllers are evaluated in SMIB and multi-machine power system subjected to various transient disturbances. To show the effectiveness and robustness of the proposed design approach, simulation results are presented and compared with some recently published approaches such as Differential Evolution (DE and Particle Swarm Optimization (PSO. It is observed that the proposed approach yield superior damping performance compared to some recently reported approaches.

  13. Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).

    Science.gov (United States)

    Goodheart, Jessica A; Bazinet, Adam L; Valdés, Ángel; Collins, Allen G; Cummings, Michael P

    2017-10-26

    The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of marine specialized consumers for which reliable phylogenies exist hampers attempts to test the role of trophic specialization in evolution. In this study, RNA-Seq data is used to produce a phylogeny of Cladobranchia, a group of marine invertebrates that feed on a diverse array of prey taxa but mostly specialize on cnidarians. The broad range of prey type preferences allegedly present in two major groups within Cladobranchia suggest that prey type shifts are relatively common over evolutionary timescales. In the present study, we generated a well-supported phylogeny of the major lineages within Cladobranchia using RNA-Seq data, and used ancestral state reconstruction analyses to better understand the evolution of prey preference. These analyses answered several fundamental questions regarding the evolutionary relationships within Cladobranchia, including support for a clade of species from Arminidae as sister to Tritoniidae (which both preferentially prey on Octocorallia). Ancestral state reconstruction analyses supported a cladobranchian ancestor with a preference for Hydrozoa and show that the few transitions identified only occur from lineages that prey on Hydrozoa to those that feed on other types of prey. There is strong phylogenetic correlation with prey preference within Cladobranchia, suggesting that prey type specialization within this group has inertia. Shifts between different types of prey have occurred rarely throughout the evolution of

  14. HIERARCHICAL ADAPTIVE ROOD PATTERN SEARCH FOR MOTION ESTIMATION AT VIDEO SEQUENCE ANALYSIS

    Directory of Open Access Journals (Sweden)

    V. T. Nguyen

    2016-05-01

    Full Text Available Subject of Research.The paper deals with the motion estimation algorithms for the analysis of video sequences in compression standards MPEG-4 Visual and H.264. Anew algorithm has been offered based on the analysis of the advantages and disadvantages of existing algorithms. Method. Thealgorithm is called hierarchical adaptive rood pattern search (Hierarchical ARPS, HARPS. This new algorithm includes the classic adaptive rood pattern search ARPS and hierarchical search MP (Hierarchical search or Mean pyramid. All motion estimation algorithms have been implemented using MATLAB package and tested with several video sequences. Main Results. The criteria for evaluating the algorithms were: speed, peak signal to noise ratio, mean square error and mean absolute deviation. The proposed method showed a much better performance at a comparable error and deviation. The peak signal to noise ratio in different video sequences shows better and worse results than characteristics of known algorithms so it requires further investigation. Practical Relevance. Application of this algorithm in MPEG-4 and H.264 codecs instead of the standard can significantly reduce compression time. This feature enables to recommend it in telecommunication systems for multimedia data storing, transmission and processing.

  15. A Game of Hide and Seek: Expectations of Clumpy Resources Influence Hiding and Searching Patterns.

    Directory of Open Access Journals (Sweden)

    Andreas Wilke

    Full Text Available Resources are often distributed in clumps or patches in space, unless an agent is trying to protect them from discovery and theft using a dispersed distribution. We uncover human expectations of such spatial resource patterns in collaborative and competitive settings via a sequential multi-person game in which participants hid resources for the next participant to seek. When collaborating, resources were mostly hidden in clumpy distributions, but when competing, resources were hidden in more dispersed (random or hyperdispersed patterns to increase the searching difficulty for the other player. More dispersed resource distributions came at the cost of higher overall hiding (as well as searching times, decreased payoffs, and an increased difficulty when the hider had to recall earlier hiding locations at the end of the experiment. Participants' search strategies were also affected by their underlying expectations, using a win-stay lose-shift strategy appropriate for clumpy resources when searching for collaboratively-hidden items, but moving equally far after finding or not finding an item in competitive settings, as appropriate for dispersed resources. Thus participants showed expectations for clumpy versus dispersed spatial resources that matched the distributions commonly found in collaborative versus competitive foraging settings.

  16. Derivation of Optimal Cropping Pattern in Part of Hirakud Command using Cuckoo Search

    Science.gov (United States)

    Rath, Ashutosh; Biswal, Sudarsan; Samantaray, Sandeep; Swain, Prakash Chandra, PROF.

    2017-08-01

    The economicgrowth of a Nation depends on agriculture which relies on the obtainable water resources, available land and crops. The contribution of water in an appropriate quantity at appropriate time plays avitalrole to increase the agricultural production. Optimal utilization of available resources can be achieved by proper planning and management of water resources projects and adoption of appropriate technology. In the present work, the command area of Sambalpur distribrutary System is taken up for investigation. Further, adoption of a fixed cropping pattern causes the reduction of yield. The present study aims at developing different crop planning strategies to increase the net benefit from the command area with minimum investment. Optimization models are developed for Kharif season using LINDO and Cuckoo Search (CS) algorithm for maximization of the net benefits. In process of development of Optimization model the factors such as cultivable land, seeds, fertilizers, man power, water cost, etc. are taken as constraints. The irrigation water needs of major crops and the total available water through canals in the command of Sambalpur Distributary are estimated. LINDO and Cuckoo Search models are formulated and used to derive the optimal cropping pattern yielding maximum net benefits. The net benefits of Rs.585.0 lakhs in Kharif Season are obtained by adopting LINGO and 596.07 lakhs from Cuckoo Search, respectively, whereas the net benefits of 447.0 lakhs is received by the farmers of the locality with the adopting present cropping pattern.

  17. Representation, searching and discovery of patterns of bases in complex RNA structures

    Science.gov (United States)

    Harrison, Anne-Marie; South, Darren R.; Willett, Peter; Artymiuk, Peter J.

    2003-08-01

    We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.

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

    Directory of Open Access Journals (Sweden)

    Guoqin Mai

    2016-01-01

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

  19. Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom

    Science.gov (United States)

    Song, Xiaoming; Duan, Weike; Huang, Zhinan; Liu, Gaofeng; Wu, Peng; Liu, Tongkun; Li, Ying; Hou, Xilin

    2015-09-01

    In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in Brassica rapa (BraCOL genes), the key flowering genes; (iii) exploration of the evolution of COL genes in plant kingdom and construction of the evolutionary pattern of COL genes; (iv) comparative analysis of CO and FT genes between Brassicaceae and Grass, which identified several family-specific amino acids, and revealed that CO and FT protein structures were similar in B. rapa and Arabidopsis but different in rice; and (v) expression analysis of photoperiod pathway-related genes in B. rapa under different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern of COL genes. In addition, this genome-wide comparative study of COL genes may also provide clues for evolution of other flowering genes.

  20. Ice age climate, evolutionary constraints and diversity patterns of European dung beetles

    DEFF Research Database (Denmark)

    Hortal, Joaquín; Diniz-Filho, José Alexandre F.; Bini, Luis Mauricio

    2011-01-01

    Current climate and Pleistocene climatic changes are both known to be associated with geographical patterns of diversity. We assess their associations with the European Scarabaeinae dung beetles, a group with high dispersal ability and well-known adaptations to warm environments. By assessing...

  1. Evolutionary convergence of the patterns of international research collaborations across scientific fields

    NARCIS (Netherlands)

    Wang, L.; Coccia, M.

    2015-01-01

    Frame and Carpenter (1979) analysed the pattern of international research collaboration among scientific fields in 1970s. Starting from this pioneering work, this paper investigates international collaborations over 1997-2012 and compares the critical results with earlier studies to detect the

  2. Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus

    Science.gov (United States)

    Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

    2012-01-01

    Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history. PMID:22822436

  3. Evolutionary plasticity of habenular asymmetry with a conserved efferent connectivity pattern.

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    Aldo Villalón

    Full Text Available The vertebrate habenulae (Hb is an evolutionary conserved dorsal diencephalic nuclear complex that relays information from limbic and striatal forebrain regions to the ventral midbrain. One key feature of this bilateral nucleus is the presence of left-right differences in size, cytoarchitecture, connectivity, neurochemistry and/or gene expression. In teleosts, habenular asymmetry has been associated with preferential innervation of left-right habenular efferents into dorso-ventral domains of the midbrain interpeduncular nucleus (IPN. However, the degree of conservation of this trait and its relation to the structural asymmetries of the Hb are currently unknown. To address these questions, we performed the first systematic comparative analysis of structural and connectional asymmetries of the Hb in teleosts. We found striking inter-species variability in the overall shape and cytoarchitecture of the Hb, and in the frequency, strength and to a lesser degree, laterality of habenular volume at the population level. Directional asymmetry of the Hb was either to the left in D. rerio, E. bicolor, O. latipes, P. reticulata, B. splendens, or to the right in F. gardneri females. In contrast, asymmetry was absent in P. scalare and F. gardneri males at the population level, although in these species the Hb displayed volumetric asymmetries at the individual level. Inter-species variability was more pronounced across orders than within a single order, and coexisted with an overall conserved laterotopic representation of left-right habenular efferents into dorso-ventral domains of the IPN. These results suggest that the circuit design involving the Hb of teleosts promotes structural flexibility depending on developmental, cognitive and/or behavioural pressures, without affecting the main midbrain connectivity output, thus unveiling a key conserved role of this connectivity trait in the function of the circuit. We propose that ontogenic plasticity in habenular

  4. Fitness-maximizing foragers can use information about patch quality to decide how to search for and within patches: optimal Levy walk searching patterns from optimal foraging theory.

    Science.gov (United States)

    Reynolds, A M

    2012-07-07

    Optimal foraging theory shows how fitness-maximizing foragers can use information about patch quality to decide how to search within patches. It is amply supported by empirical studies. Nonetheless, the theory largely ignores the fact that foragers may need to search for patches as well as for the targets within them. Here, using an exact but simple mathematical argument, it is shown how foragers can use information about patch quality to facilitate the execution of Lévy walk movement patterns with μ = 2 at inter-patch scales. These movement patterns are advantageous when searching for patches that are not depleted or rejected once visited but instead remain profitable. The analytical results are verified by the results of numerical simulations. The findings bring forth an innovative theoretical synthesis of searching for and within patches and, suggest that foragers' memories may be adaptive under spatially heterogeneous reward schedules.

  5. Amphibian species traits, evolutionary history and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk.

    Science.gov (United States)

    Greenberg, Dan A; Palen, Wendy J; Mooers, Arne Ø

    2017-12-01

    The fungal pathogen Batrachochytrium dendrobatidis (B. dendrobatidis) has emerged as a major agent of amphibian extinction, requiring conservation intervention for many susceptible species. Identifying susceptible species is challenging, but many aspects of species biology are predicted to influence the evolution of host resistance, tolerance, or avoidance strategies towards disease. In turn, we may expect species exhibiting these distinct strategies to differ in their ability to survive epizootic disease outbreaks. Here, we test for phylogenetic and trait-based patterns of B. dendrobatidis infection risk and infection intensity among 302 amphibian species by compiling a global data set of B. dendrobatidis infection surveys across 95 sites. We then use best-fit models that associate traits, taxonomy and environment with B. dendrobatidis infection risk and intensity to predict host disease mitigation strategies (tolerance, resistance, avoidance) for 122 Neotropical amphibian species that experienced epizootic B. dendrobatidis outbreaks, and noted species persistence or extinction from these events. Aspects of amphibian species life history, habitat use and climatic niche were consistently linked to variation in B. dendrobatidis infection patterns across sites around the world. However, predicted B. dendrobatidis infection risk and intensity based on site environment and species traits did not reveal a consistent pattern between the predicted host disease mitigation strategy and extinction outcome. This suggests that either tolerant or resistant species may have no advantage in ameliorating disease during epizootic events, or that other factors drive the persistence of amphibian populations during chytridiomycosis outbreaks. These results suggest that using a trait-based approach may allow us to identify species with resistance or tolerance to endemic B. dendrobatidis infections, but that this approach may be insufficient to ultimately identify species at

  6. Venoms of Micrurus coral snakes: Evolutionary trends in compositional patterns emerging from proteomic analyses.

    Science.gov (United States)

    Lomonte, Bruno; Rey-Suárez, Paola; Fernández, Julián; Sasa, Mahmood; Pla, Davinia; Vargas, Nancy; Bénard-Valle, Melisa; Sanz, Libia; Corrêa-Netto, Carlos; Núñez, Vitelbina; Alape-Girón, Alberto; Alagón, Alejandro; Gutiérrez, José María; Calvete, Juan J

    2016-11-01

    The application of proteomic tools to the study of snake venoms has led to an impressive growth in the knowledge about their composition (venomics), immunogenicity (antivenomics), and toxicity (toxicovenomics). About one-third of all venomic studies have focused on elapid species, especially those of the Old World. The New World elapids, represented by coral snakes, have been less studied. In recent years, however, a number of venomic studies on Micrurus species from North, Central, and South America have been conducted. An overview of these studies is presented, highlighting the emergence of some patterns and trends concerning their compositional, functional, and immunological characteristics. Results gathered to date, encompassing 18 out of the approximately 85 species of Micrurus, reveal a dichotomy of venom phenotypes regarding the relative abundance of the omnipresent phospholipases A 2 (PLA 2 ) and 'three-finger' toxins (3FTx): a group of species express a PLA 2 -predominant venom composition, while others display a 3FTx-predominant compositional pattern. These two divergent toxin expression phenotypes appear to be related to phylogenetic positions and geographical distributions along a North-South axis in the Americas, but further studies encompassing a higher number of species are needed to assess these hypotheses. The two contrasting phenotypes also show correlations with some toxic functionalities, complexity in the diversity of proteoforms, and immunological cross-recognition patterns. The biological significance for the emergence of a dichotomy of venom compositions within Micrurus, in some cases observed even among sympatric species that inhabit relatively small geographic areas, represents a puzzling and challenging area of research which warrants further studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. A Unique Pattern of HCV Genotype Distribution on Hainan Island in China Revealed by Evolutionary Analysis.

    Science.gov (United States)

    Wu, Tao; Xiong, Lu; Wang, Fuli; Xu, Xiaozhen; Wang, Jiao; Lin, Feng; Li, Chunhua; Lu, Ling; Zhou, Yuanping

    2016-01-01

    Different genotypes of HCV may differ in both disease progression and response to antiviral therapies. Hainan Island has been inhabited by the "Li" aboriginal minority for centuries. We aimed to provide a better understanding of HCV infection on Hainan Island, so that the information would help improve strategies for HCV prevention and control on the island and in the wider country. Using RT-PCR and DNA sequencing, we determined HCV sequences from 100 patients living on Hainan Island. Phylogenetic analysis classified these sequences into six subtypes: 6a (n=35), 1b (n=31), 3b (n=16), 2a (n=8), 3a (n=6), and 1a (n=4). By including reference sequences reported from elsewhere in China, phylogeographic trees were reconstructed to indicate their migration patterns. While the predominant 6a isolates were estimated to have origins in Guangdong and Guangxi provinces, the increase in 3b strains must have resulted from IDU network transmission from the southwest. A Bayesian Skyline Plot for subtype 1a, which is rare in China, showed a rapid population growth since 1998. Although slowed in rate around 2005, this growth continued to the present. Not found for any other HCV lineage. Overall, a delayed growth pattern may indicate the unique history of 1a dissemination in China and its recently increasing prevalence, despite measures taken to improve HCV prevention. © 2016 The Author(s) Published by S. Karger AG, Basel.

  8. Evolutionary and developmental aspects of avian-specific traits in limb skeletal pattern.

    Science.gov (United States)

    Seki, Ryohei; Kamiyama, Namiko; Tadokoro, Ayumi; Nomura, Naoki; Tsuihiji, Takanobu; Manabe, Makoto; Tamura, Koji

    2012-10-01

    The two sets of paired appendages, called limbs, are locomotory organs in tetrapods that are used for various functions (e.g., walking, running, crawling, digging, climbing, diving, swimming, and flying). Unlike such organs as the eye, which contain specialized tissues such as the lens and photoreceptor, the limb does not have any specialized cells or tissues, but consists of common tissues, such as bone, cartilage, muscle, blood vessels, and dermis. However, limb morphology is highly specialized and varies to provide species-specific modes of locomotion. As do the vertebrae and skull, the limb skeleton varies in morphology among species. The diversity of limb skeletal morphology provides examples of material for studies on morphogenesis. Avian forelimbs have evolved into wings for flight. The skeletal pattern in the avian limb has many traits that are unique among extant species of vertebrates; some of such traits are avian-specific, others are shared with more basal members of Theropoda, to which Aves belongs. Since such avian traits generally form during ontogenic development, determining when and how they appear in the developing embryonic limbs or limb buds provides important insights into the mechanisms underlying the generation of vertebrate morphological diversity. Here, we present an overview of several features of the skeletal pattern in the avian limb and discuss the developmental mechanisms responsible for their unique and lineage-specific traits.

  9. A Unique Pattern of HCV Genotype Distribution on Hainan Island in China Revealed by Evolutionary Analysis

    Directory of Open Access Journals (Sweden)

    Tao Wu

    2016-06-01

    Full Text Available Background/Aims: Different genotypes of HCV may differ in both disease progression and response to antiviral therapies. Hainan Island has been inhabited by the “Li” aboriginal minority for centuries. We aimed to provide a better understanding of HCV infection on Hainan Island, so that the information would help improve strategies for HCV prevention and control on the island and in the wider country. Methods: Using RT-PCR and DNA sequencing, we determined HCV sequences from 100 patients living on Hainan Island. Results: Phylogenetic analysis classified these sequences into six subtypes: 6a (n=35, 1b (n=31, 3b (n=16, 2a (n=8, 3a (n=6, and 1a (n=4. By including reference sequences reported from elsewhere in China, phylogeographic trees were reconstructed to indicate their migration patterns. While the predominant 6a isolates were estimated to have origins in Guangdong and Guangxi provinces, the increase in 3b strains must have resulted from IDU network transmission from the southwest. A Bayesian Skyline Plot for subtype 1a, which is rare in China, showed a rapid population growth since 1998. Although slowed in rate around 2005, this growth continued to the present. Not found for any other HCV lineage. Conclusions: Overall, a delayed growth pattern may indicate the unique history of 1a dissemination in China and its recently increasing prevalence, despite measures taken to improve HCV prevention.

  10. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

    Directory of Open Access Journals (Sweden)

    Kyle Dexter

    2016-09-01

    Full Text Available Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

  11. Shelves around the Iberian Peninsula (II): Evolutionary sedimentary patterns; Las plataformas continentales de la Peninsula Iberica (II): Patrones sedimentarios evolutivos

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, F. J.; Duran, R.; Roque, C.; Ribo, M.; Carrera, G.; Mendes, I.; Ferrin, A.; Fernandez-Salas, L. M.; Garcia-Gil, S.; Galpalsoro, I.; Rosa, F.; Barcenas, P.

    2015-07-01

    We present a synthetic view of continental-shelf evolutionary patterns around the Iberian Peninsula, focusing on proposed sequence stratigraphy interpretations and attempting a comparison between Atlantic- and Mediterranean-type shelf-margin constructions. Most of the studied shelves show a dominance of regressive to low stand deposition through successive pro gradations, particularly evident in the Pliocene-Quaternary, documenting the influence of glacio-eustasy. Transgressive to high stand development predating the Last Glacial Maximum seems to be favoured off major rivers, but the highest variability is seen during post glacial evolution. Transgressive deposits tend to show a higher spatial variability, ranging from pro graded para sequences to extensive sand sheets. Holocene high- stand deposits usually show a more homogeneous character, with development of proximal wedge-shaped deposits and a distal sheet-like deposition. Atlantic continental shelves off Iberia display three different types of shelf growth: depositional shelves, shelves with restricted pro gradation and erosional shelves. They result from the interplay between depositional and hydrodynamic regimes, with the occurrence of a latitudinal gradation from erosional shelves in the Cantabrian continental shelf to depositional shelves in the northern Gulf of Cadiz shelf. Some shelf sectors do not correspond to this general pattern, as shelf sedimentation is mainly controlled by morpho-structural features (e.g., ria environments and shelves crossed by major tectonic accidents). The Mediterranean continental shelves of Iberia show two basic types, high- versus low-supply shelves, and their growth patterns are mainly a response to the amount of fluvial supply. The low-supply style is clearly the most frequent type, and it may show further complexity according to the occurrence of submarine canyons and/or morpho-structural control. (Author)

  12. Searching for full power control rod patterns in a boiling water reactor using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Jose Luis [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: jlmt@nuclear.inin.mx; Ortiz, Juan Jose [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: jjortiz@nuclear.inin.mx; Requena, Ignacio [Departamento Ciencias Computacion e I.A. ETSII, Informatica, Universidad de Granada, C. Daniel Saucedo Aranda s/n. 18071 Granada (Spain)]. E-mail: requena@decsai.ugr.es; Perusquia, Raul [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: rpc@nuclear.inin.mx

    2004-11-01

    One of the most important questions related to both safety and economic aspects in a nuclear power reactor operation, is without any doubt its reactivity control. During normal operation of a boiling water reactor, the reactivity control of its core is strongly determined by control rods patterns efficiency. In this paper, GACRP system is proposed based on the concepts of genetic algorithms for full power control rod patterns search. This system was carried out using LVNPP transition cycle characteristics, being applied too to an equilibrium cycle. Several operation scenarios, including core water flow variation throughout the cycle and different target axial power distributions, are considered. Genetic algorithm fitness function includes reactor security parameters, such as MLHGR, MCPR, reactor k{sub eff} and axial power density.

  13. Cellular automaton and Kalman filter based track search in the HERA-B pattern tracker

    CERN Document Server

    Abt, I; Gorbounov, I; Kisel, I

    2002-01-01

    The paper describes track reconstruction package OTR/ITR-CATS developed for the Pattern Tracker of the HERA-B experiment. This package employs a combined approach for track reconstruction based on the use of a cellular automaton for track searching and the Kalman filter techniques for track fitting. A similar reconstruction strategy is already successfully applied to the Vertex Detector System (VDS) (Nucl. Instr. and Meth. A 489 (2002) 389). However, hit efficiencies and resolutions of the Pattern Tracker lower than those of the VDS require much more delicate implementation of the method. The package developed has been tested on simulated data. The results of the tests regarding reconstruction efficiency, accuracy of estimates and computing time are presented.

  14. Distinguishing the Transcription Regulation Patterns in Promoters of Human Genes with Different Function or Evolutionary Age

    KAUST Repository

    Alam, Tanvir

    2012-07-01

    Distinguishing transcription regulatory patterns of different gene groups is a common problem in various bioinformatics studies. In this work we developed a methodology to deal with such a problem based on machine learning techniques. We applied our method to two biologically important problems related to detecting a difference in transcription regulation of: a/ protein-coding and long non-coding RNAs (lncRNAs) in human, as well as b/ a difference between primate-specific and non-primate-specific long non-coding RNAs. Our method is capable to classify RNAs using various regulatory features of genes that transcribe into these RNAs, such as nucleotide frequencies, transcription factor binding sites, de novo sequence motifs, CpG islands, repetitive elements, histone modification marks, and others. Ten-fold cross-validation tests suggest that our model can distinguish protein-coding and non-coding RNAs with accuracy above 80%. Twenty-fold cross-validation tests suggest that our model can distinguish primate-specific from non-primate-specific promoters of lncRNAs with accuracy above 80%. Consequently, we can hypothesize that transcription of the groups of genes mentioned above are regulated by different mechanisms. Feature selection techniques allowed us to reduce the number of features significantly while keeping the accuracy around 80%. Consequently, we can conclude that selected features play significant role in transcription regulation of coding and non-coding genes, as well as primate-specific and non-primate-specific lncRNA genes.

  15. Google vs. the Library (Part II): Student Search Patterns and Behaviors When Using Google and a Federated Search Tool

    Science.gov (United States)

    Georgas, Helen

    2014-01-01

    This study examines the information-seeking behavior of undergraduate students within a research context. Student searches were recorded while the participants used Google and a library (federated) search tool to find sources (one book, two articles, and one other source of their choosing) for a selected topic. The undergraduates in this study…

  16. Evolutionary patterns of codon usage in the chloroplast gene rbcL.

    Science.gov (United States)

    Wall, Dennis P; Herbeck, Joshua T

    2003-06-01

    In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum likelihood-ratio tests to compare the performance of two models, one in which a single codon is overrepresented and one in which two codons are overrepresented. The measure allowed us to analyze both the extent of bias in each lineage and the evolution of codon choice across the phylogeny. Despite predictions based primarily on the low G + C content of the chloroplast and the high functional importance of rbcL, we found large differences in the extent of bias, suggesting differential molecular selection that is clade specific. The seed plants and simple leafy liverworts each independently derived a low level of bias in rbcL, perhaps indicating relaxed selectional constraint on molecular changes in the gene. Overrepresentation of a single codon was typically plesiomorphic, and transitions to overrepresentation of two codons occurred commonly across the phylogeny, possibly indicating biochemical selection. The total codon bias in each taxon, when regressed against the total bias of each amino acid, suggested that twofold amino acids play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds compose a minority of residues in this gene. Those amino acids that contributed most to the total codon usage bias of each taxon are known through amino acid knockout and replacement to be of high functional importance. This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness.

  17. Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

    Science.gov (United States)

    Campo, Daniel; García-Vázquez, Eva

    2012-01-01

    The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

  18. The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns

    Directory of Open Access Journals (Sweden)

    Miller Suzanne FC

    2007-09-01

    Full Text Available Abstract Background Leucine-rich repeats (LRRs are highly versatile and evolvable protein-ligand interaction motifs found in a large number of proteins with diverse functions, including innate immunity and nervous system development. Here we catalogue all of the extracellular LRR (eLRR proteins in worms, flies, mice and humans. We use convergent evidence from several transmembrane-prediction and motif-detection programs, including a customised algorithm, LRRscan, to identify eLRR proteins, and a hierarchical clustering method based on TribeMCL to establish their evolutionary relationships. Results This yields a total of 369 proteins (29 in worm, 66 in fly, 135 in mouse and 139 in human, many of them of unknown function. We group eLRR proteins into several classes: those with only LRRs, those that cluster with Toll-like receptors (Tlrs, those with immunoglobulin or fibronectin-type 3 (FN3 domains and those with some other domain. These groups show differential patterns of expansion and diversification across species. Our analyses reveal several clusters of novel genes, including two Elfn genes, encoding transmembrane proteins with eLRRs and an FN3 domain, and six genes encoding transmembrane proteins with eLRRs only (the Elron cluster. Many of these are expressed in discrete patterns in the developing mouse brain, notably in the thalamus and cortex. We have also identified a number of novel fly eLRR proteins with discrete expression in the embryonic nervous system. Conclusion This study provides the necessary foundation for a systematic analysis of the functions of this class of genes, which are likely to include prominently innate immunity, inflammation and neural development, especially the specification of neuronal connectivity.

  19. An impatient evolutionary algorithm with probabilistic tabu search for unified solution of some NP-hard problems in graph and set theory via clique finding.

    Science.gov (United States)

    Guturu, Parthasarathy; Dantu, Ram

    2008-06-01

    Many graph- and set-theoretic problems, because of their tremendous application potential and theoretical appeal, have been well investigated by the researchers in complexity theory and were found to be NP-hard. Since the combinatorial complexity of these problems does not permit exhaustive searches for optimal solutions, only near-optimal solutions can be explored using either various problem-specific heuristic strategies or metaheuristic global-optimization methods, such as simulated annealing, genetic algorithms, etc. In this paper, we propose a unified evolutionary algorithm (EA) to the problems of maximum clique finding, maximum independent set, minimum vertex cover, subgraph and double subgraph isomorphism, set packing, set partitioning, and set cover. In the proposed approach, we first map these problems onto the maximum clique-finding problem (MCP), which is later solved using an evolutionary strategy. The proposed impatient EA with probabilistic tabu search (IEA-PTS) for the MCP integrates the best features of earlier successful approaches with a number of new heuristics that we developed to yield a performance that advances the state of the art in EAs for the exploration of the maximum cliques in a graph. Results of experimentation with the 37 DIMACS benchmark graphs and comparative analyses with six state-of-the-art algorithms, including two from the smaller EA community and four from the larger metaheuristics community, indicate that the IEA-PTS outperforms the EAs with respect to a Pareto-lexicographic ranking criterion and offers competitive performance on some graph instances when individually compared to the other heuristic algorithms. It has also successfully set a new benchmark on one graph instance. On another benchmark suite called Benchmarks with Hidden Optimal Solutions, IEA-PTS ranks second, after a very recent algorithm called COVER, among its peers that have experimented with this suite.

  20. Surveillance Tools Emerging From Search Engines and Social Media Data for Determining Eye Disease Patterns.

    Science.gov (United States)

    Deiner, Michael S; Lietman, Thomas M; McLeod, Stephen D; Chodosh, James; Porco, Travis C

    2016-09-01

    Internet-based search engine and social media data may provide a novel complementary source for better understanding the epidemiologic factors of infectious eye diseases, which could better inform eye health care and disease prevention. To assess whether data from internet-based social media and search engines are associated with objective clinic-based diagnoses of conjunctivitis. Data from encounters of 4143 patients diagnosed with conjunctivitis from June 3, 2012, to April 26, 2014, at the University of California San Francisco (UCSF) Medical Center, were analyzed using Spearman rank correlation of each weekly observation to compare demographics and seasonality of nonallergic conjunctivitis with allergic conjunctivitis. Data for patient encounters with diagnoses for glaucoma and influenza were also obtained for the same period and compared with conjunctivitis. Temporal patterns of Twitter and Google web search data, geolocated to the United States and associated with these clinical diagnoses, were compared with the clinical encounters. The a priori hypothesis was that weekly internet-based searches and social media posts about conjunctivitis may reflect the true weekly clinical occurrence of conjunctivitis. Weekly total clinical diagnoses at UCSF of nonallergic conjunctivitis, allergic conjunctivitis, glaucoma, and influenza were compared using Spearman rank correlation with equivalent weekly data on Tweets related to disease or disease-related keyword searches obtained from Google Trends. Seasonality of clinical diagnoses of nonallergic conjunctivitis among the 4143 patients (2364 females [57.1%] and 1776 males [42.9%]) with 5816 conjunctivitis encounters at UCSF correlated strongly with results of Google searches in the United States for the term pink eye (ρ, 0.68 [95% CI, 0.52 to 0.78]; P < .001) and correlated moderately with Twitter results about pink eye (ρ, 0.38 [95% CI, 0.16 to 0.56]; P < .001) and with clinical diagnosis of influenza (ρ, 0

  1. Complex Evolutionary and Genetic Patterns Characterize the Loss of Scleral Ossification in the Blind Cavefish Astyanax mexicanus

    Science.gov (United States)

    O’Quin, Kelly E.; Doshi, Pooja; Lyon, Anastasia; Hoenemeyer, Emma; Yoshizawa, Masato; Jeffery, William R.

