Evolutionary process of deep-sea bathymodiolus mussels.

Directory of Open Access Journals (Sweden)

Jun-Ichi Miyazaki

Full Text Available BACKGROUND: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. METHODOLOGY/PRINCIPAL FINDING: We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI and NADH dehydrogenase subunit 4 (ND4 genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. CONCLUSIONS/SIGNIFICANCE: The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of

Using Ancient DNA to Understand Evolutionary and Ecological Processes

DEFF Research Database (Denmark)

Orlando, Ludovic Antoine Alexandre; Cooper, Alan

2014-01-01

Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of ...

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

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Ivanchenko Hennadii F.

2016-08-01

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

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

2012-03-01

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.

Natural history collections as windows on evolutionary processes.

Science.gov (United States)

Holmes, Michael W; Hammond, Talisin T; Wogan, Guinevere O U; Walsh, Rachel E; LaBarbera, Katie; Wommack, Elizabeth A; Martins, Felipe M; Crawford, Jeremy C; Mack, Katya L; Bloch, Luke M; Nachman, Michael W

2016-02-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. © 2016 John Wiley & Sons Ltd.

Interpreting Evolutionary Diagrams: When Topology and Process Conflict

Science.gov (United States)

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

2010-01-01

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

Sustainability and the anthropogenic alteration of evolutionary processes

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John Cairns, Jr.

2004-08-01

Full Text Available Persuasive evidence indicates that Earth is now experiencing a major biotic crisis. Even if humankind ceases severe stress on natural systems, the crisis will probably disrupt the basic evolutionary processes that characterized the period preceding the agricultural and industrial revolutions.Proliferation of drug and pesticide resistant species and opportunistic species that thrive in human-dominated ecosystems will become increasingly common. The effect on humankind of altering basic evolutionary processes is uncertain because the understanding of these processes is not robust. The probable result will not be an environment as favorable to humans as the one that has existed for most of human history. Humans probably have altered the environment since Homo sapiens first appeared. However, only in the last two centuries has the degree and rate of change reached levels now considered by many people to be ‘normal’, even though the record shows they are not.Greatly improved technology has facilitated increased exploitation of natural resources to unsustainablelevels. This exploitation, in turn, has led to exponential human population growth, which has depleted natural capital (living systems and the services they provide. Economic globalization has ensured that ecosystems far distant from consumers can be and are profitably exploited. Economicgrowth has become a universal mantra that is coupled with a conviction that such growth can continue indefinitely on a finite planet. A major paradigm shift is essential if sustainable use of the planet is to become a reality.

Freud: the first evolutionary psychologist?

Science.gov (United States)

LeCroy, D

2000-04-01

An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation.

The Riddle of a Human Being: A Human Singularity of Co-evolutionary Processes

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Helena N. Knyazeva

2008-10-01

Full Text Available span style="font-size: 10pt; font-family: #39;Times New Roman#39;"The theory of self-organization of complex systems studies laws of sustainable co-evolutionary development of structures having different speeds of development as well as laws of assembling of a complex evolutionary whole from parts when some elements of ldquo;memoryrdquo; (the biological memory, i.e. DNA, the memory of culture, i.e. the cultural and historical traditions, etc. must be included. The theory reveals general rules of nonlinear synthesis of complex evolutionary structures. The most important and paradoxical consequences of the holistic view, including an approach to solving the riddle of human personality, are as follows: 1 the explanation why and under what conditions a part (a human can be more complex than a whole (society; 2 in order to reconstruct society it is necessary to change an individual but not by cutting off the supposed undesirable past, since a human being as a microcosm is the synthesis of all previous stages of evolution, and as a result of repression of, it would seem, the wild past one can extinguish a ldquo;divine sparkrdquo; in his soul; 3 in the physical sense, singularity denotes a moment of instability, phase transition; one can talk about the human singularity of co-evolutionary processes, since in such a moment of instability individual actions of a human can play a key role in determining a channel of further development as well as in appearance of a new pattern of collective behavior in society; 4 as the models of nonlinear dynamics, elaborated at the Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences in Moscow, show, there is a possibility of a direct influence of the future and even a touch of an infinitely remote future in certain evolutionary regimes and under rigorously definite conditions, more over, it turns out that such a possibility exists only for a human (admittedly, through a specific state of being

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

International Nuclear Information System (INIS)

Quan Ji; Wang Xianjia

2011-01-01

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

Applied evolutionary economics and economic geography

OpenAIRE

Peter Sunley

2008-01-01

Applied Evolutionary Economics and Economic Geography aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and sociologists, all of whom share an interest in explaining the uneven distribution of economic activities in space and the historical processes that have produced these patterns.

On Reciprocal Causation in the Evolutionary Process.

Science.gov (United States)

Svensson, Erik I

2018-01-01

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

Incorporating evolutionary principles into environmental management and policy

DEFF Research Database (Denmark)

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

2011-01-01

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

Improving the reviewing process in Ecology and Evolutionary Biology

Directory of Open Access Journals (Sweden)

Grossman, G. D.

2014-06-01

Full Text Available I discuss current issues in reviewing and editorial practices in ecology and evolutionary biology and suggest possible solutions for current problems. The reviewing crisis is unlikely to change unless steps are taken by journals to provide greater inclusiveness and incentives to reviewers. In addition, both journals and institutions should reduce their emphasis on publication numbers (least publishable units and impact factors and focus instead on article synthesis and quality which will require longer publications. Academic and research institutions should consider reviewing manuscripts and editorial positions an important part of a researcher’s professional activities and reward them accordingly. Rewarding reviewers either monetarily or via other incentives such as free journal subscriptions may encourage participation in the reviewing process for both profit and non–profit journals. Reviewer performance will likely be improved by measures that increase inclusiveness, such as sending reviews and decision letters to reviewers. Journals may be able to evaluate the efficacy of their reviewing process by comparing citations of rejected but subsequently published papers with those published within the journal at similar times. Finally, constructive reviews: 1 identify important shortcomings and suggest solutions when possible, 2 distinguish trivial from non–trivial problems, and 3 include editor’s evaluations of the reviews including identification of trivial versus substantive comments (i.e., those that must be addressed.

Evolutionary pets: offspring numbers reveal speciation process in domesticated chickens.

Directory of Open Access Journals (Sweden)

Inga Tiemann

Full Text Available Since Darwin, the nature of the relationship between evolution and domestication has been debated. Evolution offers different mechanisms of selection that lead to adaptation and may end in the origin of new species as defined by the biological species concept. Domestication has given rise to numerous breeds in almost every domesticated species, including chickens. At the same time, so-called artificial selection seems to exclude mechanisms of sexual selection by the animals themselves. We want to forward the question to the animal itself: With whom do you reproduce successfully? This study focused on the sexual behavior of the domestic chicken Gallus gallus f.dom., particularly the White Crested Polish breed. Experiments on mate choice and the observation of fertilization and hatching rates of mixed-breeding groups revealed breed-specific preferences. In breeding groups containing White Crested Polish and a comparative breed, more purebred chicks hatched than hybrids (number of eggs collected: 1059. Mating was possible in equal shares, but in relation to the number of eggs collected, purebred offspring (62.75% ± 7.10%, M ± SE hatched to a greater extend compared to hybrid offspring (28.75% ± 15.32%, M ± SE. These data demonstrate that the mechanism of sexual selection is still present in domestic chicken breeds, which includes the alteration of gene frequencies typical for domestication and evolutionary speciation. Due to selection and mate choice we state that breeding in principle can generate new species. Therefore, we see domestication as an evolutionary process that integrates human interests of animal breeding with innate mate choice by the animal.

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

Science.gov (United States)

Toju, Hirokazu; Sota, Teiji

2009-09-01

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

Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus

Science.gov (United States)

Fan, Wentao; Sun, Zhaoyu; Shen, Tongtong; Xu, Danning; Huang, Kehe; Zhou, Jiyong; Song, Suquan; Yan, Liping

2017-01-01

Waterfowl parvoviruses are classified into goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) according to their antigenic features and host preferences. A novel duck parvovirus (NDPV), identified as a new variant of GPV, is currently infecting ducks, thus causing considerable economic loss. This study analyzed the molecular evolution and population dynamics of the emerging parvovirus capsid gene to investigate the evolutionary processes concerning the host shift of NDPV. Two important amino acids changes (Asn-489 and Asn-650) were identified in NDPV, which may be responsible for host shift of NDPV. Phylogenetic analysis indicated that the currently circulating NDPV originated from the GPV lineage. The Bayesian Markov chain Monte Carlo tree indicated that the NDPV diverged from GPV approximately 20 years ago. Evolutionary rate analyses demonstrated that GPV evolved with 7.674 × 10-4 substitutions/site/year, and the data for MDPV was 5.237 × 10-4 substitutions/site/year, whereas the substitution rate in NDPV branch was 2.25 × 10-3 substitutions/site/year. Meanwhile, viral population dynamics analysis revealed that the GPV major clade, including NDPV, grew exponentially at a rate of 1.717 year-1. Selection pressure analysis showed that most sites are subject to strong purifying selection and no positively selected sites were found in NDPV. The unique immune-epitopes in waterfowl parvovirus were also estimated, which may be helpful for the prediction of antibody binding sites against NDPV in ducks. PMID:28352261

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.

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.

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

Evolutionary patterns and processes in the radiation of phyllostomid bats

Directory of Open Access Journals (Sweden)

Monteiro Leandro R

2011-05-01

Full Text Available Abstract Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores or the relative size of tooth rows and mandibular processes (sanguivores and frugivores, which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya, larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory. Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the

Evolutionary patterns and processes in the radiation of phyllostomid bats

Science.gov (United States)

2011-01-01

Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were

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.

Influence of different positive emotions on persuasion processing: a functional evolutionary approach.

Science.gov (United States)

Griskevicius, Vladas; Shiota, Michelle N; Neufeld, Samantha L

2010-04-01

Much research has found that positive affect facilitates increased reliance on heuristics in cognition. However, theories proposing distinct evolutionary fitness-enhancing functions for specific positive emotions also predict important differences among the consequences of different positive emotion states. Two experiments investigated how six positive emotions influenced the processing of persuasive messages. Using different methods to induce emotions and assess processing, we showed that the positive emotions of anticipatory enthusiasm, amusement, and attachment love tended to facilitate greater acceptance of weak persuasive messages (consistent with previous research), whereas the positive emotions of awe and nurturant love reduced persuasion by weak messages. In addition, a series of mediation analyses suggested that the effects distinguishing different positive emotions from a neutral control condition were best accounted for by different mediators rather than by one common mediator. These findings build upon approaches that link affective valence to certain types of processing, documenting emotion-specific effects on cognition that are consistent with functional evolutionary accounts of discrete positive emotions. Copyright 2010 APA, all rights reserved.

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.

Can An Evolutionary Process Create English Text?

Energy Technology Data Exchange (ETDEWEB)

Bailey, David H.

2008-10-29

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

Building v/s Exploring Models: Comparing Learning of Evolutionary Processes through Agent-based Modeling

Science.gov (United States)

Wagh, Aditi

Two strands of work motivate the three studies in this dissertation. Evolutionary change can be viewed as a computational complex system in which a small set of rules operating at the individual level result in different population level outcomes under different conditions. Extensive research has documented students' difficulties with learning about evolutionary change (Rosengren et al., 2012), particularly in terms of levels slippage (Wilensky & Resnick, 1999). Second, though building and using computational models is becoming increasingly common in K-12 science education, we know little about how these two modalities compare. This dissertation adopts agent-based modeling as a representational system to compare these modalities in the conceptual context of micro-evolutionary processes. Drawing on interviews, Study 1 examines middle-school students' productive ways of reasoning about micro-evolutionary processes to find that the specific framing of traits plays a key role in whether slippage explanations are cued. Study 2, which was conducted in 2 schools with about 150 students, forms the crux of the dissertation. It compares learning processes and outcomes when students build their own models or explore a pre-built model. Analysis of Camtasia videos of student pairs reveals that builders' and explorers' ways of accessing rules, and sense-making of observed trends are of a different character. Builders notice rules through available blocks-based primitives, often bypassing their enactment while explorers attend to rules primarily through the enactment. Moreover, builders' sense-making of observed trends is more rule-driven while explorers' is more enactment-driven. Pre and posttests reveal that builders manifest a greater facility with accessing rules, providing explanations manifesting targeted assembly. Explorers use rules to construct explanations manifesting non-targeted assembly. Interviews reveal varying degrees of shifts away from slippage in both

Democratizing evolutionary biology, lessons from insects

DEFF Research Database (Denmark)

Dunn, Robert Roberdeau; Beasley, DeAnna E.

2016-01-01

The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This ...

Individual-based modeling of ecological and evolutionary processes

Science.gov (United States)

DeAngelis, Donald L.; Mooij, Wolf M.

2005-01-01

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

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

OpenAIRE

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

2015-01-01

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

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

Science.gov (United States)

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

2012-01-01

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

Polymorphic Evolutionary Games.

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Fishman, Michael A

2016-06-07

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

Biomimetic design processes in architecture: morphogenetic and evolutionary computational design

International Nuclear Information System (INIS)

Menges, Achim

2012-01-01

Design computation has profound impact on architectural design methods. This paper explains how computational design enables the development of biomimetic design processes specific to architecture, and how they need to be significantly different from established biomimetic processes in engineering disciplines. The paper first explains the fundamental difference between computer-aided and computational design in architecture, as the understanding of this distinction is of critical importance for the research presented. Thereafter, the conceptual relation and possible transfer of principles from natural morphogenesis to design computation are introduced and the related developments of generative, feature-based, constraint-based, process-based and feedback-based computational design methods are presented. This morphogenetic design research is then related to exploratory evolutionary computation, followed by the presentation of two case studies focusing on the exemplary development of spatial envelope morphologies and urban block morphologies. (paper)

Evolutionary Computing Methods for Spectral Retrieval

Science.gov (United States)

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

2009-01-01

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

Evolutionary heritage influences Amazon tree ecology

Science.gov (United States)

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

2016-01-01

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

Evolutionary heritage influences Amazon tree ecology.

Science.gov (United States)

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

2016-12-14

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

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

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

Science.gov (United States)

List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

2016-08-20

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to

Evolutionary process development towards next generation crystalline silicon solar cells : a semiconductor process toolbox application

Directory of Open Access Journals (Sweden)

Tous L.

2012-08-01

Full Text Available Bulk crystalline Silicon solar cells are covering more than 85% of the world’s roof top module installation in 2010. With a growth rate of over 30% in the last 10 years this technology remains the working horse of solar cell industry. The full Aluminum back-side field (Al BSF technology has been developed in the 90’s and provides a production learning curve on module price of constant 20% in average. The main reason for the decrease of module prices with increasing production capacity is due to the effect of up scaling industrial production. For further decreasing of the price per wattpeak silicon consumption has to be reduced and efficiency has to be improved. In this paper we describe a successive efficiency improving process development starting from the existing full Al BSF cell concept. We propose an evolutionary development includes all parts of the solar cell process: optical enhancement (texturing, polishing, anti-reflection coating, junction formation and contacting. Novel processes are benchmarked on industrial like baseline flows using high-efficiency cell concepts like i-PERC (Passivated Emitter and Rear Cell. While the full Al BSF crystalline silicon solar cell technology provides efficiencies of up to 18% (on cz-Si in production, we are achieving up to 19.4% conversion efficiency for industrial fabricated, large area solar cells with copper based front side metallization and local Al BSF applying the semiconductor toolbox.

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

Science.gov (United States)

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

2015-07-01

The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.

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

Directory of Open Access Journals (Sweden)

Toshihiko Kishimoto

2015-07-01

Full Text Available The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.

Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology.

Science.gov (United States)

Badyaev, Alexander V

2011-07-07

In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.

Evolutionary learning processes as the foundation for behaviour change.

Science.gov (United States)

Crutzen, Rik; Peters, Gjalt-Jorn Ygram

2018-03-01

We argue that the active ingredients of behaviour change interventions, often called behaviour change methods (BCMs) or techniques (BCTs), can usefully be placed on a dimension of psychological aggregation. We introduce evolutionary learning processes (ELPs) as fundamental building blocks that are on a lower level of psychological aggregation than BCMs/BCTs. A better understanding of ELPs is useful to select the appropriate BCMs/BCTs to target determinants of behaviour, or vice versa, to identify potential determinants targeted by a given BCM/BCT, and to optimally translate them into practical applications. Using these insights during intervention development may increase the likelihood of developing effective interventions - both in terms of behaviour change as well as maintenance of behaviour change.

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.

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

Science.gov (United States)

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

2017-11-23

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

Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.

Science.gov (United States)

Lymbery, A J

2017-01-01

An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prediction of strong earthquake motions on rock surface using evolutionary process models

International Nuclear Information System (INIS)

Kameda, H.; Sugito, M.

1984-01-01

Stochastic process models are developed for prediction of strong earthquake motions for engineering design purposes. Earthquake motions with nonstationary frequency content are modeled by using the concept of evolutionary processes. Discussion is focused on the earthquake motions on bed rocks which are important for construction of nuclear power plants in seismic regions. On this basis, two earthquake motion prediction models are developed, one (EMP-IB Model) for prediction with given magnitude and epicentral distance, and the other (EMP-IIB Model) to account for the successive fault ruptures and the site location relative to the fault of great earthquakes. (Author) [pt

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

[Evolutionary process unveiled by the maximum genetic diversity hypothesis].

Science.gov (United States)

Huang, Yi-Min; Xia, Meng-Ying; Huang, Shi

2013-05-01

As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature.

Evolutionary principles and their practical application.

Science.gov (United States)

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

2011-03-01

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

Wavelet-Based Methodology for Evolutionary Spectra Estimation of Nonstationary Typhoon Processes

Directory of Open Access Journals (Sweden)

Guang-Dong Zhou

2015-01-01

Full Text Available Closed-form expressions are proposed to estimate the evolutionary power spectral density (EPSD of nonstationary typhoon processes by employing the wavelet transform. Relying on the definition of the EPSD and the concept of the wavelet transform, wavelet coefficients of a nonstationary typhoon process at a certain time instant are interpreted as the Fourier transform of a new nonstationary oscillatory process, whose modulating function is equal to the modulating function of the nonstationary typhoon process multiplied by the wavelet function in time domain. Then, the EPSD of nonstationary typhoon processes is deduced in a closed form and is formulated as a weighted sum of the squared moduli of time-dependent wavelet functions. The weighted coefficients are frequency-dependent functions defined by the wavelet coefficients of the nonstationary typhoon process and the overlapping area of two shifted wavelets. Compared with the EPSD, defined by a sum of the squared moduli of the wavelets in frequency domain in literature, this paper provides an EPSD estimation method in time domain. The theoretical results are verified by uniformly modulated nonstationary typhoon processes and non-uniformly modulated nonstationary typhoon processes.

Darwin in Mind: New Opportunities for Evolutionary Psychology

Science.gov (United States)

Bolhuis, Johan J.; Brown, Gillian R.; Richardson, Robert C.; Laland, Kevin N.

2011-01-01

Evolutionary Psychology (EP) views the human mind as organized into many modules, each underpinned by psychological adaptations designed to solve problems faced by our Pleistocene ancestors. We argue that the key tenets of the established EP paradigm require modification in the light of recent findings from a number of disciplines, including human genetics, evolutionary biology, cognitive neuroscience, developmental psychology, and paleoecology. For instance, many human genes have been subject to recent selective sweeps; humans play an active, constructive role in co-directing their own development and evolution; and experimental evidence often favours a general process, rather than a modular account, of cognition. A redefined EP could use the theoretical insights of modern evolutionary biology as a rich source of hypotheses concerning the human mind, and could exploit novel methods from a variety of adjacent research fields. PMID:21811401

Holistic Darwinism: the new evolutionary paradigm and some implications for political science.

Science.gov (United States)

Corning, Peter A

2008-03-01

Holistic Darwinism is a candidate name for a major paradigm shift that is currently underway in evolutionary biology and related disciplines. Important developments include (1) a growing appreciation for the fact that evolution is a multilevel process, from genes to ecosystems, and that interdependent coevolution is a ubiquitous phenomenon in nature; (2) a revitalization of group selection theory, which was banned (prematurely) from evolutionary biology over 30 years ago (groups may in fact be important evolutionary units); (3) a growing respect for the fact that the genome is not a "bean bag" (in biologist Ernst Mayr's caricature), much less a gladiatorial arena for competing selfish genes, but a complex, interdependent, cooperating system; (4) an increased recognition that symbiosis is an important phenomenon in nature and that symbiogenesis is a major source of innovation in evolution; (5) an array of new, more advanced game theory models, which support the growing evidence that cooperation is commonplace in nature and not a rare exception; (6) new research and theoretical work that stresses the role of nurture in evolution, including developmental processes, phenotypic plasticity, social information transfer (culture), and especially the role of behavioral innovations as pacemakers of evolutionary change (e.g., niche construction theory, which is concerned with the active role of organisms in shaping the evolutionary process, and gene-culture coevolution theory, which relates especially to the dynamics of human evolution); (7) and, not least, a broad effort to account for the evolution of biological complexity--from major transition theory to the "Synergism Hypothesis." Here I will briefly review these developments and will present a case for the proposition that this paradigm shift has profound implications for the social sciences, including specifically political theory, economic theory, and political science as a discipline. Interdependent superorganisms, it

Historical change and evolutionary theory.

Science.gov (United States)

Masters, Roger D

2007-09-01

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

The application of evolutionary medicine principles for sustainable malaria control: a scoping study.

Science.gov (United States)

Ocampo, Denise; Booth, Mark

2016-07-22

Current interventions against malaria have significantly reduced the number of people infected and the number of deaths. Concerns about emerging resistance of both mosquitoes and parasites to intervention have been raised, and questions remain about how best to generate wider knowledge of the underlying evolutionary processes. The pedagogical and research principles of evolutionary medicine may provide an answer to this problem. Eight programme managers and five academic researchers were interviewed by telephone or videoconference to elicit their first-hand views and experiences of malaria control given that evolution is a constant threat to sustainable control. Interviewees were asked about their views on the relationship between practit groups and academics and for their thoughts on whether or not evolutionary medicine may provide a solution to reported tensions. There was broad agreement that evolution of both parasites and vectors presents an obstacle to sustainable control. It was also widely agreed that through more efficient monitoring, evolution could be widely monitored. Interviewees also expressed the view that even well planned interventions may fail if the evolutionary biology of the disease is not considered, potentially making current tools redundant. This scoping study suggests that it is important to make research, including evolutionary principles, available and easily applicable for programme managers and key decision-makers, including donors and politicians. The main conclusion is that sharing knowledge through the educational and research processes embedded within evolutionary medicine has potential to relieve tensions and facilitate sustainable control of malaria and other parasitic infections.

Evolutionary principles and their practical application

DEFF Research Database (Denmark)

Hendry, A. P.; Kinnison, M. T.; Heino, M.

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...

Individual-based modeling of ecological and evolutionary processes

NARCIS (Netherlands)

DeAngelis, D.L.; Mooij, W.M.

2005-01-01

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential and difference equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis

Core principles of evolutionary medicine

Science.gov (United States)

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

2018-01-01

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

Practical advantages of evolutionary computation

Science.gov (United States)

Fogel, David B.

1997-10-01

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

Fixation of strategies with the Moran and Fermi processes in evolutionary games

Science.gov (United States)

Liu, Xuesong; He, Mingfeng; Kang, Yibin; Pan, Qiuhui

2017-10-01

A model of stochastic evolutionary game dynamics with finite population was built. It combines the standard Moran and Fermi rules with two strategies cooperation and defection. We obtain the expressions of fixation probabilities and fixation times. The one-third rule which has been found in the frequency dependent Moran process also holds for our model. We obtain the conditions of strategy being an evolutionarily stable strategy in our model, and then make a comparison with the standard Moran process. Besides, the analytical results show that compared with the standard Moran process, fixation occurs with higher probabilities under a prisoner's dilemma game and coordination game, but with lower probabilities under a coexistence game. The simulation result shows that the fixation time in our mixed process is lower than that in the standard Fermi process. In comparison with the standard Moran process, fixation always takes more time on average in spatial populations, regardless of the game. In addition, the fixation time decreases with the growth of the number of neighbors.

Ecological and evolutionary processes at expanding range margins.

Science.gov (United States)

Thomas, C D; Bodsworth, E J; Wilson, R J; Simmons, A D; Davies, Z G; Musche, M; Conradt, L

2001-05-31

Many animals are regarded as relatively sedentary and specialized in marginal parts of their geographical distributions. They are expected to be slow at colonizing new habitats. Despite this, the cool margins of many species' distributions have expanded rapidly in association with recent climate warming. We examined four insect species that have expanded their geographical ranges in Britain over the past 20 years. Here we report that two butterfly species have increased the variety of habitat types that they can colonize, and that two bush cricket species show increased fractions of longer-winged (dispersive) individuals in recently founded populations. Both ecological and evolutionary processes are probably responsible for these changes. Increased habitat breadth and dispersal tendencies have resulted in about 3- to 15-fold increases in expansion rates, allowing these insects to cross habitat disjunctions that would have represented major or complete barriers to dispersal before the expansions started. The emergence of dispersive phenotypes will increase the speed at which species invade new environments, and probably underlies the responses of many species to both past and future climate change.

Species co-evolutionary algorithm: a novel evolutionary algorithm based on the ecology and environments for optimization

DEFF Research Database (Denmark)

Li, Wuzhao; Wang, Lei; Cai, Xingjuan

2015-01-01

and affect each other in many ways. The relationships include competition, predation, parasitism, mutualism and pythogenesis. In this paper, we consider the five relationships between solutions to propose a co-evolutionary algorithm termed species co-evolutionary algorithm (SCEA). In SCEA, five operators...

Applied evolutionary economics and economic geography

NARCIS (Netherlands)

Frenken, K.

2007-01-01

Applied Evolutionary Economics and Economic Geography" aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and

Evolutionary engineering for industrial microbiology.

Science.gov (United States)

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

2012-01-01

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

Fixation Time for Evolutionary Graphs

Science.gov (United States)

Nie, Pu-Yan; Zhang, Pei-Ai

Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

Application study of evolutionary operation methods in optimization of process parameters for mosquito coils industry

Science.gov (United States)

Ginting, E.; Tambunanand, M. M.; Syahputri, K.

2018-02-01

Evolutionary Operation Methods (EVOP) is a method that is designed used in the process of running or operating routinely in the company to enables high productivity. Quality is one of the critical factors for a company to win the competition. Because of these conditions, the research for products quality has been done by gathering the production data of the company and make a direct observation to the factory floor especially the drying department to identify the problem which is the high water content in the mosquito incense coil. PT.X which is producing mosquito coils attempted to reduce product defects caused by the inaccuracy of operating conditions. One of the parameters of good quality insect repellent that is water content, that if the moisture content is too high then the product easy to mold and broken, and vice versa if it is too low the products are easily broken and burn shorter hours. Three factors that affect the value of the optimal water content, the stirring time, drying temperature and drying time. To obtain the required conditions Evolutionary Operation (EVOP) methods is used. Evolutionary Operation (EVOP) is used as an efficient technique for optimization of two or three variable experimental parameters using two-level factorial designs with center point. Optimal operating conditions in the experiment are stirring time performed for 20 minutes, drying temperature at 65°C, and drying time for 130 minutes. The results of the analysis based on the method of Evolutionary Operation (EVOP) value is the optimum water content of 6.90%, which indicates the value has approached the optimal in a production plant that is 7%.

Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

Directory of Open Access Journals (Sweden)

Saito Shigeru

2010-05-01

Full Text Available Abstract Background Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages. Results In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events. Conclusions Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

Temporal knowledge and autobiographical memory: an evolutionary perspective

OpenAIRE

Skowronski, John J.; Sedikides, Constantine

2007-01-01

Section I: Philosophical issues 1. Evolutionary pyschology in the round , Robin Dunbar & Louise Barrett 2. The power of culture , Henry Plotkin 3. Evolution and psychology in philosophical perspective , Matteo Mameli 4. Niche construction, human behavioural ecology and evolutionary psychology , Kevin N Laland 5. Group level evolutionary processes , David Sloan Wilson Section II: The comparative Approach 6. Homologizing the mind , Drew Rendall, Hugh Nottman & John ...

Conceptual Barriers to Progress Within Evolutionary Biology.

Science.gov (United States)

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

2009-08-01

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

Evolutionary design optimization of traffic signals applied to Quito city.

Science.gov (United States)

Armas, Rolando; Aguirre, Hernán; Daolio, Fabio; Tanaka, Kiyoshi

2017-01-01

This work applies evolutionary computation and machine learning methods to study the transportation system of Quito from a design optimization perspective. It couples an evolutionary algorithm with a microscopic transport simulator and uses the outcome of the optimization process to deepen our understanding of the problem and gain knowledge about the system. The work focuses on the optimization of a large number of traffic lights deployed on a wide area of the city and studies their impact on travel time, emissions and fuel consumption. An evolutionary algorithm with specialized mutation operators is proposed to search effectively in large decision spaces, evolving small populations for a short number of generations. The effects of the operators combined with a varying mutation schedule are studied, and an analysis of the parameters of the algorithm is also included. In addition, hierarchical clustering is performed on the best solutions found in several runs of the algorithm. An analysis of signal clusters and their geolocation, estimation of fuel consumption, spatial analysis of emissions, and an analysis of signal coordination provide an overall picture of the systemic effects of the optimization process.

Research traditions and evolutionary explanations in medicine.

Science.gov (United States)

Méthot, Pierre-Olivier

2011-02-01

In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

Evolutionary computation in zoology and ecology.

Science.gov (United States)

Boone, Randall B

2017-12-01

Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.

The evolutionary ecology of molecular replicators.

Science.gov (United States)

Nee, Sean

2016-08-01

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

The eco-evolutionary impacts of domestication and agricultural practices on wild species.

Science.gov (United States)

Turcotte, Martin M; Araki, Hitoshi; Karp, Daniel S; Poveda, Katja; Whitehead, Susan R

2017-01-19

Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause non-selective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

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

KAUST Repository

Choat, John. H.; klanten, Oya. S.; Van Herwerden, Lynne; Robertson, D. Ross; Clements, Kendall D.

2012-01-01

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.

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.

A Common, Conceptual Framework for Behavioral Ecology and Evolutionary Psychology

Directory of Open Access Journals (Sweden)

Donald W. White

2007-04-01

Full Text Available Since evolutionary psychology and behavioral ecology have much in common despite their using different objects for their study, one might expect these disciplines to share a common conceptual framework with associated definitions. Unfortunately, such agreement does not entirely exist. To address the problem, we propose a common, conceptual framework, the Adaptive Behavioral System (ABS, which organizes behavior within an evolutionary framework around an organism's life history tasks. An ABS includes strategies that use decision rules and employs tactics administered by a hypothesized construct, the Evolved Processing Unit (EPU. The ABS also includes observed or predicted behavior which can be tested experimentally – the ultimate test of construct validity. Use of the proposed framework should help the two disciplines focus on their common, core business of behavior and, ultimately, be to the benefit of both.

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

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

Science.gov (United States)

Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

2014-11-11

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

Evolutionary genetics: the Drosophila model

Indian Academy of Sciences (India)

Unknown

Evolutionary genetics straddles the two fundamental processes of life, ... of the genus Drosophila have been used extensively as model systems in experimental ... issue will prove interesting, informative and thought-provoking for both estab-.

EVOLUTIONARY THEORY AND THE MARKET COMPETITION

Directory of Open Access Journals (Sweden)

SIRGHI Nicoleta

2014-12-01

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

Evolutionary accounts of human behavioural diversity

Science.gov (United States)

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

2011-01-01

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

Integrated evolutionary computation neural network quality controller for automated systems

Energy Technology Data Exchange (ETDEWEB)

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

1999-06-01

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

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.

Clonality and evolutionary history of rhabdomyosarcoma.

Directory of Open Access Journals (Sweden)

Li Chen

2015-03-01

Full Text Available To infer the subclonality of rhabdomyosarcoma (RMS and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS.

On the evolutionary relationship between chondrocytes and osteoblasts

Directory of Open Access Journals (Sweden)

Patsy eGomez-Picos

2015-09-01

Full Text Available Vertebrates are the only animals that produce bone, but the molecular genetic basis for this evolutionary novelty remains obscure. Here, we synthesize information from traditional evolutionary and modern molecular genetic studies in order to generate a working hypothesis on the evolution of the gene regulatory network (GRN underlying bone formation. To make this argument, we focus on three skeletal tissues that comprise the majority of the vertebrate skeleton: immature cartilage, mature cartilage, and bone. Immature cartilage is produced during early stages of cartilage differentiation and can persist into adulthood, whereas mature cartilage undergoes additional stages of differentiation, including hypertrophy and mineralization. Functionally, histologically, and embryologically, these three skeletal tissues are very similar, yet unique, suggesting that one might have evolved from another. Traditional studies of the fossil record, comparative anatomy and embryology demonstrate clearly that immature cartilage evolved before mature cartilage or bone. Modern molecular approaches show that the GRNs regulating differentiation of these three skeletal cell fates are similar, yet unique, just like the functional and histological features of the tissues themselves. Intriguingly, the Sox9 GRN driving cartilage formation appears to be dominant to the Runx2 GRN of bone. Emphasizing an embryological and evolutionary transcriptomic view, we hypothesize that the Runx2 GRN underlying bone formation was co-opted from mature cartilage. We discuss how modern molecular genetic experiments, such as comparative transcriptomics, can test this hypothesis directly, meanwhile permitting levels of constraint and adaptation to be evaluated quantitatively. Therefore, comparative transcriptomics may revolutionize understanding of not only the clade-specific evolution of skeletal cells, but also the generation of evolutionary novelties, providing a modern paradigm for the

Evolutionary origins and early development of number processing

CERN Document Server

Geary, David C; Mann Koepke, Kathleen

2014-01-01

The first volume in this ground-breaking series focuses on the origins and early development of numerical cognition in non-human primates, lower vertebrates, human infants, and preschool children. The text will help readers understand the nature and complexity of these foundational quantitative concepts and skills along with evolutionary precursors and early developmental trajectories. Brings together and focuses the efforts and research of multiple disciplines working in math cognition.The contributors bring vast knowledge and experience to bear on resolving extant

An Efficient Evolutionary Based Method For Image Segmentation

OpenAIRE

Aslanzadeh, Roohollah; Qazanfari, Kazem; Rahmati, Mohammad

2017-01-01

The goal of this paper is to present a new efficient image segmentation method based on evolutionary computation which is a model inspired from human behavior. Based on this model, a four layer process for image segmentation is proposed using the split/merge approach. In the first layer, an image is split into numerous regions using the watershed algorithm. In the second layer, a co-evolutionary process is applied to form centers of finals segments by merging similar primary regions. In the t...