    2015-01-01

    may control the severity and onset of lens degeneration in cavefishes. We conclude that complex evolutionary and genetic patterns underlie the loss of scleral ossification in Astyanax cavefish. PMID:26649887

  2. Serotonin-containing neurons in basal insects: In search of ground patterns among tetraconata.

    Science.gov (United States)

    Stemme, Torben; Stern, Michael; Bicker, Gerd

    2017-01-01

    The ventral nerve cord of Tetraconata contains a comparably low number of serotonin-immunoreactive neurons, facilitating individual identification of cells and their characteristic neurite morphology. This offers the rather unique possibility of establishing homologies at the single cell level. Because phylogenetic relationships within Tetraconata are still discussed controversially, comparisons of individually identifiable neurons can help to unravel these issues. Serotonin immunoreactivity has been investigated in numerous tetraconate taxa, leading to reconstructions of hypothetical ground patterns for major lineages. However, detailed descriptions of basal insects are still missing, but are crucial for meaningful evolutionary considerations. We investigated the morphology of individually identifiable serotonin-immunoreactive neurons in the ventral nerve cord of Zygentoma (Thermobia domestica, Lepisma saccharina, Atelura formicaria) and Archaeognatha (Machilis germanica, Dilta hibernica). To improve immunocytochemical resolution, we also performed preincubation experiments with 5-hydroxy-L-tryptophan and serotonin. Additionally, we checked for immunolabeling of tryptophan hydroxylase, an enzyme associated with the synthesis of serotonin. Besides the generally identified groups of anterolateral, medial, and posterolateral neurons within each ganglion of the ventral nerve cord, we identified several other immunoreactive cells, which seem to have no correspondence in other tetraconates. Furthermore, we show that not all immunoreactive neurons produce serotonin, but have the capability for serotonin uptake. Comparisons with the patterns of serotonin-containing neurons in major tetraconate taxa suggest a close phylogenetic relationship of Remipedia, Cephalocarida, and Hexapoda, supporting the Miracrustacea hypothesis. J. Comp. Neurol., 2016. © 2016 Wiley Periodicals, Inc. J. Comp. Neurol. 525:79-115, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals

  3. Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress.

    Science.gov (United States)

    Verma, Giti; Dhar, Yogeshwar Vikram; Srivastava, Dipali; Kidwai, Maria; Chauhan, Puneet Singh; Bag, Sumit Kumar; Asif, Mehar Hasan; Chakrabarty, Debasis

    2017-01-01

    Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution. Overall, 65 DHNs were identified by a genome-wide survey of 11 rice species, and 3 DHNs were found to be highly conserved. The correlation of a conserved pattern of DHNs with domestication and diversification of wild to cultivated rice was validated by synonymous substitution rates, indicating that Oryza rufipogon and Oryza sativa ssp. japonica follow an adaptive evolutionary pattern; whereas Oryza nivara and Oryza sativa ssp. indica demonstrate a conserved evolutionary pattern. A comprehensive analysis of tissue-specific expression of DHN genes in japonica and their expression profiles in normal and PEG (poly ethylene glycol)-induced dehydration stress exhibited a spatiotemporal expression pattern. Their interaction network reflects the cross-talk between gene expression and the physiological processes mediating adaptation to dehydration stress. The results obtained strongly indicated the importance of DHNs, as they are conserved during the course of domestication.

  4. Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress.

    Directory of Open Access Journals (Sweden)

    Giti Verma

    Full Text Available Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs play an important role in combating dehydration stress. Rice (Oryza sativa L., which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution. Overall, 65 DHNs were identified by a genome-wide survey of 11 rice species, and 3 DHNs were found to be highly conserved. The correlation of a conserved pattern of DHNs with domestication and diversification of wild to cultivated rice was validated by synonymous substitution rates, indicating that Oryza rufipogon and Oryza sativa ssp. japonica follow an adaptive evolutionary pattern; whereas Oryza nivara and Oryza sativa ssp. indica demonstrate a conserved evolutionary pattern. A comprehensive analysis of tissue-specific expression of DHN genes in japonica and their expression profiles in normal and PEG (poly ethylene glycol-induced dehydration stress exhibited a spatiotemporal expression pattern. Their interaction network reflects the cross-talk between gene expression and the physiological processes mediating adaptation to dehydration stress. The results obtained strongly indicated the importance of DHNs, as they are conserved during the course of domestication.

  5. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  6. Automatic boiling water reactor control rod pattern design using particle swarm optimization algorithm and local search

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Cheng-Der, E-mail: jdwang@iner.gov.tw [Nuclear Engineering Division, Institute of Nuclear Energy Research, No. 1000, Wenhua Rd., Jiaan Village, Longtan Township, Taoyuan County 32546, Taiwan, ROC (China); Lin, Chaung [National Tsing Hua University, Department of Engineering and System Science, 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan (China)

    2013-02-15

    Highlights: ► The PSO algorithm was adopted to automatically design a BWR CRP. ► The local search procedure was added to improve the result of PSO algorithm. ► The results show that the obtained CRP is the same good as that in the previous work. -- Abstract: This study developed a method for the automatic design of a boiling water reactor (BWR) control rod pattern (CRP) using the particle swarm optimization (PSO) algorithm. The PSO algorithm is more random compared to the rank-based ant system (RAS) that was used to solve the same BWR CRP design problem in the previous work. In addition, the local search procedure was used to make improvements after PSO, by adding the single control rod (CR) effect. The design goal was to obtain the CRP so that the thermal limits and shutdown margin would satisfy the design requirement and the cycle length, which is implicitly controlled by the axial power distribution, would be acceptable. The results showed that the same acceptable CRP found in the previous work could be obtained.

  7. Characterizing Diagnostic Search Patterns in Digital Breast Pathology: Scanners and Drillers.

    Science.gov (United States)

    Mercan, Ezgi; Shapiro, Linda G; Brunyé, Tad T; Weaver, Donald L; Elmore, Joann G

    2017-07-05

    Following a baseline demographic survey, 87 pathologists interpreted 240 digital whole slide images of breast biopsy specimens representing a range of diagnostic categories from benign to atypia, ductal carcinoma in situ, and invasive cancer. A web-based viewer recorded pathologists' behaviors while interpreting a subset of 60 randomly selected and randomly ordered slides. To characterize diagnostic search patterns, we used the viewport location, time stamp, and zoom level data to calculate four variables: average zoom level, maximum zoom level, zoom level variance, and scanning percentage. Two distinct search strategies were confirmed: scanning is characterized by panning at a constant zoom level, while drilling involves zooming in and out at various locations. Statistical analysis was applied to examine the associations of different visual interpretive strategies with pathologist characteristics, diagnostic accuracy, and efficiency. We found that females scanned more than males, and age was positively correlated with scanning percentage, while the facility size was negatively correlated. Throughout 60 cases, the scanning percentage and total interpretation time per slide decreased, and these two variables were positively correlated. The scanning percentage was not predictive of diagnostic accuracy. Increasing average zoom level, maximum zoom level, and zoom variance were correlated with over-interpretation.

  8. Evolutionary patterns and processes

    DEFF Research Database (Denmark)

    Leonardi, Michela; Sanz, Pablo Librado; Der Sarkissian, Clio

    2017-01-01

    Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, ...

  9. Host generalists and specialists emerging side by side: an analysis of evolutionary patterns in the cosmopolitan chewing louse genus Menacanthus.

    Science.gov (United States)

    Martinů, Jana; Sychra, Oldřich; Literák, Ivan; Čapek, Miroslav; Gustafsson, Daniel L; Štefka, Jan

    2015-01-01

    Parasites with wide host spectra provide opportunities to study the ecological parameters of speciation, as well as the process of the evolution of host specificity. The speciose and cosmopolitan louse genus Menacanthus comprises both multi-host and specialised species, allowing exploration of the ecological and historical factors affecting the evolution of parasites using a comparative approach. We used phylogenetic analysis to reconstruct evolutionary relationships in 14 species of Menacanthus based on the sequences of one mitochondrial and one nuclear gene. The results allowed us to validate species identification based on morphology, as well as to explore host distribution by assumed generalist and specialist species. Our analyses confirmed a narrow host use for several species, however in some cases, the supposed host specialists had a wider host spectrum than anticipated. In one case a host generalist (Menacanthus eurysternus) was clustered terminally on a clade almost exclusively containing host specialists. Such a clade topology indicates that the process of host specialisation may not be irreversible in parasite evolution. Finally, we compared patterns of population genetic structure, geographic distribution and host spectra between two selected species, M. eurysternus and Menacanthus camelinus, using haplotype networks. Menacanthus camelinus showed limited geographical distribution in combination with monoxenous host use, whereas M. eurysternus showed a global distribution and lack of host specificity. It is suggested that frequent host switching maintains gene flow between M. eurysternus populations on unrelated hosts in local populations. However, gene flow between geographically distant localities was restricted, suggesting that geography rather than host-specificity is the main factor defining the global genetic diversity of M. eurysternus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  10. Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa.

    Science.gov (United States)

    Duan, Weike; Song, Xiaoming; Liu, Tongkun; Huang, Zhinan; Ren, Jun; Hou, Xilin; Du, Jianchang; Li, Ying

    2014-12-31

    Ascorbic acid (AsA) is an important antioxidant in plants and an essential vitamin for humans. Extending the study of AsA-related genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution of AsA in plants and inform crop breeding. In this study, we conducted whole-genome annotation, molecular-evolution and gene-expression analyses of all known AsA-related genes in B. rapa. The nucleobase-ascorbate transporter (NAT) gene family and AsA l-galactose pathway genes were also compared among plant species. Four important insights gained are that: 1) 102 AsA-related gene were identified in B. rapa and they mainly diverged 12-18 Ma accompanied by the Brassica-specific genome triplication event; 2) during their evolution, these AsA-related genes were preferentially retained, consistent with the gene dosage hypothesis; 3) the putative proteins were highly conserved, but their expression patterns varied; and 4) although the number of AsA-related genes is higher in B. rapa than in A. thaliana, the AsA contents and the numbers of expressed genes in leaves of both species are similar, the genes that are not generally expressed may serve as substitutes during emergencies. In summary, this study provides genome-wide insights into evolutionary history and mechanisms of AsA-related genes following whole-genome triplication in B. rapa. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Internet search patterns of human immunodeficiency virus and the digital divide in the Russian Federation: infoveillance study.

    Science.gov (United States)

    Zheluk, Andrey; Quinn, Casey; Hercz, Daniel; Gillespie, James A

    2013-11-12

    Human immunodeficiency virus (HIV) is a serious health problem in the Russian Federation. However, the true scale of HIV in Russia has long been the subject of considerable debate. Using digital surveillance to monitor diseases has become increasingly popular in high income countries. But Internet users may not be representative of overall populations, and the characteristics of the Internet-using population cannot be directly ascertained from search pattern data. This exploratory infoveillance study examined if Internet search patterns can be used for disease surveillance in a large middle-income country with a dispersed population. This study had two main objectives: (1) to validate Internet search patterns against national HIV prevalence data, and (2) to investigate the relationship between search patterns and the determinants of Internet access. We first assessed whether online surveillance is a valid and reliable method for monitoring HIV in the Russian Federation. Yandex and Google both provided tools to study search patterns in the Russian Federation. We evaluated the relationship between both Yandex and Google aggregated search patterns and HIV prevalence in 2011 at national and regional tiers. Second, we analyzed the determinants of Internet access to determine the extent to which they explained regional variations in searches for the Russian terms for "HIV" and "AIDS". We sought to extend understanding of the characteristics of Internet searching populations by data matching the determinants of Internet access (age, education, income, broadband access price, and urbanization ratios) and searches for the term "HIV" using principal component analysis (PCA). We found generally strong correlations between HIV prevalence and searches for the terms "HIV" and "AIDS". National correlations for Yandex searches for "HIV" were very strongly correlated with HIV prevalence (Spearman rank-order coefficient [rs]=.881, P ≤ .001) and strongly correlated for "AIDS" (rs

  12. Affective evolutionary music composition with MetaCompose

    DEFF Research Database (Denmark)

    Scirea, Marco; Togelius, Julian; Eklund, Peter

    2017-01-01

    express different mood-states, which we achieve through a unique combination of a graph traversal-based chord sequence generator, a search-based melody generator, a pattern-based accompaniment generator, and a theory for mood expression. Melody generation uses a novel evolutionary technique combining FI-2...

  13. Molecular modeling of directed self-assembly of block copolymers: Fundamental studies of processing conditions and evolutionary pattern design

    Science.gov (United States)

    Khaira, Gurdaman Singh

    Rapid progress in the semi-conductor industry has pushed for smaller feature sizes on integrated electronic circuits. Current photo-lithographic techniques for nanofabrication have reached their technical limit and are problematic when printing features small enough to meet future industrial requirements. "Bottom-up'' techniques, such as the directed self-assembly (DSA) of block copolymers (BCP), are the primary contenders to compliment current "top-down'' photo-lithography ones. For industrial requirements, the defect density from DSA needs to be less than 1 defect per 10 cm by 10 cm. Knowledge of both material synthesis and the thermodynamics of the self-assembly process are required before optimal operating conditions can be found to produce results adequate for industry. The work present in this thesis is divided into three chapters, each discussing various aspects of DSA as studied via a molecular model that contains the essential physics of BCP self-assembly. Though there are various types of guiding fields that can be used to direct BCPs over large wafer areas with minimum defects, this study focuses only on chemically patterned substrates. The first chapter addresses optimal pattern design by describing a framework where molecular simulations of various complexities are coupled with an advanced optimization technique to find a pattern that directs a target morphology. It demonstrates the first ever study where BCP self-assembly on a patterned substrate is optimized using a three-dimensional description of the block-copolymers. For problems pertaining to DSA, the methodology is shown to converge much faster than the traditional random search approach. The second chapter discusses the metrology of BCP thin films using TEM tomography and X-ray scattering techniques, such as CDSAXS and GISAXS. X-ray scattering has the advantage of being able to quickly probe the average structure of BCP morphologies over large wafer areas; however, deducing the BCP morphology

  14. Lévy flight and Brownian search patterns of a free-ranging predator reflect different prey field characteristics.

    Science.gov (United States)

    Sims, David W; Humphries, Nicolas E; Bradford, Russell W; Bruce, Barry D

    2012-03-01

    1. Search processes play an important role in physical, chemical and biological systems. In animal foraging, the search strategy predators should use to search optimally for prey is an enduring question. Some models demonstrate that when prey is sparsely distributed, an optimal search pattern is a specialised random walk known as a Lévy flight, whereas when prey is abundant, simple Brownian motion is sufficiently efficient. These predictions form part of what has been termed the Lévy flight foraging hypothesis (LFF) which states that as Lévy flights optimise random searches, movements approximated by optimal Lévy flights may have naturally evolved in organisms to enhance encounters with targets (e.g. prey) when knowledge of their locations is incomplete. 2. Whether free-ranging predators exhibit the movement patterns predicted in the LFF hypothesis in response to known prey types and distributions, however, has not been determined. We tested this using vertical and horizontal movement data from electronic tagging of an apex predator, the great white shark Carcharodon carcharias, across widely differing habitats reflecting different prey types. 3. Individual white sharks exhibited movement patterns that predicted well the prey types expected under the LFF hypothesis. Shark movements were best approximated by Brownian motion when hunting near abundant, predictable sources of prey (e.g. seal colonies, fish aggregations), whereas movements approximating truncated Lévy flights were present when searching for sparsely distributed or potentially difficult-to-detect prey in oceanic or shelf environments, respectively. 4. That movement patterns approximated by truncated Lévy flights and Brownian behaviour were present in the predicted prey fields indicates search strategies adopted by white sharks appear to be the most efficient ones for encountering prey in the habitats where such patterns are observed. This suggests that C. carcharias appears capable of exhibiting

  15. Investigating User Search Tactic Patterns and System Support in Using Digital Libraries

    Science.gov (United States)

    Joo, Soohyung

    2013-01-01

    This study aims to investigate users' search tactic application and system support in using digital libraries. A user study was conducted with sixty digital library users. The study was designed to answer three research questions: 1) How do users engage in a search process by applying different types of search tactics while conducting different…

  16. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

    NARCIS (Netherlands)

    Aab, A.; Abreu, P.; Aglietta, M.; Ahn, E. J.; Samarai, I. Al; Albuquerque, I. F. M.; Allekotte, I.; Allen, J.; Allison, P.; Almela, A.; Alvarez Castillo, J.; Alvarez-Muniz, J.; Alves Batista, R.; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Aramo, C.; Aranda, V. M.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Awal, N.; Badescu, A. M.; Barber, K. B.; Baeuml, J.; Baus, C.; Beatty, J. J.; Becker, K. H.; Bellido, J. A.; Berat, C.; Bertaina, M. E.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blaess, S.; Blanco, M.; Bleve, C.; Bluemer, H.; Bohacova, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brancus, I.; Bridgeman, A.; Brogueira, P.; Brown, W. C.; Buchholz, P.; Bueno, A.; Buitink, S.; Buscemi, M.; Caballero-Mora, K. S.; Caccianiga, B.; Caccianiga, L.; Candusso, M.; Caramete, L.; Caruso, R.; Castellina, A.; Cataldi, G.; Cazon, L.; Cester, R.; Chavez, A. G.; Chiavassa, A.; Chinellato, J. A.; Chudoba, J.; Cilmo, M.; Clay, R. W.; Cocciolo, G.; Colalillo, R.; Coleman, A.; Collica, L.; Coluccia, M. R.; Conceicao, R.; Contreras, F.; Cooper, M. J.; Cordier, A.; Coutu, S.; Covault, C. E.; Cronin, J.; Curutiu, A.; Dallier, R.; Daniel, B.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; De Domenico, M.; de Jong, S. J.; de Mello Neto, J. R. T.; De Mitri, I.; de Oliveira, J.; de Souza, V.; del Peral, L.; Deligny, O.; Dembinski, H.; Dhital, N.; Di Giulio, C.; Di Matteo, A.; Diaz, J. C.; Diaz Castro, M. L.; Diogo, F.; Dobrigkeit, C.; Docters, W.; D'Olivo, J. C.; Dorofeev, A.; Dorosti Hasankiadeh, Q.; Dova, M. T.; Ebr, J.; Engel, R.; Erdmann, M.; Erfani, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Luis, P. Facal San; Falcke, H.; Fang, K.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Fernandes, M.; Fick, B.; Figueira, J. M.; Filevich, A.; Filipcic, A.; Fox, B. D.; Fratu, O.; Froehlich, U.; Fuchs, B.; Fujii, T.; Gaior, R.; Garcia, B.; Garcia Roca, S. T.; Garcia-Gamez, D.; Garcia-Pinto, D.; Garilli, G.; Gascon Bravo, A.; Gate, F.; Gemmeke, H.; Ghia, P. L.; Giaccari, U.; Giammarchi, M.; Giller, M.; Glaser, C.; Glass, H.; Gomez Berisso, M.; Gomez Vitale, P. F.; Goncalves, P.; Gonzalez, J. G.; Gonzalez, N.; Gookin, B.; Gordon, J.; Gorgi, A.; Gorham, P.; Gouffon, P.; Grebe, S.; Griffith, N.; Grillo, A. F.; Grubb, T. D.; Guarino, F.; Guedes, G. P.; Hampel, M. R.; Hansen, P.; Harari, D.; Harrison, T. A.; Hartmann, S.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Heimann, P.; Herve, A. E.; Hill, G. C.; Hojvat, C.; Hollon, N.; Holt, E.; Homola, P.; Horandel, J. R.; Horvath, P.; Hrabovsky, M.; Huber, D.; Huege, T.; Insolia, A.; Isar, P. G.; Jandt, I.; Jansen, S.; Jarne, C.; Josebachuili, M.; Kaeaepae, A.; Kambeitz, O.; Kampert, K. H.; Kasper, P.; Katkov, I.; Kegl, B.; Keilhauer, B.; Keivani, A.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Krause, R.; Krohm, N.; Kroemer, O.; Kruppke-Hansen, D.; Kuempel, D.; Kunka, N.; LaHurd, D.; Latronico, L.; Lauer, R.; Lauscher, M.; Lautridou, P.; Le Coz, S.; Leao, M. S. A. B.; Lebrun, D.; Lebrun, P.; Leigui de Oliveira, M. A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; Lopez, R.; Lopez Agueera, A.; Louedec, K.; Lozano Bahilo, J.; Lu, L.; Lucero, A.; Ludwig, M.; Malacari, M.; Maldera, S.; Mallamaci, M.; Maller, J.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, V.; Maris, I. C.; Marsella, G.; Martello, D.; Martin, L.; Martinez, H.; Martinez Bravo, O.; Martraire, D.; Masias Meza, J. J.; Mathes, H. J.; Mathys, S.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurel, D.; Maurizio, D.; Mayotte, E.; Mazur, P. O.; Medina, C.; Medina-Tanco, G.; Meissner, R.; Melissas, M.; Melo, D.; Menshikov, A.; Messina, S.; Meyhandan, R.; Micanovic, S.; Micheletti, M. I.; Middendorf, L.; Minaya, I. A.; Miramonti, L.; Mitrica, B.; Molina-Bueno, L.; Mollerach, S.; Monasor, M.; Monnier Ragaigne, D.; Montanet, F.; Morello, C.; Mostafa, M.; Moura, C. A.; Muller, M. A.; Mueller, G.; Mueller, S.; Muenchmeyer, M.; Mussa, R.; Navarra, G.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Nguyen, P.; Niechciol, M.; Niemietz, L.; Niggemann, T.; Nitz, D.; Nosek, D.; Novotny, V.; Nozka, L.; Ochilo, L.; Olinto, A.; Oliveira, M.; Pacheco, N.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Palmieri, N.; Papenbreer, P.; Parente, G.; Parra, A.; Paul, T.; Pech, M.; Pekala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Petermann, E.; Peters, C.; Petrera, S.; Petrov, Y.; Phuntsok, J.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Plum, M.; Porcelli, A.; Porowski, C.; Prado, R. R.; Privitera, P.; Prouza, M.; Purrello, V.; Quel, E. J.; Querchfeld, S.; Quinn, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rizi, V.; Rodrigues de Carvalho, W.; Rodriguez Cabo, I.; Rodriguez Fernandez, G.; Rodriguez Rojo, J.; Rodriguez-Frias, M. D.; Rogozin, D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Roulet, E.; Rovero, A. C.; Saffi, S. J.; Saftoiu, A.; Salamida, F.; Salazar, H.; Saleh, A.; Salesa Greus, F.; Salina, G.; Sanchez, F.; Sanchez-Lucas, P.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, B.; Sarmento, R.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, D.; Schroeder, F. G.; Scholten, O.; Schoorlemmer, H.; Schovanek, P.; Schulz, A.; Schulz, J.; Schumacher, J.; Sciutto, S. J.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Sima, O.; Kowski, A. Smial; Smida, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Squartini, R.; Srivastava, Y. N.; Stanic, S.; Stapleton, J.; Stasielak, J.; Stephan, M.; Stutz, A.; Suarez, F.; Suomijaervi, T.; Supanitsky, A. D.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Szuba, M.; Taborda, O. A.; Tapia, A.; Tartare, M.; Tepe, A.; Theodoro, V. M.; Timmermans, C.; Todero Peixoto, C. J.; Toma, G.; Tomankova, L.; Tome, B.; Tonachini, A.; Torralba Elipe, G.; Torres Machado, D.; Travnicek, P.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Valdes Galicia, J. F.; Valino, I.; Valore, L.; van Aar, G.; van Bodegom, P.; van den Berg, A. M.; van Velzen, S.; van Vliet, A.; Varela, E.; Vargas Cardenas, B.; Varner, G.; Vazquez, J. R.; Vazquez, R. A.; Veberic, D.; Verzi, V.; Vicha, J.; Videla, M.; Villasenor, L.; Vlcek, B.; Vorobiov, S.; Wahlberg, H.; Wainberg, O.; Walz, D.; Watson, A. A.; Weber, M.; Weidenhaupt, K.; Weindl, A.; Werner, F.; Widom, A.; Wiencke, L.; Wilczynska, B.; Wilczynski, H.; Will, M.; Williams, C.; Winchen, T.; Wittkowski, D.; Wundheiler, B.; Wykes, S.; Yamamoto, T.; Yapici, T.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Zhou, J.; Zhu, Y.; Zimbres Silva, M.; Ziolkowski, M.; Zuccarello, F.

    2015-01-01

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with E >= 6 x 10(19) eV by analyzing cosmic rays with energies above E >= 5 x 10(18) eV arriving within

  17. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory.

    Science.gov (United States)

    Aab, A; Abreu, P; Aglietta, M; Ahn, E J; Samarai, I Al; Albuquerque, I F M; Allekotte, I; Allen, J; Allison, P; Almela, A; Castillo, J Alvarez; Alvarez-Muñiz, J; Batista, R Alves; Ambrosio, M; Aminaei, A; Anchordoqui, L; Andringa, S; Aramo, C; Aranda, V M; Arqueros, F; Asorey, H; Assis, P; Aublin, J; Ave, M; Avenier, M; Avila, G; Awal, N; Badescu, A M; Barber, K B; Bäuml, J; Baus, C; Beatty, J J; Becker, K H; Bellido, J A; Berat, C; Bertaina, M E; Bertou, X; Biermann, P L; Billoir, P; Blaess, S; Blanco, M; Bleve, C; Blümer, H; Boháčová, M; Boncioli, D; Bonifazi, C; Bonino, R; Borodai, N; Brack, J; Brancus, I; Bridgeman, A; Brogueira, P; Brown, W C; Buchholz, P; Bueno, A; Buitink, S; Buscemi, M; Caballero-Mora, K S; Caccianiga, B; Caccianiga, L; Candusso, M; Caramete, L; Caruso, R; Castellina, A; Cataldi, G; Cazon, L; Cester, R; Chavez, A G; Chiavassa, A; Chinellato, J A; Chudoba, J; Cilmo, M; Clay, R W; Cocciolo, G; Colalillo, R; Coleman, A; Collica, L; Coluccia, M R; Conceição, R; Contreras, F; Cooper, M J; Cordier, A; Coutu, S; Covault, C E; Cronin, J; Curutiu, A; Dallier, R; Daniel, B; Dasso, S; Daumiller, K; Dawson, B R; Almeida, R M de; Domenico, M De; Jong, S J de; Neto, J R T de Mello; Mitri, I De; Oliveira, J de; Souza, V de; Peral, L Del; Deligny, O; Dembinski, H; Dhital, N; Giulio, C Di; Matteo, A Di; Diaz, J C; Castro, M L Díaz; Diogo, F; Dobrigkeit, C; Docters, W; D'Olivo, J C; Dorofeev, A; Hasankiadeh, Q Dorosti; Dova, M T; Ebr, J; Engel, R; Erdmann, M; Erfani, M; Escobar, C O; Espadanal, J; Etchegoyen, A; Luis, P Facal San; Falcke, H; Fang, K; Farrar, G; Fauth, A C; Fazzini, N; Ferguson, A P; Fernandes, M; Fick, B; Figueira, J M; Filevich, A; Filipčič, A; Fox, B D; Fratu, O; Fröhlich, U; Fuchs, B; Fujii, T; Gaior, R; García, B; Roca, S T Garcia; Garcia-Gamez, D; Garcia-Pinto, D; Garilli, G; Bravo, A Gascon; Gate, F; Gemmeke, H; Ghia, P L; Giaccari, U; Giammarchi, M; Giller, M; Glaser, C; Glass, H; Berisso, M Gómez; Vitale, P F Gómez; Gonçalves, P; Gonzalez, J G; González, N; Gookin, B; Gordon, J; Gorgi, A; Gorham, P; Gouffon, P; Grebe, S; Griffith, N; Grillo, A F; Grubb, T D; Guarino, F; Guedes, G P; Hampel, M R; Hansen, P; Harari, D; Harrison, T A; Hartmann, S; Harton, J L; Haungs, A; Hebbeker, T; Heck, D; Heimann, P; Herve, A E; Hill, G C; Hojvat, C; Hollon, N; Holt, E; Homola, P; Hörandel, J R; Horvath, P; Hrabovský, M; Huber, D; Huege, T; Insolia, A; Isar, P G; Jandt, I; Jansen, S; Jarne, C; Josebachuili, M; Kääpä, A; Kambeitz, O; Kampert, K H; Kasper, P; Katkov, I; Kégl, B; Keilhauer, B; Keivani, A; Kemp, E; Kieckhafer, R M; Klages, H O; Kleifges, M; Kleinfeller, J; Krause, R; Krohm, N; Krömer, O; Kruppke-Hansen, D; Kuempel, D; Kunka, N; LaHurd, D; Latronico, L; Lauer, R; Lauscher, M; Lautridou, P; Coz, S Le; Leão, M S A B; Lebrun, D; Lebrun, P; Oliveira, M A Leigui de; Letessier-Selvon, A; Lhenry-Yvon, I; Link, K; López, R; Agüera, A Lopez; Louedec, K; Bahilo, J Lozano; Lu, L; Lucero, A; Ludwig, M; Malacari, M; Maldera, S; Mallamaci, M; Maller, J; Mandat, D; Mantsch, P; Mariazzi, A G; Marin, V; Mariş, I C; Marsella, G; Martello, D; Martin, L; Martinez, H; Bravo, O Martínez; Martraire, D; Meza, J J Masías; Mathes, H J; Mathys, S; Matthews, J; Matthews, J A J; Matthiae, G; Maurel, D; Maurizio, D; Mayotte, E; Mazur, P O; Medina, C; Medina-Tanco, G; Meissner, R; Melissas, M; Melo, D; Menshikov, A; Messina, S; Meyhandan, R; Mićanović, S; Micheletti, M I; Middendorf, L; Minaya, I A; Miramonti, L; Mitrica, B; Molina-Bueno, L; Mollerach, S; Monasor, M; Ragaigne, D Monnier; Montanet, F; Morello, C; Mostafá, M; Moura, C A; Muller, M A; Müller, G; Müller, S; Münchmeyer, M; Mussa, R; Navarra, G; Navas, S; Necesal, P; Nellen, L; Nelles, A; Neuser, J; Nguyen, P; Niechciol, M; Niemietz, L; Niggemann, T; Nitz, D; Nosek, D; Novotny, V; Nožka, L; Ochilo, L; Olinto, A; Oliveira, M; Pacheco, N; Selmi-Dei, D Pakk; Palatka, M; Pallotta, J; Palmieri, N; Papenbreer, P; Parente, G; Parra, A; Paul, T; Pech, M; Pȩkala, J; Pelayo, R; Pepe, I M; Perrone, L; Petermann, E; Peters, C; Petrera, S; Petrov, Y; Phuntsok, J; Piegaia, R; Pierog, T; Pieroni, P; Pimenta, M; Pirronello, V; Platino, M; Plum, M; Porcelli, A; Porowski, C; Prado, R R; Privitera, P; Prouza, M; Purrello, V; Quel, E J; Querchfeld, S; Quinn, S; Rautenberg, J; Ravel, O; Ravignani, D; Revenu, B; Ridky, J; Riggi, S; Risse, M; Ristori, P; Rizi, V; Carvalho, W Rodrigues de; Cabo, I Rodriguez; Fernandez, G Rodriguez; Rojo, J Rodriguez; Rodríguez-Frías, M D; Rogozin, D; Ros, G; Rosado, J; Rossler, T; Roth, M; Roulet, E; Rovero, A C; Saffi, S J; Saftoiu, A; Salamida, F; Salazar, H; Saleh, A; Greus, F Salesa; Salina, G; Sánchez, F; Sanchez-Lucas, P; Santo, C E; Santos, E; Santos, E M; Sarazin, F; Sarkar, B; Sarmento, R; Sato, R; Scharf, N; Scherini, V; Schieler, H; Schiffer, P; Schmidt, D; Schröder, F G; Scholten, O; Schoorlemmer, H; Schovánek, P; Schulz, A; Schulz, J; Schumacher, J; Sciutto, S J; Segreto, A; Settimo, M; Shadkam, A; Shellard, R C; Sidelnik, I; Sigl, G; Sima, O; Kowski, A Śmiał; Šmída, R; Snow, G R; Sommers, P; Sorokin, J; Squartini, R; Srivastava, Y N; Stanič, S; Stapleton, J; Stasielak, J; Stephan, M; Stutz, A; Suarez, F; Suomijärvi, T; Supanitsky, A D; Sutherland, M S; Swain, J; Szadkowski, Z; Szuba, M; Taborda, O A; Tapia, A; Tartare, M; Tepe, A; Theodoro, V M; Timmermans, C; Peixoto, C J Todero; Toma, G; Tomankova, L; Tomé, B; Tonachini, A; Elipe, G Torralba; Machado, D Torres; Travnicek, P; Trovato, E; Tueros, M; Ulrich, R; Unger, M; Urban, M; Galicia, J F Valdés; Valiño, I; Valore, L; Aar, G van; Bodegom, P van; Berg, A M van den; Velzen, S van; Vliet, A van; Varela, E; Vargas Cárdenas, B; Varner, G; Vázquez, J R; Vázquez, R A; Veberič, D; Verzi, V; Vicha, J; Videla, M; Villaseñor, L; Vlcek, B; Vorobiov, S; Wahlberg, H; Wainberg, O; Walz, D; Watson, A A; Weber, M; Weidenhaupt, K; Weindl, A; Werner, F; Widom, A; Wiencke, L; Wilczyńska, B; Wilczyński, H; Will, M; Williams, C; Winchen, T; Wittkowski, D; Wundheiler, B; Wykes, S; Yamamoto, T; Yapici, T; Yuan, G; Yushkov, A; Zamorano, B; Zas, E; Zavrtanik, D; Zavrtanik, M; Zaw, I; Zepeda, A; Zhou, J; Zhu, Y; Silva, M Zimbres; Ziolkowski, M; Zuccarello, F

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with [Formula: see text] eV by analyzing cosmic rays with energies above [Formula: see text] eV arriving within an angular separation of approximately 15[Formula: see text]. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources.

  18. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

    Science.gov (United States)

    Aab, A.; Abreu, P.; Aglietta, M.; Ahn, E. J.; Samarai, I. Al; Albuquerque, I. F. M.; Allekotte, I.; Allen, J.; Allison, P.; Almela, A.; Castillo, J. Alvarez; Alvarez-Muñiz, J.; Batista, R. Alves; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Aramo, C.; Aranda, V. M.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Awal, N.; Badescu, A. M.; Barber, K. B.; Bäuml, J.; Baus, C.; Beatty, J. J.; Becker, K. H.; Bellido, J. A.; Berat, C.; Bertaina, M. E.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blaess, S.; Blanco, M.; Bleve, C.; Blümer, H.; Boháčová, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brancus, I.; Bridgeman, A.; Brogueira, P.; Brown, W. C.; Buchholz, P.; Bueno, A.; Buitink, S.; Buscemi, M.; Caballero-Mora, K. S.; Caccianiga, B.; Caccianiga, L.; Candusso, M.; Caramete, L.; Caruso, R.; Castellina, A.; Cataldi, G.; Cazon, L.; Cester, R.; Chavez, A. G.; Chiavassa, A.; Chinellato, J. A.; Chudoba, J.; Cilmo, M.; Clay, R. W.; Cocciolo, G.; Colalillo, R.; Coleman, A.; Collica, L.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cooper, M. J.; Cordier, A.; Coutu, S.; Covault, C. E.; Cronin, J.; Curutiu, A.; Dallier, R.; Daniel, B.; Dasso, S.; Daumiller, K.; Dawson, B. R.; Almeida, R. M. de; Domenico, M. De; Jong, S. J. de; Neto, J. R. T. de Mello; Mitri, I. De; Oliveira, J. de; Souza, V. de; Peral, L. del; Deligny, O.; Dembinski, H.; Dhital, N.; Giulio, C. Di; Matteo, A. Di; Diaz, J. C.; Castro, M. L. Díaz; Diogo, F.; Dobrigkeit, C.; Docters, W.; D'Olivo, J. C.; Dorofeev, A.; Hasankiadeh, Q. Dorosti; Dova, M. T.; Ebr, J.; Engel, R.; Erdmann, M.; Erfani, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Luis, P. Facal San; Falcke, H.; Fang, K.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Fernandes, M.; Fick, B.; Figueira, J. M.; Filevich, A.; Filipčič, A.; Fox, B. D.; Fratu, O.; Fröhlich, U.; Fuchs, B.; Fujii, T.; Gaior, R.; García, B.; Roca, S. T. Garcia; Garcia-Gamez, D.; Garcia-Pinto, D.; Garilli, G.; Bravo, A. Gascon; Gate, F.; Gemmeke, H.; Ghia, P. L.; Giaccari, U.; Giammarchi, M.; Giller, M.; Glaser, C.; Glass, H.; Berisso, M. Gómez; Vitale, P. F. Gómez; Gonçalves, P.; Gonzalez, J. G.; González, N.; Gookin, B.; Gordon, J.; Gorgi, A.; Gorham, P.; Gouffon, P.; Grebe, S.; Griffith, N.; Grillo, A. F.; Grubb, T. D.; Guarino, F.; Guedes, G. P.; Hampel, M. R.; Hansen, P.; Harari, D.; Harrison, T. A.; Hartmann, S.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Heimann, P.; Herve, A. E.; Hill, G. C.; Hojvat, C.; Hollon, N.; Holt, E.; Homola, P.; Hörandel, J. R.; Horvath, P.; Hrabovský, M.; Huber, D.; Huege, T.; Insolia, A.; Isar, P. G.; Jandt, I.; Jansen, S.; Jarne, C.; Josebachuili, M.; Kääpä, A.; Kambeitz, O.; Kampert, K. H.; Kasper, P.; Katkov, I.; Kégl, B.; Keilhauer, B.; Keivani, A.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Krause, R.; Krohm, N.; Krömer, O.; Kruppke-Hansen, D.; Kuempel, D.; Kunka, N.; LaHurd, D.; Latronico, L.; Lauer, R.; Lauscher, M.; Lautridou, P.; Coz, S. Le; Leão, M. S. A. B.; Lebrun, D.; Lebrun, P.; Oliveira, M. A. Leigui de; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; López, R.; Agüera, A. Lopez; Louedec, K.; Bahilo, J. Lozano; Lu, L.; Lucero, A.; Ludwig, M.; Malacari, M.; Maldera, S.; Mallamaci, M.; Maller, J.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, V.; Mariş, I. C.; Marsella, G.; Martello, D.; Martin, L.; Martinez, H.; Bravo, O. Martínez; Martraire, D.; Meza, J. J. Masías; Mathes, H. J.; Mathys, S.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurel, D.; Maurizio, D.; Mayotte, E.; Mazur, P. O.; Medina, C.; Medina-Tanco, G.; Meissner, R.; Melissas, M.; Melo, D.; Menshikov, A.; Messina, S.; Meyhandan, R.; Mićanović, S.; Micheletti, M. I.; Middendorf, L.; Minaya, I. A.; Miramonti, L.; Mitrica, B.; Molina-Bueno, L.; Mollerach, S.; Monasor, M.; Ragaigne, D. Monnier; Montanet, F.; Morello, C.; Mostafá, M.; Moura, C. A.; Muller, M. A.; Müller, G.; Müller, S.; Münchmeyer, M.; Mussa, R.; Navarra, G.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Nguyen, P.; Niechciol, M.; Niemietz, L.; Niggemann, T.; Nitz, D.; Nosek, D.; Novotny, V.; Nožka, L.; Ochilo, L.; Olinto, A.; Oliveira, M.; Pacheco, N.; Selmi-Dei, D. Pakk; Palatka, M.; Pallotta, J.; Palmieri, N.; Papenbreer, P.; Parente, G.; Parra, A.; Paul, T.; Pech, M.; Pȩkala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Petermann, E.; Peters, C.; Petrera, S.; Petrov, Y.; Phuntsok, J.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Plum, M.; Porcelli, A.; Porowski, C.; Prado, R. R.; Privitera, P.; Prouza, M.; Purrello, V.; Quel, E. J.; Querchfeld, S.; Quinn, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rizi, V.; Carvalho, W. Rodrigues de; Cabo, I. Rodriguez; Fernandez, G. Rodriguez; Rojo, J. Rodriguez; Rodríguez-Frías, M. D.; Rogozin, D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Roulet, E.; Rovero, A. C.; Saffi, S. J.; Saftoiu, A.; Salamida, F.; Salazar, H.; Saleh, A.; Greus, F. Salesa; Salina, G.; Sánchez, F.; Sanchez-Lucas, P.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, B.; Sarmento, R.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, D.; Schröder, F. G.; Scholten, O.; Schoorlemmer, H.; Schovánek, P.; Schulz, A.; Schulz, J.; Schumacher, J.; Sciutto, S. J.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Sima, O.; kowski, A. Śmiał; Šmída, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Squartini, R.; Srivastava, Y. N.; Stanič, S.; Stapleton, J.; Stasielak, J.; Stephan, M.; Stutz, A.; Suarez, F.; Suomijärvi, T.; Supanitsky, A. D.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Szuba, M.; Taborda, O. A.; Tapia, A.; Tartare, M.; Tepe, A.; Theodoro, V. M.; Timmermans, C.; Peixoto, C. J. Todero; Toma, G.; Tomankova, L.; Tomé, B.; Tonachini, A.; Elipe, G. Torralba; Machado, D. Torres; Travnicek, P.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Galicia, J. F. Valdés; Valiño, I.; Valore, L.; Aar, G. van; Bodegom, P. van; Berg, A. M. van den; Velzen, S. van; Vliet, A. van; Varela, E.; Vargas Cárdenas, B.; Varner, G.; Vázquez, J. R.; Vázquez, R. A.; Veberič, D.; Verzi, V.; Vicha, J.; Videla, M.; Villaseñor, L.; Vlcek, B.; Vorobiov, S.; Wahlberg, H.; Wainberg, O.; Walz, D.; Watson, A. A.; Weber, M.; Weidenhaupt, K.; Weindl, A.; Werner, F.; Widom, A.; Wiencke, L.; Wilczyńska, B.; Wilczyński, H.; Will, M.; Williams, C.; Winchen, T.; Wittkowski, D.; Wundheiler, B.; Wykes, S.; Yamamoto, T.; Yapici, T.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Zhou, J.; Zhu, Y.; Silva, M. Zimbres; Ziolkowski, M.; Zuccarello, F.

    2015-06-01

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with eV by analyzing cosmic rays with energies above eV arriving within an angular separation of approximately 15. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources.

  19. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Aab, A.; Buchholz, P.; Erfani, M.; Froehlich, U.; Heimann, P.; Niechciol, M.; Ochilo, L.; Risse, M.; Tepe, A.; Yushkov, A.; Ziolkowski, M. [Universitaet Siegen, Siegen (Germany); Abreu, P.; Andringa, S.; Assis, P.; Brogueira, P.; Cazon, L.; Conceicao, R.; Diogo, F.; Espadanal, J.; Goncalves, P.; Oliveira, M.; Pimenta, M.; Santo, C.E.; Sarmento, R.; Tome, B. [Universidade de Lisboa - UL, Laboratorio de Instrumentacao e Fisica Experimental de Particulas - LIP and Instituto Superior Tecnico - IST, Lisbon (Portugal); Aglietta, M.; Bertaina, M.E.; Bonino, R.; Castellina, A.; Chiavassa, A.; Gorgi, A.; Latronico, L.; Maldera, S.; Morello, C.; Navarra, G. [Universita di Torino, Osservatorio Astrofisico di Torino (INAF), Torino (Italy); INFN, Torino (Italy); Ahn, E.J.; Fazzini, N.; Glass, H.; Hojvat, C.; Kasper, P.; Lebrun, P.; Mantsch, P.; Mazur, P.O. [Fermilab, Batavia, IL (United States); Al Samarai, I.; Deligny, O.; Lhenry-Yvon, I.; Martraire, D.; Salamida, F.; Suomijaervi, T. [Universite Paris 11, CNRS-IN2P3, Institut de Physique Nucleaire d' Orsay (IPNO), Orsay (France); Albuquerque, I.F.M.; Gouffon, P.; Santos, E.M. [Universidade de Sao Paulo, Instituto de Fisica, Sao Paulo, SP (Brazil); Allekotte, I.; Asorey, H.; Bertou, X.; Berisso, M.G.; Harari, D.; Mollerach, S.; Purrello, V.; Roulet, E.; Sidelnik, I.; Taborda, O.A. [Centro Atomico Bariloche and Instituto Balseiro (CNEA-UNCuyo-CONICET), San Carlos de Bariloche (Argentina); Allen, J.; Awal, N.; Farrar, G.; Zaw, I. [New York University, New York, NY (United States); Allison, P.; Beatty, J.J.; Gordon, J.; Griffith, N.; Stapleton, J.; Sutherland, M.S. [Ohio State University, Columbus, OH (United States); Almela, A.; Etchegoyen, A.; Wainberg, O. [Instituto de Tecnologias en Deteccion y Astroparticulas (CNEA, CONICET, UNSAM), Buenos Aires (Argentina); Universidad Tecnologica Nacional - Facultad Regional Buenos Aires, Buenos Aires (Argentina); Castillo, J.A.; D' Olivo, J.C.; Medina-Tanco, G.; Nellen, L.; Galicia, J.F.V.; Vargas Cardenas, B. [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico); Alvarez-Muniz, J.; Ave, M.; Roca, S.T.G.; Agueera, A.L.; Parente, G.; Parra, A.; Carvalho, W.R. de; Cabo, I.R.; Elipe, G.T.; Tueros, M.; Valino, I.; Vazquez, R.A.; Zas, E. [Universidad de Santiago de Compostela, Santiago de Compostela (Spain); Batista, R.A.; Schiffer, P.; Sigl, G.; Vliet, A. van [Universitaet Hamburg, Hamburg (Germany); Ambrosio, M.; Aramo, C.; Buscemi, M.; Cilmo, M.; Colalillo, R.; Guarino, F.; Valore, L. [Universita di Napoli ' ' Federico II' ' , Napoli (Italy); INFN, Napoli (Italy); Aminaei, A.; Buitink, S.; Schulz, J.; Aar, G. van; Velzen, S. van; Wykes, S. [IMAPP, Radboud University Nijmegen, Nijmegen (Netherlands); Anchordoqui, L. [City University of New York, Department of Physics and Astronomy, New York (United States); Aranda, V.M.; Arqueros, F.; Garcia-Pinto, D.; Minaya, I.A.; Rosado, J.; Vazquez, J.R. [Universidad Complutense de Madrid, Madrid (Spain); Aublin, J.; Billoir, P.; Blanco, M.; Caccianiga, L.; Gaior, R.; Ghia, P.L.; Letessier-Selvon, A.; Muenchmeyer, M.; Settimo, M. [Universites Paris 6 et Paris 7, CNRS-IN2P3, Laboratoire de Physique Nucleaire et de Hautes Energies (LPNHE), Paris (France); Avenier, M.; Berat, C.; Le Coz, S.; Lebrun, D.; Louedec, K.; Montanet, F.; Stutz, A.; Tartare, M. [Universite Grenoble-Alpes, CNRS/IN2P3, Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Grenoble (France); Avila, G.; Vitale, P.F.G. [Observatorio Pierre Auger and Comision Nacional de Energia Atomica, Malarguee (Argentina); Badescu, A.M.; Fratu, O. [University Politehnica of Bucharest, Bucharest (Romania); Barber, K.B.; Bellido, J.A.; Blaess, S.; Clay, R.W.; Cooper, M.J.; Dawson, B.R.; Grubb, T.D.; Harrison, T.A.; Hill, G.C.; Malacari, M.; Nguyen, P.; Saffi, S.J.; Sorokin, J.; Bodegom, P. van [University of Adelaide, Adelaide, SA (Australia); Baeuml, J.; Baus, C.; Fuchs, B.; Gonzalez, J.G.; Huber, D.; Kambeitz, O.; Katkov, I.; Link, K.; Ludwig, M.; Maurel, D.; Melissas, M.; Palmieri, N.; Werner, F. [Karlsruhe Institute of Technology - Campus South - Institut fuer Experimentelle, Kernphysik (IEKP), Karlsruhe (Germany); Becker, K.H.; Homola, P.; Jandt, I.; Kaeaepae, A.; Kampert, K.H.; Krohm, N.; Kruppke-Hansen, D.; Mathys, S.; Neuser, J.; Niemietz, L.; Papenbreer, P.; Querchfeld, S.; Rautenberg, J.; Sarkar, B.; Winchen, T.; Wittkowski, D. [Bergische Universitaet Wuppertal, Wuppertal (Germany); Biermann, P.L.; Caramete, L.; Curutiu, A. [Max-Planck-Institut fuer Radioastronomie, Bonn (Germany); Bleve, C.; Cataldi, G.; Cocciolo, G.; Coluccia, M.R.; De Mitri, I.; Marsella, G.; Martello, D.; Perrone, L.; Scherini, V. [Dipartimento di Matematica e Fisica ' ' E. De Giorgi' ' , Universita del Salento, Lecce (Italy); INFN, Lecce (Italy); and others

    2015-06-15

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with E ≥ 6 x 10{sup 19} eV by analyzing cosmic rays with energies above E ≥ 5 x 10{sup 18} eVarriving within an angular separation of approximately 15 {sup circle}. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources. (orig.)

  20. GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm.

    Directory of Open Access Journals (Sweden)

    Leonardo Bottolo

    Full Text Available Genome-wide association studies (GWAS yielded significant advances in defining the genetic architecture of complex traits and disease. Still, a major hurdle of GWAS is narrowing down multiple genetic associations to a few causal variants for functional studies. This becomes critical in multi-phenotype GWAS where detection and interpretability of complex SNP(s-trait(s associations are complicated by complex Linkage Disequilibrium patterns between SNPs and correlation between traits. Here we propose a computationally efficient algorithm (GUESS to explore complex genetic-association models and maximize genetic variant detection. We integrated our algorithm with a new Bayesian strategy for multi-phenotype analysis to identify the specific contribution of each SNP to different trait combinations and study genetic regulation of lipid metabolism in the Gutenberg Health Study (GHS. Despite the relatively small size of GHS (n  =  3,175, when compared with the largest published meta-GWAS (n > 100,000, GUESS recovered most of the major associations and was better at refining multi-trait associations than alternative methods. Amongst the new findings provided by GUESS, we revealed a strong association of SORT1 with TG-APOB and LIPC with TG-HDL phenotypic groups, which were overlooked in the larger meta-GWAS and not revealed by competing approaches, associations that we replicated in two independent cohorts. Moreover, we demonstrated the increased power of GUESS over alternative multi-phenotype approaches, both Bayesian and non-Bayesian, in a simulation study that mimics real-case scenarios. We showed that our parallel implementation based on Graphics Processing Units outperforms alternative multi-phenotype methods. Beyond multivariate modelling of multi-phenotypes, our Bayesian model employs a flexible hierarchical prior structure for genetic effects that adapts to any correlation structure of the predictors and increases the power to identify

  1. The topology of evolutionary novelty and innovation in macroevolution.

    Science.gov (United States)

    Erwin, Douglas H

    2017-12-05

    Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Authors.

  2. A System for Automated Extraction of Metadata from Scanned Documents using Layout Recognition and String Pattern Search Models.

    Science.gov (United States)

    Misra, Dharitri; Chen, Siyuan; Thoma, George R

    2009-01-01

    One of the most expensive aspects of archiving digital documents is the manual acquisition of context-sensitive metadata useful for the subsequent discovery of, and access to, the archived items. For certain types of textual documents, such as journal articles, pamphlets, official government records, etc., where the metadata is contained within the body of the documents, a cost effective method is to identify and extract the metadata in an automated way, applying machine learning and string pattern search techniques.At the U. S. National Library of Medicine (NLM) we have developed an automated metadata extraction (AME) system that employs layout classification and recognition models with a metadata pattern search model for a text corpus with structured or semi-structured information. A combination of Support Vector Machine and Hidden Markov Model is used to create the layout recognition models from a training set of the corpus, following which a rule-based metadata search model is used to extract the embedded metadata by analyzing the string patterns within and surrounding each field in the recognized layouts.In this paper, we describe the design of our AME system, with focus on the metadata search model. We present the extraction results for a historic collection from the Food and Drug Administration, and outline how the system may be adapted for similar collections. Finally, we discuss some ongoing enhancements to our AME system.

  3. Phylogenetic patterns of human coxsackievirus B5 arise from population dynamics between two genogroups and reveal evolutionary factors of molecular adaptation and transmission.

    Science.gov (United States)

    Henquell, Cécile; Mirand, Audrey; Richter, Jan; Schuffenecker, Isabelle; Böttiger, Blenda; Diedrich, Sabine; Terletskaia-Ladwig, Elena; Christodoulou, Christina; Peigue-Lafeuille, Hélène; Bailly, Jean-Luc

    2013-11-01

    The aim of this study was to gain insights into the tempo and mode of the evolutionary processes that sustain genetic diversity in coxsackievirus B5 (CVB5) and into the interplay with virus transmission. We estimated phylodynamic patterns with a large sample of virus strains collected in Europe by Bayesian statistical methods, reconstructed the ancestral states of genealogical nodes, and tested for selection. The genealogies estimated with the structural one-dimensional gene encoding the VP1 protein and nonstructural 3CD locus allowed the precise description of lineages over time and cocirculating virus populations within the two CVB5 clades, genogroups A and B. Strong negative selection shaped the evolution of both loci, but compelling phylogenetic data suggested that immune selection pressure resulted in the emergence of the two genogroups with opposed evolutionary pathways. The genogroups also differed in the temporal occurrence of the amino acid changes. The virus strains of genogroup A were characterized by sequential acquisition of nonsynonymous changes in residues exposed at the virus 5-fold axis. The genogroup B viruses were marked by selection of three changes in a different domain (VP1 C terminus) during its early emergence. These external changes resulted in a selective sweep, which was followed by an evolutionary stasis that is still ongoing after 50 years. The inferred population history of CVB5 showed an alternation of the prevailing genogroup during meningitis epidemics across Europe and is interpreted to be a consequence of partial cross-immunity.

  4. Understanding Visual Search Patterns of Dermatologists Assessing Pigmented Skin Lesions Before and After Online Training

    National Research Council Canada - National Science Library

    Krupinski, Elizabeth A; Chao, Joseph; Hofmann-Wellenhof, Rainer; Morrison, Lynne; Curiel-Lewandrowski, Clara

    2014-01-01

    The goal of this investigation was to explore the feasibility of characterizing the visual search characteristics of dermatologists evaluating images corresponding to single pigmented skin lesions (PSLs...

  5. Googling in anatomy education: Can google trends inform educators of national online search patterns of anatomical syllabi?

    Science.gov (United States)

    Phelan, Nigel; Davy, Shane; O'Keeffe, Gerard W; Barry, Denis S

    2017-03-01

    The role of e-learning platforms in anatomy education continues to expand as self-directed learning is promoted in higher education. Although a wide range of e-learning resources are available, determining student use of non-academic internet resources requires novel approaches. One such approach that may be useful is the Google Trends© web application. To determine the feasibility of Google Trends to gain insights into anatomy-related online searches, Google Trends data from the United States from January 2010 to December 2015 were analyzed. Data collected were based on the recurrence of keywords related to head and neck anatomy generated from the American Association of Clinical Anatomists and the Anatomical Society suggested anatomy syllabi. Relative search volume (RSV) data were analyzed for seasonal periodicity and their overall temporal trends. Following exclusions due to insufficient search volume data, 29 out of 36 search terms were analyzed. Significant seasonal patterns occurred in 23 search terms. Thirty-nine seasonal peaks were identified, mainly in October and April, coinciding with teaching periods in anatomy curricula. A positive correlation of RSV with time over the 6-year study period occurred in 25 out of 29 search terms. These data demonstrate how Google Trends may offer insights into the nature and timing of online search patterns of anatomical syllabi and may potentially inform the development and timing of targeted online supports to ensure that students of anatomy have the opportunity to engage with online content that is both accurate and fit for purpose. Anat Sci Educ 10: 152-159. © 2016 American Association of Anatomists. © 2016 American Association of Anatomists.

  6. The differential pattern of tissue-specific expression of ruminant pancreatic type ribonucleases may help to understand the evolutionary history of their genes.

    Science.gov (United States)

    Sasso, M P; Lombardi, M; Confalone, E; Carsana, A; Palmieri, M; Furia, A

    1999-02-18

    Molecular evolutionary analyses of mammalian ribonucleases have shown that gene duplication events giving three paralogous genes occurred in ruminant ancestors. The enzymes of the bovine species encoded by these genes, isolated from pancreas, brain and seminal vesicles, present similar enzymological properties but distinct structural features. In other ruminant species, genomic sequences orthologous to the bovine genes of pancreas and brain ribonucleases encode active enzymes. In mammalian species other than ruminant artiodactyls, only one gene encoding ribonuclease of the pancreatic type is generally present. In this work, we describe a differential pattern of transcriptional expression of the pancreas and brain ribonuclease genes in the ox species and report transcription of the human ribonuclease gene in brain as well as in pancreas and in mammary gland. We also report the molecular cloning of the gene encoding the bovine seminal ribonuclease in which the structural organization already described for the two paralogous genes is conserved. The seminal RNAase is exclusively expressed in seminal vesicles of Bos taurus, whereas in other ruminant species, the orthologous sequence is a pseudogene. Previous studies from a number of research groups demonstrated that, unlike other mammalian ribonucleases, the seminal enzyme is a covalent dimer, and its unique quaternary structure correlates with special biological activities. The major determinant of dimer formation, i.e. the presence of two adjacent cysteine residues, is absent in the pseudogenes. We advance the hypothesis that the differentiation of distinct expression patterns could represent an important evolutionary determinant for the genes encoding pancreas and brain ribonucleases in ruminants, whereas the differentiation of a quaternary structure endowed with new biological functions could be the main determinant for the evolutionary success of the seminal gene in the bovine species.

  7. Chunking versus foraging search patterns by rats in the hierarchically baited radial maze.

    Science.gov (United States)

    Cohen, Jerome; Pardy, Sandra; Solway, Heidi; Graham, Harold

    2003-06-01

    Rats were exposed to a radial maze containing six black smooth arms and six wire-grid-covered arms and a striped 'exit arm' in experiment 1. The probability of a black or grid arm being baited (5/6 vs 1/6) with sunflower seeds was associated with its proximal cue for some rats (the Relevant Arm Cue group) but not for others (the Irrelevant Arm Cue group). All rats could terminate a trial and receive a highly preferred morsel of apple by entering the exit arm only after having sampled all six seed-baited arms. Relevant Arm Cue rats usually chose some arms from the more densely baited set before choosing an arm from the less densely baited set and made fewer reentries than Irrelevant Arm Cue rats. Although such clustered, higher choice accuracy in the Relevant Arm Cue group corresponds to human clustered, better recall of verbal items from lists hierarchically organized by categories, these rats did not similarly exhaustively retrieve items (arm locations). That is, when required to terminate a trial by entering the 'exit' arm for an apple morsel after having sampled all seed-baited arms, both groups were equally unable to withhold making nonrewarded premature exits. This nonexhaustive foraging search pattern was maintained in the next two experiments in which the radial maze was reduced to three black and three grid arms along with the striped 'exit' arm and in which black and grid arm cues were paired with number of seeds (eight or one) in an arm for Relevant Arm Cue rats. Although Relevant Arm Cue rats displayed perfect clustering by entering all eight-seeded arms before a one-seeded arm, they made more premature exits and reentries into eight-seeded arms in experiment 2 or when forced to enter all eight-seeded arms in experiment 3 than did Irrelevant Arm Cue rats. These foraging tendencies prevent accurate estimations of the amount of information (i.e., arm locations) rats can 'chunk'.

  8. Comparing search patterns in digital breast tomosynthesis and full-field digital mammography: an eye tracking study.

    Science.gov (United States)

    Aizenman, Avi; Drew, Trafton; Ehinger, Krista A; Georgian-Smith, Dianne; Wolfe, Jeremy M

    2017-10-01

    As a promising imaging modality, digital breast tomosynthesis (DBT) leads to better diagnostic performance than traditional full-field digital mammograms (FFDM) alone. DBT allows different planes of the breast to be visualized, reducing occlusion from overlapping tissue. Although DBT is gaining popularity, best practices for search strategies in this medium are unclear. Eye tracking allowed us to describe search patterns adopted by radiologists searching DBT and FFDM images. Eleven radiologists examined eight DBT and FFDM cases. Observers marked suspicious masses with mouse clicks. Eye position was recorded at 1000 Hz and was coregistered with slice/depth plane as the radiologist scrolled through the DBT images, allowing a 3-D representation of eye position. Hit rate for masses was higher for tomography cases than 2-D cases and DBT led to lower false positive rates. However, search duration was much longer for DBT cases than FFDM. DBT was associated with longer fixations but similar saccadic amplitude compared with FFDM. When comparing radiologists' eye movements to a previous study, which tracked eye movements as radiologists read chest CT, we found DBT viewers did not align with previously identified "driller" or "scanner" strategies, although their search strategy most closely aligns with a type of vigorous drilling strategy.

  9. The search for evolutionary developmental origins of aging in zebrafish: a novel intersection of developmental and senescence biology in the zebrafish model system.

    Science.gov (United States)

    Kishi, Shuji

    2011-09-01

    regulation. We wish to ascertain whether we can identify such genes promptly in a comprehensive manner. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes and small molecular compounds that can be linked to the senescence phenotype and thereby facilitates searching for the evolutionary and developmental origins of aging in vertebrates. Copyright © 2011 Wiley-Liss, Inc.

  10. Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development.

    Science.gov (United States)

    Miyazawa, Hideyuki; Ueda, Chiaki; Yahata, Kensuke; Su, Zhi-Hui

    2014-02-18

    Myriapoda, a subphylum of Arthropoda, comprises four classes, Chilopoda, Diplopoda, Pauropoda, and Symphyla. While recent molecular evidence has shown that Myriapoda is monophyletic, the internal phylogeny, which is pivotal for understanding the evolutionary history of myriapods, remains unresolved. Here we report the results of phylogenetic analyses and estimations of divergence time and ancestral state of myriapods. Phylogenetic analyses were performed based on three nuclear protein-coding genes determined from 19 myriapods representing the four classes (17 orders) and 11 outgroup species. The results revealed that Symphyla whose phylogenetic position has long been debated is the sister lineage to all other myriapods, and that the interordinal relationships within classes were consistent with traditional classifications. Ancestral state estimation based on the tree topology suggests that myriapods evolved from an ancestral state that was characterized by a hemianamorphic mode of post-embryonic development and had a relatively low number of body segments and legs.

  11. eHealth Search Patterns: A Comparison of Private and Public Health Care Markets Using Online Panel Data.