Making evolutionary biology a basic science for medicine

Science.gov (United States)

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

2010-01-01

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

The pathway between conflict and reconciliation: coexistence as an evolutionary process.

Science.gov (United States)

Sluzki, Carlos E

2010-02-01

A normative sequence of six stages is proposed to describe the process of evolution from open conflict to harmonious coexistence, as well at its devolution from the latter to the former. The stages may be termed Confrontation, Truce, Collaboration, Cooperation, Interdependence and Integration. Each of the six stages constitutes an amalgam of practices, narratives and prevalent emotions in a relational "game" that tends to resist change. At the stage of Confrontation, each party assumes that any act of the other is motivated by ill intent, and active hostility prevails. In Truce or Freeze, acts of hostility are curtailed by a real or virtual "neutral zone" controlled by powerful third parties. The dominant emotions are resentment, anger, and mistrust. Collaboration retains some assumptions of ill intent while certain activities in common are carried out. The third party looses visibility, and the dominant emotions include ambivalence. Cooperation entails the assumption of neutral intent of self and other, while activities in common are planned and carried out. Key emotions include cautious compassion for the other. Interdependence is characterized by active involvement in planning toward the common good. The dominant emotions are trust and forgiveness. At the other end of the spectrum, parties at the stage of Integration are actively involved in projects aimed at the common good and each supports the other's growth. The dominant emotions are solidarity and a friendly trust. Movement from one stage to another shares certain characteristics with other complex systems. For professionals aiming to facilitate evolutionary change, whether in interpersonal or in international relations, the systemic cohesion of each stage constitutes the main challenge, and the promise of similar cohesion at the next stage provides the main hope.

Evolutionary epistemology, rationality, and the sociology of knowledge

CERN Document Server

Bartley, W W

1993-01-01

This collection of essays in support of the theory of evolutionary epistemology includes articles by Karl Popper, Peter Munz and Gerhard Vollmer. This volume attempts to show how an evolutionary and non-justificational approach affects the sociology of knowledge.

Core principles of evolutionary medicine: A Delphi study.

Science.gov (United States)

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

2018-01-01

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

Space cannot be cut-why self-identity naturally includes neighbourhood.

Science.gov (United States)

Rayner, Alan David

2011-06-01

Psychology is not alone in its struggle with conceptualizing the dynamic relationship between space and individual or collective identity. This general epistemological issue haunts biology where it has a specific focus in evolutionary arguments. It arises because of the incompatibility between definitive logical systems of 'contradiction or unity', which can only apply to inert material systems, and natural evolutionary processes of cumulative energetic transformation. This incompatibility makes any attempt to apply definitive logic to evolutionary change unrealistic and paradoxical. It is important to recognise, because discrete perceptions of self and group, based on the supposition that any distinguishable identity can be completely cut free, as an 'independent singleness', from the space it inescapably includes and is included in, are a profound but unnecessary source of psychological, social and environmental conflict. These perceptions underlie Darwin's definition of 'natural selection' as 'the preservation of favoured races in the struggle for life'. They result in precedence being given to striving for homogeneous supremacy, through the competitive suppression of others, instead of seeking sustainable, co-creative evolutionary relationship in spatially and temporally heterogeneous communities. Here, I show how 'natural inclusion', a new, post-dialectic understanding of evolutionary process, becomes possible through recognising space as a limitless, indivisible, receptive (non-resistive) 'intangible presence' vital for movement and communication, not as empty distance between one tangible thing and another. The fluid boundary logic of natural inclusion as the co-creative, fluid dynamic transformation of all through all in receptive spatial context, allows all form to be understood as flow-form, distinctive but dynamically continuous, not singularly discrete. This simple move from regarding space and boundaries as sources of discontinuity and discrete

The extended evolutionary synthesis: its structure, assumptions and predictions

Science.gov (United States)

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

2015-01-01

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

An evolutionary ecology of individual differences

Science.gov (United States)

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

2014-01-01

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

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,

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...

An evolutionary approach to financial history.

Science.gov (United States)

Ferguson, N

2009-01-01

Financial history is not conventionally thought of in evolutionary terms, but it should be. Traditional ways of thinking about finance, dating back to Hilferding, emphasize the importance of concentration and economies of scale. But these approaches overlook the rich "biodiversity" that characterizes the financial world. They also overlook the role of natural selection. To be sure, natural selection in the financial world is not exactly analogous to the processes first described by Darwin and elaborated on by modern biologists. There is conscious adaptation as well as random mutation. Moreover, there is something resembling "intelligent design" in finance, whereby regulators and legislators act in a quasidivine capacity, putting dinosaurs on life support. The danger is that such interventions in the natural processes of the market may ultimately distort the evolutionary process, by getting in the way of Schumpeter's "creative destruction."

Cryptic Genetic Variation in Evolutionary Developmental Genetics

Directory of Open Access Journals (Sweden)

Annalise B. Paaby

2016-06-01

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

Evolutionary Ship Track Planning within Traffic Separation Schemes – Evaluation of Individuals

Directory of Open Access Journals (Sweden)

Rafal Szlapczynski

2013-06-01

Full Text Available The paper presents an extended version of the author’s Evolutionary Sets of Safe Ship Trajectories method. The method plans safe tracks of all ships involved in an encounter including speed reduction maneuvers, if necessary, and taking into account Rule 10 of COLREGS, which specifies ships’ behavior within Traffic Separation Schemes governed by IMO. The paper focuses on the evaluation phase of the evolutionary process and shows how fitness function is designed to compare various possible tracks as well as to assess the quality of a final solution. The impact of the fitness function on the method’s results is illustrated by examples.

How cultural evolutionary theory can inform social psychology and vice versa.

Science.gov (United States)

Mesoudi, Alex

2009-10-01

Cultural evolutionary theory is an interdisciplinary field in which human culture is viewed as a Darwinian process of variation, competition, and inheritance, and the tools, methods, and theories developed by evolutionary biologists to study genetic evolution are adapted to study cultural change. It is argued here that an integration of the theories and findings of mainstream social psychology and of cultural evolutionary theory can be mutually beneficial. Social psychology provides cultural evolution with a set of empirically verified microevolutionary cultural processes, such as conformity, model-based biases, and content biases, that are responsible for specific patterns of cultural change. Cultural evolutionary theory provides social psychology with ultimate explanations for, and an understanding of the population-level consequences of, many social psychological phenomena, such as social learning, conformity, social comparison, and intergroup processes, as well as linking social psychology with other social science disciplines such as cultural anthropology, archaeology, and sociology.

Evolutionary thinking

Science.gov (United States)

Hunt, Tam

2014-01-01

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

Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

Science.gov (United States)

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

2016-05-03

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

Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics.

Science.gov (United States)

Bybee, Seth; Córdoba-Aguilar, Alex; Duryea, M Catherine; Futahashi, Ryo; Hansson, Bengt; Lorenzo-Carballa, M Olalla; Schilder, Ruud; Stoks, Robby; Suvorov, Anton; Svensson, Erik I; Swaegers, Janne; Takahashi, Yuma; Watts, Phillip C; Wellenreuther, Maren

2016-01-01

Odonata (dragonflies and damselflies) present an unparalleled insect model to integrate evolutionary genomics with ecology for the study of insect evolution. Key features of Odonata include their ancient phylogenetic position, extensive phenotypic and ecological diversity, several unique evolutionary innovations, ease of study in the wild and usefulness as bioindicators for freshwater ecosystems worldwide. In this review, we synthesize studies on the evolution, ecology and physiology of odonates, highlighting those areas where the integration of ecology with genomics would yield significant insights into the evolutionary processes that would not be gained easily by working on other animal groups. We argue that the unique features of this group combined with their complex life cycle, flight behaviour, diversity in ecological niches and their sensitivity to anthropogenic change make odonates a promising and fruitful taxon for genomics focused research. Future areas of research that deserve increased attention are also briefly outlined.

Entrepreneurs and Evolutionary Biology: The Relationship between Testosterone and New Venture Creation

Science.gov (United States)

White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth

2006-01-01

Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

Science.gov (United States)

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

Evolutionary dynamics with fluctuating population sizes and strong mutualism

Science.gov (United States)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

Science.gov (United States)

Chotibut, Thiparat; Nelson, David R

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Using Evolutionary Theory to Guide Mental Health Research.

Science.gov (United States)

Durisko, Zachary; Mulsant, Benoit H; McKenzie, Kwame; Andrews, Paul W

2016-03-01

Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. © The Author(s) 2016.

Extended evolutionary psychology: the importance of transgenerational developmental plasticity

Directory of Open Access Journals (Sweden)

Karola eStotz

2014-08-01

Full Text Available What kind mechanisms one deems central for the evolutionary process deeply influences one’s understanding of the nature of organisms, including cognition. Reversely, adopting a certain approach to the nature of life and cognition and the relationship between them or between the organism and its environment should affect one’s view of evolutionary theory. This paper explores this reciprocal relationship in more detail. In particular it argues that the view of living and cognitive systems, especially humans, as deeply integrated beings embedded in and transformed by their genetic, epigenetic (molecular and cellular, behavioral, ecological, socio-cultural and cognitive-symbolic legacies calls for an extended evolutionary synthesis that goes beyond either a theory of genes juxtaposed against a theory of cultural evolution and or even more sophisticated theories of gene-culture coevolution and niche construction. Environments, particularly in the form of developmental environments, do not just select for variation, they also create new variation by influencing development through the reliable transmission of non-genetic but heritable information. This paper stresses particularly views of embodied, embedded, enacted and extended cognition, and their relationship to those aspects of extended inheritance that lie between genetic and cultural inheritance, the still grey area of epigenetic and behavioral inheritance systems that play a role in parental effect. These are the processes that can be regarded as transgenerational developmental plasticity and that I think can most fruitfully contribute to, and be investigated by, developmental psychology.

Extended evolutionary psychology: the importance of transgenerational developmental plasticity.

Science.gov (United States)

Stotz, Karola

2014-01-01

What kind mechanisms one deems central for the evolutionary process deeply influences one's understanding of the nature of organisms, including cognition. Reversely, adopting a certain approach to the nature of life and cognition and the relationship between them or between the organism and its environment should affect one's view of evolutionary theory. This paper explores this reciprocal relationship in more detail. In particular it argues that the view of living and cognitive systems, especially humans, as deeply integrated beings embedded in and transformed by their genetic, epigenetic (molecular and cellular), behavioral, ecological, socio-cultural and cognitive-symbolic legacies calls for an extended evolutionary synthesis that goes beyond either a theory of genes juxtaposed against a theory of cultural evolution and or even more sophisticated theories of gene-culture coevolution and niche construction. Environments, particularly in the form of developmental environments, do not just select for variation, they also create new variation by influencing development through the reliable transmission of non-genetic but heritable information. This paper stresses particularly views of embodied, embedded, enacted and extended cognition, and their relationship to those aspects of extended inheritance that lie between genetic and cultural inheritance, the still gray area of epigenetic and behavioral inheritance systems that play a role in parental effect. These are the processes that can be regarded as transgenerational developmental plasticity and that I think can most fruitfully contribute to, and be investigated by, developmental psychology.

The four cornerstones of Evolutionary Toxicology.

Science.gov (United States)

Bickham, John W

2011-05-01

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

Evolutionary Stable Strategy

Indian Academy of Sciences (India)

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

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.

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.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

Science.gov (United States)

Werren, John H

2011-06-28

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

Evolutionary theory of ageing and the problem of correlated Gompertz parameters.

Science.gov (United States)

Burger, Oskar; Missov, Trifon I

2016-11-07

The Gompertz mortality model is often used to evaluate evolutionary theories of ageing, such as the Medawar-Williams' hypothesis that high extrinsic mortality leads to faster ageing. However, fits of the Gompertz mortality model to data often find the opposite result that mortality is negatively correlated with the rate of ageing. This negative correlation has been independently discovered in several taxa and is known in actuarial studies of ageing as the Strehler-Mildvan correlation. We examine the role of mortality selection in determining late-life variation in susceptibility to death, which has been suggested to be the cause of this negative correlation. We demonstrate that fixed-frailty models that account for heterogeneity in frailty do not remove the correlation and that the correlation is an inherent statistical property of the Gompertz distribution. Linking actuarial and biological rates of ageing will continue to be a pressing challenge, but the Strehler-Mildvan correlation itself should not be used to diagnose any biological, physiological, or evolutionary process. These findings resolve some key tensions between theory and data that affect evolutionary and biological studies of ageing and mortality. Tests of evolutionary theories of ageing should include direct measures of physiological performance or condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary medicine: its scope, interest and potential.

Science.gov (United States)

Stearns, Stephen C

2012-11-07

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

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

Science.gov (United States)

Chen, Bor-Sen; Yeh, Chin-Hsun

2017-12-01

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

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...

Fixation times in evolutionary games under weak selection

International Nuclear Information System (INIS)

Altrock, Philipp M; Traulsen, Arne

2009-01-01

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

A Semiotic Analysis of the Interface between Evolutionary and Developmental Processes

Directory of Open Access Journals (Sweden)

Eugenio Andrade

2008-07-01

Full Text Available This work proposes the notion of organisms as Evolving Developing Agents (EDA in order to ground an internalist model in which evolution and development are conceived as aspects of a general transformative tendency driven by organism's need to cope with environmental uncertainty. It is shown how the integration Evo/Devo contributes to an expanded evolutionary synthesis that accounts for divergent evolution in terms of development, without disregarding the role of genes and natural selection. However this integration has to be seen as a specific case that contributes to the contextualization of C.S.Peirce's evolutionary ontology founded on three universal categories and six space/time/function relations, as described by Taborsky. The role played by the EDA is characterized by the Secondness as firstness relation for it merges the internal/ external, and individual/population and present/past/ progressive cuts that permeate the discourse of biology.

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer.

Science.gov (United States)

Boto, Luis

2015-06-01

Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.

Embodied artificial evolution: Artificial evolutionary systems in the 21st Century.

Science.gov (United States)

Eiben, A E; Kernbach, S; Haasdijk, Evert

2012-12-01

Evolution is one of the major omnipresent powers in the universe that has been studied for about two centuries. Recent scientific and technical developments make it possible to make the transition from passively understanding to actively using evolutionary processes. Today this is possible in Evolutionary Computing, where human experimenters can design and manipulate all components of evolutionary processes in digital spaces. We argue that in the near future it will be possible to implement artificial evolutionary processes outside such imaginary spaces and make them physically embodied. In other words, we envision the "Evolution of Things", rather than just the evolution of digital objects, leading to a new field of Embodied Artificial Evolution (EAE). The main objective of this paper is to present a unifying vision in order to aid the development of this high potential research area. To this end, we introduce the notion of EAE, discuss a few examples and applications, and elaborate on the expected benefits as well as the grand challenges this developing field will have to address.

The drug target genes show higher evolutionary conservation than non-target genes.

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Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

[Evolutionary perspective in precocious puberty].

Science.gov (United States)

Hochberg, Ze'ev

2014-10-01

Pubertal development is subject to substantial heritability, but much variation remains to be explained, including fast changes over the last 150 years, that cannot be explained by changes of gene frequency in the population. This article discusses the influence of environmental factors to adjust maturational tempo in the service of fitness goals. Utilizing evolutionary development thinking (evo-devo), the author examines adolescence as an evolutionary life-history stage in its developmental context. The transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, social needs of adolescence and maturation toward youth and adulthood. Using Belsky's evolutionary theory of socialization, I show that familial psychosocial environment during the infancy-childhood and childhood-juvenility transitions foster a fast life-history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. The implications of the evo-devo framework for theory building, illuminates new directions in the understanding of precocious puberty other than a diagnosis of a disease.

Evolutionary perspectives on ageing.

Science.gov (United States)

Reichard, Martin

2017-10-01

From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ecological opportunity and predator-prey interactions: linking eco-evolutionary processes and diversification in adaptive radiations.