    Science.gov (United States)

    Schneider, Janina Anne; Holland, Christopher Patrick

    2017-04-13

    Patient and consumer access to eHealth information is of crucial importance because of its role in patient-centered medicine and to improve knowledge about general aspects of health and medical topics. The objectives were to analyze and compare eHealth search patterns in a private (United States) and a public (United Kingdom) health care market. A new taxonomy of eHealth websites is proposed to organize the largest eHealth websites. An online measurement framework is developed that provides a precise and detailed measurement system. Online panel data are used to accurately track and analyze detailed search behavior across 100 of the largest eHealth websites in the US and UK health care markets. The health, medical, and lifestyle categories account for approximately 90% of online activity, and e-pharmacies, social media, and professional categories account for the remaining 10% of online activity. Overall search penetration of eHealth websites is significantly higher in the private (United States) than the public market (United Kingdom). Almost twice the number of eHealth users in the private market have adopted online search in the health and lifestyle categories and also spend more time per website than those in the public market. The use of medical websites for specific conditions is almost identical in both markets. The allocation of search effort across categories is similar in both the markets. For all categories, the vast majority of eHealth users only access one website within each category. Those that conduct a search of two or more websites display very narrow search patterns. All users spend relatively little time on eHealth, that is, 3-7 minutes per website. The proposed online measurement framework exploits online panel data to provide a powerful and objective method of analyzing and exploring eHealth behavior. The private health care system does appear to have an influence on eHealth search behavior in terms of search penetration and time spent per

  12. Analysis of Nondeterministic Search Patterns for Minimization of UAV Counter-Targeting

    Science.gov (United States)

    2013-03-01

    64 Figure 4.9 Procerus Unicorn UAV [48] used in multi-UAV look-ahead Levy search demonstration conducted at 13-2 JIFX in February, 2013...to the Procerus Unicorn UAV employed during these flight experiments, shown in Figure 4.9. Figure 4.10 shows the straight-line path between the major...Figure 4.9: Procerus Unicorn UAV [48] used in multi-UAV look-ahead Levy search demonstration conducted at 13-2 JIFX in February, 2013. for display in

  13. Fractal reorientation clocks: Linking animal behavior to statistical patterns of search.

    Science.gov (United States)

    Bartumeus, Frederic; Levin, Simon A

    2008-12-09

    The movement ecology framework depicts animal movement as the result of the combined effects of internal and external constraints on animal navigation and motion capacities. Nevertheless, there are still fundamental problems to understand how these modulations take place and how they might be translated into observed statistical properties of animal trajectories. Of particular interest, here, is the general idea of intermittence in animal movement. Intermittent locomotion assumes that animal movement is, in essence, discrete. The existence of abrupt interruptions in an otherwise continuous flow of movement allows for the possibility of reorientations, that is, to break down previous directional memories of the trajectory. In this study, we explore the potential links between intermittent locomotion, reorientation behavior, and search efficiency. By means of simulations we show that the incorporation of Lévy intermittence in an otherwise nonintermittent search strongly modifies encounter rates. The result is robust to different types of landscapes (i.e., target density and spatial distribution), and spatial dimensions (i.e., 2D, 3D). We propose that Lévy intermittence may come from reorientation mechanisms capable of organizing directional persistence on time (i.e., fractal reorientation clocks), and we rationalize that the explicit distinction between scanning and reorientation mechanisms is essential to make accurate statistical inferences from animal search behavior. Finally, we provide a statistical tool to judge the existence of episodic and strong reorientation behaviors capable of modifying relevant properties of stochastic searches, ultimately controlling the chances of finding unknown located items.

  14. Optimal Mixing Evolutionary Algorithms

    NARCIS (Netherlands)

    D. Thierens (Dirk); P.A.N. Bosman (Peter); N. Krasnogor

    2011-01-01

    htmlabstractA key search mechanism in Evolutionary Algorithms is the mixing or juxtaposing of partial solutions present in the parent solutions. In this paper we look at the efficiency of mixing in genetic algorithms (GAs) and estimation-of-distribution algorithms (EDAs). We compute the mixing

  15. Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.

    Science.gov (United States)

    Smoly, Ilan; Carmel, Amir; Shemer-Avni, Yonat; Yeger-Lotem, Esti; Ziv-Ukelson, Michal

    2016-03-01

    Network querying is a powerful approach to mine molecular interaction networks. Most state-of-the-art network querying tools either confine the search to a prespecified topology in the form of some template subnetwork, or do not specify any topological constraints at all. Another approach is grammar-based queries, which are more flexible and expressive as they allow for expressing the topology of the sought pattern according to some grammar-based logic. Previous grammar-based network querying tools were confined to the identification of paths. In this article, we extend the patterns identified by grammar-based query approaches from paths to trees. For this, we adopt a higher order query descriptor in the form of a regular tree grammar (RTG). We introduce a novel problem and propose an algorithm to search a given graph for the k highest scoring subgraphs matching a tree accepted by an RTG. Our algorithm is based on the combination of dynamic programming with color coding, and includes an extension of previous k-best parsing optimization approaches to avoid isomorphic trees in the output. We implement the new algorithm and exemplify its application to mining viral infection patterns within molecular interaction networks. Our code is available online.

  16. Optimizing Search Patterns for Multiple Searchers Prosecuting a Single Contact In the South China Sea

    Science.gov (United States)

    2016-09-01

    and classify submarines in the area. 1.1 History SDT originated in World War II (WWII) and represented the birth of operations analysis...search and rescue operations [3]. The following research focuses on the aspects of stochastic processes, use and interpretation of sweep widths, and...limited only by the imagination of the analyst utilizing it. While it is exercised in the form of a naval problem for this research, many research papers

  17. Peering into the Deep: Characterizing the Internet Search Patterns of Patients with Gynecologic Cancers.

    Science.gov (United States)

    McLeod, Jane; Yu, Irene; Ingledew, Paris-Ann

    2017-03-01

    Cancer patients are increasingly using the Internet to learn about their disease, connect with others undergoing similar treatments and obtain support outside of the clinical encounter. The goal of this project was to explore how patients with gynecological cancers (ovarian, cervical, and endometrial) used the Internet as an information resource and how this influenced their treatment decisions and interactions with their health care specialists. From 2013 to 2014, ovarian, endometrial, and cervical cancer patients attending a comprehensive cancer centre were invited to complete a 24-item paper questionnaire detailing their experiences in searching the Internet. Twenty-eight patients completed survey. The largest portion of participants had an ovarian cancer diagnosis (61 %), followed by endometrial (29 %) and cervical cancer (11 %). Results indicate that the majority (85 %) of patients used the Internet as a resource to learn about their gynecological cancers. Most respondents (89 %) used Google as their search engine, and some used multiple search engines. The most frequently searched topics included treatment information (85 %), management of symptoms/treatment toxicity (59 %), and alternative treatments (37 %). Many patients (74 %) felt that the Internet was a useful tool for understanding their diagnosis; however, 33 % reported that the Internet was somewhat hard to understand. Most (78 %) patients reported that Internet information increased their understanding of their diagnosis, and 56 % felt it did not affect their decision-making. This study highlights how gynecological patients are accessing cancer information online and how physicians may support this within the clinical setting.

  18. Understanding visual search patterns of dermatologists assessing pigmented skin lesions before and after online training.

    Science.gov (United States)

    Krupinski, Elizabeth A; Chao, Joseph; Hofmann-Wellenhof, Rainer; Morrison, Lynne; Curiel-Lewandrowski, Clara

    2014-12-01

    The goal of this investigation was to explore the feasibility of characterizing the visual search characteristics of dermatologists evaluating images corresponding to single pigmented skin lesions (PSLs) (close-ups and dermoscopy) as a venue to improve training programs for dermoscopy. Two Board-certified dermatologists and two dermatology residents participated in a phased study. In phase I, they viewed a series of 20 PSL cases ranging from benign nevi to melanoma. The close-up and dermoscopy images of the PSL were evaluated sequentially and rated individually as benign or malignant, while eye position was recorded. Subsequently, the participating subjects completed an online dermoscopy training module that included a pre- and post-test assessing their dermoscopy skills (phase 2). Three months later, the subjects repeated their assessment on the 20 PSLs presented during phase I of the study. Significant differences in viewing time and eye-position parameters were observed as a function of level of expertise. Dermatologists overall have more efficient search than residents generating fewer fixations with shorter dwells. Fixations and dwells associated with decisions changing from benign to malignant or vice versa from photo to dermatoscopic viewing were longer than any other decision, indicating increased visual processing for those decisions. These differences in visual search may have implications for developing tools to teach dermatologists and residents about how to better utilize dermoscopy in clinical practice.

  19. Evolutionary pattern of mutation in the factor IX genes of great apes: How does it compare to the pattern of recent germline mutation in patients with hemophilia B?

    Energy Technology Data Exchange (ETDEWEB)

    Grouse, L.H.; Ketterling, R.P.; Sommer, S.S. [Mayo Clinic/Foundation, Rochester, MN (United States)

    1994-09-01

    Most mutations causing hemophilia B have arisen within the past 150 years. By correcting for multiple biases, the underlying rates of spontaneous germline mutation have been estimated in the factor IX gene. From these rates, an underlying pattern of mutation has emerged. To determine if this pattern compares to a underlying pattern found in the great apes, sequence changes were determined in intronic regions of the factor IX gene. The following species were studied: Gorilla gorilla, Pan troglodytes (chimpanzee), Pongo pygmacus (orangutan) and Homo sapiens. Intronic sequences at least 200 bp from a splice junction were randomly chosen, amplified by cross-species PCR, and sequenced. These regions are expected to be subject to little if any selective pressure. Early diverged species of Old World monkeys were also studied to help determine the direction of mutational changes. A total of 62 sequence changes were observed. Initial data suggest that the average pattern since evolution of the great apes has a paucity of transitions at CpG dinucleotides and an excess of microinsertions to microdeletions when compared to the pattern observed in humans during the past 150 years (p<.05). A larger study is in progress to confirm these results.

  20. Pattern Search in Multi-structure Data: A Framework for the Next-Generation Evidence-based Medicine

    Energy Technology Data Exchange (ETDEWEB)

    Sukumar, Sreenivas R [ORNL; Ainsworth, Keela C [ORNL

    2014-01-01

    With the advent of personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledge-bases) to predict diagnostic risks is fast emerging. Addressing this need, we pose and address the following questions (i) How can we jointly analyze both qualitative and quantitative data ? (ii) Is the fusion of multi-structure data expected to provide better insights than either of them individually ? We present experiments on two bio-medical data sets - mammography and traumatic brain studies to demonstrate architectures and tools for evidence-pattern search.

  1. Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3 reveal no contribution to reproductive isolation between bovine species

    Directory of Open Access Journals (Sweden)

    Beja-Pereira Albano

    2011-01-01

    Full Text Available Abstract Background It has been established that mammalian egg zona pellucida (ZP glycoproteins are responsible for species-restricted binding of sperm to unfertilized eggs, inducing the sperm acrosome reaction, and preventing polyspermy. In mammals, ZP apparently represents a barrier to heterospecific fertilization and thus probably contributes to reproductive isolation between species. The evolutionary relationships between some members of the tribe Bovini are complex and highly debatable, particularly, those involving Bos and Bison species for which interspecific hybridization is extensively documented. Because reproductive isolation is known to be a major precursor of species divergence, testing evolutionary patterns of ZP glycoproteins may shed some light into the speciation process of these species. To this end, we have examined intraspecific and interspecific genetic variation of two ZP genes (Zp2 and Zp3 for seven representative species (111 individuals from the Bovini tribe, including five species from Bos and Bison, and two species each from genera Bubalus and Syncerus. Results A pattern of low levels of intraspecific polymorphism and interspecific divergence was detected for the two sequenced fragments each for Zp2 and Zp3. At intraspecific level, none of neutrality tests detected deviations from neutral equilibrium expectations for the two genes. Several haplotypes in both genes were shared by multiple species from Bos and Bison. Conclusions Here we argue that neither ancestral polymorphism nor introgressive hybridization alone can fully account for haplotype sharing among species from Bos and Bison, and that both scenarios have contributed to such a pattern of haplotype sharing observed here. Additionally, codon-based tests revealed strong evidence for purifying selection in the Zp3 coding haplotype sequences and weak evidence for purifying selection in the Zp2 coding haplotype sequences. Contrary to a general genetic pattern that

  2. HYBRID GREY WOLF OPTIMIZATION-PATTERN SEARCH (hGWO-PS) OPTIMIZED 2DOF-PID CONTROLLERS FOR LOAD FREQUENCY CONTROL (LFC) IN INTERCONNECTED THERMAL POWER PLANTS

    National Research Council Canada - National Science Library

    V, Soni; G, Parmar; M, Kumar; S, Panda

    2016-01-01

    The combination of Grey Wolf Optimization and Pattern Search Technique (hGWO-PS) has been introduced to optimize the parameters of two Degree of Freedom Proportional-Integral-Derivative Controller (2DOF-PID...

  3. Affective evolutionary music composition with MetaCompose

    DEFF Research Database (Denmark)

    Scirea, Marco; Togelius, Julian; Eklund, Peter

    2017-01-01

    express different mood-states, which we achieve through a unique combination of a graph traversal-based chord sequence generator, a search-based melody generator, a pattern-based accompaniment generator, and a theory for mood expression. Melody generation uses a novel evolutionary technique combining FI-2...... affective state. This system, which can reliably generate affect-expressive music, can subsequently be integrated in any kind of interactive application (e.g., games) to create an adaptive and dynamic soundtrack....

  4. C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.

    Science.gov (United States)

    Sowpati, Divya Tej; Srivastava, Surabhi; Dhawan, Jyotsna; Mishra, Rakesh K

    2017-09-13

    Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

  5. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

    Directory of Open Access Journals (Sweden)

    Otten Celine

    2008-06-01

    Full Text Available Abstract Background Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. Results G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. Conclusion Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.

  6. A Five Species Cyclically Dominant Evolutionary Game with Fixed Direction: A New Way to Produce Self-Organized Spatial Patterns

    Directory of Open Access Journals (Sweden)

    Yibin Kang

    2016-08-01

    Full Text Available Cyclically dominant systems are hot issues in academia, and they play an important role in explaining biodiversity in Nature. In this paper, we construct a five-strategy cyclically dominant system. Each individual in our system changes its strategy along a fixed direction. The dominant strategy can promote a change in the dominated strategy, and the dominated strategy can block a change in the dominant strategy. We use mean-field theory and cellular automaton simulation to discuss the evolving characters of the system. In the cellular automaton simulation, we find the emergence of spiral waves on spatial patterns without a migration rate, which suggests a new way to produce self-organized spatial patterns.

  7. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

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

  8. Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Elodie eGazave

    2016-04-01

    Full Text Available The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP, winter Europe (WE, and winter Asia (WA. Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  9. Searching for three-dimensional secondary structural patterns in proteins with ProSMoS.

    Science.gov (United States)

    Shi, Shuoyong; Zhong, Yi; Majumdar, Indraneel; Sri Krishna, S; Grishin, Nick V

    2007-06-01

    Many evolutionarily distant, but functionally meaningful links between proteins come to light through comparison of spatial structures. Most programs that assess structural similarity compare two proteins to each other and find regions in common between them. Structural classification experts look for a particular structural motif instead. Programs base similarity scores on superposition or closeness of either Cartesian coordinates or inter-residue contacts. Experts pay more attention to the general orientation of the main chain and mutual spatial arrangement of secondary structural elements. There is a need for a computational tool to find proteins with the same secondary structures, topological connections and spatial architecture, regardless of subtle differences in 3D coordinates. We developed ProSMoS--a Protein Structure Motif Search program that emulates an expert. Starting from a spatial structure, the program uses previously delineated secondary structural elements. A meta-matrix of interactions between the elements (parallel or antiparallel) minding handedness of connections (left or right) and other features (e.g. element lengths and hydrogen bonds) is constructed prior to or during the searches. All structures are reduced to such meta-matrices that contain just enough information to define a protein fold, but this definition remains very general and deviations in 3D coordinates are tolerated. User supplies a meta-matrix for a structural motif of interest, and ProSMoS finds all proteins in the protein data bank (PDB) that match the meta-matrix. ProSMoS performance is compared to other programs and is illustrated on a beta-Grasp motif. A brief analysis of all beta-Grasp-containing proteins is presented. Program availability: ProSMoS is freely available for non-commercial use from ftp://iole.swmed.edu/pub/ProSMoS.

  10. Evidence From Web-Based Dietary Search Patterns to the Role of B12 Deficiency in Non-Specific Chronic Pain: A Large-Scale Observational Study.

    Science.gov (United States)

    Giat, Eitan; Yom-Tov, Elad

    2018-01-05

    Profound vitamin B12 deficiency is a known cause of disease, but the role of low or intermediate levels of B12 in the development of neuropathy and other neuropsychiatric symptoms, as well as the relationship between eating meat and B12 levels, is unclear. The objective of our study was to investigate the role of low or intermediate levels of B12 in the development of neuropathy and other neuropsychiatric symptoms. We used food-related Internet search patterns from a sample of 8.5 million people based in the US as a proxy for B12 intake and correlated these searches with Internet searches related to possible effects of B12 deficiency. Food-related search patterns were highly correlated with known consumption and food-related searches (ρ=.69). Awareness of B12 deficiency was associated with a higher consumption of B12-rich foods and with queries for B12 supplements. Searches for terms related to neurological disorders were correlated with searches for B12-poor foods, in contrast with control terms. Popular medicines, those having fewer indications, and those which are predominantly used to treat pain, were more strongly correlated with the ability to predict neuropathic pain queries using the B12 contents of food. Our findings show that Internet search patterns are a useful way of investigating health questions in large populations, and suggest that low B12 intake may be associated with a broader spectrum of neurological disorders than previously thought.

  11. Co-evolutionary patterns of variation in small and large RNA segments of Crimean-Congo hemorrhagic fever virus.

    Science.gov (United States)

    Chamberlain, John; Cook, Nicola; Lloyd, Graham; Mioulet, Valerie; Tolley, Howard; Hewson, Roger

    2005-12-01

    The genus Nairovirus of the family Bunyaviridae includes the Crimean-Congo haemorrhagic fever (CCHF) species group. The species is predominated by the hazard-group 4 pathogens, from which the name and majority of strain entries are derived. Additionally, the species embraces hazard-group 2 viruses that are classified as members by antigenic cross-reactivity. CCHF viruses have a tripartite RNA genome consisting of large (L), medium (M) and small (S) segments. Here, the sequence characterization of previously undescribed L and S segments from novel strains originating in the Middle East and Africa is reported. Further scrutiny of this data with phylogenetic tools, in the context of other publicly available sequence information, reveals analogous grouping patterns between the L and S segments. These groups correlate with the geographical distribution of strain isolation and indicate that the L and S segments of CCHF viruses have evolved together.

  12. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.

    Science.gov (United States)

    Malik, Assaf; Korol, Abraham; Hübner, Sariel; Hernandez, Alvaro G; Thimmapuram, Jyothi; Ali, Shahjahan; Glaser, Fabian; Paz, Arnon; Avivi, Aaron; Band, Mark

    2011-01-01

    The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.

  13. Non-LTR R2 element evolutionary patterns: phylogenetic incongruences, rapid radiation and the maintenance of multiple lineages.

    Directory of Open Access Journals (Sweden)

    Andrea Luchetti

    Full Text Available Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850-600 Million years ago placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host's 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the "library" model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.

  14. Fitness-maximizing foragers can use information about patch quality to decide how to search for and within patches: optimal Lévy walk searching patterns from optimal foraging theory

    Science.gov (United States)

    Reynolds, A. M.

    2012-01-01

    Optimal foraging theory shows how fitness-maximizing foragers can use information about patch quality to decide how to search within patches. It is amply supported by empirical studies. Nonetheless, the theory largely ignores the fact that foragers may need to search for patches as well as for the targets within them. Here, using an exact but simple mathematical argument, it is shown how foragers can use information about patch quality to facilitate the execution of Lévy walk movement patterns with μ = 2 at inter-patch scales. These movement patterns are advantageous when searching for patches that are not depleted or rejected once visited but instead remain profitable. The analytical results are verified by the results of numerical simulations. The findings bring forth an innovative theoretical synthesis of searching for and within patches and, suggest that foragers' memories may be adaptive under spatially heterogeneous reward schedules. PMID:22258553

  15. GENERALIZED ANALYSIS OF THE RESULTS OF GENETICALLY ENGINEERED BIOLOGICAL THERAPY: SEARCHES FOR NEW PATTERNS

    Directory of Open Access Journals (Sweden)

    Yakov Aleksandrovich Sigidin

    2013-01-01

    Full Text Available The clinical analysis of the results of genetically engineered biological therapy identifies a number of patterns of the mechanism of action of this therapy and the pathogenetic features of rheumatic diseases. The results of using genetically engineered biological agents (GEBA having different mechanisms of action allow one to identify categories of rheumatoid arthritis patients with different pathogenetic features. Various cytokines can play a major pathogenic role in a clinically similar inflammatory process. The therapeutic effect of tumor necrosis factor-α (TNF-α inhibitors exhibits the predominance of their nonspecific anti-inflammatory activity over the immunosuppressive one. Contrary to the previous ideas of cytokine hierarchy, TNF-α neutralization does not block the effects of interleukin 6 (IL-6. Anti-B-cell therapy is most effective in patients with significant autoimmune disorders; a contrary pattern is observed when TNF-α inhibitors are used. TNF-α is very important in the development of an inflammatory process in ankylosing spondylitis (AS while the role of IL6 is insignificant. Autoimmune disorders in AS are not marked; whereby predominantly immunotropic GEBAs (rituximab and abatacept are ineffective in this disease. The blocking of a biological reaction to inflammation cannot coincide with the suppression of the inflammatory process proper.

  16. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.

    Directory of Open Access Journals (Sweden)

    Marc W Allard

    Full Text Available Facile laboratory tools are needed to augment identification in contamination events to trace the contamination back to the source (traceback of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis. Understanding the evolution and diversity within and among outbreak strains is the first step towards this goal. To this end, we collected 106 new S. Enteriditis isolates within S. Enteriditis Pulsed-Field Gel Electrophoresis (PFGE pattern JEGX01.0004 and close relatives, and determined their genome sequences. Sources for these isolates spanned food, clinical and environmental farm sources collected during the 2010 S. Enteritidis shell egg outbreak in the United States along with closely related serovars, S. Dublin, S. Gallinarum biovar Pullorum and S. Gallinarum. Despite the highly homogeneous structure of this population, S. Enteritidis isolates examined in this study revealed thousands of SNP differences and numerous variable genes (n = 366. Twenty-one of these genes from the lineages leading to outbreak-associated samples had nonsynonymous (causing amino acid changes changes and five genes are putatively involved in known Salmonella virulence pathways. While chromosome synteny and genome organization appeared to be stable among these isolates, genome size differences were observed due to variation in the presence or absence of several phages and plasmids, including phage RE-2010, phage P125109, plasmid pSEEE3072_19 (similar to pSENV, plasmid pOU1114 and two newly observed mobile plasmid elements pSEEE1729_15 and pSEEE0956_35. These differences produced modifications to the assembled bases for these draft genomes in the size range of approximately 4.6 to 4.8 mbp, with S. Dublin being larger (∼4.9 mbp and S. Gallinarum smaller (4.55 mbp when compared to S. Enteritidis. Finally, we identified variable S. Enteritidis genes associated with virulence pathways that may be useful markers for the development of rapid surveillance

  17. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae.

    Science.gov (United States)

    Turmel, M; Lemieux, C; Burger, G; Lang, B F; Otis, C; Plante, I; Gray, M W

    1999-09-01

    Green plants appear to comprise two sister lineages, Chlorophyta (classes Chlorophyceae, Ulvophyceae, Trebouxiophyceae, and Prasinophyceae) and Streptophyta (Charophyceae and Embryophyta, or land plants). To gain insight into the nature of the ancestral green plant mitochondrial genome, we have sequenced the mitochondrial DNAs (mtDNAs) of Nephroselmis olivacea and Pedinomonas minor. These two green algae are presumptive members of the Prasinophyceae. This class is thought to include descendants of the earliest diverging green algae. We find that Nephroselmis and Pedinomonas mtDNAs differ markedly in size, gene content, and gene organization. Of the green algal mtDNAs sequenced so far, that of Nephroselmis (45,223 bp) is the most ancestral (minimally diverged) and occupies the phylogenetically most basal position within the Chlorophyta. Its repertoire of 69 genes closely resembles that in the mtDNA of Prototheca wickerhamii, a later diverging trebouxiophycean green alga. Three of the Nephroselmis genes (nad10, rpl14, and rnpB) have not been identified in previously sequenced mtDNAs of green algae and land plants. In contrast, the 25,137-bp Pedinomonas mtDNA contains only 22 genes and retains few recognizably ancestral features. In several respects, including gene content and rate of sequence divergence, Pedinomonas mtDNA resembles the reduced mtDNAs of chlamydomonad algae, with which it is robustly affiliated in phylogenetic analyses. Our results confirm the existence of two radically different patterns of mitochondrial genome evolution within the green algae.

  18. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: Utility and potential for the discovery of novel evolutionary patterns

    KAUST Repository

    Malik, Assaf

    2011-08-12

    The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ~12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat. 2011 Malik et al.

  19. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.

    Directory of Open Access Journals (Sweden)

    Assaf Malik

    Full Text Available The blind subterranean mole rat (Spalax ehrenbergi superspecies is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.

  20. Pattern search in multi-structure data: a framework for the next-generation evidence-based medicine

    Science.gov (United States)

    Sukumar, Sreenivas R.; Ainsworth, Keela C.

    2014-03-01

    With the impetus towards personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledgebase, etc.) to predict diagnostic risks is fast emerging. Addressing this need, we pose and answer the following questions: (i) How can we jointly analyze and explore measurement data in context with qualitative domain knowledge? (ii) How can we search and hypothesize patterns (not known apriori) from such multi-structure data? (iii) How can we build predictive models by integrating weakly-associated multi-relational multi-structure data? We propose a framework towards answering these questions. We describe a software solution that leverages hardware for scalable in-memory analytics and applies next-generation semantic query tools on medical data.

  1. COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes.

    Science.gov (United States)

    Maccari, Giuseppe; Gemignani, Federica; Landi, Stefano

    2010-07-15

    The complete sequencing of the human genome shows that only 1% of the entire genome encodes for proteins. The major part of the genome is made up of non-coding DNA, regulatory elements and junk DNA. Transcriptional regulation plays a central role in a multitude of critical cellular processes and responses, and it is a central force in the development and differentiation of multicellular organisms. Identifying regulatory elements is one of the major tasks in this challenge. To accomplish this task, we developed a solid and simple suite that allows direct access to genomic database and immediate result check. We introduce COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for motif search in entire genomes. Motifs can be partially degenerated and interrupted by spacers of variable length. We demonstrate through real biological data mining the simplicity and robustness of this tool. The test was performed on two well-known protein domains and a highly variable cis-acting element. COMPASSS successfully identifies both protein domains and cis-acting semi-conserved elements. The COMPASSS suite is available for Windows free of charge from our web sites: compasss.sourceforge.net/; www.stefanolandi.eu/

  2. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

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

  3. The impact of arbuscular mycorrhizal fungi on plant growth following herbivory: A search for pattern

    Science.gov (United States)

    Borowicz, Victoria A.

    2013-10-01

    Arbuscular mycorrhizal (AM) fungi can facilitate nutrient uptake and increase host plant growth but also place constraints on the host's carbon budget. When plants are stressed by herbivory the net effect of the symbiosis may be altered tolerance. Individual experiments manipulating AM fungi and herbivory have demonstrated increased, decreased, and no effect on tolerance but patterns with respect to plant, herbivore, or fungus characteristics have not emerged. Meta-analysis of published results from factorial experiments was used to describe the size of the effects of herbivory and of AM fungi on host growth when factors such as cause of damage, inoculum, and host characteristics are considered, and to determine whether AM fungi alter the effects of herbivory. Also, the correlation between the effect of AM fungi on tolerance and resistance was tested with data from studies that examined insect performance. Herbivory strongly and consistently reduced shoot and root growth, especially in perennial plants and crops. AM fungi increased shoot growth of perennials but not annuals, and when insects caused damage but not when artificial defoliation was applied. Root growth was consistently greater with AM fungi. The interaction of AM fungi and herbivory, which indicates whether AM fungi alter the effects of herbivory, was variable and never significant overall but homogeneity tests indicated underlying structure. In experiments that used single species inoculum, Glomus intraradices increased, whereas Glomus mosseae reduced, effects of herbivory on shoot growth. Multispecies inocula magnified effects of herbivory on root growth whereas single species inocula ameliorated effects. The impact of AM fungi on resistance to herbivory was positively correlated with the impact on tolerance; however AM fungi reduced both tolerance and resistance in many cases. Review of these results with respect to the types of systems studied suggests directions for future investigation.

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

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    2016-11-01

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

  5. Archaeogenetics in evolutionary medicine.

    Science.gov (United States)

    Bouwman, Abigail; Rühli, Frank

    2016-09-01

    Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.

  6. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation.

    Science.gov (United States)

    Pereira, Tiago José; Baldwin, James Gordon

    2016-05-01

    Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    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.

  8. The Assessment of Current Biogeographic Patterns of Coral Reef Fishes in the Red Sea by Incorporating Their Evolutionary and Ecological Background

    KAUST Repository

    Robitzch Sierra, Vanessa S. N.

    2017-03-01

    The exceptional environment of the Red Sea has lead to high rates of endemism and biodiversity. Located at the periphery of the world’s coral reefs distribution, its relatively young reefs offer an ideal opportunity to study biogeography and underlying evolutionary and ecological triggers. Here, I provide baseline information on putative seasonal recruitment patterns of reef fishes along a cross shelf gradient at an inshore, mid-shelf, and shelf-edge reef in the central Saudi Arabian Red Sea. I propose a basic comparative model to resolve biogeographic patterns in endemic and cosmopolitan reef fishes. Therefore, I chose the genetically, biologically, and ecologically similar coral-dwelling damselfishes Dascyllus aruanus and D. marginatus as a model species-group. As a first step, basic information on the distribution, population structure, and genetic diversity is evaluated within and outside the Red Sea along most of their global distribution. Second, pelagic larval durations (PLDs) within the Red Sea environmental gradient are explored. For the aforementioned, PLDs of the only other Red Sea Dascyllus, D. trimaculatus, are included for a more comprehensive comparison. Third, to further assess ongoing pathways of connectivity and geneflow related to larval behavior and dispersal in Red Sea reef fishes, the genetic composition and kinship of a single recruitment cohort of D. aruanus arriving together at one single reef is quantified using single nuclear polymorphisms (SNPs). Genetic diversity and relatedness of the recruits are compared to that of the standing population at the settlement reef, providing insight into putative dispersal strategies and behavior of coral reef fish larvae. As a fourth component to study traits shaping biogeography, the ecology and adaptive potential of the cosmopolitan D. aruanus is described by studying morphometric-geometrics of the body structure in relation to the stomach content and prey type from specimen along the cross

  9. Strontium-isotope stratigraphy of Upper Cretaceous rudist bivalves: Biozones, evolutionary patterns and sea-level change calibrated to numerical ages

    Science.gov (United States)

    Steuber, Thomas; Schlüter, Malte

    2012-08-01

    Numerical ages derived from strontium-isotope stratigraphy of 81 Late Turonian-Maastrichtian rudist localities from the Caribbean to Oman are used to establish stratigraphical ranges of readily identifiable taxa of rudist bivalves (Hippuritida). Based on these ranges, seven biozones for the Turonian-Maastrichtian of the central-eastern Mediterranean Tethys, and three biozones for the mid-Campanian-Maastrichtian of the Arabian Plate are established. Most of these are interval zones, each based on the first stratigraphical appearance of the nominal taxon. Micro-evolutionary patterns such as phyletic size increase have been demonstrated for some of the nominal species, as well as a trend of stratigraphical range expansion from the Turonian to the Maastrichtian. Implications of the geochronology of Late Cretaceous carbonate platforms for the biostratigraphy of other benthic fossils are briefly discussed. Three significant gaps in the stratigraphical distribution of rudist localities in the lower, middle, and uppermost Campanian, respectively, correlate with other records of sea-level change, indicating that they correspond to major eustatic sea-level falls. Only a limited number of rudist taxa is evaluated here, but the early and latest Campanian sea-level falls correspond to faunal turnover and extinction of characteristic associations of Late Cretaceous Hippuritida. The final extinction of the Hippuritida at the Cretaceous/Paleogene boundary is evaluated based on the available numerical ages of eighteen Late Maastrichtian localities. Eighteen genera are recorded at the six youngest localities, which thus have a species richness similar to older Late Cretaceous localities. While the ultimate cause for extinction of the Hippuritida must be evaluated on time scales beyond the resolution of strontium-isotope stratigraphy, the data set evaluated provides some insight into the pattern of their demise, which is considered to be the result of a high degree of endemism

  10. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

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

  11. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

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

  12. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

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

  13. Design of binary patterns for speckle reduction in holographic display with compressive sensing and direct-binary search algorithm

    Science.gov (United States)

    Leportier, Thibault; Hwang, Do Kyung; Park, Min-Chul

    2017-08-01

    One problem common to imaging techniques based on coherent light is speckle noise. This phenomenon is caused mostly by random interference of light scattered by rough surfaces. Speckle noise can be avoided by using advanced holographic imaging techniques such as optical scanning holography. A more widely known method is to capture several holograms of the same object and to perform an averaging operation so that the signal to noise ratio can be improved. Several digital filters were also proposed to reduce noise in the numerical reconstruction plane of holograms, even though they usually require finding a compromise between noise reduction and edge preservation. In this study, we used a digital filter based on compressive sensing algorithm. This approach enables to obtain results equivalent to the average of multiple holograms, but only a single hologram is needed. Filters for speckle reduction are applied on numerical reconstructions of hologram, and not on the hologram itself. Then, optical reconstruction cannot be performed. We propose a method based on direct-binary search (DBS) algorithm to generate binary holograms that can be reconstructed optically after application of a speckle reduction filter. Since the optimization procedure of the DBS algorithm is performed in the image plane, speckle reduction techniques can be applied on the complex hologram and used as a reference to obtain a binary pattern where the speckle noise generated during the recording of the hologram has been filtered.

  14. Selectionist and evolutionary approaches to brain function: a critical appraisal.

    Science.gov (United States)

    Fernando, Chrisantha; Szathmáry, Eörs; Husbands, Phil

    2012-01-01

    We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman's theory of neuronal group selection, Changeux's theory of synaptic selection and selective stabilization of pre-representations, Seung's Darwinian synapse, Loewenstein's synaptic melioration, Adam's selfish synapse, and Calvin's replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price's covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity, and variability) as the most powerful mechanism for search in a sparsely occupied search space. Examples are given of cases where parallel competitive search with information transfer among the units is more efficient than search without information transfer between units. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.

  15. Optimal search behavior and classic foraging theory

    Energy Technology Data Exchange (ETDEWEB)

    Bartumeus, F [Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ (United States); Catalan, J [Centre d' Estudis Avancats de Blanes CEAB-CSIC, C/Acces a la Cala Sant Francesc 14, 17300 Blanes, Catalonia (Spain)

    2009-10-30

    Random walk methods and diffusion theory pervaded ecological sciences as methods to analyze and describe animal movement. Consequently, statistical physics was mostly seen as a toolbox rather than as a conceptual framework that could contribute to theory on evolutionary biology and ecology. However, the existence of mechanistic relationships and feedbacks between behavioral processes and statistical patterns of movement suggests that, beyond movement quantification, statistical physics may prove to be an adequate framework to understand animal behavior across scales from an ecological and evolutionary perspective. Recently developed random search theory has served to critically re-evaluate classic ecological questions on animal foraging. For instance, during the last few years, there has been a growing debate on whether search behavior can include traits that improve success by optimizing random (stochastic) searches. Here, we stress the need to bring together the general encounter problem within foraging theory, as a mean for making progress in the biological understanding of random searching. By sketching the assumptions of optimal foraging theory (OFT) and by summarizing recent results on random search strategies, we pinpoint ways to extend classic OFT, and integrate the study of search strategies and its main results into the more general theory of optimal foraging.

  16. Utilizing mixed methods research in analyzing Iranian researchers’ informarion search behaviour in the Web and presenting current pattern

    Directory of Open Access Journals (Sweden)

    Maryam Asadi

    2015-12-01

    Full Text Available Using mixed methods research design, the current study has analyzed Iranian researchers’ information searching behaviour on the Web.Then based on extracted concepts, the model of their information searching behavior was revealed. . Forty-four participants, including academic staff from universities and research centers were recruited for this study selected by purposive sampling. Data were gathered from questionnairs including ten questions and semi-structured interview. Each participant’s memos were analyzed using grounded theory methods adapted from Strauss & Corbin (1998. Results showed that the main objectives of subjects were doing a research, writing a paper, studying, doing assignments, downloading files and acquiring public information in using Web. The most important of learning about how to search and retrieve information were trial and error and get help from friends among the subjects. Information resources are identified by searching in information resources (e.g. search engines, references in papers, and search in Online database… communications facilities & tools (e.g. contact with colleagues, seminars & workshops, social networking..., and information services (e.g. RSS, Alerting, and SDI. Also, Findings indicated that searching by search engines, reviewing references, searching in online databases, and contact with colleagues and studying last issue of the electronic journals were the most important for searching. The most important strategies were using search engines and scientific tools such as Google Scholar. In addition, utilizing from simple (Quick search method was the most common among subjects. Using of topic, keywords, title of paper were most important of elements for retrieval information. Analysis of interview showed that there were nine stages in researchers’ information searching behaviour: topic selection, initiating search, formulating search query, information retrieval, access to information

  17. Obtention control bars patterns for a BWR using Tabo search; Obtencion de patrones de barras de control para un BWR usando busqueda Tabu

    Energy Technology Data Exchange (ETDEWEB)

    Castillo, A.; Ortiz, J.J.; Alonso, G. [Instituto Nacional de Investigaciones Nucleares, Km. 36.5 Carretera Mexico-Toluca, Ocoyoacac, Estado de Mexico 52045 (Mexico); Morales, L.B. [UNAM, IIMAS, Ciudad Universitaria, D. F. 04510 (Mexico); Valle, E. del [IPN, ESFM, Unidad Profesional ' Adolfo Lopez Mateos' , Col. Lindavista 07738, D. F. (Mexico)]. e-mail: jacm@nuclear.inin.mx

    2004-07-01

    The obtained results when implementing the technique of tabu search, for to optimize patterns of control bars in a BWR type reactor, using the CM-PRESTO code are presented. The patterns of control bars were obtained for the designs of fuel reloads obtained in a previous work, using the same technique. The obtained results correspond to a cycle of 18 months using 112 fresh fuels enriched at the 3.53 of U-235. The used technique of tabu search, prohibits recently visited movements, in the position that correspond to the axial positions of the control bars, additionally the tiempo{sub t}abu matrix is used for to manage a size of variable tabu list and the objective function is punished with the frequency of the forbidden movements. The obtained patterns of control bars improve the longitude of the cycle with regard to the reference values and they complete the restrictions of safety. (Author)

  18. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

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

  19. Evolutionary history of the little fire ant Wasmannia auropunctata before global invasion: inferring dispersal patterns, niche requirements and past and present distribution within its native range.

    Science.gov (United States)

    Chifflet, L; Rodriguero, M S; Calcaterra, L A; Rey, O; Dinghi, P A; Baccaro, F B; Souza, J L P; Follett, P; Confalonieri, V A

    2016-04-01

    The evolutionary history of invasive species within their native range may involve key processes that allow them to colonize new habitats. Therefore, phylogeographic studies of invasive species within their native ranges are useful to understand invasion biology in an evolutionary context. Here we integrated classical and Bayesian phylogeographic methods using mitochondrial and nuclear DNA markers with a palaeodistribution modelling approach, to infer the phylogeographic history of the invasive ant Wasmannia auropunctata across its native distribution in South America. We discuss our results in the context of the recent establishment of this mostly tropical species in the Mediterranean region. Our Bayesian phylogeographic analysis suggests that the common ancestor of the two main clades of W. auropunctata occurred in central Brazil during the Pliocene. Clade A would have differentiated northward and clade B southward, followed by a secondary contact beginning about 380,000 years ago in central South America. There were differences in the most suitable habitats among clades when considering three distinct climatic periods, suggesting that genetic differentiation was accompanied by changes in niche requirements, clade A being a tropical lineage and clade B a subtropical and temperate lineage. Only clade B reached more southern latitudes, with a colder climate than that of northern South America. This is concordant with the adaptation of this originally tropical ant species to temperate climates prior to its successful establishment in the Mediterranean region. This study highlights the usefulness of exploring the evolutionary history of invasive species within their native ranges to better understand biological invasions. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  20. Pro-eating disorder search patterns: the possible influence of celebrity eating disorder stories in the media

    National Research Council Canada - National Science Library

    Lewis, Stephen P; Klauninger, Laura; Marcincinova, Ivana

    2016-01-01

    .... The current study was conducted to examine whether news media stories covering eating disorder disclosures of celebrities corresponded with increases in Internet searches for pro eating disorder material...

  1. Pro-eating disorder search patterns: the possible influence of celebrity eating disorder stories in the media.

    Science.gov (United States)

    Lewis, Stephen P; Klauninger, Laura; Marcincinova, Ivana

    2016-01-01

    Pro eating disorder websites often contain celebrity-focused content (e.g., images) used as thinspiration to engage in unhealthy eating disorder behaviours. The current study was conducted to examine whether news media stories covering eating disorder disclosures of celebrities corresponded with increases in Internet searches for pro eating disorder material. Results indicated that search volumes for pro eating disorder terms spiked in the month immediately following such news coverage but only for particularly high-profile celebrities. Hence, there may be utility in providing recovery-oriented resources within the search results for pro-eating disorder Internet searches and within news stories of this nature.

  2. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

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

  3. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  4. A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

    Science.gov (United States)

    Favre, Patrick; Bapaume, Laure; Bossolini, Eligio; Delorenzi, Mauro; Falquet, Laurent; Reinhardt, Didier

    2014-12-03

    Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic

  5. Identification of volatile and semivolatile compounds in chemical ionization GC-MS using a mass-to-structure (MTS) Search Engine with integral isotope pattern ranking.

    Science.gov (United States)

    Liao, Wenta; Draper, William M

    2013-02-21

    The mass-to-structure or MTS Search Engine is an Access 2010 database containing theoretical molecular mass information for 19,438 compounds assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. This database, which contains no experimental mass spectral data, was developed as an aid to identification of compounds in atmospheric pressure ionization (API)-LC-MS. This paper describes a powerful upgrade to this database, a fully integrated utility for filtering or ranking candidates based on isotope ratios and patterns. The new MTS Search Engine is applied here to the identification of volatile and semivolatile compounds including pesticides, nitrosoamines and other pollutants. Methane and isobutane chemical ionization (CI) GC-MS spectra were obtained from unit mass resolution mass spectrometers to determine MH(+) masses and isotope ratios. Isotopes were measured accurately with errors of Search Engine and details performance testing with over 50 model compounds.

  6. MetaCompose: A Compositional Evolutionary Music Composer

    DEFF Research Database (Denmark)

    Scirea, Marco; Togelius, Julian; Eklund, Peter

    2016-01-01

    This paper describes a compositional, extensible framework for music composition and a user study to systematically evaluate its core components. These components include a graph traversal-based chord sequence generator, a search-based melody generator and a pattern-based accompaniment generator....... An important contribution of this paper is the melody generator which uses a novel evolutionary technique combining FI-2POP and multi-objective optimization. A participant-based evaluation overwhelmingly confirms that all current components of the framework combine effectively to create harmonious, pleasant...

  7. Evolutionary and Ecological Consequences of Interspecific Hybridization in Cladocerans

    NARCIS (Netherlands)

    Schwenk, K.; Spaak, P.

    1995-01-01

    The evolutionary process of interspecific hybridization in cladocerans is reviewed based on ecological and population genetic data. The evolutionary consequences of hybridization, biogeographic patterns and fitness comparisons are analyzed within the conceptual framework of theories on

  8. A Hybrid Chaotic Quantum Evolutionary Algorithm

    DEFF Research Database (Denmark)

    Cai, Y.; Zhang, M.; Cai, H.

    2010-01-01

    A hybrid chaotic quantum evolutionary algorithm is proposed to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm. The proposed algorithm adopts the chaotic initialization method to generate initial population which will form...... and enhance the global search ability. A large number of tests show that the proposed algorithm has higher convergence speed and better optimizing ability than quantum evolutionary algorithm, real-coded quantum evolutionary algorithm and hybrid quantum genetic algorithm. Tests also show that when chaos...... is introduced to quantum evolutionary algorithm, the hybrid chaotic search strategy is superior to the carrier chaotic strategy, and has better comprehensive performance than the chaotic mutation strategy in most of cases. Especially, the proposed algorithm is the only one that has 100% convergence rate in all...

  9. Pro-eating disorder search patterns: the possible influence of celebrity eating disorder stories in the media

    OpenAIRE

    Lewis, Stephen P.; Klauninger, Laura; Marcincinova, Ivana

    2016-01-01

    Pro eating disorder websites often contain celebrity-focused content (e.g., images) used as thinspiration to engage in unhealthy eating disorder behaviours. The current study was conducted to examine whether news media stories covering eating disorder disclosures of celebrities corresponded with increases in Internet searches for pro eating disorder material. Results indicated that search volumes for pro eating disorder terms spiked in the month immediately following such news coverage but on...

  10. Co-evolutionary patterns and diversification of ant-fungus associations in the asexual fungus-farming ant Mycocepurus smithii in Panama.

    Science.gov (United States)

    Kellner, K; Fernández-Marín, H; Ishak, H D; Sen, R; Linksvayer, T A; Mueller, U G

    2013-06-01

    Partner fidelity through vertical symbiont transmission is thought to be the primary mechanism stabilizing cooperation in the mutualism between fungus-farming (attine) ants and their cultivated fungal symbionts. An alternate or additional mechanism could be adaptive partner or symbiont choice mediating horizontal cultivar transmission or de novo domestication of free-living fungi. Using microsatellite genotyping for the attine ant Mycocepurus smithii and ITS rDNA sequencing for fungal cultivars, we provide the first detailed population genetic analysis of local ant-fungus associations to test for the relative importance of vertical vs. horizontal transmission in a single attine species. M. smithii is the only known asexual attine ant, and it is furthermore exceptional because it cultivates a far greater cultivar diversity than any other attine ant. Cultivar switching could permit the ants to re-acquire cultivars after garden loss, to purge inferior cultivars that are locally mal-adapted or that accumulated deleterious mutations under long-term asexuality. Compared to other attine ants, symbiont choice and local adaptation of ant-fungus combinations may play a more important role than partner-fidelity feedback in the co-evolutionary process of M. smithii and its fungal symbionts. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  11. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  12. Evolutionary genomics of Entamoeba

    Science.gov (United States)

    Weedall, Gareth D.; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it. PMID:21288488

  13. Evolutionary theory and teleology.

    Science.gov (United States)

    O'Grady, R T

    1984-04-21

    The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

  14. Neuronal boost to evolutionary dynamics.

    Science.gov (United States)

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

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

  15. Selectionist and evolutionary approaches to brain function: a critical appraisal

    Directory of Open Access Journals (Sweden)

    Chrisantha Thomas Fernando

    2012-04-01

    Full Text Available We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity and variability as the most powerful mechanism in a sparsely occupied search space. Examples of why parallel competitive search with information transfer among the units is efficient are given. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.

  16. Evolutionary developmental psychology

    National Research Council Canada - National Science Library

    King, Ashley C; Bjorklund, David F

    2010-01-01

    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...

  17. PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Pontarotti Pierre

    2009-09-01

    Full Text Available Abstract Background To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted. Results Here, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii the search for user-defined patterns in large phylogenetic trees, iii the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other. Conclusion PhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.

  18. Pattern Recognition-Assisted Infrared Library Searching of the Paint Data Query Database to Enhance Lead Information from Automotive Paint Trace Evidence.

    Science.gov (United States)

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Weakley, Andrew

    2017-03-01

    Multilayered automotive paint fragments, which are one of the most complex materials encountered in the forensic science laboratory, provide crucial links in criminal investigations and prosecutions. To determine the origin of these paint fragments, forensic automotive paint examiners have turned to the paint data query (PDQ) database, which allows the forensic examiner to compare the layer sequence and color, texture, and composition of the sample to paint systems of the original equipment manufacturer (OEM). However, modern automotive paints have a thin color coat and this layer on a microscopic fragment is often too thin to obtain accurate chemical and topcoat color information. A search engine has been developed for the infrared (IR) spectral libraries of the PDQ database in an effort to improve discrimination capability and permit quantification of discrimination power for OEM automotive paint comparisons. The similarity of IR spectra of the corresponding layers of various records for original finishes in the PDQ database often results in poor discrimination using commercial library search algorithms. A pattern recognition approach employing pre-filters and a cross-correlation library search algorithm that performs both a forward and backward search has been used to significantly improve the discrimination of IR spectra in the PDQ database and thus improve the accuracy of the search. This improvement permits inter-comparison of OEM automotive paint layer systems using the IR spectra alone. Such information can serve to quantify the discrimination power of the original automotive paint encountered in casework and further efforts to succinctly communicate trace evidence to the courts.

  19. The Evolving Theory of Evolutionary Radiations.

    Science.gov (United States)

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  1. Searching for globular cluster-like abundance patterns in young massive clusters - II. Results from the Antennae galaxies

    Science.gov (United States)

    Lardo, C.; Cabrera-Ziri, I.; Davies, B.; Bastian, N.

    2017-06-01

    The presence of multiple populations (MPs) with distinctive light element abundances is a widespread phenomenon in clusters older than 6 Gyr. Clusters with masses, luminosities, and sizes comparable to those of ancient globulars are still forming today. None the less, the presence of light element variations has been poorly investigated in such young systems, even if the knowledge of the age at which this phenomenon develops is crucial for theoretical models on MPs. We use J-band integrated spectra of three young (7-40 Myr) clusters in NGC 4038 to look for Al variations indicative of MPs. Assuming that the large majority (≥70 per cent) of stars are characterized by high Al content - as observed in Galactic clusters with comparable mass; we find that none of the studied clusters show significant Al variations. Small Al spreads have been measured in all the six young clusters observed in the near-infrared. While it is unlikely that young clusters only show low Al whereas old ones display different levels of Al variations; this suggests the possibility that MPs are not present at such young ages at least among the high-mass stellar component. Alternatively, the fraction of stars with field-like chemistry could be extremely large, mimicking low Al abundances in the integrated spectrum. Finally, since the near-infrared stellar continuum of young clusters is almost entirely due to luminous red supergiants, we can also speculate that MPs only manifest themselves in low-mass stars due to some evolutionary mechanism.

  2. Erythropoietin improves place learning in fimbria-fornix-transected rats and modifies the search pattern of normal rats

    DEFF Research Database (Denmark)

    Mogensen, Jesper; Miskowiak, Kamilla; Sørensen, Thomas Alrik

    2004-01-01

    -associated impairment. The two sham-operated groups did not differ with respect to the proficiency of task acquisition. But administration of EPO to intact animals caused a significant modification of swim patterns-apparently reflecting a somewhat modified strategy of task solution. It is concluded that systemic...

  3. Azcatl-CRP: An ant colony-based system for searching full power control rod patterns in BWRs

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz, Juan Jose [Dpto. Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Salazar, Edo. de Mexico (Mexico)]. E-mail: jjortiz@nuclear.inin.mx; Requena, Ignacio [Dpto. Ciencias Computacion e I.A. ETSII Informatica, University of Granada, C. Daniel Saucedo Aranda s/n, 18071 Granada (Spain)]. E-mail: requena@decsai.ugr.es

    2006-01-15

    We show a new system named AZCATL-CRP to design full power control rod patterns in BWRs. Azcatl-CRP uses an ant colony system and a reactor core simulator for this purpose. Transition and equilibrium cycles of Laguna Verde Nuclear Power Plant (LVNPP) reactor core in Mexico were used to test Azcatl-CRP. LVNPP has 109 control rods grouped in four sequences and currently uses control cell core (CCC) strategy in its fuel reload design. With CCC method only one sequence is employed for reactivity control at full power operation. Several operation scenarios are considered, including core water flow variation throughout the cycle, target different axial power distributions and Haling conditions. Azcatl-CRP designs control rod patterns (CRP) taking into account safety aspects such as k {sub eff} core value and thermal limits. Axial power distributions are also adjusted to a predetermined power shape.

  4. Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

    Science.gov (United States)

    Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

    2005-01-01

    As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

  5. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  6. Algorithmic Mechanism Design of Evolutionary Computation.

    Science.gov (United States)

    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.

  7. Anxiety: an evolutionary approach.

    Science.gov (United States)

    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.

  8. Evolutionary reconstruction of pattern formation in 98 Dictyostelium species reveals that cell-type specialization by lateral inhibition is a derived trait.

    Science.gov (United States)

    Schilde, Christina; Skiba, Anna; Schaap, Pauline

    2014-01-01

    Multicellularity provides organisms with opportunities for cell-type specialization, but requires novel mechanisms to position correct proportions of different cell types throughout the organism. Dictyostelid social amoebas display an early form of multicellularity, where amoebas aggregate to form fruiting bodies, which contain only spores or up to four additional cell-types. These cell types will form the stalk and support structures for the stalk and spore head. Phylogenetic inference subdivides Dictyostelia into four major groups, with the model organism D. discoideum residing in group 4. In D. discoideum differentiation of its five cell types is dominated by lateral inhibition-type mechanisms that trigger scattered cell differentiation, with tissue patterns being formed by cell sorting. To reconstruct the evolution of pattern formation in Dictyostelia, we used cell-type specific antibodies and promoter-reporter fusion constructs to investigate pattern formation in 98 species that represent all groupings. Our results indicate that in all early diverging Dictyostelia and most members of groups 1-3, cells differentiate into maximally two cell types, prestalk and prespore cells, with pattern formation being dominated by position-dependent transdifferentiation of prespore cells into prestalk cells. In clade 2A, prestalk and stalk cell differentiation are lost and the prespore cells construct an acellular stalk. Group 4 species set aside correct proportions of prestalk and prespore cells early in development, and differentiate into up to three more supporting cell types. Our experiments show that positional transdifferentiation is the ancestral mode of pattern formation in Dictyostelia. The early specification of a prestalk population equal to the number of stalk cells is a derived trait that emerged in group 4 and a few late diverging species in the other groups. Group 4 spore masses are larger than those of other groups and the differentiation of supporting cell

  9. Advanced Modeling System for Optimization of Wind Farm Layout and Wind Turbine Sizing Using a Multi-Level Extended Pattern Search Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    DuPont, Bryony; Cagan, Jonathan; Moriarty, Patrick

    2016-07-01

    This paper presents a system of modeling advances that can be applied in the computational optimization of wind plants. These modeling advances include accurate cost and power modeling, partial wake interaction, and the effects of varying atmospheric stability. To validate the use of this advanced modeling system, it is employed within an Extended Pattern Search (EPS)-Multi-Agent System (MAS) optimization approach for multiple wind scenarios. The wind farm layout optimization problem involves optimizing the position and size of wind turbines such that the aerodynamic effects of upstream turbines are reduced, which increases the effective wind speed and resultant power at each turbine. The EPS-MAS optimization algorithm employs a profit objective, and an overarching search determines individual turbine positions, with a concurrent EPS-MAS determining the optimal hub height and rotor diameter for each turbine. Two wind cases are considered: (1) constant, unidirectional wind, and (2) three discrete wind speeds and varying wind directions, each of which have a probability of occurrence. Results show the advantages of applying the series of advanced models compared to previous application of an EPS with less advanced models to wind farm layout optimization, and imply best practices for computational optimization of wind farms with improved accuracy.

  10. Analysis of NCL Proteins from an Evolutionary Standpoint

    Science.gov (United States)

    Muzaffar, Neda E; Pearce, David A

    2008-01-01

    The Neuronal Ceroid Lipofuscinoses (NCLs) are the most common group of neurodegenerative disorders of childhood. While mutations in eight different genes have been shown to be responsible for these clinically distinct types of NCL, the NCLs share many clinical and pathological similarities. We have conducted an exhaustive Basic Local Alignment Search Tool (BLAST) analysis of the human protein sequences for each of the eight known NCL proteins- CLN1, CLN2, CLN3, CLN5, CLN6, CLN7, CLN8 and CLN10. The number of homologous species per CLN-protein identified by BLAST searches varies depending on the parameters set for the BLAST search. For example, a lower threshold is able to pull up more homologous sequences whereas a higher threshold decreases this number. Nevertheless, the clade confines are consistent despite this variation in BLAST searching parameters. Further phylogenetic analyses on the appearance of NCL proteins through evolution reveals a different time line for the appearance of the CLN-proteins. Moreover, divergence of each protein shows a different pattern, providing important clues on the evolving role of these proteins. We present and review in-depth bioinformatic analysis of the NCL proteins and classify the CLN-proteins into families based on their structures and evolutionary relationships, respectively. Based on these analyses, we have grouped the CLN-proteins into common clades indicating a common evolving pathway within the evolutionary tree of life. CLN2 is grouped in Eubacteria, CLN1 and CLN10 in Viridiplantae, CLN3 in Fungi/ Metazoa, CLN7 in Bilateria and CLN5, CLN6 and CLN8 in Euteleostomi. PMID:19440452

  11. Temporal mortality-colonization dynamic can influence the coexistence and persistence patterns of cooperators and defectors in an evolutionary game model

    Directory of Open Access Journals (Sweden)

    YouHua Chen

    2014-03-01

    Full Text Available In the present report, the coexistence and persistence time patterns of Prisoners' Dilemma game players were explored in 2D spatial grid systems by considering the impacts of the mortality-colonization temporal dynamic specifically. Our results showed that the waiting time for triggering a colonization event could remarkably influence and change the extinction patterns of both cooperators and defectors. Interestingly, a relatively high frequency of stochastic colonization events could promote the persistence of defectors but not cooperators. In contrast, a low frequency of stochastic- or constant-time colonization events could facilitate the persistence of cooperators but not defectors. However, a long waiting time would be detrimental to the survival of both game players and drives them to go extinction in faster rates. At last, it was found that colonization strength played a relatively weak role on influencing the coexistence scenarios of both game players, but should be kept small if the coexistence of game players is needed to maintain. In conclusion, our study provides evidence showing that the temporal trade-off of mortality and colonization activities would influence the evolution of PD game and the persistence of cooperators and defectors.

  12. Sources for Imanishi Kinji's views of sociality and evolutionary ...

    Indian Academy of Sciences (India)

    2007-05-10

    May 10, 2007 ... Prior to the contribution of genetics or the modern evolutionary synthesis (MES) to natural selection theory, social ecologists searched for factors in addition to natural selection that could influence species change. The idea that sociality, not just biology, was important in determining evolutionary outcomes ...

  13. A Fast Evolutionary Metaheuristic for VRP with Time Windows

    NARCIS (Netherlands)

    Bräysy, Olli; Dullaert, Wout

    2003-01-01

    This paper presents a new evolutionary metaheuristic for the vehicle routing problem with time windiows. Ideas on multi-start local search, ejection chains, simulated annealing and evolutionary computation are combined in a heuristic that is both robust and efficient. the proposed method produces

  14. Hardy–Weinberg Equilibrium and the Foundations of Evolutionary ...

    Indian Academy of Sciences (India)

    Srimath

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

  15. Comparing Evolutionary Algorithms on Binary Constraint Satisfaction Problems

    NARCIS (Netherlands)

    Craenen, B.G.W.; Eiben, A.E.; van Hemert, J.I.

    2003-01-01

    Constraint handling is not straightforward in evolutionary algorithms (EAs) since the usual search operators, mutation and recombination, are 'blind' to constraints. Nevertheless, the issue is highly relevant, for many challenging problems involve constraints. Over the last decade, numerous EAs for

  16. Complex evolutionary patterns of two rare human G3P[9] rotavirus strains possessing a feline/canine-like H6 genotype on an AU-1-like genotype constellation.

    Science.gov (United States)

    Wang, Yuan-Hong; Pang, Bei-Bei; Zhou, Xuan; Ghosh, Souvik; Tang, Wei-Feng; Peng, Jin-Song; Hu, Quan; Zhou, Dun-Jin; Kobayashi, Nobumichi

    2013-06-01

    The group A rotavirus (RVA) G3P[9] is a rare VP7-VP4 genotype combination, detected occasionally in humans and cats. Other than the prototype G3P[9] strain, RVA/Human- tc/JPN/AU-l/1982/G3P3[9], the whole genomes of only two human G3P[9] RVA strains and two feline G3P[9] RVA strains have been analyzed so far, revealing complex evolutionary patterns, distinct from that of AU-1. We report here the whole genomic analyses of two human G3P[9] RVA strains, RVA/Human-tc/CHN/L621/2006/G3P[9] and RVA/Human-wt/CHN/E2451/2011/G3P[9], detected in patients with diarrhea in China. Strains L621 and E2451 possessed a H6 NSP5 genotype on an AU-1-like genotype constellation, not reported previously. However, not all the genes of L621 and E2451 were closely related to those of AU-1, or to each other, revealing different evolutionary patterns among the AU-1-like RVAs. The VP7, VP4, VP6 and NSP4 genes of E2451 and L621 were found to cluster together with human G3P[9] RVA strains believed to be of possible feline/canine origin, and feline or raccoon dog RVA strains. The VP1, VP3, NSP2 and NSP5 genes of E2451 and L621 formed distinct clusters in genotypes typically found in feline/canine RVA strains or RVA strains from other host species which are believed to be of feline/canine RVA origin. The VP2 genes of E2451 and L621, and NSP3 gene of L621 clustered among RVA strains from different host species which are believed to have a complete or partial feline/canine RVA origin. The NSP1 genes of E2451 and L621, and NSP3 gene of E2451 clustered with AU-1 and several other strains possessing a complete or partial feline RVA strain BA222-05-like genotype constellation. Taken together, these observations suggest that nearly all the eleven gene segments of G3P[9] RVA strains L621 and E2451 might have originated from feline/canine RVAs, and that reassortments may have occurred among these feline/canine RVA strains, before being transmitted to humans. Copyright © 2013 Elsevier B.V. All rights

  17. Evolutionary molecular medicine.

    Science.gov (United States)

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

    2012-05-01

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

  18. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns.

    Science.gov (United States)

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-04-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes. © 2016 American Society of Plant Biologists. All Rights Reserved.