Science.gov (United States)

Pontarp, Mikael; Petchey, Owen L

2018-03-14

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses. © 2018 The Authors.

Soft tissue freezing process. Identification of the dual-phase lag model parameters using the evolutionary algorithm

Science.gov (United States)

Mochnacki, Bohdan; Majchrzak, Ewa; Paruch, Marek

2018-01-01

In the paper the soft tissue freezing process is considered. The tissue sub-domain is subjected to the action of cylindrical cryoprobe. Thermal processes proceeding in the domain considered are described using the dual-phase lag equation (DPLE) supplemented by the appropriate boundary and initial conditions. DPLE results from the generalization of the Fourier law in which two lag times are introduced (relaxation and thermalization times). The aim of research is the identification of these parameters on the basis of measured cooling curves at the set of points selected from the tissue domain. To solve the problem the evolutionary algorithms are used. The paper contains the mathematical model of the tissue freezing process, the very short information concerning the numerical solution of the basic problem, the description of the inverse problem solution and the results of computations.

How evolutionary principles improve the understanding of human health and disease.

Science.gov (United States)

Gluckman, Peter D; Low, Felicia M; Buklijas, Tatjana; Hanson, Mark A; Beedle, Alan S

2011-03-01

An appreciation of the fundamental principles of evolutionary biology provides new insights into major diseases and enables an integrated understanding of human biology and medicine. However, there is a lack of awareness of their importance amongst physicians, medical researchers, and educators, all of whom tend to focus on the mechanistic (proximate) basis for disease, excluding consideration of evolutionary (ultimate) reasons. The key principles of evolutionary medicine are that selection acts on fitness, not health or longevity; that our evolutionary history does not cause disease, but rather impacts on our risk of disease in particular environments; and that we are now living in novel environments compared to those in which we evolved. We consider these evolutionary principles in conjunction with population genetics and describe several pathways by which evolutionary processes can affect disease risk. These perspectives provide a more cohesive framework for gaining insights into the determinants of health and disease. Coupled with complementary insights offered by advances in genomic, epigenetic, and developmental biology research, evolutionary perspectives offer an important addition to understanding disease. Further, there are a number of aspects of evolutionary medicine that can add considerably to studies in other domains of contemporary evolutionary studies.

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

Science.gov (United States)

Lion, Sébastien

2018-01-01

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

Structured synthesis of MEMS using evolutionary approaches

DEFF Research Database (Denmark)

Fan, Zhun; Wang, Jiachuan; Achiche, Sofiane

2008-01-01

In this paper, we discuss the hierarchy that is involved in a typical MEMS design and how evolutionary approaches can be used to automate the hierarchical synthesis process for MEMS. The paper first introduces the flow of a structured MEMS design process and emphasizes that system-level lumped...

Evolutionary Process for Integrating COTS-Based Systems (EPIC): An Overview. Key Elements in Building, Fielding, and Supporting Commercial-off-the-Shelf (COTS) Based Solutions

National Research Council Canada - National Science Library

Albert, Cecilia

2002-01-01

.... The Evolutionary Process for Integrating COTS-based systems (EPIC) redefines acquisition, management, and engineering practices to more effectively leverage the COTS marketplace and other sources of pre-existing components...

Robust and Flexible Scheduling with Evolutionary Computation

DEFF Research Database (Denmark)

Jensen, Mikkel T.

Over the last ten years, there have been numerous applications of evolutionary algorithms to a variety of scheduling problems. Like most other research on heuristic scheduling, the primary aim of the research has been on deterministic formulations of the problems. This is in contrast to real world...... scheduling problems which are usually not deterministic. Usually at the time the schedule is made some information about the problem and processing environment is available, but this information is uncertain and likely to change during schedule execution. Changes frequently encountered in scheduling...... environments include machine breakdowns, uncertain processing times, workers getting sick, materials being delayed and the appearance of new jobs. These possible environmental changes mean that a schedule which was optimal for the information available at the time of scheduling can end up being highly...

Toward a general evolutionary theory of oncogenesis.

Science.gov (United States)

Ewald, Paul W; Swain Ewald, Holly A

2013-01-01

We propose an evolutionary framework, the barrier theory of cancer, which is based on the distinction between barriers to oncogenesis and restraints. Barriers are defined as mechanisms that prevent oncogenesis. Restraints, which are more numerous, inhibit but do not prevent oncogenesis. Processes that compromise barriers are essential causes of cancer; those that interfere with restraints are exacerbating causes. The barrier theory is built upon the three evolutionary processes involved in oncogenesis: natural selection acting on multicellular organisms to mold barriers and restraints, natural selection acting on infectious organisms to abrogate these protective mechanisms, and oncogenic selection which is responsible for the evolution of normal cells into cancerous cells. The barrier theory is presented as a first step toward the development of a general evolutionary theory of cancer. Its attributes and implications for intervention are compared with those of other major conceptual frameworks for understanding cancer: the clonal diversification model, the stem cell theory and the hallmarks of cancer. The barrier theory emphasizes the practical value of distinguishing between essential and exacerbating causes. It also stresses the importance of determining the scope of infectious causation of cancer, because individual pathogens can be responsible for multiple essential causes in infected cells.

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.

[Evolutionary medicine: an introduction. Evolutionary biology, a missing element in medical teaching].

Science.gov (United States)

Swynghedauw, Bernard

2009-05-01

The aim of this brief review article is to help to reconcile medicine with evolutionary biology, a subject that should be taught in medical school. Evolutionary medicine takes the view that contemporary ills are related to an incompatibility between the environment in which humans currently live and their genomes, which have been shaped by diferent environmental conditions during biological evolution. Human activity has recently induced acute environmental modifications that have profoundly changed the medical landscape. Evolutionary biology is an irreversible, ongoing and discontinuous process characterized by periods of stasis followed by accelerations. Evolutionary biology is determined by genetic mutations, which are selected either by Darwinian selective pressure or randomly by genetic drift. Most medical events result from a genome/environment conflict. Some may be purely genetic, as in monogenic diseases, and others purely environmental, such as traffic accidents. Nevertheless, in most common diseases the clinical landscape is determined by the conflict between these two factors, the genetic elements of which are gradually being unraveled Three examples are examined in depth:--The medical consequences of the greenhouse effect. The absence of excess mortality during recent heat waves suggests that the main determinant of mortality in the 2003 heatwave was heatstroke and old age. The projected long-term effects of global warming call for research on thermolysis, a forgotten branch of physiology.--The hygiene hypothesis postulates that the exponential rise in autoimmune and allergic diseases is linked to lesser exposure to infectious agents, possibly involving counter-regulatory factors such as IL-10.--The recent rise in the incidence of obesity and type 2 diabetes in rich countries can be considered to result from a conflict between a calorie-rich environment and gene variants that control appetite. These variants are currently being identified by genome

Evolutionary heritage influences amazon tree ecology

NARCIS (Netherlands)

Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of

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

Science.gov (United States)

Shackelford, Todd K; Liddle, James R

2014-05-01

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

Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.

Science.gov (United States)

Wang, Jiguang; Khiabanian, Hossein; Rossi, Davide; Fabbri, Giulia; Gattei, Valter; Forconi, Francesco; Laurenti, Luca; Marasca, Roberto; Del Poeta, Giovanni; Foà, Robin; Pasqualucci, Laura; Gaidano, Gianluca; Rabadan, Raul

2014-12-11

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

IDEA: Interactive Display for Evolutionary Analyses.

Science.gov (United States)

Egan, Amy; Mahurkar, Anup; Crabtree, Jonathan; Badger, Jonathan H; Carlton, Jane M; Silva, Joana C

2008-12-08

The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

Evolutionary speed limited by water in arid Australia.

Science.gov (United States)

Goldie, Xavier; Gillman, Len; Crisp, Mike; Wright, Shane

2010-09-07

The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.

A study of driver's route choice behavior based on evolutionary game theory.

Science.gov (United States)

Jiang, Xiaowei; Ji, Yanjie; Du, Muqing; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Nature vs. Nurture: The Role of Environmental Resources in Evolutionary Deep Intelligence

OpenAIRE

Chung, Audrey G.; Fieguth, Paul; Wong, Alexander

2018-01-01

Evolutionary deep intelligence synthesizes highly efficient deep neural networks architectures over successive generations. Inspired by the nature versus nurture debate, we propose a study to examine the role of external factors on the network synthesis process by varying the availability of simulated environmental resources. Experimental results were obtained for networks synthesized via asexual evolutionary synthesis (1-parent) and sexual evolutionary synthesis (2-parent, 3-parent, and 5-pa...

[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.

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

NARCIS (Netherlands)

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

2017-01-01

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

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

Science.gov (United States)

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

2016-09-01

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

Applying evolutionary anthropology.

Science.gov (United States)

Gibson, Mhairi A; Lawson, David W

2015-01-01

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

Applying Evolutionary Anthropology

Science.gov (United States)

Gibson, Mhairi A; Lawson, David W

2015-01-01

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

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.

Indoor Thermal Comfort, an Evolutionary Biology Perspective

Energy Technology Data Exchange (ETDEWEB)

Stoops, John L.

2006-04-15

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

Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome.

Science.gov (United States)

Saida, Satoshi; Watanabe, Ken-ichiro; Sato-Otsubo, Aiko; Terui, Kiminori; Yoshida, Kenichi; Okuno, Yusuke; Toki, Tsutomu; Wang, RuNan; Shiraishi, Yuichi; Miyano, Satoru; Kato, Itaru; Morishima, Tatsuya; Fujino, Hisanori; Umeda, Katsutsugu; Hiramatsu, Hidefumi; Adachi, Souichi; Ito, Etsuro; Ogawa, Seishi; Ito, Mamoru; Nakahata, Tatsutoshi; Heike, Toshio

2013-05-23

Transient abnormal myelopoiesis (TAM) is a clonal preleukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, interleukin (IL)-2Rγ(null) mice. Serial engraftment after transplantation of cells from a TAM patient who developed ML-DS a year later demonstrated their self-renewal capacity. A GATA1 mutation and no copy number alterations (CNAs) were detected in the primary patient sample by conventional genomic sequencing and CNA profiling. However, in serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. Detailed genomic analysis identified minor subclones with a 16q deletion or this distinct GATA1 mutation in the primary patient sample. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Our xenograft model of TAM may provide unique insight into the evolutionary process of leukemia.

An evolutionary framework for the Jovian and Saturnian satellites

International Nuclear Information System (INIS)

Stevenson, R.J.

1987-01-01

The position of the satellite within the protonebula, the influence of the parent planet, particularly the relative effects of tidal (gravitational) as opposed to radiogenic (internal) heat generating processes, as well as the type of ice, exert a control on the evolutionary histories of the Jovian and Saturnian satellites. The landscapes of the moons are modified by surface deformational processes (tectonic activity derived from within the body) and externally derived cratering. The geological history of the Galilean satellites is deduced from surface stratigraphic successions of geological units. Io and Europa, with crater-free surfaces, are tectonically more advanced than crater-saturated Callisto. Two thermal-drive models are proposed based on: an expression for externally derived gravitational influences between two bodies; and internal heat generation via radiogenic decay (expressed by surface area/volume ratio). Both parameters, for the Galilean satellites, are plotted against an inferred product of tectonic processes - the age of the surface terrain. From these diagrams, the tectonic evolutionary state of the more distant Saturnian system are predicted. These moons are fitted into an evolutionary framework for the Solar System. 34 refs.; 4 figs.; 2 tabs

Evolutionary Expectations

DEFF Research Database (Denmark)

Nash, Ulrik William

2014-01-01

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

Evolutionary Awareness

Directory of Open Access Journals (Sweden)

Gregory Gorelik

2014-10-01

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

Promoter Motifs in NCLDVs: An Evolutionary Perspective

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Graziele Pereira Oliveira

2017-01-01

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

Promoter Motifs in NCLDVs: An Evolutionary Perspective

Science.gov (United States)

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

2017-01-01

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

Species packing in eco-evolutionary models of seasonally fluctuating environments.

Science.gov (United States)

Kremer, Colin T; Klausmeier, Christopher A

2017-09-01

As ecology and evolution become ever more entwined, many areas of ecological theory are being re-examined. Eco-evolutionary analyses of classic coexistence mechanisms are yielding new insights into the structure and stability of communities. We examine fluctuation-dependent coexistence models, identifying communities that are both ecologically and evolutionarily stable. Members of these communities possess distinct environmental preferences, revealing widespread patterns of limiting similarity. This regularity leads to consistent changes in the structure of communities across fluctuation regimes. However, at high amplitudes, subtle differences in the form of fluctuations dramatically affect the collapse of communities. We also show that identical fluctuations can support multiple evolutionarily stable communities - a novel example of alternative stable states within eco-evolutionary systems. Consequently, the configuration of communities will depend on historical contingencies, including details of the adaptive process. Integrating evolution into the study of coexistence offers new insights, while enriching our understanding of ecology. © 2017 John Wiley & Sons Ltd/CNRS.

IDEA: Interactive Display for Evolutionary Analyses

Directory of Open Access Journals (Sweden)

Carlton Jane M

2008-12-01

Full Text Available Abstract Background The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. Results We have developed IDEA (Interactive Display for Evolutionary Analyses, an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. Conclusion IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

Bone Adaptation as an Evolutionary Process

DEFF Research Database (Denmark)

Bagge, Mette

1998-01-01

. The memory of past loadings is included in themodel to account for the delay in the bone response from the loadchanges. The remodeling rate equation is derived from the structuraloptimization task of maximizing the stiffness in each time step. Additional informationscan be extracted from the optimization...... process; the remodelingequilibrium parameter where no apposition or resorption takes place is defined asthe element optimality conditions and the optimal design is used as aninitial design for the onset ofthe remodeling simulation. Some examples of boneadaptation resulting from load changes is given....

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

Science.gov (United States)

Yaroslavsky, Leonid P.

1996-11-01

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

Attractive evolutionary equilibria

NARCIS (Netherlands)

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

2011-01-01

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

An Improved SPEA2 Algorithm with Adaptive Selection of Evolutionary Operators Scheme for Multiobjective Optimization Problems

Directory of Open Access Journals (Sweden)

Fuqing Zhao

2016-01-01

Full Text Available A fixed evolutionary mechanism is usually adopted in the multiobjective evolutionary algorithms and their operators are static during the evolutionary process, which causes the algorithm not to fully exploit the search space and is easy to trap in local optima. In this paper, a SPEA2 algorithm which is based on adaptive selection evolution operators (AOSPEA is proposed. The proposed algorithm can adaptively select simulated binary crossover, polynomial mutation, and differential evolution operator during the evolutionary process according to their contribution to the external archive. Meanwhile, the convergence performance of the proposed algorithm is analyzed with Markov chain. Simulation results on the standard benchmark functions reveal that the performance of the proposed algorithm outperforms the other classical multiobjective evolutionary algorithms.

Applying ecological and evolutionary theory to cancer: a long and winding road.

Science.gov (United States)

Thomas, Frédéric; Fisher, Daniel; Fort, Philippe; Marie, Jean-Pierre; Daoust, Simon; Roche, Benjamin; Grunau, Christoph; Cosseau, Céline; Mitta, Guillaume; Baghdiguian, Stephen; Rousset, François; Lassus, Patrice; Assenat, Eric; Grégoire, Damien; Missé, Dorothée; Lorz, Alexander; Billy, Frédérique; Vainchenker, William; Delhommeau, François; Koscielny, Serge; Itzykson, Raphael; Tang, Ruoping; Fava, Fanny; Ballesta, Annabelle; Lepoutre, Thomas; Krasinska, Liliana; Dulic, Vjekoslav; Raynaud, Peggy; Blache, Philippe; Quittau-Prevostel, Corinne; Vignal, Emmanuel; Trauchessec, Hélène; Perthame, Benoit; Clairambault, Jean; Volpert, Vitali; Solary, Eric; Hibner, Urszula; Hochberg, Michael E

2013-01-01

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed on applications of evolutionary biology to understanding and controlling neoplastic progression and to prevent therapeutic failures. This is now beginning to change, and there is a growing international interest in the interface between cancer and evolutionary biology. The objective of this introduction is first to describe the basic ideas and concepts linking evolutionary biology to cancer. We then present four major fronts where the evolutionary perspective is most developed, namely laboratory and clinical models, mathematical models, databases, and techniques and assays. Finally, we discuss several of the most promising challenges and future prospects in this interdisciplinary research direction in the war against cancer.