  19. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns1

    Science.gov (United States)

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-01-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes. PMID:26839128

  20. GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal).

    Science.gov (United States)

    Parreira, Ricardo; Branco, Cristina; Piedade, João; Esteves, Aida

    2012-01-01

    GBV-C is a non-pathogenic virus that is largely dispersed in different human populations. The phylogenetic analysis of the 5'-untranslated region (5'UTR) of the GBV-C genome has led to the segregation of viral strains into six genotypes, but incongruent results are frequently obtained depending on the genome region analyzed. In this report, different phylogenetic approaches and multivariate statistics were combined to disclose evolutionary patterns that contribute to shape GBV-C evolution. The data here presented indicate: (i) that the phylogenetic noise was mostly determined by the size of the analyzed sequence, rather than by its position on the viral genome; (ii) that most genomic segments in the coding sequence seemed to evolve under a similar evolution model, which was different from that which best fits the 5'UTR, with overall large heterogeneity of rate change across the sequence; (iii) that due to saturation of transversions occurring in the 5'UTR at genetic distances GBV-C evolution extensively, this being shown for both reference genomes and NS5B GBV-C sequences amplified from Portuguese residents. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Direct and Evolutionary Approaches for Optimal Receiver Function Inversion

    Science.gov (United States)

    Dugda, Mulugeta Tuji

    Receiver functions are time series obtained by deconvolving vertical component seismograms from radial component seismograms. Receiver functions represent the impulse response of the earth structure beneath a seismic station. Generally, receiver functions consist of a number of seismic phases related to discontinuities in the crust and upper mantle. The relative arrival times of these phases are correlated with the locations of discontinuities as well as the media of seismic wave propagation. The Moho (Mohorovicic discontinuity) is a major interface or discontinuity that separates the crust and the mantle. In this research, automatic techniques to determine the depth of the Moho from the earth's surface (the crustal thickness H) and the ratio of crustal seismic P-wave velocity (Vp) to S-wave velocity (Vs) (kappa= Vp/Vs) were developed. In this dissertation, an optimization problem of inverting receiver functions has been developed to determine crustal parameters and the three associated weights using evolutionary and direct optimization techniques. The first technique developed makes use of the evolutionary Genetic Algorithms (GA) optimization technique. The second technique developed combines the direct Generalized Pattern Search (GPS) and evolutionary Fitness Proportionate Niching (FPN) techniques by employing their strengths. In a previous study, Monte Carlo technique has been utilized for determining variable weights in the H-kappa stacking of receiver functions. Compared to that previously introduced variable weights approach, the current GA and GPS-FPN techniques have tremendous advantages of saving time and these new techniques are suitable for automatic and simultaneous determination of crustal parameters and appropriate weights. The GA implementation provides optimal or near optimal weights necessary in stacking receiver functions as well as optimal H and kappa values simultaneously. Generally, the objective function of the H-kappa stacking problem

  2. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

    Science.gov (United States)

    Edmunds, Richard C.; Su, Baofeng; Balhoff, James P.; Eames, B. Frank; Dahdul, Wasila M.; Lapp, Hilmar; Lundberg, John G.; Vision, Todd J.; Dunham, Rex A.; Mabee, Paula M.; Westerfield, Monte

    2016-01-01

    Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

  3. Evolutionary ecology of virus emergence.

    Science.gov (United States)

    Dennehy, John J

    2017-02-01

    The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

  4. Global Pattern Search at Scale

    Science.gov (United States)

    2015-06-29

    detection algorithms to process the free text. For visualization, the tool displays an interactive web application to the user, featuring a map overlaid...behavior, as well as allow for deep exploration of the raw data while maintaining scalability. B. Utilizing Open-Source Datasets Intelligence analysts are...collect these articles, we set up a collection pipeline to scrape articles from these news outlets’ published RSS feeds using the Python feedparser1

  5. Remembering the evolutionary Freud.

    Science.gov (United States)

    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.

  6. From bioinformatic pattern analysis to evolutionary dynamics

    NARCIS (Netherlands)

    Hogeweg, P.|info:eu-repo/dai/nl/073710725

    Ribonucleïnezuur (RNA) vervult twee verschillende rollen binnen een cel. Enerzijds heeft het molecuul de functie om informatie op te slaan (net zoals desoxyribonucleïnezuur (DNA)), anderzijds dient het als katalysator (op een manier zoals ook eiwit deze rol vervult). Bovendien kan RNA optreden als

  7. Cube search, revisited

    Science.gov (United States)

    Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

    2015-01-01

    Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with “equivalent” 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. PMID:25780063

  8. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 11. Evolutionary Biology Today - The Domain of Evolutionary Biology. Amitabh Joshi. Series Article Volume 7 Issue 11 November 2002 pp 8-17. Fulltext. Click here to view fulltext PDF. Permanent link:

  9. Evolutionary Biology Today

    Indian Academy of Sciences (India)

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

  10. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  11. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  12. Applying evolutionary anthropology

    OpenAIRE

    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 h...

  13. Identification of a Robust Lichen Index for the Deconvolution of Lichen and Rock Mixtures Using Pattern Search Algorithm (case Study: Greenland)

    Science.gov (United States)

    Salehi, S.; Karami, M.; Fensholt, R.

    2016-06-01

    Lichens are the dominant autotrophs of polar and subpolar ecosystems commonly encrust the rock outcrops. Spectral mixing of lichens and bare rock can shift diagnostic spectral features of materials of interest thus leading to misinterpretation and false positives if mapping is done based on perfect spectral matching methodologies. Therefore, the ability to distinguish the lichen coverage from rock and decomposing a mixed pixel into a collection of pure reflectance spectra, can improve the applicability of hyperspectral methods for mineral exploration. The objective of this study is to propose a robust lichen index that can be used to estimate lichen coverage, regardless of the mineral composition of the underlying rocks. The performance of three index structures of ratio, normalized ratio and subtraction have been investigated using synthetic linear mixtures of pure rock and lichen spectra with prescribed mixing ratios. Laboratory spectroscopic data are obtained from lichen covered samples collected from Karrat, Liverpool Land, and Sisimiut regions in Greenland. The spectra are then resampled to Hyperspectral Mapper (HyMAP) resolution, in order to further investigate the functionality of the indices for the airborne platform. In both resolutions, a Pattern Search (PS) algorithm is used to identify the optimal band wavelengths and bandwidths for the lichen index. The results of our band optimization procedure revealed that the ratio between R894-1246 and R1110 explains most of the variability in the hyperspectral data at the original laboratory resolution (R2=0.769). However, the normalized index incorporating R1106-1121 and R904-1251 yields the best results for the HyMAP resolution (R2=0.765).

  14. IDENTIFICATION OF A ROBUST LICHEN INDEX FOR THE DECONVOLUTION OF LICHEN AND ROCK MIXTURES USING PATTERN SEARCH ALGORITHM (CASE STUDY: GREENLAND

    Directory of Open Access Journals (Sweden)

    S. Salehi

    2016-06-01

    Full Text Available Lichens are the dominant autotrophs of polar and subpolar ecosystems commonly encrust the rock outcrops. Spectral mixing of lichens and bare rock can shift diagnostic spectral features of materials of interest thus leading to misinterpretation and false positives if mapping is done based on perfect spectral matching methodologies. Therefore, the ability to distinguish the lichen coverage from rock and decomposing a mixed pixel into a collection of pure reflectance spectra, can improve the applicability of hyperspectral methods for mineral exploration. The objective of this study is to propose a robust lichen index that can be used to estimate lichen coverage, regardless of the mineral composition of the underlying rocks. The performance of three index structures of ratio, normalized ratio and subtraction have been investigated using synthetic linear mixtures of pure rock and lichen spectra with prescribed mixing ratios. Laboratory spectroscopic data are obtained from lichen covered samples collected from Karrat, Liverpool Land, and Sisimiut regions in Greenland. The spectra are then resampled to Hyperspectral Mapper (HyMAP resolution, in order to further investigate the functionality of the indices for the airborne platform. In both resolutions, a Pattern Search (PS algorithm is used to identify the optimal band wavelengths and bandwidths for the lichen index. The results of our band optimization procedure revealed that the ratio between R894-1246 and R1110 explains most of the variability in the hyperspectral data at the original laboratory resolution (R2=0.769. However, the normalized index incorporating R1106-1121 and R904-1251 yields the best results for the HyMAP resolution (R2=0.765.

  15. HYBRID GREY WOLF OPTIMIZATION-PATTERN SEARCH (hGWO-PS OPTIMIZED 2DOF-PID CONTROLLERS FOR LOAD FREQUENCY CONTROL (LFC IN INTERCONNECTED THERMAL POWER PLANTS

    Directory of Open Access Journals (Sweden)

    V Soni

    2016-04-01

    Full Text Available The combination of Grey Wolf Optimization and Pattern Search Technique (hGWO-PS has been introduced to optimize the parameters of two Degree of Freedom Proportional-Integral-Derivative Controller (2DOF-PID for controlling the load frequency in Automatic Generation Control (AGC for interconnected power system. The interconnected two area power system of non-reheat thermal power plants consisting of 2DOF-PID controller in each area has been considered for design and analysis. Firstly, the proposed approach has been implemented in the aforementioned standard test system and thereafter, the robustness of the system consisting 2DOF-PID controller optimized by proposed technique has been estimated using the sensitivity analysis for the same. The robustness of the system consisting of 2DOF-PID controller optimized by proposed scheme is examined by varying the parameters of standard test system, loading conditions during operation, size and location of the disturbances. The performance of the 2DOF-PID controller optimized by proposed approach has also been compared with recently published approaches in the literature. The simulation results show that the proposed hGWOPS optimized 2DOF-PID controller shows far better performance than recently published approaches in the literature in terms of dynamic response. The simulation results also show that system performances hardly change when the operating load condition and system parameters are changed by ±50% from their nominal values, i.e. the proposed controllers are quite robust for a wide range of the system parameters and operating load conditions from their nominal values.

  16. Evidential significance of automotive paint trace evidence using a pattern recognition based infrared library search engine for the Paint Data Query Forensic Database.

    Science.gov (United States)

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Fasasi, Ayuba; Weakley, Andrew

    2016-10-01

    A prototype library search engine has been further developed to search the infrared spectral libraries of the paint data query database to identify the line and model of a vehicle from the clear coat, surfacer-primer, and e-coat layers of an intact paint chip. For this study, search prefilters were developed from 1181 automotive paint systems spanning 3 manufacturers: General Motors, Chrysler, and Ford. The best match between each unknown and the spectra in the hit list generated by the search prefilters was identified using a cross-correlation library search algorithm that performed both a forward and backward search. In the forward search, spectra were divided into intervals and further subdivided into windows (which corresponds to the time lag for the comparison) within those intervals. The top five hits identified in each search window were compiled; a histogram was computed that summarized the frequency of occurrence for each library sample, with the IR spectra most similar to the unknown flagged. The backward search computed the frequency and occurrence of each line and model without regard to the identity of the individual spectra. Only those lines and models with a frequency of occurrence greater than or equal to 20% were included in the final hit list. If there was agreement between the forward and backward search results, the specific line and model common to both hit lists was always the correct assignment. Samples assigned to the same line and model by both searches are always well represented in the library and correlate well on an individual basis to specific library samples. For these samples, one can have confidence in the accuracy of the match. This was not the case for the results obtained using commercial library search algorithms, as the hit quality index scores for the top twenty hits were always greater than 99%. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Evolutionary convergence and biologically embodied cognition

    NARCIS (Netherlands)

    Keijzer, Franciscus

    2017-01-01

    The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in

  18. The Impact of Parametrization on Randomized Search Heuristics

    DEFF Research Database (Denmark)

    Gießen, Christian

    optimization algorithms. We consider the following topics. Escaping local optima using local search. We analyze memetic algorithms, i.e. evolutionary algorithms equipped with a local search after mutation. To this end we consider the (1+1) EA equipped with Standard Local Search (SLS) and Variable-Depth Search...

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

    Science.gov (United States)

    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.

  20. Evolutionary Theorising on Technological Change and Sustainable Development

    NARCIS (Netherlands)

    C.H. Reschke; P. Mulder (Peter); R. Kemp (René)

    2003-01-01

    textabstractThis paper examines the significance of evolutionary theorising on technological change for (technology) policies aiming to move society into a more ecologically sustainable direction. It is argued that fundamental changes in production processes and consumption patterns underpinned by

  1. Evolutionary Models for Simple Biosystems

    Science.gov (United States)

    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.

  2. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Advances of evolutionary computation methods and operators

    CERN Document Server

    Cuevas, Erik; Oliva Navarro, Diego Alberto

    2016-01-01

    The goal of this book is to present advances that discuss alternative Evolutionary Computation (EC) developments and non-conventional operators which have proved to be effective in the solution of several complex problems. The book has been structured so that each chapter can be read independently from the others. The book contains nine chapters with the following themes: 1) Introduction, 2) the Social Spider Optimization (SSO), 3) the States of Matter Search (SMS), 4) the collective animal behavior (CAB) algorithm, 5) the Allostatic Optimization (AO) method, 6) the Locust Search (LS) algorithm, 7) the Adaptive Population with Reduced Evaluations (APRE) method, 8) the multimodal CAB, 9) the constrained SSO method.

  4. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

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

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-19

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

  6. Numerical and Evolutionary Optimization Workshop

    CERN Document Server

    Trujillo, Leonardo; Legrand, Pierrick; Maldonado, Yazmin

    2017-01-01

    This volume comprises a selection of works presented at the Numerical and Evolutionary Optimization (NEO) workshop held in September 2015 in Tijuana, Mexico. The development of powerful search and optimization techniques is of great importance in today’s world that requires researchers and practitioners to tackle a growing number of challenging real-world problems. In particular, there are two well-established and widely known fields that are commonly applied in this area: (i) traditional numerical optimization techniques and (ii) comparatively recent bio-inspired heuristics. Both paradigms have their unique strengths and weaknesses, allowing them to solve some challenging problems while still failing in others. The goal of the NEO workshop series is to bring together people from these and related fields to discuss, compare and merge their complimentary perspectives in order to develop fast and reliable hybrid methods that maximize the strengths and minimize the weaknesses of the underlying paradigms. Throu...

  7. Evaluation of User Interface of DL + Federated Search Engine from the Perspective of M.A / M.S.C Students in Al-Zahra University in order to Provide Federated Search Engines User Interface Pattern

    Directory of Open Access Journals (Sweden)

    Amir Ghaebi

    2014-02-01

    The results showed that the major component from graduate students' perspective is guidance and navigation and searched filter components. Results indicate that more than 50 percent of students the importance of 74 criteria of 96 criteria considered high and very high and, (therefore the majority of the criteria in the study from the viewpoints are acceptable. However, findings also showed that among the four components of this study, the search filter, display and record review, consolidation and guidance is a positive relation, and between the views of different faculties is not significant difference about the importance of criterias and components.

  8. Evolutionary Mechanisms for Loneliness

    Science.gov (United States)

    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

  9. Evolutionary behavioral genetics.

    Science.gov (United States)

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

    2015-04-01

    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.

  10. Marine mammals: evolutionary biology

    National Research Council Canada - National Science Library

    Berta, Annalisa; Sumich, James L; Kovacs, Kit M

    2015-01-01

    The third edition of Marine Mammals: Evolutionary Biology provides a comprehensive and current assessment of the diversity, evolution, and biology of marine mammals, while highlighting the latest tools and techniques for their study...

  11. Evolutionary triangulation: informing genetic association studies with evolutionary evidence.

    Science.gov (United States)

    Huang, Minjun; Graham, Britney E; Zhang, Ge; Harder, Reed; Kodaman, Nuri; Moore, Jason H; Muglia, Louis; Williams, Scott M

    2016-01-01

    Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with

  12. SEARCH and a computational perspective of evolution

    Energy Technology Data Exchange (ETDEWEB)

    Kargupta, H.

    1996-05-01

    This paper develops an alternate perspective of natural evolution using the SEARCH (Search Envisioned As Relation and Class Hierarchizing) framework (Kargupta, 1995). Some problems of existing views about evolutionary computation are noted. An attempt is made to fulfill these deficiencies using a new computational perspective of gene expression based on a decomposition of blackbox optimization in terms of relations, classes, samples, and partial ordering.

  13. An Evolutionary Psychology Approach to Consumer Choice

    Directory of Open Access Journals (Sweden)

    ZURINA BT MOHAIDIN

    2013-07-01

    Full Text Available Human behaviour can be explained not only through experience and environments but also by incorporating evolutionary explanation. Consumer behaviour could not be understood accurately without infusing Darwinian evolutionary theory which has contributed in the knowledge of human nature. Evolutionary psychology revolves around the human’s evolved mental and the impact on human’s traits and behaviour where the influence of the environment to our genes would determine our individual behaviour and traits, resulting in variation among us. Foraging which is a part of behavioural ecology involves many sequences or repetitions of animals’ activities and decision making which is useful to relate these patterns of activities to the decisions made in human consumption. The aim of this research is to investigate the similarities of human consumption and ecological behaviour by employing interpretative and comparative approach. It is hoped that by applying the evolutionary theory in explaining consumer choice, this study is able to contribute to the development of behavioural ecology in human consumption. The analysis of the data is done aggregately for 200 consumers and individually for 20 consumers, who have purchased four product categories over a year. This study concludes that the theories of evolutionary psychology can fit to the consumers’ buying behaviour implicating its usefulness in explaining the consumers’ choice.

  14. Proteomics in evolutionary ecology.

    Science.gov (United States)

    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

  15. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

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

  16. Evolutionary synthetic biology.

    Science.gov (United States)

    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.

  17. Total Integrative Evolutionary Communication

    DEFF Research Database (Denmark)

    Nedergaard Thomsen, Ole; Brier, Søren

    2014-01-01

    In this paper we outline a cybersemiotic foundation for the trend of pragmatics-based functional linguistics, Functional Discourse Grammar. Cybersemiotics is a substantial inter- and transdisciplinary semiotic theory which integrates, on the one hand, second-order cybernetics and autopoiesis theory...... and, on the other, Peircean biosemiotics. According to Cybersemiotics, language is primarily a creative process of total integrative evolutionary communication. It comprises three evolutionary stages: (1) biological reflexive languaging (the reflexive foundation of social coordination), (2......). In this inclusive hierarchy language games subsume the other stages, and thus human evolutionary communication is primarily a symbolic-conventional practice. It is intertwined with the practice of living, that is, with different life forms, including other forms of semiotic behavior. Together they form a coherent...

  18. Teaching evolutionary biology

    Directory of Open Access Journals (Sweden)

    Rosana Tidon

    2004-01-01

    Full Text Available Evolutionary Biology integrates several disciplines of Biology in a complex and interactive manner, where a deep understanding of the subject demands knowledge in diverse areas. Since this knowledge is often inaccessible to the majority of specialized professionals, including the teachers, we present some reflections in order to stimulate discussions aimed at the improvement of the conditions of education in this area. We examine the profile of evolutionary teaching in Brazil, based on questionnaires distributed to teachers in Secondary Education in the Federal District, on data provided by the "National Institute for Educational Studies and Research", and on information collected from teachers working in various regions of this country. Issues related to biological misconceptions, curriculum and didactic material are discussed, and some proposals are presented with the objective of aiding discussions aimed at the improvement of the teaching of evolutionary biology.

  19. Evolutionary Design in Art

    Science.gov (United States)

    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.

  20. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  1. Comparing Usage Patterns Recorded between an Electronic Reference and an Electronic Monograph Collection: The Differences in Searches and Full-Text Content Viewings

    Science.gov (United States)

    Lamothe, Alain R.

    2012-01-01

    This paper presents the results from a quantitative and systematic analysis comparing the online usage of an e-reference and an e-monograph collection. A very strong relationship exists between size and usage: the larger the collection, the greater the usage. An equally strong relationship exists between searches and viewings, meaning that the…

  2. Piaget, Pedagogy, and Evolutionary Psychology

    Directory of Open Access Journals (Sweden)

    Jeremy E. C. Genovese

    2003-01-01

    Full Text Available Constructivist pedagogy draws on Piaget's developmental theory. Because Piaget depicted the emergence of formal reasoning skills in adolescence as part of the normal developmental pattern, many constructivists have assumed that intrinsic motivation is possible for all academic tasks. This paper argues that Piaget's concept of a formal operational stage has not been empirically verified and that the cognitive skills associated with that stage are in fact “biologically secondary abilities” (Geary and Bjorklund, 2000 culturally determined abilities that are difficult to acquire. Thus, it is unreasonable to expect that intrinsic motivation will suffice for most students for most higher level academic tasks. In addition, a case is made that educational psychology must incorporate the insights of evolutionary psychology.

  3. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    Science.gov (United States)

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

    2015-01-01

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

  4. When development matters: From evolutionary psychology to evolutionary developmental psychology

    OpenAIRE

    Hernández Blasi, Carlos; Gardiner, Amy K.; Bjorklund, David F.

    2008-01-01

    This article presents evolutionary developmental psychology (EDP) as an emerging field of evolutionary psychology (EP). In describing the core tenets of both approaches and the differences between them, we emphasize the important roles that evolution and development have in understanding human behaviour. We suggest that developmental psychologists should pay more attention to evolutionary issues and, conversely, evolutionary psychologists should take development seriously. Key words: evol...

  5. Personalized Search

    CERN Document Server

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  6. Social Search: A Taxonomy of, and a User-Centred Approach to, Social Web Search

    Science.gov (United States)

    McDonnell, Michael; Shiri, Ali

    2011-01-01

    Purpose: The purpose of this paper is to introduce the notion of social search as a new concept, drawing upon the patterns of web search behaviour. It aims to: define social search; present a taxonomy of social search; and propose a user-centred social search method. Design/methodology/approach: A mixed method approach was adopted to investigate…

  7. Cenozoic climate change influences mammalian evolutionary dynamics

    OpenAIRE

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

    2011-01-01

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

  8. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... I define an evolutionary transition as a shift in the hierarchical level at which heritable fitness variance ... life, for example in eusocial insects, around 150 million years ago. None of these transformations was ...... affecting and heritable trait, and to introduce a mechanism which inhibits them from subsequent ...

  9. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    IAS Admin

    After Maynard-Smith and Price [1] mathematically derived why a given behaviour or strategy was adopted by a certain proportion of the population at a given time, it was shown that a strategy which is currently stable in a population need not be stable in evolutionary time (across generations). Additionally it was sug-.

  10. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  11. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...

  12. Origins of evolutionary transitions.

    Science.gov (United States)

    Clarke, Ellen

    2014-04-01

    An 'evolutionary transition in individuality' or 'major transition' is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started.

  13. Learning: An Evolutionary Analysis

    Science.gov (United States)

    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…

  14. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

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

    2016-01-01

    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

  15. Editorial overview: Evolutionary psychology

    NARCIS (Netherlands)

    Gangestad, S.W.; Tybur, J.M.

    2016-01-01

    Functional approaches in psychology - which ask what behavior is good for - are almost as old as scientific psychology itself. Yet sophisticated, generative functional theories were not possible until developments in evolutionary biology in the mid-20th century. Arising in the last three decades,

  16. Evolutionary Developmental Psychology.

    Science.gov (United States)

    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. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    An `evolutionary transition in individuality' or `major transition' is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can ...

  18. Evolutionary Theory under Fire.

    Science.gov (United States)

    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)

  19. Evolutionary developmental psychology.

    Science.gov (United States)

    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.

  20. Evolutionary Theories of Detection

    Energy Technology Data Exchange (ETDEWEB)

    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. Automated Antenna Design with Evolutionary Algorithms

    Science.gov (United States)

    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

  2. Visual search

    NARCIS (Netherlands)

    Toet, A.; Bijl, P.

    2003-01-01

    Visual search, with or without the aid of optical or electro-optical instruments, plays a significant role in various types of military and civilian operations (e.g., reconnaissance, surveillance, and search and rescue). Advance knowledge of human visual search and target acquisition performance is

  3. Turbopump Performance Improved by Evolutionary Algorithms

    Science.gov (United States)

    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.

  4. MELEC: Meta-Level Evolutionary Composer

    Directory of Open Access Journals (Sweden)

    Andres Calvo

    2011-02-01

    Full Text Available Genetic algorithms (GA’s are global search mechanisms that have been applied to many disciplines including music composition. Computer system MELEC composes music using evolutionary computation on two levels: the object and the meta. At the object-level, MELEC employs GAs to compose melodic motifs and iteratively refine them through evolving generations. At the meta-level, MELEC forms the overall musical structure by concatenating the generated motifs in an order that depends on the evolutionary process. In other words, the structure of the music is determined by a geneological traversal of the algorithm’s execution sequence. In this implementation, we introduce a new data structure that tracks the execution of the GA, the Genetic Algorithm Traversal Tree, and uses its traversal to define the musical structure. Moreover, we employ a Fibonacci-based fitness function to shape the melodic evolution.

  5. Evolutionary computation techniques a comparative perspective

    CERN Document Server

    Cuevas, Erik; Oliva, Diego

    2017-01-01

    This book compares the performance of various evolutionary computation (EC) techniques when they are faced with complex optimization problems extracted from different engineering domains. Particularly focusing on recently developed algorithms, it is designed so that each chapter can be read independently. Several comparisons among EC techniques have been reported in the literature, however, they all suffer from one limitation: their conclusions are based on the performance of popular evolutionary approaches over a set of synthetic functions with exact solutions and well-known behaviors, without considering the application context or including recent developments. In each chapter, a complex engineering optimization problem is posed, and then a particular EC technique is presented as the best choice, according to its search characteristics. Lastly, a set of experiments is conducted in order to compare its performance to other popular EC methods.

  6. Evolutionary Thinking in Environmental Economics

    NARCIS (Netherlands)

    van den Bergh, J.C.J.M.

    2007-01-01

    Evolutionary and environmental economics have a potentially close relationship. This paper reviews past and identifies potential applications of evolutionary concepts and methods to environmental economics. This covers a number of themes: resource use and ecosystem management; growth and

  7. The evolutionary ecology of the Lygaeidae

    Science.gov (United States)

    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. [Charles Darwin and the problem of evolutionary progress].

    Science.gov (United States)

    Iordanskiĭ, N N

    2010-01-01

    According to Ch. Darwin's evolutionary theory, evolutionary progress (interpreted as morpho-physiological progress or arogenesis in recent terminology) is one of logical results of natural selection. At the same time, natural selection does not hold any factors especially promoting evolutionary progress. Darwin emphasized that the pattern of evolutionary changes depends on organism nature more than on the pattern of environment changes. Arogenesis specificity is determined by organization of rigorous biological systems - integral organisms. Onward progressive development is determined by fundamental features of living organisms: metabolism and homeostasis. The concept of social Darwinism differs fundamentally from Darwin's ideas about the most important role of social instincts in progress of mankind. Competition and selection play secondary role in socio-cultural progress of human society.

  9. A Fast Evolutionary Metaheuristic for the Vehicle Routing Problem with Time Windows

    NARCIS (Netherlands)

    Bräysy, Olli; Dullaert, W.

    2003-01-01

    This paper presents a new evolutionary metaheuristic for the vehicle routing problem with time windows. Ideas on multi-start local search, ejection chains, simulated annealing and evolutionary computation are combined in a heuristic that is both robust and efficient. The proposed method produces

  10. Evolutionary Psychology and Intelligence Research Cannot Be Integrated the Way Kanazawa (2010) Suggested

    Science.gov (United States)

    Penke, Lars; Borsboom, Denny; Johnson, Wendy; Kievit, Rogier A.; Ploeger, Annemie; Wicherts, Jelte M.

    2011-01-01

    This article shares the authors' comments on a record by Kanazawa. Evolutionary psychologists search for human universals, differential psychologists for variation around common human themes. So far, evolutionary psychology and differential psychology seem somewhat disparate and unconnected, although Kanazawa is certainly not the first to attempt…

  11. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America.

    Science.gov (United States)

    Marcellini, Sylvain; González, Favio; Sarrazin, Andres F; Pabón-Mora, Natalia; Benítez, Mariana; Piñeyro-Nelson, Alma; Rezende, Gustavo L; Maldonado, Ernesto; Schneider, Patricia Neiva; Grizante, Mariana B; Da Fonseca, Rodrigo Nunes; Vergara-Silva, Francisco; Suaza-Gaviria, Vanessa; Zumajo-Cardona, Cecilia; Zattara, Eduardo E; Casasa, Sofia; Suárez-Baron, Harold; Brown, Federico D

    2017-01-01

    Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community. © 2016 Wiley Periodicals, Inc.

  12. Exploiting Lagrangian coherent structures (LCS) for the calculation of oil spill and search-and-rescue drift patterns in the ocean

    Energy Technology Data Exchange (ETDEWEB)

    Beegle-Krause, CJ [Environmental Research for Decision, Inc (United States)], email: cjbk@research4d.org; Peacock, Thomas; Allshouse, Michael [Massachusetts Institute of Technology (United States)

    2011-07-01

    This study emphasizes the benefits of using the Lagrangian Coherent Structure (LCS) approach in predicting oil spill flow patterns. The goal of this study is to show the importance of such numerical model in revealing how particles in an unsteady flow move, and how this can be applied in predicting the trajectory of oil particles in water when there is an oil spill. A particular case of vortex behavior, the double gyre, was incorporated into the LCS method to generate the skeleton of a flow in complex forward and backward time-dependent fields. This model was used later on to simulate the oil spill flow pattern of the MC 252 incident from May 24 to May 26, 2010. Results were then compared to the actual patterns. It was affirmed that forward-time calculations predict regions with intense changes beforehand, whereas backward-time calculations reveal the accordance between LCS and ultimate particle cluster.

  13. Solution of optimal power flow using evolutionary-based algorithms

    African Journals Online (AJOL)

    Due to the drawbacks in classical methods, the artificial intelligence (AI) techniques have been introduced to solve the OPF problem. The AI-based optimization has become an important approach for determining the global optimal solution. One of the most important intelligent search techniques is called evolutionary ...

  14. Adaptive radiations, ecological specialization, and the evolutionary integration of complex morphological structures.

    Science.gov (United States)

    Monteiro, Leandro R; Nogueira, Marcelo R

    2010-03-01

    The evolutionary integration of complex morphological structures is a macroevolutionary pattern in which morphogenetic components evolve in a coordinated fashion, which can result from the interplay among processes of developmental, genetic integration, and different types of selection. We tested hypotheses of ecological versus developmental factors underlying patterns of within-species and evolutionary integration in the mandible of phyllostomid bats, during the most impressive ecological and morphological radiation among mammals. Shape variation of mandibular morphogenetic components was associated with diet, and the transition of integration patterns from developmental to within-species to evolutionary was examined. Within-species (as a proxy to genetic) integration in different lineages resembled developmental integration regardless of diet specialization, however, evolutionary integration patterns reflected selection in different mandibular components. For dietary specializations requiring extensive functional changes in mastication patterns or biting, such as frugivores and sanguivores, the evolutionary integration pattern was not associated with expected within-species or developmental integration. On the other hand, specializations with lower mastication demands or without major functional reorganization (such as nectarivores and carnivores), presented evolutionary integration patterns similar to the expected developmental pattern. These results show that evolutionary integration patterns are largely a result of independent selection on specific components regardless of developmental modules.

  15. Are hotspots of evolutionary potential adequately protected in southern California?

    Science.gov (United States)

    Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

    2008-01-01

    Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

  16. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    Darwinian evolution by natural selection is driven primarily by differential survival and reproduction among individuals in a population. When the evolutionary interest of an individual is in conflict with the interests of the population, the genes increasing individual fitness at the cost...... performance are not in conflict, it is unlikely that plant breeding can radically improve the results of millions of years of evolution through natural selection. However, efforts to improve crops can be very successful, when breeding is directed towards goals diverging from natural selection. The potential...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  17. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

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

  18. Heuristic Search Theory and Applications

    CERN Document Server

    Edelkamp, Stefan

    2011-01-01

    Search has been vital to artificial intelligence from the very beginning as a core technique in problem solving. The authors present a thorough overview of heuristic search with a balance of discussion between theoretical analysis and efficient implementation and application to real-world problems. Current developments in search such as pattern databases and search with efficient use of external memory and parallel processing units on main boards and graphics cards are detailed. Heuristic search as a problem solving tool is demonstrated in applications for puzzle solving, game playing, constra

  19. Anxiety: an evolutionary approach.

    OpenAIRE

    Bateson, M; Brilot, B; Nettle, D.