A New DG Multiobjective Optimization Method Based on an Improved Evolutionary Algorithm

Directory of Open Access Journals (Sweden)

Wanxing Sheng

2013-01-01

Full Text Available A distribution generation (DG multiobjective optimization method based on an improved Pareto evolutionary algorithm is investigated in this paper. The improved Pareto evolutionary algorithm, which introduces a penalty factor in the objective function constraints, uses an adaptive crossover and a mutation operator in the evolutionary process and combines a simulated annealing iterative process. The proposed algorithm is utilized to the optimize DG injection models to maximize DG utilization while minimizing system loss and environmental pollution. A revised IEEE 33-bus system with multiple DG units was used to test the multiobjective optimization algorithm in a distribution power system. The proposed algorithm was implemented and compared with the strength Pareto evolutionary algorithm 2 (SPEA2, a particle swarm optimization (PSO algorithm, and nondominated sorting genetic algorithm II (NGSA-II. The comparison of the results demonstrates the validity and practicality of utilizing DG units in terms of economic dispatch and optimal operation in a distribution power system.

Exponential Expansion in Evolutionary Economics

DEFF Research Database (Denmark)

Frederiksen, Peter; Jagtfelt, Tue

2013-01-01

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

An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

Directory of Open Access Journals (Sweden)

Afnizanfaizal Abdullah

Full Text Available The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

Science.gov (United States)

Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N V

2013-01-01

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

A Study of Driver’s Route Choice Behavior Based on Evolutionary Game Theory

Directory of Open Access Journals (Sweden)

Xiaowei Jiang

2014-01-01

Full Text Available This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers’ route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver’s route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver’s route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Open Issues in Evolutionary Robotics.

Science.gov (United States)

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

2016-01-01

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

Incorporating Development Into Evolutionary Psychology

Directory of Open Access Journals (Sweden)

David F. Bjorklund

2016-09-01

Full Text Available Developmental thinking is gradually becoming integrated within mainstream evolutionary psychology. This is most apparent with respect to the role of parenting, with proponents of life history theory arguing that cognitive and behavioral plasticity early in life permits children to select different life history strategies, with such strategies being adaptive solutions to different fitness trade-offs. I argue that adaptations develop and are based on the highly plastic nature of infants’ and children’s behavior/cognition/brains. The concept of evolved probabilistic cognitive mechanisms is introduced, defined as information processing mechanisms evolved to solve recurrent problems faced by ancestral populations that are expressed in a probabilistic fashion in each individual in a generation and are based on the continuous and bidirectional interaction over time at all levels of organization, from the genetic through the cultural. Early perceptual/cognitive biases result in behavior that, when occurring in a species-typical environment, produce continuous adaptive changes in behavior (and cognition, yielding adaptive outcomes. Examples from social learning and tool use are provided, illustrating the development of adaptations via evolved probabilistic cognitive mechanisms. The integration of developmental concepts into mainstream evolutionary psychology (and evolutionary concepts into mainstream developmental psychology will provide a clearer picture of what it means to be human.

Evolutionary games under incompetence.

Science.gov (United States)

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

2018-02-26

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

Human compulsivity: A perspective from evolutionary medicine.

Science.gov (United States)

Stein, Dan J; Hermesh, Haggai; Eilam, David; Segalas, Cosi; Zohar, Joseph; Menchon, Jose; Nesse, Randolph M

2016-05-01

Biological explanations address not only proximal mechanisms (for example, the underlying neurobiology of obsessive-compulsive disorder), but also distal mechanisms (that is, a consideration of how particular neurobiological mechanisms evolved). Evolutionary medicine has emphasized a series of explanations for vulnerability to disease, including constraints, mismatch, and tradeoffs. The current paper will consider compulsive symptoms in obsessive-compulsive and related disorders and behavioral addictions from this evolutionary perspective. It will argue that while obsessive-compulsive disorder (OCD) is typically best conceptualized as a dysfunction, it is theoretically and clinically valuable to understand some symptoms of obsessive-compulsive and related disorders in terms of useful defenses. The symptoms of behavioral addictions can also be conceptualized in evolutionary terms (for example, mismatch), which in turn provides a sound foundation for approaching assessment and intervention. Copyright © 2016. Published by Elsevier B.V.

On the evolution of misunderstandings about evolutionary psychology.

Science.gov (United States)

Young, J; Persell, R

2000-04-01

Some of the controversy surrounding evolutionary explanations of human behavior may be due to cognitive information-processing patterns that are themselves the result of evolutionary processes. Two such patterns are (1) the tendency to oversimplify information so as to reduce demand on cognitive resources and (2) our strong desire to generate predictability and stability from perceptions of the external world. For example, research on social stereotyping has found that people tend to focus automatically on simplified social-categorical information, to use such information when deciding how to behave, and to rely on such information even in the face of contradictory evidence. Similarly, an undying debate over nature vs. nurture is shaped by various data-reduction strategies that frequently oversimplify, and thus distort, the intent of the supporting arguments. This debate is also often marked by an assumption that either the nature or the nurture domain may be justifiably excluded at an explanatory level because one domain appears to operate in a sufficiently stable and predictable way for a particular argument. As a result, critiques in-veighed against evolutionary explanations of behavior often incorporate simplified--and erroneous--assumptions about either the mechanics of how evolution operates or the inevitable implications of evolution for understanding human behavior. The influences of these tendencies are applied to a discussion of the heritability of behavioral characteristics. It is suggested that the common view that Mendelian genetics can explain the heritability of complex behaviors, with a one-gene-one-trait process, is misguided. Complex behaviors are undoubtedly a product of a more complex interaction between genes and environment, ensuring that both nature and nurture must be accommodated in a yet-to-be-developed post-Mendelian model of genetic influence. As a result, current public perceptions of evolutionary explanations of behavior are

Langley's CSI evolutionary model: Phase O

Science.gov (United States)

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

1991-01-01

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

A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

Science.gov (United States)

Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

2014-01-01

Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research

Science.gov (United States)

Piperno, Dolores R.

2017-01-01

The development of agricultural societies, one of the most transformative events in human and ecological history, was made possible by plant and animal domestication. Plant domestication began 12,000–10,000 y ago in a number of major world areas, including the New World tropics, Southwest Asia, and China, during a period of profound global environmental perturbations as the Pleistocene epoch ended and transitioned into the Holocene. Domestication is at its heart an evolutionary process, and for many prehistorians evolutionary theory has been foundational in investigating agricultural origins. Similarly, geneticists working largely with modern crops and their living wild progenitors have documented some of the mechanisms that underwrote phenotypic transformations from wild to domesticated species. Ever-improving analytic methods for retrieval of empirical data from archaeological sites, together with advances in genetic, genomic, epigenetic, and experimental research on living crop plants and wild progenitors, suggest that three fields of study currently little applied to plant domestication processes may be necessary to understand these transformations across a range of species important in early prehistoric agriculture. These fields are phenotypic (developmental) plasticity, niche construction theory, and epigenetics with transgenerational epigenetic inheritance. All are central in a controversy about whether an Extended Evolutionary Synthesis is needed to reconceptualize how evolutionary change occurs. An exploration of their present and potential utility in domestication study shows that all three fields have considerable promise in elucidating important issues in plant domestication and in agricultural origin and dispersal research and should be increasingly applied to these issues. PMID:28576881

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

Science.gov (United States)

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

2016-01-01

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

Ecological and evolutionary consequences of niche construction for its agent.

Science.gov (United States)

Kylafis, Grigoris; Loreau, Michel

2008-10-01

Niche construction can generate ecological and evolutionary feedbacks that have been underinvestigated so far. We present an eco-evolutionary model that incorporates the process of niche construction to reveal its effects on the ecology and evolution of the niche-constructing agent. We consider a simple plant-soil nutrient ecosystem in which plants have the ability to increase the input of inorganic nutrient as an example of positive niche construction. On an ecological time scale, the model shows that niche construction allows the persistence of plants under infertile soil conditions that would otherwise lead to their extinction. This expansion of plants' niche, however, requires a high enough rate of niche construction and a high enough initial plant biomass to fuel the positive ecological feedback between plants and their soil environment. On an evolutionary time scale, we consider that the rates of niche construction and nutrient uptake coevolve in plants while a trade-off constrains their values. Different evolutionary outcomes are possible depending on the shape of the trade-off. We show that niche construction results in an evolutionary feedback between plants and their soil environment such that plants partially regulate soil nutrient content. The direct benefit accruing to plants, however, plays a crucial role in the evolutionary advantage of niche construction.

Spatial evolutionary epidemiology of spreading epidemics.

Science.gov (United States)

Lion, S; Gandon, S

2016-10-26

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

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

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Sandra Olliges

2010-10-01

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

The Explanatory Value of Inclusive Fitness for Evolutionary Theory

OpenAIRE

Rubin, Hannah

2017-01-01

At the heart of evolutionary theory is the concept of 'fitness', which is, standardly, an organism's reproductive success. Many evolutionary theorists argue, however, that to explain the evolution of social traits, such as altruism, we must use a different notion of fitness. This 'inclusive fitness', which includes the reproductive success of relatives, is seen as indispensable for studying social evolution. Recently, however, both biologists and philosophers have critically scrutinized its s...

Towards Automatic Controller Design using Multi-Objective Evolutionary Algorithms

DEFF Research Database (Denmark)

Pedersen, Gerulf

of evolutionary computation, a choice was made to use multi-objective algorithms for the purpose of aiding in automatic controller design. More specifically, the choice was made to use the Non-dominated Sorting Genetic Algorithm II (NSGAII), which is one of the most potent algorithms currently in use...... for automatic controller design. However, because the field of evolutionary computation is relatively unknown in the field of control engineering, this thesis also includes a comprehensive introduction to the basic field of evolutionary computation as well as a description of how the field has previously been......In order to design the controllers of tomorrow, a need has risen for tools that can aid in the design of these. A desire to use evolutionary computation as a tool to achieve that goal is what gave inspiration for the work contained in this thesis. After having studied the foundations...

Using Evolutionary Data in Developing Phylogenetic Trees: A Scaffolded Approach with Authentic Data

Science.gov (United States)

Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

2015-01-01

Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships between ungulates, then construct a scientific argument…

Extrapolating Weak Selection in Evolutionary Games

Science.gov (United States)

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

2013-01-01

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

Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

International Nuclear Information System (INIS)

Mahony, Jennifer; Ainsworth, Stuart; Stockdale, Stephen; Sinderen, Douwe van

2012-01-01

Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

Energy Technology Data Exchange (ETDEWEB)

Mahony, Jennifer, E-mail: j.mahony@ucc.ie [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Ainsworth, Stuart; Stockdale, Stephen [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Sinderen, Douwe van, E-mail: d.vansinderen@ucc.ie [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Western Road, Cork (Ireland)

2012-12-20

Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

Universal Darwinism As a Process of Bayesian Inference.

Science.gov (United States)

Campbell, John O

2016-01-01

Many of the mathematical frameworks describing natural selection are equivalent to Bayes' Theorem, also known as Bayesian updating. By definition, a process of Bayesian Inference is one which involves a Bayesian update, so we may conclude that these frameworks describe natural selection as a process of Bayesian inference. Thus, natural selection serves as a counter example to a widely-held interpretation that restricts Bayesian Inference to human mental processes (including the endeavors of statisticians). As Bayesian inference can always be cast in terms of (variational) free energy minimization, natural selection can be viewed as comprising two components: a generative model of an "experiment" in the external world environment, and the results of that "experiment" or the "surprise" entailed by predicted and actual outcomes of the "experiment." Minimization of free energy implies that the implicit measure of "surprise" experienced serves to update the generative model in a Bayesian manner. This description closely accords with the mechanisms of generalized Darwinian process proposed both by Dawkins, in terms of replicators and vehicles, and Campbell, in terms of inferential systems. Bayesian inference is an algorithm for the accumulation of evidence-based knowledge. This algorithm is now seen to operate over a wide range of evolutionary processes, including natural selection, the evolution of mental models and cultural evolutionary processes, notably including science itself. The variational principle of free energy minimization may thus serve as a unifying mathematical framework for universal Darwinism, the study of evolutionary processes operating throughout nature.

Evolutionary Dynamics and Diversity in Microbial Populations

Science.gov (United States)

Thompson, Joel; Fisher, Daniel

2013-03-01

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

The Role of Affordances in the Evolutionary Process Reconsidered A Niche Construction Perspective

NARCIS (Netherlands)

Withagen, Rob; van Wermeskerken, Margot

Gibson asserted that affordances are the primary objects of perception. Although this assertion is especially attractive when considered in the context of evolutionary theory, the role that affordances play in the evolution of animals' perceptual and action systems is still unclear. Trying to

Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping.

Directory of Open Access Journals (Sweden)

Yoshinobu Uno

Full Text Available Comparative genome analysis of non-avian reptiles and amphibians provides important clues about the process of genome evolution in tetrapods. However, there is still only limited information available on the genome structures of these organisms. Consequently, the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes in tetrapods remain poorly understood. We constructed chromosome maps of functional genes for the Chinese soft-shelled turtle (Pelodiscus sinensis, the Siamese crocodile (Crocodylus siamensis, and the Western clawed frog (Xenopus tropicalis and compared them with genome and/or chromosome maps of other tetrapod species (salamander, lizard, snake, chicken, and human. This is the first report on the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes inferred from comparative genomic analysis of vertebrates, which cover all major non-avian reptilian taxa (Squamata, Crocodilia, Testudines. The eight largest macrochromosomes of the turtle and chicken were equivalent, and 11 linkage groups had also remained intact in the crocodile. Linkage groups of the chicken macrochromosomes were also highly conserved in X. tropicalis, two squamates, and the salamander, but not in human. Chicken microchromosomal linkages were conserved in the squamates, which have fewer microchromosomes than chicken, and also in Xenopus and the salamander, which both lack microchromosomes; in the latter, the chicken microchromosomal segments have been integrated into macrochromosomes. Our present findings open up the possibility that the ancestral amniotes and tetrapods had at least 10 large genetic linkage groups and many microchromosomes, which corresponded to the chicken macro- and microchromosomes, respectively. The turtle and chicken might retain the microchromosomes of the amniote protokaryotype almost intact. The decrease in number and/or disappearance of microchromosomes by repeated

Darwin’s legacy in South African evolutionary biology

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S. D. Johnson

2010-02-01

Full Text Available In the two decades after publication of the Origin of Species, Charles Darwin facilitated the publication of numerous scientific papers by settler naturalists in South Africa. This helped to establish the strong tradition of natural history which has characterised evolutionary research in South African museums, herbaria and universities. Significant developments in the early 20th century included the hominid fossil discoveries of Raymond Dart, Robert Broom, and others, but there was otherwise very little South African involvement in the evolutionary synthesis of the 1930s and 1940s. Evolutionary biology developed into a distinct discipline in South Africa during the 1970s and 1980s when it was dominated by mammalian palaeontology and a vigorous debate around species concepts. In the post-apartheid era, the main focus of evolutionary biology has been the construction of phylogenies for African plants and animals using molecular data, and the use of these phylogenies to answer questions about taxonomic classification and trait evolution. South African biologists have also recently contributed important evidence for some of Darwin’s ideas about plant–animal coevolution, sexual selection, and the role of natural selection in speciation. A bibliographic analysis shows that South African authors produce 2–3% of the world’s publications in the field of evolutionary biology, which is much higher than the value of about 0.5% for publications in all sciences. With its extraordinary biodiversity and well-developed research infrastructure, South Africa is an ideal laboratory from which to advance evolutionary research.

Symbionticism revisited: a discussion of the evolutionary impact of intracellular symbioses.

Science.gov (United States)

Taylor, F J

1979-04-11

Wallin (1927) first published the notion that the fusion of bacteria with host cells was the principal source of genetic novelty for speciation. He suggested that mitochondria are transitional elements in this process. While the significance that he attributed to symbiosis now seem excessive, he was one of the first authors to be aware of the evolutionary potential of symbiotic events and his view of mitochondria may not seem strange to many cell biologist today. The most significant evolutionary development which has been attributed to intracellular symbiosis is the origin of eukaryotic cellular organization. The current status of the 'serial endosymbiosis hypothesis' is briefly review. The case for the symbiotic origin of the chloroplast, based principally on 16 S RNA oligonucleotide cataloguing, is very strong. Mitochondrial origins are more obscure but also appear to be symbiotic due to recent 18 S cataloguing from wheat embryos. The probablility of the multiple origin of some eukaryotic organelles is also examined, the processes in question being the acquisition of distinct stocks of chloroplasts from disparate photosynthetic prokaryotes and the secondary donation of organelles from degenerate eukaryotic endosymbionts to their hosts, with specific reference to the dinoflagellates Peridinium balticum, Kryptoperidinium foliaceum and the ciliate Mesodinium rubrum. It is concluded that the evolutionary potential of intracellular symbiosis ('cytobiosis': a term introduced in this paper) is great, with the best established influence being on the origin of eukaryotic chloroplasts. Together with the potential effects of viral vectors, symbiosis serves as a supplementary speciation mechanism capable of producing directed evolutionary changes. It is likely that these processes will explain some of the apparent anomalies in evolutionary rates and direction which are not readily explicable by the conventional synthetic theory of evolution.