    2011-01-01

    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 ...

  20. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

    Full Text Available Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  1. Evolutionary mysteries in meiosis.

    Science.gov (United States)

    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'. © 2016 The Author(s).

  2. Asymmetric Evolutionary Games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-08-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  3. Faceted Search

    CERN Document Server

    Tunkelang, Daniel

    2009-01-01

    We live in an information age that requires us, more than ever, to represent, access, and use information. Over the last several decades, we have developed a modern science and technology for information retrieval, relentlessly pursuing the vision of a "memex" that Vannevar Bush proposed in his seminal article, "As We May Think." Faceted search plays a key role in this program. Faceted search addresses weaknesses of conventional search approaches and has emerged as a foundation for interactive information retrieval. User studies demonstrate that faceted search provides more

  4. Beyond the search process

    DEFF Research Database (Denmark)

    Hyldegård, Jette

    2009-01-01

    This paper reports on the findings from a longitudinal case study exploring Kuhlthau's information search process (ISP)-model in a group based academic setting. The research focus is on group members' activities and cognitive and emotional experiences during the task process of writing an assignm......This paper reports on the findings from a longitudinal case study exploring Kuhlthau's information search process (ISP)-model in a group based academic setting. The research focus is on group members' activities and cognitive and emotional experiences during the task process of writing...... seeking, the cognitive pattern associated with focus formulation and the tendency towards an increase in writing activities while searching activities decreased. Differences in behavior were also found, which were associated with contextual and social factors beyond the mere search process...

  5. The Development of Expertise in Radiology: In Chest Radiograph Interpretation, "Expert" Search Pattern May Predate "Expert" Levels of Diagnostic Accuracy for Pneumothorax Identification.

    Science.gov (United States)

    Kelly, Brendan S; Rainford, Louise A; Darcy, Sarah P; Kavanagh, Eoin C; Toomey, Rachel J

    2016-07-01

    Purpose To investigate the development of chest radiograph interpretation skill through medical training by measuring both diagnostic accuracy and eye movements during visual search. Materials and Methods An institutional exemption from full ethical review was granted for the study. Five consultant radiologists were deemed the reference expert group, and four radiology registrars, five senior house officers (SHOs), and six interns formed four clinician groups. Participants were shown 30 chest radiographs, 14 of which had a pneumothorax, and were asked to give their level of confidence as to whether a pneumothorax was present. Receiver operating characteristic (ROC) curve analysis was carried out on diagnostic decisions. Eye movements were recorded with a Tobii TX300 (Tobii Technology, Stockholm, Sweden) eye tracker. Four eye-tracking metrics were analyzed. Variables were compared to identify any differences between groups. All data were compared by using the Friedman nonparametric method. Results The average area under the ROC curve for the groups increased with experience (0.947 for consultants, 0.792 for registrars, 0.693 for SHOs, and 0.659 for interns; P = .009). A significant difference in diagnostic accuracy was found between consultants and registrars (P = .046). All four eye-tracking metrics decreased with experience, and there were significant differences between registrars and SHOs. Total reading time decreased with experience; it was significantly lower for registrars compared with SHOs (P = .046) and for SHOs compared with interns (P = .025). Conclusion Chest radiograph interpretation skill increased with experience, both in terms of diagnostic accuracy and visual search. The observed level of experience at which there was a significant difference was higher for diagnostic accuracy than for eye-tracking metrics. (©) RSNA, 2016 Online supplemental material is available for this article.

  6. Stride lengths, speed and energy costs in walking of Australopithecus afarensis: using evolutionary robotics to predict locomotion of early human ancestors

    OpenAIRE

    Sellers, William I; Cain, Gemma M; Wang, Weijie; Crompton, Robin H

    2005-01-01

    This paper uses techniques from evolutionary robotics to predict the most energy-efficient upright walking gait for the early human relative Australopithecus afarensis, based on the proportions of the 3.2 million year old AL 288-1 ‘Lucy’ skeleton, and matches predictions against the nearly contemporaneous (3.5–3.6 million year old) Laetoli fossil footprint trails. The technique creates gaits de novo and uses genetic algorithm optimization to search for the most efficient patterns of simulated...

  7. Analysis of the uniform augmentation of the flow through the nucleus in the searching process of the patterns of objective control bars in a BWR; Analisis del aumento uniforme del caudal a traves del nucleo en el proceso de busqueda de los patrones de barras de control objetivo en un BWR

    Energy Technology Data Exchange (ETDEWEB)

    Montes, J.L.; Ortiz, J.J.; Perusquia, R. [ININ, Carretera Mexico-Toluca Km. 36.5, 52045 Estado de Mexico (Mexico)]. e-mail: jlmt@nuclear.inin.mx

    2004-07-01

    The search of the patterns of control bars (PBCs) in a power reactor of boiling water, requires to investigate a very wide space of solutions, in principle they are had of the order of 3 x 10{sup 152} possible configurations to establish the PBC in a point given before reaching the end of the cycle. This situation suggests to define those restrictions and conditions initial appropriately so that the search converges toward the desirable results. Presently work the results of the search of patterns of bars based on different flow scenarios through the nucleus are presented. The Cycle 10 is analysed (C10) of the Unit One of the Nuclear Power station Laguna Verde (CNLV), which presents an interesting mixture of diverse designs of control bars used in operation to power. The search of the patterns of bars of objective control is carried out applying the GACRP program which is based on the calculation technique known as genetic algorithms. (Author)

  8. Evolutionary Cost-Sensitive Extreme Learning Machine.

    Science.gov (United States)

    Zhang, Lei; Zhang, David

    2017-12-01

    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.

  9. Towards an evolutionary model of transcription networks.

    Directory of Open Access Journals (Sweden)

    Dan Xie

    2011-06-01

    Full Text Available DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs, we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates.

  10. Advanced Search

    African Journals Online (AJOL)

    Items 151 - 200 of 500 ... Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more ...

  11. Search Results

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  12. Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  13. How does resource supply affect evolutionary diversification?

    Science.gov (United States)

    Hall, Alex R; Colegrave, Nick

    2006-01-01

    The availability of different resources in the environment can affect the outcomes of evolutionary diversification. A unimodal distribution of diversity with resource supply has been widely observed and explained previously in the context of selection acting in a spatially heterogeneous environment. Here, we propose an alternative mechanism to explain the relationship between resource supply and diversification that is based on selection for exploitation of different resources. To test this mechanism, we conducted a selection experiment using the bacterium Pseudomonas fluorescens in spatially homogeneous environments over a wide range of resource supply rates. Our results show that niche diversification peaks at intermediate levels of resource availability. We suggest that this unimodal relationship is due to evolutionary diversification that is driven by competition for resources but constrained by the ecological opportunity represented by different resource types. These processes may underlie some general patterns of diversity, including latitudinal gradients in species richness and the effects of anthropogenic enrichment of the environment. PMID:17015335

  14. Evolutionary Theory's Increasing Role in Personality and Social Psychology

    Directory of Open Access Journals (Sweden)

    Gregory D. Webster

    2007-01-01

    Full Text Available Has the emergence of evolutionary psychology had an increasing impact on personality and social psychological research published over the past two decades? If so, is its growing influence substantially different from that of other emerging psychological areas? These questions were addressed in the present study by conducting a content analysis of the Journal of Personality and Social Psychology (JPSP from 1985 to 2004 using the PsycINFO online abstract database. Specifically, keyword searches for “evol*” or “Darwin*” revealed that the percentage of JPSP articles drawing on evolutionary theory was modest, but increased significantly between 1985 and 2004. To compare the growing impact of evolutionary psychology with other psychological areas, similar keywords searches were performed in JPSP for emotion and motivation, judgment and decision making, neuroscience and psychophysiology, stereotyping and prejudice, and terror management theory. The increase in evolutionary theory in JPSP over time was practically equal to the mean increase over time for the other five areas. Thus, evolutionary psychology has played an increasing role in shaping personality and social psychological research over the past 20 years, and is growing at a rate consistent with other emerging psychological areas.

  15. Comparative genomics and evolutionary biology.

    Science.gov (United States)

    Kondrashov, A S

    1999-12-01

    Data of large-scale DNA sequencing are relevant to some of the most fundamental issues in evolutionary biology: suboptimality, homology, hierarchy, ancestry, novelties, the role of natural selection, and the relative importance of directional versus stabilizing selection. Already, these data provided the best available evidence for some evolutionary phenomena, and in several cases led to refinement of old concepts. Still, the Darwinian evolutionary paradigm will successfully accommodate comparative genomics.

  16. Evolutionary status of Polaris

    Science.gov (United States)

    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.

  17. Cenozoic climate change influences mammalian evolutionary dynamics.

    Science.gov (United States)

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

    2012-01-17

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

  18. Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses

    Directory of Open Access Journals (Sweden)

    Sorribas Albert

    2009-11-01

    Full Text Available Abstract Background Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investigating the evolution of metabolic adaptation to environmental changes. Although biological systems have evolved by natural selection and result in well-adapted systems, we can hardly expect that actual metabolic processes are at the theoretical optimum that could result from an optimization analysis. More likely, natural systems are to be found in a feasible region compatible with global physiological requirements. Results We first present a new method for globally optimizing nonlinear models of metabolic pathways that are based on the Generalized Mass Action (GMA representation. The optimization task is posed as a nonconvex nonlinear programming (NLP problem that is solved by an outer-approximation algorithm. This method relies on solving iteratively reduced NLP slave subproblems and mixed-integer linear programming (MILP master problems that provide valid upper and lower bounds, respectively, on the global solution to the original NLP. The capabilities of this method are illustrated through its application to the anaerobic fermentation pathway in Saccharomyces cerevisiae. We next introduce a method to identify the feasibility parametric regions that allow a system to meet a set of physiological constraints that can be represented in mathematical terms through algebraic equations. This technique is based on applying the outer-approximation based algorithm iteratively over a reduced search space in order to identify regions that contain feasible solutions to the problem and discard others in which no feasible solution exists. As an example, we characterize the feasible enzyme activity changes that are compatible with an appropriate adaptive response of yeast Saccharomyces cerevisiae to heat shock Conclusion Our results

  19. Evolutionary dynamics under interactive diversity

    Science.gov (United States)

    Su, Qi; Li, Aming; Wang, Long

    2017-10-01

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

  20. Human adoption in evolutionary perspective.

    Science.gov (United States)

    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.

  1. Evolutionary advantages of adaptive rewarding

    Science.gov (United States)

    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.

  2. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    driven towards diversity (instead of optimality). Extinctions amplify diversity-generation by creating unpredictable evolutionary bottlenecks. Persisting through multiple such bottlenecks is more likely for lineages that diversify across many niches, resulting in indirect selection pressure...... events may provide a simple and effective mechanism to enhance performance of divergent search algorithms....

  3. Autonomous search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Autonomous combinatorial search (AS) represents a new field in combinatorial problem solving. Its major standpoint and originality is that it considers that problem solvers must be capable of self-improvement operations. This is the first book dedicated to AS.

  4. Evolutionary explanations for natural language: criteria from evolutionary biology

    NARCIS (Netherlands)

    Zuidema, W.; de Boer, B.

    2008-01-01

    Theories of the evolutionary origins of language must be informed by empirical and theoretical results from a variety of different fields. Complementing recent surveys of relevant work from linguistics, animal behaviour and genetics, this paper surveys the requirements on evolutionary scenarios that

  5. Evolutionary origins of hepatitis A virus in small mammals

    Science.gov (United States)

    Drexler, Jan Felix; Corman, Victor M.; Lukashev, Alexander N.; van den Brand, Judith M. A.; Gmyl, Anatoly P.; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M.; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G.; Lemon, Stanley M.; Drosten, Christian

    2015-01-01

    Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3Dpol sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses. PMID:26575627

  6. Evolutionary origins of hepatitis A virus in small mammals.

    Science.gov (United States)

    Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

    2015-12-08

    Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

  7. Evolutionary Perspective on Collective Decision Making

    Science.gov (United States)

    Farrell, Dene; Sayama, Hiroki; Dionne, Shelley D.; Yammarino, Francis J.; Wilson, David Sloan

    Team decision making dynamics are investigated from a novel perspective by shifting agency from decision makers to representations of potential solutions. We provide a new way to navigate social dynamics of collective decision making by interpreting decision makers as constituents of an evolutionary environment of an ecology of evolving solutions. We demonstrate distinct patterns of evolution with respect to three forms of variation: (1) Results with random variations in utility functions of individuals indicate that groups demonstrating minimal internal variation produce higher true utility values of group solutions and display better convergence; (2) analysis of variations in behavioral patterns within a group shows that a proper balance between selective and creative evolutionary forces is crucial to producing adaptive solutions; and (3) biased variations of the utility functions diminish the range of variation for potential solution utility, leaving only the differential of convergence performance static. We generally find that group cohesion (low random variation within a group) and composition (appropriate variation of behavioral patterns within a group) are necessary for a successful navigation of the solution space, but performance in both cases is susceptible to group level biases.

  8. Evolutionary contingency and SETI revisited

    Science.gov (United States)

    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.

  9. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    Resonance – Journal of Science Education. Current Issue : Vol. 23, Issue 2. Current Issue Volume 23 | Issue 2. February 2018. Home · Volumes & Issues · Categories · Special Issues · Search · Editorial Board · Information for Authors · Subscription ...

  10. Intelligence's likelihood and evolutionary time frame

    Science.gov (United States)

    Bogonovich, Marc

    2011-04-01

    This paper outlines hypotheses relevant to the evolution of intelligent life and encephalization in the Phanerozoic. If general principles are inferable from patterns of Earth life, implications could be drawn for astrobiology. Many of the outlined hypotheses, relevant data, and associated evolutionary and ecological theory are not frequently cited in astrobiological journals. Thus opportunity exists to evaluate reviewed hypotheses with an astrobiological perspective. A quantitative method is presented for testing one of the reviewed hypotheses (hypothesis i; the diffusion hypothesis). Questions are presented throughout, which illustrate that the question of intelligent life's likelihood can be expressed as multiple, broadly ranging, more tractable questions.

  11. Information theory, evolutionary innovations and evolvability.

    Science.gov (United States)

    Wagner, Andreas

    2017-12-05

    How difficult is it to 'discover' an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of 'progress' in Darwinian evolution.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

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

    Science.gov (United States)

    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. Diabetes and Obesity—An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Sylvia Kirchengast

    2017-01-01

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

  14. An evolutionary developmental approach to cultural evolution.

    Science.gov (United States)

    Andersson, Claes; Törnberg, Anton; Törnberg, Petter

    2014-04-01

    Evolutionary developmental theories in biology see the processes and organization of organisms as crucial for understanding the dynamic behavior of organic evolution. Darwinian forces are seen as necessary but not sufficient for explaining observed evolutionary patterns. We here propose that the same arguments apply with even greater force to culture vis-à-vis cultural evolution. In order not to argue entirely in the abstract, we demonstrate the proposed approach by combining a set of different models into a provisional synthetic theory and by applying this theory to a number of short case studies. What emerges is a set of concepts and models that allow us to consider entirely new types of explanations for the evolution of cultures. For example, we see how feedback relations--both within societies and between societies and their ecological environment--have the power to shape evolutionary history in profound ways. The ambition here is not to produce a definitive statement on what such a theory should look like but rather to propose a starting point along with an argumentation and demonstration of its potential.

  15. Evolutionary games on multilayer networks: a colloquium

    Science.gov (United States)

    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.

  16. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... living in the future could occur, if built spaces could evolve and adapt alongside inhabitants. As such, present study explores the interdisciplinary possibilities in utilizing computational power to co-create with users and generate designs based on human input. We argue that this could lead...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  17. Topics of Evolutionary Computation 2001

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem......This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem...

  18. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

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

    2016-01-01

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

  19. Conceptual foundations of evolutionary thought

    Indian Academy of Sciences (India)

    K. P. MOHANAN

    2017-07-04

    Jul 4, 2017 ... This article seeks to explore the conceptual foundations of evolutionary thought in the physical, biological, and human sciences. Viewing evolution as symmetry breaking, it explores the concepts of change, history, and evolutionary history, and outlines a concept of biological macroevolution.

  20. Evolutionary dynamics in structured populations

    Science.gov (United States)

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

    2010-01-01

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

  1. Child Development and Evolutionary Psychology.

    Science.gov (United States)

    Bjorklund, David F.; Pellegrini, Anthony D.

    2000-01-01

    Argues that an evolutionary account provides insight into developmental function and individual differences. Outlines some assumptions of evolutionary psychology related to development. Introduces the developmental systems approach, differential influence of natural selection at different points in ontogeny, and development of evolved…

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

    Science.gov (United States)

    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.

  3. In Search of the E. coli Compounds that Change the Antibiotic Production Pattern of Streptomyces coelicolor During Inter-species Interaction.

    Science.gov (United States)

    Mavituna, Ferda; Luti, Khalid Jaber Kadhum; Gu, Lixing

    2016-08-01

    The aim of this work was to investigate the interaction between E.coli and Streptomyces coelicolor A3 (2) for the increased production of undecylprodigiosin and identify the E. coli actives mediating this inter-species interaction. The antibiotics of interest were the red-pigmented undecylprodigiosin and blue-pigmented actinorhodin. Pure cultures of S. coelicolor in a defined medium produced higher concentrations of actinorhodin compared to those of undecylprodigiosin. The latter however, is more important due to its immunosuppressive and antitumor properties. As a strategy to increase undecylprodigiosin production, we added separately, live cells and heat-killed cells of E. coli C600, and the cell-free supernatant of E. coli culture to S. coelicolor cultures in shake flasks. The interaction with live cells of E. coli altered the antibiotic production pattern and undecylprodigiosin production was enhanced by 3.5-fold compared to the pure cultures of S. coelicolor and actinorhodin decreased by 15-fold. The heat-killed cells of E. coli however, had no effect on antibiotic production. In all cases, growth and glucose consumption of S. coelicolor remained almost the same as those observed in the pure culture indicating that the changes in antibiotic production were not due to nutritional stress. Results with cell-free supernatant of E. coli culture indicated that the interaction between S. coelicolor and E. coli was mediated via diffusible molecule(s). Using a set of extraction procedures and agar-well diffusion bioassays, we isolated and preliminarily identified a class of compounds. For the preliminary verification, we added the compound which was the common chemical structural moiety in this class of compounds to the pure S. coelicolor cultures. We observed similar effects on antibiotic production as with the live E. coli cells and their supernatant indicating that this class of compounds secreted by E. coli indeed could act as actives during interspecies

  4. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

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

  5. $A$ searches

    CERN Document Server

    Beacham, James

    The Standard Model of particle physics encompasses three of the four known fundamental forces of nature, and has remarkably withstood all of the experimental tests of its predictions, a fact solidified by the discovery, in 2012, of the Higgs boson. However, it cannot be the complete picture. Many measurements have been made that hint at physics beyond the Standard Model, and the main task of the high- energy experimental physics community is to conduct searches for new physics in as many di↵erent places and regimes as possible. I present three searches for new phenomena in three di↵erent high-energy collider experiments, namely, a search for events with at least three photons in the final state, which is sensitive to an exotic decay of a Higgs boson into four photons via intermediate pseudoscalar particles, a, with ATLAS, at the Large Hadron Collider; a search for a dark photon, also known as an A0 , with APEX, at Thomas Je↵erson National Accelerator Facility; and a search for a Higgs decaying into four...

  6. Evolutionary aspects of life forms in angiosperm families

    NARCIS (Netherlands)

    Kremer, P; VanAndel, J

    1995-01-01

    The distribution patterns of life forms among extant families, subclasses and classes are described with the aim of detecting evolutionary trends. The explosive diversification of angiosperms constrains the possibilities for detecting such trends. Moreover, the extant groups of seed plants are only

  7. Evolutionary history of the somatostatin and somatostatin receptors

    Indian Academy of Sciences (India)

    ... growth through their control pattern of secretion of growth hormone, but the evolutionary history of somatostatin and somatostatin receptors are ill defined. We used comparative whole genome analysis of Danio rerio, Carassius auratus, Xenopus tropicalis, Gallus gallus, Monodelphis domestica, Homo sapiens, Sus scrofa, ...

  8. New advances in spatial network modelling: towards evolutionary algorithms

    NARCIS (Netherlands)

    Reggiani, A; Nijkamp, P.; Sabella, E.

    2001-01-01

    This paper discusses analytical advances in evolutionary methods with a view towards their possible applications in the space-economy. For this purpose, we present a brief overview and illustration of models actually available in the spatial sciences which attempt to map the complex patterns of

  9. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)

    NARCIS (Netherlands)

    Dermitzakis, ET; Reymond, A; Scamuffa, N; Ucla, C; Kirkness, E; Rossier, C; Antonarakis, SE

    2003-01-01

    Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species.

  10. The Evolutionary Legacy of Diversification Predicts Ecosystem Function.

    Science.gov (United States)

    Yguel, Benjamin; Jactel, Hervé; Pearse, Ian S; Moen, Daniel; Winter, Marten; Hortal, Joaquin; Helmus, Matthew R; Kühn, Ingolf; Pavoine, Sandrine; Purschke, Oliver; Weiher, Evan; Violle, Cyrille; Ozinga, Wim; Brändle, Martin; Bartish, Igor; Prinzing, Andreas

    2016-10-01

    Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.

  11. Human genomic disease variants: a neutral evolutionary explanation.

    Science.gov (United States)

    Dudley, Joel T; Kim, Yuseob; Liu, Li; Markov, Glenn J; Gerold, Kristyn; Chen, Rong; Butte, Atul J; Kumar, Sudhir

    2012-08-01

    Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.

  12. Human genomic disease variants: A neutral evolutionary explanation

    Science.gov (United States)

    Dudley, Joel T.; Kim, Yuseob; Liu, Li; Markov, Glenn J.; Gerold, Kristyn; Chen, Rong; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease. PMID:22665443

  13. Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

    Science.gov (United States)

    Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

    2012-11-06

    All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

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

    Science.gov (United States)

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

    2016-11-01

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

  15. A Novel Self-Adaptive Harmony Search Algorithm

    Directory of Open Access Journals (Sweden)

    Kaiping Luo

    2013-01-01

    Full Text Available The harmony search algorithm is a music-inspired optimization technology and has been successfully applied to diverse scientific and engineering problems. However, like other metaheuristic algorithms, it still faces two difficulties: parameter setting and finding the optimal balance between diversity and intensity in searching. This paper proposes a novel, self-adaptive search mechanism for optimization problems with continuous variables. This new variant can automatically configure the evolutionary parameters in accordance with problem characteristics, such as the scale and the boundaries, and dynamically select evolutionary strategies in accordance with its search performance. The new variant simplifies the parameter setting and efficiently solves all types of optimization problems with continuous variables. Statistical test results show that this variant is considerably robust and outperforms the original harmony search (HS, improved harmony search (IHS, and other self-adaptive variants for large-scale optimization problems and constrained problems.

  16. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  17. Functionality of intergenic transcription: an evolutionary comparison.

    Directory of Open Access Journals (Sweden)

    Philipp Khaitovich

    2006-10-01

    Full Text Available Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.

  18. Evolutionary medicine: update on the relevance to family practice.

    Science.gov (United States)

    Naugler, Christopher T

    2008-09-01

    To review the relevance of evolutionary medicine to family practice and family physician training. Articles were located through a MEDLINE search, using the key words evolution, Darwin, and adaptation. Most references presented level III evidence (expert opinion), while a minority provided level II evidence (epidemiologic studies). Evolutionary medicine deals with the interplay of biology and the environment in the understanding of human disease. Yet medical schools have virtually ignored the need for family physicians to have more than a cursory knowledge of this topic. A review of the main trends in this field most relevant to family practice revealed that a basic knowledge of evolutionary medicine might help in explaining the causation of diseases to patients. Evolutionary medicine has also proven key to explaining the reasons for the development of antibiotic resistance and has the potential to explain cancer pathogenesis. As an organizing principle, this field also has potential in the teaching of family medicine. Evolutionary medicine should be studied further and incorporated into medical training and practice. Its practical utility will be proven through the generation of testable hypotheses and their application in relation to disease causation and possible prevention.

  19. A mini-review of the evolutionary theories of aging.

    Directory of Open Access Journals (Sweden)

    2001-02-01

    Full Text Available This article reviews some studies testing evolutionary theories of aging and shows that they are not always confirmed. Nevertheless, many gerontologists consider now that these theories provide a general explanation of the aging process. In such conditions, we may wonder whether time has come to provisionally accept these theories in order to redirect the research efforts of gerontologists towards other directions, such as the search for new means to modulate the aging process.

  20. Evolutionary biology redux.

    Science.gov (United States)

    Torday, John S

    2013-01-01

    This article offers a novel, enlightened concept for determining the mechanism of evolution. It is based on homeostasis, which distinguishes life from non-life and as such is the universal mechanism for the evolution of all living organisms. This view of evolution is logical, mechanistic, non-scalar, predictive, testable, and falsifiable, and it illuminates the epistemological relationships between physics and biology, ontogeny and phylogeny, development and aging, ultimate and proximate causation, health and disease. In addition to validating Haeckel's biogenetic law and Lamarckian epigenetics, reflecting the enabling value of the cellular approach, this perspective also expresses the evolutionary process at the cell-molecular level, since the mechanism of cell communication itself is universal in biology, in keeping with a Kuhnian paradigm shift. This approach may even elucidate the nature and evolution of consciousness as a manifestation of the cellular continuum from unicellular to multicellular life. We need such a functional genomic mechanism for the process of evolution if we are to make progress in biology and medicine. Like Copernican heliocentrism, a cellular approach to evolution may fundamentally change humankind's perceptions about our place in the universe.

  1. Evolutionary biology in biodiversity science, conservation, and policy: a call to action.

    Science.gov (United States)

    Hendry, Andrew P; Lohmann, Lúcia G; Conti, Elena; Cracraft, Joel; Crandall, Keith A; Faith, Daniel P; Häuser, Christoph; Joly, Carlos A; Kogure, Kazuhiro; Larigauderie, Anne; Magallón, Susana; Moritz, Craig; Tillier, Simon; Zardoya, Rafael; Prieur-Richard, Anne-Hélène; Walther, Bruno A; Yahara, Tetsukazu; Donoghue, Michael J

    2010-05-01

    Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant. We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans. We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology. In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

  2. Discovery services: next generation of searching scholarly information

    OpenAIRE

    Keene, Chris

    2011-01-01

    The new breed of resource discovery services is an evolutionary step forward in providing library users with a ‘one-stop shop’ where they can find information sources for their research. They provide a single search box that can search a library’s online and physical content including articles, books, journals, newspaper articles, e-books, specialist collections and more. These discovery services have built on the concepts of both federated searching and next-generation catalogues.

  3. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    Whiteson, S.; Wiering, M.; van Otterlo, M.

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces,

  4. Integrating genomics into evolutionary medicine.

    Science.gov (United States)

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

    2014-12-01

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

  5. Internet Search Engines

    OpenAIRE

    Fatmaa El Zahraa Mohamed Abdou

    2004-01-01

    A general study about the internet search engines, the study deals main 7 points; the differance between search engines and search directories, components of search engines, the percentage of sites covered by search engines, cataloging of sites, the needed time for sites appearance in search engines, search capabilities, and types of search engines.

  6. Evolutionary advances in the higher fungi.

    Science.gov (United States)

    Moore, R T

    1997-10-01

    In this report the phrase 'evolutionary advances' is used in three ways: 1. to describe monophyletic changes perceived within a lineage; 2. to describe evolutionary sequences that appear to have become parallel/convergent; 3. to describe major transitions inferred between primary taxa. In monophyletic evolution the changes occur within a specific lineage that arises from a common ancestor, e.g., modern Man, horses, rusts. In parallel/convergent evolution different lineages respond similarly over time to environmental challenges and opportunities and come to acquire a great deal of comparability (e.g., Webster, 1987). Such lineages may be designated as separate taxa, e.g., similarities in marsupial and placental carnivores, or, if the polyphyleticism is cryptic, as a collective taxon, e.g., Aves, the class of birds, the obsolete Amentiferae for catkin bearing plants, the Gasteromycetes, and lichens. In major transitions there are significant paradigm shifts in which evolutionary changes from one predominant life style pattern to another are accompanied by increases in complexity (see Smith & Szatháry, 1995), e.g., symbiosis, the water to land transition, the changes between the phyla of land fungi. Three particular terms are used in evaluating evolutionary relationships (Moore, 1996a): homology, paramology, and analogy. Homology, from Darwin's theory of common descent, is the phenomenon of having a common historical origin but not necessarily the same final structure or function (e.g., vertebrate forelimbs). Paramology (Moore, 1971) applies to inferred relationships in evolutionary schemes based on contemporary forms that lack fossil antecedents, e.g., the various phylogenetic interpretations of prokaryotes, algae, and fungi; Boekhout et al. (1993) have evaluated the taxonomic resolution of a variety of morphologic, biochemical, physiological, and molecular characters (Table 1). Analogy is generally applied to similar forms that are unrelated, e.g., insect

  7. Evolutionary conceptual analysis: faith community nursing.

    Science.gov (United States)

    Ziebarth, Deborah

    2014-12-01

    The aim of the study was to report an evolutionary concept analysis of faith community nursing (FCN). FCN is a source of healthcare delivery in the USA which has grown in comprehensiveness and complexity. With increasing healthcare cost and a focus on access and prevention, FCN has extended beyond the physical walls of the faith community building. Faith communities and healthcare organizations invest in FCN and standardized training programs exist. Using Rodgers' evolutionary analysis, the literature was examined for antecedents, attributes, and consequences of the concept. This design allows for understanding the historical and social nature of the concept and how it changes over time. A search of databases using the keywords FCN, faith community nurse, parish nursing, and parish nurse was done. The concept of FCN was explored using research and theoretical literature. A theoretical definition and model were developed with relevant implications. The search results netted a sample of 124 reports of research and theoretical articles from multiple disciplines: medicine, education, religion and philosophy, international health, and nursing. Theoretical definition: FCN is a method of healthcare delivery that is centered in a relationship between the nurse and client (client as person, family, group, or community). The relationship occurs in an iterative motion over time when the client seeks or is targeted for wholistic health care with the goal of optimal wholistic health functioning. Faith integrating is a continuous occurring attribute. Health promoting, disease managing, coordinating, empowering and accessing health care are other essential attributes. All essential attributes occur with intentionality in a faith community, home, health institution and other community settings with fluidity as part of a community, national, or global health initiative. A new theoretical definition and corresponding conceptual model of FCN provides a basis for future nursing

  8. Phenotypical Behavior and Evolutionary Slavery

    OpenAIRE

    Martins, Andre C. R.

    2000-01-01

    A new evolutionary solution to Prisoner Dilemma situations is proposed in this paper. A specific genetic code may have different phenotypes, meaning different strategies for different individuals carrying that gene. This means that, under the right parameters, it is a good evolutionary solution to create two types of phenotypes with different strategies, here called as leaders and servants. In this solution, servants always cooperate with the leaders and leaders never do with the servants. In...