Creating ensembles of oblique decision trees with evolutionary algorithms and sampling

Science.gov (United States)

Cantu-Paz, Erick [Oakland, CA; Kamath, Chandrika [Tracy, CA

2006-06-13

A decision tree system that is part of a parallel object-oriented pattern recognition system, which in turn is part of an object oriented data mining system. A decision tree process includes the step of reading the data. If necessary, the data is sorted. A potential split of the data is evaluated according to some criterion. An initial split of the data is determined. The final split of the data is determined using evolutionary algorithms and statistical sampling techniques. The data is split. Multiple decision trees are combined in ensembles.

Attractive evolutionary equilibria

OpenAIRE

Roorda, Berend; Joosten, Reinoud

2011-01-01

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

Lessons in modularity: the evolutionary ecology of colonial invertebrates

Directory of Open Access Journals (Sweden)

Roger N. Hughes

2005-06-01

Full Text Available Benthic colonial invertebrates share with higher plants a modular construction and a sessile adult life. Both types of organism show parallel evolutionary responses to common selective forces, but in contrast to the long-established focus on plants, comparable study of colonial invertebrates has developed relatively recently, largely owing to the application of new techniques in image processing and molecular biology. Species whose life cycles are readily completed under laboratory conditions and whose colonies are easily propagated from cuttings provide powerful models for experimentally investigating fundamental evolutionary problems, including metabolic allometry, the manifestation of ageing and the origin of allorecognition systems. Free of the confounding influences of behavioural manipulation and costs of copulation, colonial invertebrates whose water-borne sperm fertilize retained eggs lend themselves well to the experimental study of cryptic female choice, sperm competition and sexual conflict. In these respects, it will be productive to adopt and extend theoretical frameworks developed for flowering plants to guide experimental investigation of modular animals. Since mate choice occurs at the cellular level in modular animals, reproductive isolation is uncorrelated with morphology and cryptic speciation is likely to be widespread.

The concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing.

Science.gov (United States)

Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos

2017-04-01

This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-objective evolutionary algorithms for fuzzy classification in survival prediction.

Science.gov (United States)

Jiménez, Fernando; Sánchez, Gracia; Juárez, José M

2014-03-01

This paper presents a novel rule-based fuzzy classification methodology for survival/mortality prediction in severe burnt patients. Due to the ethical aspects involved in this medical scenario, physicians tend not to accept a computer-based evaluation unless they understand why and how such a recommendation is given. Therefore, any fuzzy classifier model must be both accurate and interpretable. The proposed methodology is a three-step process: (1) multi-objective constrained optimization of a patient's data set, using Pareto-based elitist multi-objective evolutionary algorithms to maximize accuracy and minimize the complexity (number of rules) of classifiers, subject to interpretability constraints; this step produces a set of alternative (Pareto) classifiers; (2) linguistic labeling, which assigns a linguistic label to each fuzzy set of the classifiers; this step is essential to the interpretability of the classifiers; (3) decision making, whereby a classifier is chosen, if it is satisfactory, according to the preferences of the decision maker. If no classifier is satisfactory for the decision maker, the process starts again in step (1) with a different input parameter set. The performance of three multi-objective evolutionary algorithms, niched pre-selection multi-objective algorithm, elitist Pareto-based multi-objective evolutionary algorithm for diversity reinforcement (ENORA) and the non-dominated sorting genetic algorithm (NSGA-II), was tested using a patient's data set from an intensive care burn unit and a standard machine learning data set from an standard machine learning repository. The results are compared using the hypervolume multi-objective metric. Besides, the results have been compared with other non-evolutionary techniques and validated with a multi-objective cross-validation technique. Our proposal improves the classification rate obtained by other non-evolutionary techniques (decision trees, artificial neural networks, Naive Bayes, and case

The role of rules in the evolution of the market system: Hayek’s concept of evolutionary epistemology

Directory of Open Access Journals (Sweden)

Krstić Miloš

2012-01-01

Full Text Available Starting from the concept of the Darwinian paradigm that, by using Darwin’s principles of variation, selection, and retention, all domains from biology to economic systems can be explained, the advocates of modern evolutionary epistemology have analyzed the role of thoughtful institutional design in the process of cultural evolution. In light of the issue of how human intention and evolutionary forces interact in socioeconomic processes, this paper examines the views of F. A. Hayek, the most famous follower of evolutionary epistemology, on the evolution of the market economy system. In this paper special attention will be devoted to Hayek’s concept of rational liberalism and his evolutionary epistemology. [Ministarstva nauke Republike Srbije, br. 179066: Improving the Competitiveness of the Public and Private Sectors by Networking Competences in the European Integration Process of Serbia

[Evolutionary medicine: A new look on health and disease].

Science.gov (United States)

Bauduer, F

2017-03-01

Evolutionary medicine represents an innovative approach deriving from evolutionary biology. It includes the initial Darwin's view, its actualization in the light of progresses in genetics and also dissident theories (i.e. non gene-based) particularly epigenetics. This approach enables us to reconsider the pathophysiology of numerous diseases, as for instance, infection, and our so-called diseases of civilization especially obesity, type 2 diabetes, allergy or cancer. Evolutionary medicine may also improve our knowledge regarding inter-individual variation in susceptibility to disease or drugs. Furthermore, it points out the impact of our behaviors and environment on the genesis of a series of diseases. Copyright © 2016 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

Double-dealing behavior potentially promotes cooperation in evolutionary prisoner's dilemma games

Science.gov (United States)

Dai, Qionglin; Li, Haihong; Cheng, Hongyan; Li, Yuting; Yang, Junzhong

2010-11-01

We investigate the effects of double-dealing behavior on cooperation in evolutionary games. Each individual in a population has two attributes: character and action. One's action may be consistent with one's character or not. We provide analytical results by a mean-field description of evolutionary prisoner's dilemma games (PDGs). Moreover, we give numerical results on different networks, ranging from square lattices to scale-free networks (SFNs). Two important conclusions have been drawn from the results on SFNs. Firstly, if only non-influential individuals (those with low degrees) have chances of becoming double-dealers, cooperation is certain to deteriorate. Secondly, when influential individuals (those with high degrees) adopt double-dealing behavior moderately, cooperation would be enhanced, which is in opposition to the traditional belief. These results help us to understand better the social phenomenon of the existence of double-dealers. In addition to the PDG, other types of games including the snowdrift game, the stag-hunt game and the harmony game have also been studied on our model. The results for these three games are also presented, which are consistent with the results for the PDG qualitatively. Furthermore, we consider our model under the co-evolution framework, in which the probability of an individual changing into a double-dealer and the individual strategy both could evolve during the evolutionary process.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

Science.gov (United States)

Mishra, Bud; Daruwala, Raoul-Sam; Zhou, Yi; Ugel, Nadia; Policriti, Alberto; Antoniotti, Marco; Paxia, Salvatore; Rejali, Marc; Rudra, Archisman; Cherepinsky, Vera; Silver, Naomi; Casey, William; Piazza, Carla; Simeoni, Marta; Barbano, Paolo; Spivak, Marina; Feng, Jiawu; Gill, Ofer; Venkatesh, Mysore; Cheng, Fang; Sun, Bing; Ioniata, Iuliana; Anantharaman, Thomas; Hubbard, E Jane Albert; Pnueli, Amir; Harel, David; Chandru, Vijay; Hariharan, Ramesh; Wigler, Michael; Park, Frank; Lin, Shih-Chieh; Lazebnik, Yuri; Winkler, Franz; Cantor, Charles R; Carbone, Alessandra; Gromov, Mikhael

2003-01-01

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

A quantitative evolutionary theory of adaptive behavior dynamics.

Science.gov (United States)

McDowell, J J

2013-10-01

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

Evolutionary dynamics of a smoothed war of attrition game.

Science.gov (United States)

Iyer, Swami; Killingback, Timothy

2016-05-07

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

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

Science.gov (United States)

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

Evolutionary biology: a basic science for medicine in the 21st century.

Science.gov (United States)

Perlman, Robert L

2011-01-01

Evolutionary biology was a poorly developed discipline at the time of the Flexner Report and was not included in Flexner's recommendations for premedical or medical education. Since that time, however, the value of an evolutionary approach to medicine has become increasingly recognized. There are several ways in which an evolutionary perspective can enrich medical education and improve medical practice. Evolutionary considerations rationalize our continued susceptibility or vulnerability to disease; they call attention to the idea that the signs and symptoms of disease may be adaptations that prevent or limit the severity of disease; they help us understand the ways in which our interventions may affect the evolution of microbial pathogens and of cancer cells; and they provide a framework for thinking about population variation and risk factors for disease. Evolutionary biology should become a foundational science for the medical education of the future.

Biological causal links on physiological and evolutionary time scales.

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Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Universal Darwinism as a process of Bayesian inference

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John Oberon Campbell

2016-06-01

Full Text Available Many of the mathematical frameworks describing natural selection are equivalent to Bayes’ Theorem, also known as Bayesian updating. By definition, a process of Bayesian Inference is one which involves a Bayesian update, so we may conclude that these frameworks describe natural selection as a process of Bayesian inference. Thus natural selection serves as a counter example to a widely-held interpretation that restricts Bayesian Inference to human mental processes (including the endeavors of statisticians. As Bayesian inference can always be cast in terms of (variational free energy minimization, natural selection can be viewed as comprising two components: a generative model of an ‘experiment’ in the external world environment, and the results of that 'experiment' or the 'surprise' entailed by predicted and actual outcomes of the ‘experiment’. Minimization of free energy implies that the implicit measure of 'surprise' experienced serves to update the generative model in a Bayesian manner. This description closely accords with the mechanisms of generalized Darwinian process proposed both by Dawkins, in terms of replicators and vehicles, and Campbell, in terms of inferential systems. Bayesian inference is an algorithm for the accumulation of evidence-based knowledge. This algorithm is now seen to operate over a wide range of evolutionary processes, including natural selection, the evolution of mental models and cultural evolutionary processes, notably including science itself. The variational principle of free energy minimization may thus serve as a unifying mathematical framework for universal Darwinism, the study of evolutionary processes operating throughout nature.

An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

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Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

2015-01-01

Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

The Neural Systems of Forgiveness: An Evolutionary Psychological Perspective

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Joseph Billingsley

2017-05-01

Full Text Available Evolution-minded researchers posit that the suite of human cognitive adaptations may include forgiveness systems. According to these researchers, forgiveness systems regulate interpersonal motivation toward a transgressor in the wake of harm by weighing multiple factors that influence both the potential gains of future interaction with the transgressor and the likelihood of future harm. Although behavioral research generally supports this evolutionary model of forgiveness, the model’s claims have not been examined with available neuroscience specifically in mind, nor has recent neuroscientific research on forgiveness generally considered the evolutionary literature. The current review aims to help bridge this gap by using evolutionary psychology and cognitive neuroscience to mutually inform and interrogate one another. We briefly summarize the evolutionary research on forgiveness, then review recent neuroscientific findings on forgiveness in light of the evolutionary model. We emphasize neuroscientific research that links desire for vengeance to reward-based areas of the brain, that singles out prefrontal areas likely associated with inhibition of vengeful feelings, and that correlates the activity of a theory-of-mind network with assessments of the intentions and blameworthiness of those who commit harm. In addition, we identify gaps in the existing neuroscientific literature, and propose future research directions that might address them, at least in part.

Evolutionary Explanations of Eating Disorders

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Igor Kardum

2008-12-01

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

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

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Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

2018-04-24

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed

The citation field of evolutionary economics

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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

Ecological and evolutionary impacts of changing climatic variability.

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Vázquez, Diego P; Gianoli, Ernesto; Morris, William F; Bozinovic, Francisco

2017-02-01

While average temperature is likely to increase in most locations on Earth, many places will simultaneously experience higher variability in temperature, precipitation, and other climate variables. Although ecologists and evolutionary biologists widely recognize the potential impacts of changes in average climatic conditions, relatively little attention has been paid to the potential impacts of changes in climatic variability and extremes. We review the evidence on the impacts of increased climatic variability and extremes on physiological, ecological and evolutionary processes at multiple levels of biological organization, from individuals to populations and communities. Our review indicates that climatic variability can have profound influences on biological processes at multiple scales of organization. Responses to increased climatic variability and extremes are likely to be complex and cannot always be generalized, although our conceptual and methodological toolboxes allow us to make informed predictions about the likely consequences of such climatic changes. We conclude that climatic variability represents an important component of climate that deserves further attention. © 2015 Cambridge Philosophical Society.

Synthesis of logic circuits with evolutionary algorithms

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JONES,JAKE S.; DAVIDSON,GEORGE S.

2000-01-26

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

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

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Horváth, Denis; Kuscsik, Zoltán; Gmitra, Martin

2006-09-01

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

An evolutionary perspective on anti-tumor immunity

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David John Klinke

2013-01-01

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

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

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Hunt, Tam

2014-12-01

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

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

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Austen L. Krill

2007-01-01

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

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

International Nuclear Information System (INIS)

Quan Ji; Wang Xianjia

2013-01-01

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

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.

Different evolutionary pathways underlie the morphology of wrist bones in hominoids.

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Kivell, Tracy L; Barros, Anna P; Smaers, Jeroen B

2013-10-23

The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context.We identify morphological features that principally characterize primate - and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones - the scaphoid, lunate, triquetrum, capitate and hamate - are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist

Defensive traits exhibit an evolutionary trade-off and drive diversification in ants.

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Blanchard, Benjamin D; Moreau, Corrie S

2017-02-01

Evolutionary biologists have long predicted that evolutionary trade-offs among traits should constrain morphological divergence and species diversification. However, this prediction has yet to be tested in a broad evolutionary context in many diverse clades, including ants. Here, we reconstruct an expanded ant phylogeny representing 82% of ant genera, compile a new family-wide trait database, and conduct various trait-based analyses to show that defensive traits in ants do exhibit an evolutionary trade-off. In particular, the use of a functional sting negatively correlates with a suite of other defensive traits including spines, large eye size, and large colony size. Furthermore, we find that several of the defensive traits that trade off with a sting are also positively correlated with each other and drive increased diversification, further suggesting that these traits form a defensive suite. Our results support the hypothesis that trade-offs in defensive traits significantly constrain trait evolution and influence species diversification in ants. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

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

2017-10-01

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

Integrating genomics into evolutionary medicine.

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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.

Brief Communication: Quantitative- and molecular-genetic differentiation in humans and chimpanzees: implications for the evolutionary processes underlying cranial diversification.

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Weaver, Timothy D

2014-08-01

Estimates of the amount of genetic differentiation in humans among major geographic regions (e.g., Eastern Asia vs. Europe) from quantitative-genetic analyses of cranial measurements closely match those from classical- and molecular-genetic markers. Typically, among-region differences account for ∼10% of the total variation. This correspondence is generally interpreted as evidence for the importance of neutral evolutionary processes (e.g., genetic drift) in generating among-region differences in human cranial form, but it was initially surprising because human cranial diversity was frequently assumed to show a strong signature of natural selection. Is the human degree of similarity of cranial and DNA-sequence estimates of among-region genetic differentiation unusual? How do comparisons with other taxa illuminate the evolutionary processes underlying cranial diversification? Chimpanzees provide a useful starting point for placing the human results in a broader comparative context, because common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the extant species most closely related to humans. To address these questions, I used 27 cranial measurements collected on a sample of 861 humans and 263 chimpanzees to estimate the amount of genetic differentiation between pairs of groups (between regions for humans and between species or subspecies for chimpanzees). Consistent with previous results, the human cranial estimates are quite similar to published DNA-sequence estimates. In contrast, the chimpanzee cranial estimates are much smaller than published DNA-sequence estimates. It appears that cranial differentiation has been limited in chimpanzees relative to humans. © 2014 Wiley Periodicals, Inc.

Evolutionary approaches to cultural and linguistic diversity.

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Steele, James; Jordan, Peter; Cochrane, Ethan

2010-12-12

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

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

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Riboldi, M; Baroni, G; Spadea, M F; Tagaste, B; Garibaldi, C; Cambria, R; Orecchia, R; Pedotti, A

2007-01-01

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

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

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Weaver, Steven; Shank, Stephen D; Spielman, Stephanie J; Li, Michael; Muse, Spencer V; Kosakovsky Pond, Sergei L

2018-01-02

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally-executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey. org, and the underlying codebase is available from https://github.com/veg/datamonkey-js. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Attachment in Middle Childhood: An Evolutionary-Developmental Perspective

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Del Giudice, Marco

2015-01-01

Middle childhood is a key transitional stage in the development of attachment processes and representations. Here I discuss the middle childhood transition from an evolutionary-developmental perspective and show how this approach offers fresh insight into the function and organization of attachment in this life stage. I begin by presenting an…

Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

Indian Academy of Sciences (India)

A hundred years is but an instant in evolutionary time; however during his life that spanned a century, Ernst Mayr (1904-2005) made outstanding contributions to our understanding of the pat- tern and process of evolution. An ornithologist and systematist by training, Mayr embraced Darwinism and championed the cause of.

Evolutionary analysis of FAM83H in vertebrates.

Directory of Open Access Journals (Sweden)

Wushuang Huang

Full Text Available Amelogenesis imperfecta is a group of disorders causing abnormalities in enamel formation in various phenotypes. Many mutations in the FAM83H gene have been identified to result in autosomal dominant hypocalcified amelogenesis imperfecta in different populations. However, the structure and function of FAM83H and its pathological mechanism have yet to be further explored. Evolutionary analysis is an alternative for revealing residues or motifs that are important for protein function. In the present study, we chose 50 vertebrate species in public databases representative of approximately 230 million years of evolution, including 1 amphibian, 2 fishes, 7 sauropsidas and 40 mammals, and we performed evolutionary analysis on the FAM83H protein. By sequence alignment, conserved residues and motifs were indicated, and the loss of important residues and motifs of five special species (Malayan pangolin, platypus, minke whale, nine-banded armadillo and aardvark was discovered. A phylogenetic time tree showed the FAM83H divergent process. Positive selection sites in the C-terminus suggested that the C-terminus of FAM83H played certain adaptive roles during evolution. The results confirmed some important motifs reported in previous findings and identified some new highly conserved residues and motifs that need further investigation. The results suggest that the C-terminus of FAM83H contain key conserved regions critical to enamel formation and calcification.

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.

Development links psychological causes to evolutionary explanations.

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Fedyk, Mark; Kushnir, Tamar

2014-04-01

Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.

Regulatory RNA design through evolutionary computation and strand displacement.

Science.gov (United States)

Rostain, William; Landrain, Thomas E; Rodrigo, Guillermo; Jaramillo, Alfonso

2015-01-01

The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.

Evolutionary Multiplayer Games

OpenAIRE

Gokhale, Chaitanya S.; Traulsen, Arne

2014-01-01

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

Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora

Directory of Open Access Journals (Sweden)

Stephanie eBollmann

2016-03-01

Full Text Available Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL, and RNA-dependent RNA polymerase (RDR through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.

Comparative Study of Evolutionary Multi-objective Optimization Algorithms for a Non-linear Greenhouse Climate Control Problem

DEFF Research Database (Denmark)

Ghoreishi, Newsha; Sørensen, Jan Corfixen; Jørgensen, Bo Nørregaard

2015-01-01

Non-trivial real world decision-making processes usually involve multiple parties having potentially conflicting interests over a set of issues. State-of-the-art multi-objective evolutionary algorithms (MOEA) are well known to solve this class of complex real-world problems. In this paper, we...... compare the performance of state-of-the-art multi-objective evolutionary algorithms to solve a non-linear multi-objective multi-issue optimisation problem found in Greenhouse climate control. The chosen algorithms in the study includes NSGAII, eNSGAII, eMOEA, PAES, PESAII and SPEAII. The performance...... of all aforementioned algorithms is assessed and compared using performance indicators to evaluate proximity, diversity and consistency. Our insights to this comparative study enhanced our understanding of MOEAs performance in order to solve a non-linear complex climate control problem. The empirical...

Soft computing integrating evolutionary, neural, and fuzzy systems

CERN Document Server

Tettamanzi, Andrea

2001-01-01

Soft computing encompasses various computational methodologies, which, unlike conventional algorithms, are tolerant of imprecision, uncertainty, and partial truth. Soft computing technologies offer adaptability as a characteristic feature and thus permit the tracking of a problem through a changing environment. Besides some recent developments in areas like rough sets and probabilistic networks, fuzzy logic, evolutionary algorithms, and artificial neural networks are core ingredients of soft computing, which are all bio-inspired and can easily be combined synergetically. This book presents a well-balanced integration of fuzzy logic, evolutionary computing, and neural information processing. The three constituents are introduced to the reader systematically and brought together in differentiated combinations step by step. The text was developed from courses given by the authors and offers numerous illustrations as

Helminths and Cancers From the Evolutionary Perspective.

Science.gov (United States)

Scholte, Larissa L S; Pascoal-Xavier, Marcelo A; Nahum, Laila A

2018-01-01

Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes ( Schistosoma haematobium, Schistosoma japonicum , and Schistosoma mansoni ) and liver flukes ( Clonorchis sinensis and Opisthorchis viverrini ) are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine) and may contribute to parasite and cancer research.

Helminths and Cancers From the Evolutionary Perspective

Directory of Open Access Journals (Sweden)

Larissa L. S. Scholte

2018-04-01

Full Text Available Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes (Schistosoma haematobium, Schistosoma japonicum, and Schistosoma mansoni and liver flukes (Clonorchis sinensis and Opisthorchis viverrini are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine and may contribute to parasite and cancer research.

Asymmetric Evolutionary Games

Science.gov (United States)

McAvoy, Alex; Hauert, Christoph

2015-01-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

Invasion Success by Plant Breeding Evolutionary Changes as a Critical Factor for the Invasion of the Ornamental Plant Mahonia aquifolium

CERN Document Server

Ross, Christel Anne

2009-01-01

Invasive species are a major threat to global biodiversity and cause significant economic costs. Studying biological invasions is both essential for preventing future invasions and is also useful in order to understand basic ecological processes. Christel Ross investigates whether evolutionary changes by plant breeding are a relevant factor for the invasion success of Mahonia aquifolium in Germany. Her findings show that invasive populations differ from native populations in quantitative-genetic traits and molecular markers, whereas their genetic diversity is similar. She postulates that these evolutionary changes are rather a result of plant breeding, which includes interspecific hybridisation, than the result of a genetic bottleneck or the releases from specialist herbivores.

The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

Science.gov (United States)

Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

2018-03-01

Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more

Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites.

Science.gov (United States)

Ponsuwanna, Patrath; Kochakarn, Theerarat; Bunditvorapoom, Duangkamon; Kümpornsin, Krittikorn; Otto, Thomas D; Ridenour, Chase; Chotivanich, Kesinee; Wilairat, Prapon; White, Nicholas J; Miotto, Olivo; Chookajorn, Thanat

2016-01-29

Malaria parasites have evolved a series of intricate mechanisms to survive and propagate within host red blood cells. Intra-erythrocytic parasitism requires these organisms to digest haemoglobin and detoxify iron-bound haem. These tasks are executed by haemoglobin-specific proteases and haem biocrystallization factors that are components of a large multi-subunit complex. Since haemoglobin processing machineries are functionally and genetically linked to the modes of action and resistance mechanisms of several anti-malarial drugs, an understanding of their evolutionary history is important for drug development and drug resistance prevention. Maximum likelihood trees of genetic repertoires encoding haemoglobin processing machineries within Plasmodium species, and with the representatives of Apicomplexan species with various host tropisms, were created. Genetic variants were mapped onto existing three-dimensional structures. Genome-wide single nucleotide polymorphism data were used to analyse the selective pressure and the effect of these mutations at the structural level. Recent expansions in the falcipain and plasmepsin repertoires are unique to human malaria parasites especially in the Plasmodium falciparum and P. reichenowi lineage. Expansion of haemoglobin-specific plasmepsins occurred after the separation event of Plasmodium species, but the other members of the plasmepsin family were evolutionarily conserved with one copy for each sub-group in every Apicomplexan species. Haemoglobin-specific falcipains are separated from invasion-related falcipain, and their expansions within one specific locus arose independently in both P. falciparum and P. vivax lineages. Gene conversion between P. falciparum falcipain 2A and 2B was observed in artemisinin-resistant strains. Comparison between the numbers of non-synonymous and synonymous mutations suggests a strong selective pressure at falcipain and plasmepsin genes. The locations of amino acid changes from non

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

Evolutionary and ecological perspectives of Late Paleozoic ferns. Part III. Anachoropterid ferns (including Anachoropteris, Tubicaulis, the Sermayaceae, Kaplanopteridaceae and Psalixochlaenaceae)

OpenAIRE

Galtier, Jean; Phillips, Tom L.

2014-01-01

The anachoropterid ferns, previously assigned to the family Anachoropteridaceae, are a group of anatomically preserved late Paleozoic filicalean ferns characterized by a C-shaped foliar xylem with abaxially recurved arms (inversicatenalean anatomy) and two main protoxylem strands. The variously curved to strongly inrolled foliar xylem certainly reflects different evolutionary trends within the morphogenus Anachoropteris. The occurrence of two groups of Tubicaulis is supported by differences i...

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

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

Science.gov (United States)

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

2002-01-01

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

Part E: Evolutionary Computation

DEFF Research Database (Denmark)

2015-01-01

of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...

Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes.

Science.gov (United States)

Rendel, Mark D

2011-01-01

In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk - indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered. Copyright © 2010 Elsevier Inc. All rights reserved.

Application of evolutionary games to modeling carcinogenesis.

Science.gov (United States)

Swierniak, Andrzej; Krzeslak, Michal

2013-06-01

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

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

Science.gov (United States)

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

2010-01-26

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

An open future for ecological and evolutionary data?

Science.gov (United States)

Kenall, Amye; Harold, Simon; Foote, Christopher

2014-04-02

As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.

Evolutionary Science as a Method to Facilitate Higher Level Thinking and Reasoning in Medical Training.

Science.gov (United States)

Graves, Joseph L; Reiber, Chris; Thanukos, Anna; Hurtado, Magdalena; Wolpaw, Terry

2016-10-15

Evolutionary science is indispensable for understanding biological processes. Effective medical treatment must be anchored in sound biology. However, currently the insights available from evolutionary science are not adequately incorporated in either pre-medical or medical school curricula. To illuminate how evolution may be helpful in these areas, examples in which the insights of evolutionary science are already improving medical treatment and ways in which evolutionary reasoning can be practiced in the context of medicine are provided. In order to facilitate the learning of evolutionary principles, concepts derived from evolutionary science that medical students and professionals should understand are outlined. These concepts are designed to be authoritative and at the same time easily accessible for anyone with the general biological knowledge of a first-year medical student. Thus we conclude that medical practice informed by evolutionary principles will be more effective and lead to better patient outcomes.Furthermore, it is argued that evolutionary medicine complements general medical training because it provides an additional means by which medical students can practice the critical thinking skills that will be important in their future practice. We argue that core concepts from evolutionary science have the potential to improve critical thinking and facilitate more effective learning in medical training. © The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

Applications of evolutionary economic geography

NARCIS (Netherlands)

Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx

2008-01-01

This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of

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

Science.gov (United States)

Charlton, Bruce G

2007-01-01

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

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

KAUST Repository

Mineta, Katsuhiko

2015-05-01

The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

KAUST Repository

Mineta, Katsuhiko; Matsumoto, Tomotaka; Osada, Naoki; Araki, Hitoshi

2015-01-01

The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

Lysosomal enzymes and their receptors in invertebrates: an evolutionary perspective.

Science.gov (United States)

Kumar, Nadimpalli Siva; Bhamidimarri, Poorna M

2015-01-01

Lysosomal biogenesis is an important process in eukaryotic cells to maintain cellular homeostasis. The key components that are involved in the biogenesis such as the lysosomal enzymes, their modifications and the mannose 6-phosphate receptors have been well studied and their evolutionary conservation across mammalian and non-mammalian vertebrates is clearly established. Invertebrate lysosomal biogenesis pathway on the other hand is not well studied. Although, details on mannose 6-phosphate receptors and enzymes involved in lysosomal enzyme modifications were reported earlier, a clear cut pathway has not been established. Recent research on the invertebrate species involving biogenesis of lysosomal enzymes suggests a possible conserved pathway in invertebrates. This review presents certain observations based on these processes that include biochemical, immunological and functional studies. Major conclusions include conservation of MPR-dependent pathway in higher invertebrates and recent evidence suggests that MPR-independent pathway might have been more prominent among lower invertebrates. The possible components of MPR-independent pathway that may play a role in lysosomal enzyme targeting are also discussed here.

Study on Cooperative Mechanism of Prefabricated Producers Based on Evolutionary Game Theory

Directory of Open Access Journals (Sweden)

Tongyao Feng

2017-01-01

Full Text Available Good cooperation mechanism is an important guarantee for the advancement of industrialization construction. To strengthen the partnership between producers, we analyze the behavior evolution trend of both parties using an evolutionary game theory. Based on the original model, the mechanism of coordination and cooperation between prefabricated producers is explained under the condition of punishment and incentive. The results indicate that stable evolutionary strategies exist under both cooperation and noncooperation, and the evolutionary results are influenced by the initial proportion of both decision-making processes. The government can support the production enterprises to establish a solid partnership through effective punishment and incentive mechanisms to reduce the initial cost in the supply chain of prefabricated construction, resulting in a win-win situation.

Massively parallel evolutionary computation on GPGPUs

CERN Document Server

Tsutsui, Shigeyoshi

2013-01-01

Evolutionary algorithms (EAs) are metaheuristics that learn from natural collective behavior and are applied to solve optimization problems in domains such as scheduling, engineering, bioinformatics, and finance. Such applications demand acceptable solutions with high-speed execution using finite computational resources. Therefore, there have been many attempts to develop platforms for running parallel EAs using multicore machines, massively parallel cluster machines, or grid computing environments. Recent advances in general-purpose computing on graphics processing units (GPGPU) have opened u

Evolutionary disarmament in interspecific competition.

Science.gov (United States)

Kisdi, E; Geritz, S A

2001-12-22

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

Evolutionary model of an anonymous consumer durable market

Science.gov (United States)

Kaldasch, Joachim

2011-07-01

An analytic model is presented that considers the evolution of a market of durable goods. The model suggests that after introduction goods spread always according to a Bass diffusion. However, this phase will be followed by a diffusion process for durable consumer goods governed by a variation-selection-reproduction mechanism and the growth dynamics can be described by a replicator equation. The theory suggests that products play the role of species in biological evolutionary models. It implies that the evolution of man-made products can be arranged into an evolutionary tree. The model suggests that each product can be characterized by its product fitness. The fitness space contains elements of both sites of the market, supply and demand. The unit sales of products with a higher product fitness compared to the mean fitness increase. Durables with a constant fitness advantage replace other goods according to a logistic law. The model predicts in particular that the mean price exhibits an exponential decrease over a long time period for durable goods. The evolutionary diffusion process is directly related to this price decline and is governed by Gompertz equation. Therefore it is denoted as Gompertz diffusion. Describing the aggregate sales as the sum of first, multiple and replacement purchase the product life cycle can be derived. Replacement purchase causes periodic variations of the sales determined by the finite lifetime of the good (Juglar cycles). The model suggests that both, Bass- and Gompertz diffusion may contribute to the product life cycle of a consumer durable. The theory contains the standard equilibrium view of a market as a special case. It depends on the time scale, whether an equilibrium or evolutionary description is more appropriate. The evolutionary framework is used to derive also the size, growth rate and price distribution of manufacturing business units. It predicts that the size distribution of the business units (products) is lognormal

The Evolutionary Puzzle of Suicide

Directory of Open Access Journals (Sweden)

Henri-Jean Aubin

2013-12-01

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

Evolutionary economics and industry location

NARCIS (Netherlands)

Boschma, R.A.; Frenken, K.

2003-01-01

This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both

Evolutionary institutionalism.

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.

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.

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131.

Science.gov (United States)

Stoesser, Nicole; Sheppard, Anna E; Pankhurst, Louise; De Maio, Nicola; Moore, Catrin E; Sebra, Robert; Turner, Paul; Anson, Luke W; Kasarskis, Andrew; Batty, Elizabeth M; Kos, Veronica; Wilson, Daniel J; Phetsouvanh, Rattanaphone; Wyllie, David; Sokurenko, Evgeni; Manges, Amee R; Johnson, Timothy J; Price, Lance B; Peto, Timothy E A; Johnson, James R; Didelot, Xavier; Walker, A Sarah; Crook, Derrick W

2016-03-22

Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n= 215) of sequenced ST131E. coliisolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of ablaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration ofblaCTX-Mwithin subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, theblaCTX-M-14/14-likegroup. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages ofE. coli These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. Escherichia coli, perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to

Cognition and Culture in Evolutionary Context.

Science.gov (United States)

Colmenares, Fernando; Hernández-Lloreda, María Victoria

2017-01-09

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

Coevolution of Artificial Agents Using Evolutionary Computation in Bargaining Game

Directory of Open Access Journals (Sweden)

Sangwook Lee

2015-01-01

Full Text Available Analysis of bargaining game using evolutionary computation is essential issue in the field of game theory. This paper investigates the interaction and coevolutionary process among heterogeneous artificial agents using evolutionary computation (EC in the bargaining game. In particular, the game performance with regard to payoff through the interaction and coevolution of agents is studied. We present three kinds of EC based agents (EC-agent participating in the bargaining game: genetic algorithm (GA, particle swarm optimization (PSO, and differential evolution (DE. The agents’ performance with regard to changing condition is compared. From the simulation results it is found that the PSO-agent is superior to the other agents.

Compassion: An Evolutionary Analysis and Empirical Review

OpenAIRE

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

2010-01-01

What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization...

Gender Inequality in Interaction--An Evolutionary Account

Science.gov (United States)

Hopcroft, Rosemary L.