  9. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  10. FAILURE CORRECTION OF LINEAR ARRAY ANTENNA WITH MULTIPLE NULL PLACEMENT USING CUCKOO SEARCH ALGORITHM

    Directory of Open Access Journals (Sweden)

    R. Muralidaran

    2014-03-01

    Full Text Available The influence of evolutionary algorithms enhanced its scope of getting its existence in almost every complex optimization problems. In this paper, cuckoo search algorithm, an algorithm based on the brood parasite behavior along with Levy weights has been proposed for the radiation pattern correction of a linear array of isotropic antennas with uniform spacing when failed with more than one antenna element. Even though deterioration produced by the failure of antenna elements results in various undesirable effects, consideration in this paper is given to the correction of side lobe level and null placement at two places. Various articles in the past have already shown that the idea to correct the radiation pattern is to alter the amplitude weights of the remaining unfailed elements, instead of replacing the faulty elements. This approach is made use of modifying the current excitations of unfailed elements using cuckoo search algorithm such that the resulting radiation pattern is similar to the unfailed original pattern in terms of side lobe level and null placement at two places. Examples shown in this paper demonstrate the effectiveness of this algorithm in achieving the desired objectives.

  11. SEARCH, blackbox optimization, and sample complexity

    Energy Technology Data Exchange (ETDEWEB)

    Kargupta, H. [Los Alamos National Lab., NM (United States). Computational Science Methods Div.; Goldberg, D.E. [Univ. of Illinois, Urbana, IL (United States). Dept. of General Engineering

    1996-05-01

    The SEARCH (Search Envisioned As Relation and Class Hierarchizing) framework developed elsewhere (Kargupta, 1995; Kargupta and Goldberg, 1995) offered an alternate perspective toward blackbox optimization -- optimization in presence of little domain knowledge. The SEARCH framework investigates the conditions essential for transcending the limits of random enumerative search using a framework developed in terms of relations, classes and partial ordering. This paper presents a summary of some of the main results of that work. A closed form bound on the sample complexity in terms of the cardinality of the relation space, class space, desired quality of the solution and the reliability is presented. This also leads to the identification of the class of order-k delineable problems that can be solved in polynomial sample complexity. These results are applicable to any blackbox search algorithms, including evolutionary optimization techniques.

  12. Keep Searching and You’ll Find

    DEFF Research Database (Denmark)

    Laursen, Keld

    2012-01-01

    This article critically reviews and synthesizes the contributions found in theoretical and empirical studies of firm-level innovation search processes. It explores the advantages and disadvantages of local and non-local search, discusses organizational responses, and identifies potential exogenous...... different search strategies, but end up with very similar technological profiles in fast-growing technologies. The article concludes by highlighting what we have learnt from the literature and suggesting some new avenues for research....... triggers for different kinds of search. It argues that the initial focus on local search was a consequence, in part, of the attention in evolutionary economics to path-dependent behavior, but that as localized behavior was increasingly accepted as the standard mode, studies began to question whether local...

  13. Evolutionary Origin of Euglena.

    Science.gov (United States)

    Zakryś, Bożena; Milanowski, Rafał; Karnkowska, Anna

    2017-01-01

    Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids. Their plastids embedded by three membranes arose as the result of a secondary endosymbiosis between phagotrophic eukaryovorous euglenid and the Pyramimonas-related green alga. Within photosynthetic euglenids three evolutionary lineages can be distinguished. The most basal lineage is formed by one mixotrophic species, Rapaza viridis. Other photosynthetic euglenids are split into two groups: predominantly marine Eutreptiales and freshwater Euglenales. Euglenales are divided into two families: Phacaceae, comprising three monophyletic genera (Discoplastis, Lepocinclis, Phacus) and Euglenaceae with seven monophyletic genera (Euglenaformis, Euglenaria, Colacium, Cryptoglena, Strombomonas, Trachelomonas, Monomorphina) and polyphyletic genus Euglena. For 150 years researchers have been studying Euglena based solely on morphological features what resulted in hundreds of descriptions of new taxa and many artificial intra-generic classification systems. In spite of the progress towards defining Euglena, it still remains polyphyletic and morphologically almost undistinguishable from members of the recently described genus Euglenaria; members of both genera have cells undergoing metaboly (dynamic changes in cell shape), large chloroplasts with pyrenoids and monomorphic paramylon grains. Model organisms Euglena gracilis Klebs, the species of choice for addressing fundamental questions in eukaryotic biochemistry, cell and molecular biology, is a

  14. Working with Data: Discovering Knowledge through Mining and Analysis; Systematic Knowledge Management and Knowledge Discovery; Text Mining; Methodological Approach in Discovering User Search Patterns through Web Log Analysis; Knowledge Discovery in Databases Using Formal Concept Analysis; Knowledge Discovery with a Little Perspective.

    Science.gov (United States)

    Qin, Jian; Jurisica, Igor; Liddy, Elizabeth D.; Jansen, Bernard J; Spink, Amanda; Priss, Uta; Norton, Melanie J.

    2000-01-01

    These six articles discuss knowledge discovery in databases (KDD). Topics include data mining; knowledge management systems; applications of knowledge discovery; text and Web mining; text mining and information retrieval; user search patterns through Web log analysis; concept analysis; data collection; and data structure inconsistency. (LRW)

  15. The Use of Evolutionary Approaches to Understand Single Cell Genomes

    Directory of Open Access Journals (Sweden)

    Haiwei eLuo

    2015-03-01

    Full Text Available The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.

  16. MultiSeq: unifying sequence and structure data for evolutionary analysis

    Directory of Open Access Journals (Sweden)

    Wright Dan

    2006-08-01

    Full Text Available Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural

  17. Understanding evolutionary potential in virtual CPU instruction set architectures.

    Science.gov (United States)

    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. Understanding evolutionary potential in virtual CPU instruction set architectures.

    Directory of Open Access Journals (Sweden)

    David M Bryson

    Full Text Available 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

  19. Evolution of Decisions in Population Games with Sequentially Searching Individuals

    Directory of Open Access Journals (Sweden)

    Tadeas Priklopil

    2015-09-01

    Full Text Available In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.

  20. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    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.

  1. The major synthetic evolutionary transitions.

    Science.gov (United States)

    Solé, Ricard

    2016-08-19

    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'. © 2016 The Author(s).

  2. Structural symmetry in evolutionary games

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

  3. Evolutionary genomics of environmental pollution.

    Science.gov (United States)

    Whitehead, Andrew

    2014-01-01

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

  4. An Evolutionary Optimizer of libsvm Models

    Directory of Open Access Journals (Sweden)

    Dragos Horvath

    2014-11-01

    Full Text Available This user guide describes the rationale behind, and the modus operandi of a Unix script-driven package for evolutionary searching of optimal Support Vector Machine model parameters as computed by the libsvm package, leading to support vector machine models of maximal predictive power and robustness. Unlike common libsvm parameterizing engines, the current distribution includes the key choice of best-suited sets of attributes/descriptors, in addition to the classical libsvm operational parameters (kernel choice, kernel parameters, cost, and so forth, allowing a unified search in an enlarged problem space. It relies on an aggressive, repeated cross-validation scheme to ensure a rigorous assessment of model quality. Primarily designed for chemoinformatics applications, it also supports the inclusion of decoy instances, for which the explained property (bioactivity is, strictly speaking, unknown but presumably “inactive”, thus additionally testing the robustness of a model to noise. The package was developed with parallel computing in mind, supporting execution on both multi-core workstations as well as compute cluster environments. It can be downloaded from http://infochim.u-strasbg.fr/spip.php?rubrique178.

  5. Kernel method based human model for enhancing interactive evolutionary optimization.

    Science.gov (United States)

    Pei, Yan; Zhao, Qiangfu; Liu, Yong

    2015-01-01

    A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly.

  6. Performance comparison of some evolutionary algorithms on job shop scheduling problems

    Science.gov (United States)

    Mishra, S. K.; Rao, C. S. P.

    2016-09-01

    Job Shop Scheduling as a state space search problem belonging to NP-hard category due to its complexity and combinational explosion of states. Several naturally inspire evolutionary methods have been developed to solve Job Shop Scheduling Problems. In this paper the evolutionary methods namely Particles Swarm Optimization, Artificial Intelligence, Invasive Weed Optimization, Bacterial Foraging Optimization, Music Based Harmony Search Algorithms are applied and find tuned to model and solve Job Shop Scheduling Problems. To compare about 250 Bench Mark instances have been used to evaluate the performance of these algorithms. The capabilities of each these algorithms in solving Job Shop Scheduling Problems are outlined.

  7. Evolutionary lessons from California plant phylogeography

    Science.gov (United States)

    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

  8. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

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

  9. A multilevel evolutionary framework for sustainability analysis

    Directory of Open Access Journals (Sweden)

    Timothy M. Waring

    2015-06-01

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

  10. The genomic landscape of rapid repeated evolutionary ...

    Science.gov (United States)

    Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediatinggenes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversityhas likely been a crucial substrate for selective sweeps to propel rapid adaptation. This manuscript describes genomic evaluations that contribute to our understanding of the ecological and evolutionary risks associated with chronic contaminant exposures to wildlife populations. Here, we assessed genetic patterns associated with long-term response to an important class of highly toxic environmental pollutants. Specifically, chemical-specific tolerance has rapidly and repeatedly evolved in an estuarine fish species resident to estuaries of the Atlantic U.S. coast. We used laboratory studies to ch

  11. Changes in users' Web search performance after ten years ...

    African Journals Online (AJOL)

    The changes in users' Web search performance using search engines over ten years was investigated in this study. Matched data obtained from samples in 2000 and 2010 were used for the comparative analysis. The patterns of Web search engine use suggested a dominance in using a particular search engine. Statistical ...

  12. Evolutionary psychology and intelligence research.

    Science.gov (United States)

    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. Copyright 2010 APA, all rights reserved.

  13. A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset.

    Science.gov (United States)

    Joung, Je-Gun; Kim, Soo-Jin; Shin, Soo-Yong; Zhang, Byoung-Tak

    2012-01-01

    Biclustering has been utilized to find functionally important patterns in biological problem. Here a bicluster is a submatrix that consists of a subset of rows and a subset of columns in a matrix, and contains homogeneous patterns. The problem of finding biclusters is still challengeable due to computational complex trying to capture patterns from two-dimensional features. We propose a Probabilistic COevolutionary Biclustering Algorithm (PCOBA) that can cluster the rows and columns in a matrix simultaneously by utilizing a dynamic adaptation of multiple species and adopting probabilistic learning. In biclustering problems, a coevolutionary search is suitable since it can optimize interdependent subcomponents formed of rows and columns. Furthermore, acquiring statistical information on two populations using probabilistic learning can improve the ability of search towards the optimum value. We evaluated the performance of PCOBA on synthetic dataset and yeast expression profiles. The results demonstrated that PCOBA outperformed previous evolutionary computation methods as well as other biclustering methods. Our approach for searching particular biological patterns could be valuable for systematically understanding functional relationships between genes and other biological components at a genome-wide level.

  14. An Orthogonal Evolutionary Algorithm With Learning Automata for Multiobjective Optimization.

    Science.gov (United States)

    Dai, Cai; Wang, Yuping; Ye, Miao; Xue, Xingsi; Liu, Hailin

    2016-12-01

    Research on multiobjective optimization problems becomes one of the hottest topics of intelligent computation. In order to improve the search efficiency of an evolutionary algorithm and maintain the diversity of solutions, in this paper, the learning automata (LA) is first used for quantization orthogonal crossover (QOX), and a new fitness function based on decomposition is proposed to achieve these two purposes. Based on these, an orthogonal evolutionary algorithm with LA for complex multiobjective optimization problems with continuous variables is proposed. The experimental results show that in continuous states, the proposed algorithm is able to achieve accurate Pareto-optimal sets and wide Pareto-optimal fronts efficiently. Moreover, the comparison with the several existing well-known algorithms: nondominated sorting genetic algorithm II, decomposition-based multiobjective evolutionary algorithm, decomposition-based multiobjective evolutionary algorithm with an ensemble of neighborhood sizes, multiobjective optimization by LA, and multiobjective immune algorithm with nondominated neighbor-based selection, on 15 multiobjective benchmark problems, shows that the proposed algorithm is able to find more accurate and evenly distributed Pareto-optimal fronts than the compared ones.

  15. Exponential Expansion in Evolutionary Economics

    DEFF Research Database (Denmark)

    Frederiksen, Peter; Jagtfelt, Tue

    2013-01-01

    of Thomas Kuhn’s notion of scientific paradigms and criteria for a good theory (1977, 1996). The paper thus aims to augment and assimilate the fragmented and scattered body of concepts presently residing within the field of evolutionary economics, by presenting an intuitive framework, applicable within...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...

  16. The evolutionary psychology of violence.

    Science.gov (United States)

    Goetz, Aaron T

    2010-02-01

    This paper reviews theory and research on the evolutionary psychology of violence. First, I examine evidence suggesting that humans have experienced an evolutionary history of violence. Next, I discuss violence as a context-sensitive strategy that might have provided benefits to our ancestors under certain circumstances. I then focus on the two most common forms of violence that plague humans -violence over status contests and intimate partner violence- outlining psychological mechanisms involved in each. Finally, I suggest that greater progress will be made by shifting the study from contexts to mechanisms.

  17. The evolutionary psychology of hunger.

    Science.gov (United States)

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

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

  19. An evolutionary algorithm for large traveling salesman problems.

    Science.gov (United States)

    Tsai, Huai-Kuang; Yang, Jinn-Moon; Tsai, Yuan-Fang; Kao, Cheng-Yan

    2004-08-01

    This work proposes an evolutionary algorithm, called the heterogeneous selection evolutionary algorithm (HeSEA), for solving large traveling salesman problems (TSP). The strengths and limitations of numerous well-known genetic operators are first analyzed, along with local search methods for TSPs from their solution qualities and mechanisms for preserving and adding edges. Based on this analysis, a new approach, HeSEA is proposed which integrates edge assembly crossover (EAX) and Lin-Kernighan (LK) local search, through family competition and heterogeneous pairing selection. This study demonstrates experimentally that EAX and LK can compensate for each other's disadvantages. Family competition and heterogeneous pairing selections are used to maintain the diversity of the population, which is especially useful for evolutionary algorithms in solving large TSPs. The proposed method was evaluated on 16 well-known TSPs in which the numbers of cities range from 318 to 13509. Experimental results indicate that HeSEA performs well and is very competitive with other approaches. The proposed method can determine the optimum path when the number of cities is under 10,000 and the mean solution quality is within 0.0074% above the optimum for each test problem. These findings imply that the proposed method can find tours robustly with a fixed small population and a limited family competition length in reasonable time, when used to solve large TSPs.

  20. Evolutionary dynamics of rRNA gene clusters in cichlid fish

    Directory of Open Access Journals (Sweden)

    Nakajima Rafael T

    2012-10-01

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

  1. The Evolutionary Vaccination Dilemma in Complex Networks

    CERN Document Server

    Cardillo, Alessio; Naranjo, Fernando; Gómez-Gardeñes, Jesús

    2013-01-01

    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 not the vaccine upon their previous experience. Our framework thus put in competition two well-known dynamical properties of scale-free networks: the fast propagation of diseases and the promotion of cooperative behaviours. Our results show that when vaccine is perfect scale-free networks enhance the vaccination behaviour with respect to random graphs with homogeneous connectivity patterns. However, when imperfection appears we find a cross-over effect so that the number of infected (vaccinated) individuals increases (decreases) with respect to homogeneous networks, thus showing up the competition between the aforementioned properties of scale-free graphs.

  2. Human mortality improvement in evolutionary context

    DEFF Research Database (Denmark)

    Burger, Oskar; Baudisch, Annette; Vaupel, James W

    2012-01-01

    Life expectancy is increasing in most countries and has exceeded 80 in several, as low-mortality nations continue to make progress in averting deaths. The health and economic implications of mortality reduction have been given substantial attention, but the observed malleability of human mortality...... has not been placed in a broad evolutionary context. We quantify the rate and amount of mortality reduction by comparing a variety of human populations to the evolved human mortality profile, here estimated as the average mortality pattern for ethnographically observed hunter-gatherers. We show...... that human mortality has decreased so substantially that the difference between hunter-gatherers and today's lowest mortality populations is greater than the difference between hunter-gatherers and wild chimpanzees. The bulk of this mortality reduction has occurred since 1900 and has been experienced by only...

  3. Towards an evolutionary theory of language.

    Science.gov (United States)

    Nowak, M A.; Komarova, N L.

    2001-07-01

    Language is a biological trait that radically changed the performance of one species and the appearance of the planet. Understanding how human language came about is one of the most interesting tasks for evolutionary biology. Here we discuss how natural selection can guide the emergence of some basic features of human language, including arbitrary signs, words, syntactic communication and grammar. We show how natural selection can lead to the duality of patterning of human language: sequences of phonemes form words; sequences of words form sentences. Finally, we present a framework for the population dynamics of grammar acquisition, which allows us to study the cultural evolution of grammar and the biological evolution of universal grammar.

  4. Evolutionary equations with applications in natural sciences

    CERN Document Server

    Mokhtar-Kharroubi, Mustapha

    2015-01-01

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

  5. Linking metacommunity theory and symbiont evolutionary ecology.

    Science.gov (United States)

    Mihaljevic, Joseph R

    2012-06-01

    Processes that occur both within and between hosts can influence the ecological and evolutionary dynamics of symbionts, a broad term that includes parasitic and disease-causing organisms. Metacommunity theory can integrate these local- and regional-scale dynamics to explore symbiont community composition patterns across space. In this article I emphasize that symbionts should be incorporated into the metacommunity concept. I highlight the utility of metacommunity theory by discussing practical and general benefits that emerge from considering symbionts in a metacommunity framework. Specifically, investigating the local and regional drivers of symbiont community and metacommunity structure will lead to a more holistic understanding of symbiont ecology and evolution and could reveal novel insights into the roles of symbiont communities in mediating host health. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Biosequence Similarity Search on the Mercury System

    Science.gov (United States)

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. PMID:18846267

  7. Black-Box Search by Unbiased Variation

    DEFF Research Database (Denmark)

    Lehre, Per Kristian; Witt, Carsten

    2012-01-01

    The complexity theory for black-box algorithms, introduced by Droste, Jansen, and Wegener (Theory Comput. Syst. 39:525–544, 2006), describes common limits on the efficiency of a broad class of randomised search heuristics. There is an obvious trade-off between the generality of the black-box model...... and the strength of the bounds that can be proven in such a model. In particular, the original black-box model provides for well-known benchmark problems relatively small lower bounds, which seem unrealistic in certain cases and are typically not met by popular search heuristics.In this paper, we introduce a more...... restricted black-box model for optimisation of pseudo-Boolean functions which we claim captures the working principles of many randomised search heuristics including simulated annealing, evolutionary algorithms, randomised local search, and others. The key concept worked out is an unbiased variation operator...

  8. Meta Search Engines.

    Science.gov (United States)

    Garman, Nancy

    1999-01-01

    Describes common options and features to consider in evaluating which meta search engine will best meet a searcher's needs. Discusses number and names of engines searched; other sources and specialty engines; search queries; other search options; and results options. (AEF)

  9. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

  10. Selective evolutionary generation systems: Theory and applications

    Science.gov (United States)

    Menezes, Amor A.

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

  11. Primal-improv: Towards co-evolutionary musical improvisation

    DEFF Research Database (Denmark)

    Scirea, M.; Eklund, P.; Togelius, J.

    2017-01-01

    This paper describes a work in progress on co-evolving Artificial Neural Networks (ANNs) for music improvisation. Using this neuro-evolutionary approach the ANNs adapt to the changes in the human player's music as input, while still maintaining some of the structure of the musical piece previously...... arrangements than ANNs evolved without a specific objective. The emerging and interesting musical patterns that are produced by the evolved ANNs hint at the promising potential of the system....

  12. Evolutionary robotics – A review

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    MS received 26 June 2001; revised 9 May 2003. Abstract. In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system.

  13. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    Evolutionary genetics straddles the two fundamental processes of life, development (the transition from egg to adult) and reproduction (the generation of eggs from adults), and scrutinizes, from an evolu- tionary perspective, the nature .... script profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol.

  14. Current Issues in Evolutionary Paleontology.

    Science.gov (United States)

    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)

  15. Conceptual foundations of evolutionary thought

    Indian Academy of Sciences (India)

    2017-07-04

    Jul 4, 2017 ... Home; Journals; Journal of Genetics; Volume 96; Issue 3. Conceptual foundations of evolutionary thought. K. P. MOHANAN. Perspectives Volume 96 Issue 3 July 2017 pp 401-412. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/03/0401-0412. Abstract ...

  16. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  17. Haldane and modern evolutionary genetics

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 5. Haldane and modern evolutionary genetics. BRIAN CHARLESWORTH. HALDANE AT 125 Volume 96 Issue 5 November 2017 pp 773-782. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/05/0773-0782. Keywords.

  18. Evolutionary trends in directional hearing

    DEFF Research Database (Denmark)

    Carr, Catherine E; Christensen-Dalsgaard, Jakob

    2016-01-01

    Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds...

  19. Is evolutionary biology strategic science?

    Science.gov (United States)

    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.

  20. The Evolutionary Ecology of Mutualism

    NARCIS (Netherlands)

    Ivens, A.B.F.

    2012-01-01

    Mutualism, cooperation between different species, is wide-spread in nature. From bees pollinating plants to bacteria aiding digestion in the human gut: mutualism is essential for life on earth. But how does mutualism evolve? And what mechanisms keep mutualisms stable over evolutionary time and

  1. Defining fitness in evolutionary models

    Indian Academy of Sciences (India)

    The analysis of evolutionary models requires an appropriate definition for fitness. In this paper, I review such definitions in relation to the five major dimensions by which models may be described, namely. finite versus infinite (or very large) population size,; type of environment (constant, fixed length, temporally stochastic, ...

  2. Euryhalinity in an evolutionary context

    Science.gov (United States)

    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.

  3. Realism, Relativism, and Evolutionary Psychology

    NARCIS (Netherlands)

    Derksen, M.

    Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with

  4. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    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…

  5. Major evolutionary transitions in individuality

    NARCIS (Netherlands)

    West, S.A.; Fisher, R.M.; Gardner, A.; Kiers, E.T.

    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

  6. Variants of Evolutionary Algorithms for Real-World Applications

    CERN Document Server

    Weise, Thomas; Michalewicz, Zbigniew

    2012-01-01

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

  7. Classification of Automated Search Traffic

    Science.gov (United States)

    Buehrer, Greg; Stokes, Jack W.; Chellapilla, Kumar; Platt, John C.

    As web search providers seek to improve both relevance and response times, they are challenged by the ever-increasing tax of automated search query traffic. Third party systems interact with search engines for a variety of reasons, such as monitoring a web site’s rank, augmenting online games, or possibly to maliciously alter click-through rates. In this paper, we investigate automated traffic (sometimes referred to as bot traffic) in the query stream of a large search engine provider. We define automated traffic as any search query not generated by a human in real time. We first provide examples of different categories of query logs generated by automated means. We then develop many different features that distinguish between queries generated by people searching for information, and those generated by automated processes. We categorize these features into two classes, either an interpretation of the physical model of human interactions, or as behavioral patterns of automated interactions. Using the these detection features, we next classify the query stream using multiple binary classifiers. In addition, a multiclass classifier is then developed to identify subclasses of both normal and automated traffic. An active learning algorithm is used to suggest which user sessions to label to improve the accuracy of the multiclass classifier, while also seeking to discover new classes of automated traffic. Performance analysis are then provided. Finally, the multiclass classifier is used to predict the subclass distribution for the search query stream.

  8. THE THEORY OF THE FIRM AND THE EVOLUTIONARY GAMES

    Directory of Open Access Journals (Sweden)

    Sirghi Nicoleta

    2013-07-01

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

  9. Evolutionary biology of bacterial and fungal pathogens

    National Research Council Canada - National Science Library

    Baquero, F

    2008-01-01

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

  10. Towards a mechanistic foundation of evolutionary theory.

    Science.gov (United States)

    Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

    2017-02-15

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

  11. Dobzhansky and Evolutionary Cytogenetics-Pioneering ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Dobzhansky and Evolutionary Cytogenetics - Pioneering Evolutionary Studies with Chromosomes. Bimalendu B Nath. General Article Volume 5 Issue 10 October 2000 pp 61-65 ...

  12. Particle Swarm Optimization with Double Learning Patterns.

    Science.gov (United States)

    Shen, Yuanxia; Wei, Linna; Zeng, Chuanhua; Chen, Jian

    2016-01-01

    Particle Swarm Optimization (PSO) is an effective tool in solving optimization problems. However, PSO usually suffers from the premature convergence due to the quick losing of the swarm diversity. In this paper, we first analyze the motion behavior of the swarm based on the probability characteristic of learning parameters. Then a PSO with double learning patterns (PSO-DLP) is developed, which employs the master swarm and the slave swarm with different learning patterns to achieve a trade-off between the convergence speed and the swarm diversity. The particles in the master swarm and the slave swarm are encouraged to explore search for keeping the swarm diversity and to learn from the global best particle for refining a promising solution, respectively. When the evolutionary states of two swarms interact, an interaction mechanism is enabled. This mechanism can help the slave swarm in jumping out of the local optima and improve the convergence precision of the master swarm. The proposed PSO-DLP is evaluated on 20 benchmark functions, including rotated multimodal and complex shifted problems. The simulation results and statistical analysis show that PSO-DLP obtains a promising performance and outperforms eight PSO variants.

  13. Particle Swarm Optimization with Double Learning Patterns

    Directory of Open Access Journals (Sweden)

    Yuanxia Shen

    2016-01-01

    Full Text Available Particle Swarm Optimization (PSO is an effective tool in solving optimization problems. However, PSO usually suffers from the premature convergence due to the quick losing of the swarm diversity. In this paper, we first analyze the motion behavior of the swarm based on the probability characteristic of learning parameters. Then a PSO with double learning patterns (PSO-DLP is developed, which employs the master swarm and the slave swarm with different learning patterns to achieve a trade-off between the convergence speed and the swarm diversity. The particles in the master swarm and the slave swarm are encouraged to explore search for keeping the swarm diversity and to learn from the global best particle for refining a promising solution, respectively. When the evolutionary states of two swarms interact, an interaction mechanism is enabled. This mechanism can help the slave swarm in jumping out of the local optima and improve the convergence precision of the master swarm. The proposed PSO-DLP is evaluated on 20 benchmark functions, including rotated multimodal and complex shifted problems. The simulation results and statistical analysis show that PSO-DLP obtains a promising performance and outperforms eight PSO variants.

  14. Evolutionary allometry reveals a shift in selection pressure on male horn size.

    Science.gov (United States)

    Tidière, M; Lemaître, J-F; Pélabon, C; Gimenez, O; Gaillard, J-M

    2017-10-01

    How selection pressures acting within species interact with developmental constraints to shape macro-evolutionary patterns of species divergence is still poorly understood. In particular, whether or not sexual selection affects evolutionary allometry, the increase in trait size with body size across species, of secondary sexual characters, remains largely unknown. In this context, bovid horn size is an especially relevant trait to study because horns are present in both sexes, but the intensity of sexual selection acting on them is expected to vary both among species and between sexes. Using a unique data set of sex-specific horn size and body mass including 91 species of bovids, we compared the evolutionary allometry between horn size and body mass between sexes while accounting for both the intensity of sexual selection and phylogenetic relationship among species. We found a nonlinear evolutionary allometry where the allometric slope decreased with increasing species body mass. This pattern, much more pronounced in males than in females, suggests either that horn size is limited by some constraints in the largest bovids or is no longer the direct target of sexual selection in very large species. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  15. Wirelength Minimization in Partitioning and Floorplanning Using Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    I. Hameem Shanavas

    2011-01-01

    Full Text Available Minimizing the wirelength plays an important role in physical design automation of very large-scale integration (VLSI chips. The objective of wirelength minimization can be achieved by finding an optimal solution for VLSI physical design components like partitioning and floorplanning. In VLSI circuit partitioning, the problem of obtaining a minimum delay has prime importance. In VLSI circuit floorplanning, the problem of minimizing silicon area is also a hot issue. Reducing the minimum delay in partitioning and area in floorplanning helps to minimize the wirelength. The enhancements in partitioning and floorplanning have influence on other criteria like power, cost, clock speed, and so forth. Memetic Algorithm (MA is an Evolutionary Algorithm that includes one or more local search phases within its evolutionary cycle to obtain the minimum wirelength by reducing delay in partitioning and by reducing area in floorplanning. MA applies some sort of local search for optimization of VLSI partitioning and floorplanning. The algorithm combines a hierarchical design technique like genetic algorithm and constructive technique like Simulated Annealing for local search to solve VLSI partitioning and floorplanning problem. MA can quickly produce optimal solutions for the popular benchmark.

  16. Essays on nonlinear evolutionary game dynamics

    NARCIS (Netherlands)

    Ochea, M.I.

    2010-01-01

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

  17. The citation field of evolutionary economics.

    NARCIS (Netherlands)

    Dolfsma, W.; Leydesdorff, L.

    2010-01-01

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

  18. The citation field of evolutionary economics

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

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

  19. Quantum Search in Hilbert Space

    Science.gov (United States)

    Zak, Michail

    2003-01-01

    A proposed quantum-computing algorithm would perform a search for an item of information in a database stored in a Hilbert-space memory structure. The algorithm is intended to make it possible to search relatively quickly through a large database under conditions in which available computing resources would otherwise be considered inadequate to perform such a task. The algorithm would apply, more specifically, to a relational database in which information would be stored in a set of N complex orthonormal vectors, each of N dimensions (where N can be exponentially large). Each vector would constitute one row of a unitary matrix, from which one would derive the Hamiltonian operator (and hence the evolutionary operator) of a quantum system. In other words, all the stored information would be mapped onto a unitary operator acting on a quantum state that would represent the item of information to be retrieved. Then one could exploit quantum parallelism: one could pose all search queries simultaneously by performing a quantum measurement on the system. In so doing, one would effectively solve the search problem in one computational step. One could exploit the direct- and inner-product decomposability of the unitary matrix to make the dimensionality of the memory space exponentially large by use of only linear resources. However, inasmuch as the necessary preprocessing (the mapping of the stored information into a Hilbert space) could be exponentially expensive, the proposed algorithm would likely be most beneficial in applications in which the resources available for preprocessing were much greater than those available for searching.

  20. Frog tongue surface microstructures: functional and evolutionary patterns

    Science.gov (United States)

    Gorb, Stanislav N

    2016-01-01

    Summary Frogs (Lissamphibia: Anura) use adhesive tongues to capture fast moving, elusive prey. For this, the tongues are moved quickly and adhere instantaneously to various prey surfaces. Recently, the functional morphology of frog tongues was discussed in context of their adhesive performance. It was suggested that the interaction between the tongue surface and the mucus coating is important for generating strong pull-off forces. However, despite the general notions about its importance for a successful contact with the prey, little is known about the surface structure of frog tongues. Previous studies focused almost exclusively on species within the Ranidae and Bufonidae, neglecting the wide diversity of frogs. Here we examined the tongue surface in nine different frog species, comprising eight different taxa, i.e., the Alytidae, Bombinatoridae, Megophryidae, Hylidae, Ceratophryidae, Ranidae, Bufonidae, and Dendrobatidae. In all species examined herein, we found fungiform and filiform papillae on the tongue surface. Further, we observed a high degree of variation among tongues in different frogs. These differences can be seen in the size and shape of the papillae, in the fine-structures on the papillae, as well as in the three-dimensional organization of subsurface tissues. Notably, the fine-structures on the filiform papillae in frogs comprise hair-like protrusions (Megophryidae and Ranidae), microridges (Bufonidae and Dendrobatidae), or can be irregularly shaped or absent as observed in the remaining taxa examined herein. Some of this variation might be related to different degrees of adhesive performance and may point to differences in the spectra of prey items between frog taxa. PMID:27547606