2009-01-01

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

Evolutionary Algorithm for Optimal Vaccination Scheme

International Nuclear Information System (INIS)

Parousis-Orthodoxou, K J; Vlachos, D S

2014-01-01

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

Grand challenges in evolutionary and population genetics: The importance of integrating epigenetics, genomics, modeling, and experimentation

Science.gov (United States)

Samuel A. Cushman

2014-01-01

This is a time of explosive growth in the fields of evolutionary and population genetics, with whole genome sequencing and bioinformatics driving a transformative paradigm shift (Morozova and Marra, 2008). At the same time, advances in epigenetics are thoroughly transforming our understanding of evolutionary processes and their implications for populations, species and...

Evolutionary explanations in medical and health profession courses: are you answering your students' "why" questions?

Directory of Open Access Journals (Sweden)

Malyango Avelin A

2005-05-01

Full Text Available Abstract Background Medical and pre-professional health students ask questions about human health that can be answered in two ways, by giving proximate and evolutionary explanations. Proximate explanations, most common in textbooks and classes, describe the immediate scientifically known biological mechanisms of anatomical characteristics or physiological processes. These explanations are necessary but insufficient. They can be complemented with evolutionary explanations that describe the evolutionary processes and principles that have resulted in human biology we study today. The main goal of the science of Darwinian Medicine is to investigate human disease, disorders, and medical complications from an evolutionary perspective. Discussion This paper contrasts the differences between these two types of explanations by describing principles of natural selection that underlie medical questions. Thus, why is human birth complicated? Why does sickle cell anemia exist? Why do we show symptoms like fever, diarrhea, and coughing when we have infection? Why do we suffer from ubiquitous age-related diseases like arteriosclerosis, Alzheimer's and others? Why are chronic diseases like type II diabetes and obesity so prevalent in modern society? Why hasn't natural selection eliminated the genes that cause common genetic diseases like hemochromatosis, cystic fibrosis, Tay sachs, PKU and others? Summary In giving students evolutionary explanations professors should underscore principles of natural selection, since these can be generalized for the analysis of many medical questions. From a research perspective, natural selection seems central to leading hypotheses of obesity and type II diabetes and might very well explain the occurrence of certain common genetic diseases like cystic fibrosis, hemochromatosis, Tay sachs, Fragile X syndrome, G6PD and others because of their compensating advantages. Furthermore, armed with evolutionary explanations, health care

Evolutionary perspectives into placental biology and disease

Directory of Open Access Journals (Sweden)

Edward B. Chuong

2013-12-01

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

Contemporary issues in evolutionary biology

Indian Academy of Sciences (India)

We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...

An Agent-Based Co-Evolutionary Multi-Objective Algorithm for Portfolio Optimization

Directory of Open Access Journals (Sweden)

Rafał Dreżewski

2017-08-01

Full Text Available Algorithms based on the process of natural evolution are widely used to solve multi-objective optimization problems. In this paper we propose the agent-based co-evolutionary algorithm for multi-objective portfolio optimization. The proposed technique is compared experimentally to the genetic algorithm, co-evolutionary algorithm and a more classical approach—the trend-following algorithm. During the experiments historical data from the Warsaw Stock Exchange is used in order to assess the performance of the compared algorithms. Finally, we draw some conclusions from these experiments, showing the strong and weak points of all the techniques.

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

Science.gov (United States)

Zong, Hengshan; Jia, Guozhu; Cheng, Yang

2015-11-01

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

Cooperation and conflict in cancer: An evolutionary perspective

Directory of Open Access Journals (Sweden)

Jonathan Featherston

2012-09-01

Full Text Available Evolutionary approaches to carcinogenesis have gained prominence in the literature and enhanced our understanding of cancer. However, an appreciation of neoplasia in the context of evolutionary transitions, particularly the transition from independent genes to a fullyintegrated genome, is largely absent. In the gene–genome evolutionary transition, mobile genetic elements (MGEs can be studied as the extant exemplars of selfish autonomous lowerlevel units that cooperated to form a higher-level, functionally integrated genome. Here,we discuss levels of selection in cancer cells. In particular, we examine the tension between gene and genome units of selection by examining the expression profiles of MGE domains in an array of human cancers. Overall, across diverse cancers, there is an aberrant expression of several families of mobile elements, including the most common MGE in the human genome, retrotransposon LINE 1. These results indicate an alternative life-history strategy for MGEs in the cancers studied. Whether the aberrant expression is the cause or effect oftumourigenesis is unknown, although some evidence suggests that dysregulation of MGEs can play a role in cancer origin and progression. These data are interpreted in combination with phylostratigraphic reports correlating the origin of cancer genes with multicellularity and other potential increases in complexity in cancer cell populations. Cooperation and conflict between individuals at the gene, genome and cell level provide an evolutionary medicineperspective of cancer that enhances our understanding of disease pathogenesis and treatment.

The origins of pedagogy: developmental and evolutionary perspectives.

Science.gov (United States)

Skerry, Amy E; Lambert, Enoch; Powell, Lindsey J; McAuliffe, Katherine

2013-07-18

The question of whether and how information is actively transferred from knowledgeable to ignorant individuals has received much attention in psychology and evolutionary biology. Research in these fields has proceeded largely independently, with studies of nonhuman animals focusing on knowledgeable individuals and whether or not they meet a functional definition of teaching, while studies of children focus on the learner's assumptions and inferences. We argue that a comprehensive theory of teaching will benefit from integrating perspectives and empirical phenomena from evolutionary and developmental disciplines. In this review, we identify cases of seemingly purposeful information transfer (i.e. teaching) in human and nonhuman animals, discuss what is known about the cognitive processes that support teaching in different species, and highlight ways in which each discipline might be informed by extant theories and empirical tools from the other.

A Way Forward Beyond Karl Popper's and Donald T. Campbell's Dead-End Evolutionary Epistemologies.

Science.gov (United States)

Wettersten, John

2016-01-01

Theories of natural thought processes have traditionally served as foundations for philosophies of science. The source of all knowledge is passively received observations; these are combined to produce certain knowledge. After David Hume showed that this was not possible, deductivist alternatives, that is, theories that find a source of knowledge in ideas not derived from observations, from Immanuel Kant to William Whewell in the mid-1 9th century, were introduced. In response, traditional associationist and inductivist views were refurbished; a deductivist alternative was developed by the W6rzburg School. Much later Karl Popper in philosophy and Donald T. Campbell in psychology integrated this view with evolutionary theory. Campbell wanted thereby to find a justificationist view, which would reduce philosophy of science to cognitive psychology; Popper rejected both justificationism and the reduction of philosophy of science to psychology. Campbell thought all rational processes were innate psychological processes; Popper thought psychological processes were used to develop various rational processes. Campbell could not show that all rational thought was reducible to innate psychological processes, nor how some justification of scientific theories was possible. Popper could not show how evolutionary theory contributed to our knowledge of psychological thought processes. Both failed to observe that cognitive processes are social; people have learned how to think by learning how to interact in social groups seeking understanding. When innate thought processes are studied as social characteristics, evolutionary theory can contribute to both cognitive psychology and the theory of rationality, as both Popper and Campbell wanted it to do.

Connecting proximate mechanisms and evolutionary patterns: pituitary gland size and mammalian life history.

Science.gov (United States)

Kamilar, J M; Tecot, S R

2015-11-01

At the proximate level, hormones are known to play a critical role in influencing the life history of mammals, including humans. The pituitary gland is directly responsible for producing several hormones, including those related to growth and reproduction. Although we have a basic understanding of how hormones affect life history characteristics, we still have little knowledge of this relationship in an evolutionary context. We used data from 129 mammal species representing 14 orders to investigate the relationship between pituitary gland size and life history variation. Because pituitary gland size should be related to hormone production and action, we predicted that species with relatively large pituitaries should be associated with fast life histories, especially increased foetal and post-natal growth rates. Phylogenetic analyses revealed that total pituitary size and the size of the anterior lobe of the pituitary significantly predicted a life history axis that was correlated with several traits including body mass, and foetal and post-natal growth rates. Additional models directly examining the association between relative pituitary size and growth rates produced concordant results. We also found that relative pituitary size variation across mammals was best explained by an Ornstein-Uhlenbeck model of evolution, suggesting an important role of stabilizing selection. Our results support the idea that the size of the pituitary is linked to life history variation through evolutionary time. This pattern is likely due to mediating hormone levels but additional work is needed. We suggest that future investigations incorporating endocrine gland size may be critical for understanding life history evolution. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Evolutionary origin of the turtle skull.

Science.gov (United States)

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

2015-09-10

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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Science.gov (United States)

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

Mean-Potential Law in Evolutionary Games

Science.gov (United States)

Nałecz-Jawecki, Paweł; Miekisz, Jacek

2018-01-01

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

An evolutionary framework for cultural change: Selectionism versus communal exchange

Science.gov (United States)

Gabora, Liane

2013-06-01

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

Is evolutionary psychology a metatheory for psychology? A discussion of four major issues in psychology from an evolutionary developmental perspective

NARCIS (Netherlands)

Ploeger, A.; van der Maas, H.L.J.; Raijmakers, M.E.J.

2008-01-01

Evolutionary psychology has been proposed as a metatheoretical framework for psychology. We argue that evolutionary psychology should be expanded if it is to offer new insights regarding the major issues in psychology. Evolutionary developmental biology can provide valuable new insights into issues

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

Science.gov (United States)

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

2014-06-01

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

The uncertain foundation of neo-Darwinism: metaphysical and epistemological pluralism in the evolutionary synthesis.

Science.gov (United States)

Delisle, Richard G

2009-06-01

The Evolutionary Synthesis is often seen as a unification process in evolutionary biology, one which provided this research area with a solid common theoretical foundation. As such, neo-Darwinism is believed to constitute from this time onward a single, coherent, and unified movement offering research guidelines for investigations. While this may be true if evolutionary biology is solely understood as centred around evolutionary mechanisms, an entirely different picture emerges once other aspects of the founding neo-Darwinists' views are taken into consideration, aspects potentially relevant to the elaboration of an evolutionary worldview: the tree of life, the ontological distinctions of the main cosmic entities (inert matter, biological organisms, mind), the inherent properties of self-organizing matter, evolutionary ethics, and so on. Profound tensions and inconsistencies are immediately revealed in the neo-Darwinian movement once this broader perspective is adopted. This pluralism is such that it is possible to identify at least three distinct and quasi-incommensurable epistemological/metaphysical frameworks as providing a proper foundation for neo-Darwinism. The analysis of the views of Theodosius Dobzhansky, Bernhard Rensch, and Ernst Mayr will illustrate this untenable pluralism, one which requires us to conceive of the neo-Darwinian research agenda as being conducted in more than one research programme or research tradition at the same time.

Comparison of evolutionary computation algorithms for solving bi ...

Indian Academy of Sciences (India)

failure probability. Multiobjective Evolutionary Computation algorithms (MOEAs) are well-suited for Multiobjective task scheduling on heterogeneous environment. The two Multi-Objective Evolutionary Algorithms such as Multiobjective Genetic. Algorithm (MOGA) and Multiobjective Evolutionary Programming (MOEP) with.

“Ménage à Trois”: The Evolutionary Interplay between JSRV, enJSRVs and Domestic Sheep

Science.gov (United States)

Armezzani, Alessia; Varela, Mariana; Spencer, Thomas E.; Palmarini, Massimo; Arnaud, Frédérick

2014-01-01

Sheep betaretroviruses represent a fascinating model to study the complex evolutionary interplay between host and pathogen in natural settings. In infected sheep, the exogenous and pathogenic Jaagsiekte sheep retrovirus (JSRV) coexists with a variety of highly related endogenous JSRVs, referred to as enJSRVs. During evolution, some of them were co-opted by the host as they fulfilled important biological functions, including placental development and protection against related exogenous retroviruses. In particular, two enJSRV loci, enJS56A1 and enJSRV-20, were positively selected during sheep domestication due to their ability to interfere with the replication of related competent retroviruses. Interestingly, viruses escaping these transdominant enJSRVs have recently emerged, probably less than 200 years ago. Overall, these findings suggest that in sheep the process of endogenization is still ongoing and, therefore, the evolutionary interplay between endogenous and exogenous sheep betaretroviruses and their host has not yet reached an equilibrium. PMID:25502326

Testing the ecological consequences of evolutionary change using elements.

Science.gov (United States)

Jeyasingh, Punidan D; Cothran, Rickey D; Tobler, Michael

2014-02-01

Understanding the ecological consequences of evolutionary change is a central challenge in contemporary biology. We propose a framework based on the ˜25 elements represented in biology, which can serve as a conduit for a general exploration of poorly understood evolution-to-ecology links. In this framework, known as ecological stoichiometry, the quantity of elements in the inorganic realm is a fundamental environment, while the flow of elements from the abiotic to the biotic realm is due to the action of genomes, with the unused elements excreted back into the inorganic realm affecting ecological processes at higher levels of organization. Ecological stoichiometry purposefully assumes distinct elemental composition of species, enabling powerful predictions about the ecological functions of species. However, this assumption results in a simplified view of the evolutionary mechanisms underlying diversification in the elemental composition of species. Recent research indicates substantial intraspecific variation in elemental composition and associated ecological functions such as nutrient excretion. We posit that attention to intraspecific variation in elemental composition will facilitate a synthesis of stoichiometric information in light of population genetics theory for a rigorous exploration of the ecological consequences of evolutionary change.

Evolutionary model of the growth and size of firms

Science.gov (United States)

Kaldasch, Joachim

2012-07-01

The key idea of this model is that firms are the result of an evolutionary process. Based on demand and supply considerations the evolutionary model presented here derives explicitly Gibrat's law of proportionate effects as the result of the competition between products. Applying a preferential attachment mechanism for firms, the theory allows to establish the size distribution of products and firms. Also established are the growth rate and price distribution of consumer goods. Taking into account the characteristic property of human activities to occur in bursts, the model allows also an explanation of the size-variance relationship of the growth rate distribution of products and firms. Further the product life cycle, the learning (experience) curve and the market size in terms of the mean number of firms that can survive in a market are derived. The model also suggests the existence of an invariant of a market as the ratio of total profit to total revenue. The relationship between a neo-classic and an evolutionary view of a market is discussed. The comparison with empirical investigations suggests that the theory is able to describe the main stylized facts concerning the size and growth of firms.

Process, including PSA and membrane separation, for separating hydrogen from hydrocarbons

Science.gov (United States)

Baker, Richard W.; Lokhandwala, Kaaeid A.; He, Zhenjie; Pinnau, Ingo

2001-01-01

An improved process for separating hydrogen from hydrocarbons. The process includes a pressure swing adsorption step, a compression/cooling step and a membrane separation step. The membrane step relies on achieving a methane/hydrogen selectivity of at least about 2.5 under the conditions of the process.

The interaction of neutral evolutionary processes with climatically-driven adaptive changes in the 3D shape of the human os coxae.

Science.gov (United States)

Betti, Lia; von Cramon-Taubadel, Noreen; Manica, Andrea; Lycett, Stephen J

2014-08-01

Differences in the breadth of the pelvis among modern human populations and among extinct hominin species have often been interpreted in the light of thermoregulatory adaptation, whereby a larger pelvic girdle would help preserve body temperature in cold environments while a narrower pelvis would help dissipate heat in tropical climates. There is, however, a theoretical problem in interpreting a pattern of variation as evidence of selection without first accounting for the effects of neutral evolutionary processes (i.e., mutation, genetic drift and migration). Here, we analyse 3D configurations of 27 landmarks on the os coxae of 1494 modern human individuals representing 30 male and 23 female populations from five continents and a range of climatic conditions. We test for the effects of climate on the size and shape of the pelvic bone, while explicitly accounting for population history (i.e., geographically-mediated gene flow and genetic drift). We find that neutral processes account for a substantial proportion of shape variance in the human os coxae in both sexes. Beyond the neutral pattern due to population history, temperature is a significant predictor of shape and size variation in the os coxae, at least in males. The effect of climate on the shape of the pelvic bone, however, is comparatively limited, explaining only a small percentage of shape variation in males and females. In accordance with previous hypotheses, the size of the os coxae tends to increase with decreasing temperature, although the significance of the association is reduced when population history is taken into account. In conclusion, the shape and size of the human os coxae reflect both neutral evolutionary processes and climatically-driven adaptive changes. Neutral processes have a substantial effect on pelvic variation, suggesting such factors will need to be taken into account in future studies of human and fossil hominin coxal variation. Copyright © 2014 Elsevier Ltd. All rights

Academic Training: Evolutionary Heuristic Optimization: Genetic Algorithms and Estimation of Distribution Algorithms - Lecture series

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Françoise Benz

2004-01-01

ACADEMIC TRAINING LECTURE REGULAR PROGRAMME 1, 2, 3 and 4 June From 11:00 hrs to 12:00 hrs - Main Auditorium bldg. 500 Evolutionary Heuristic Optimization: Genetic Algorithms and Estimation of Distribution Algorithms V. Robles Forcada and M. Perez Hernandez / Univ. de Madrid, Spain In the real world, there exist a huge number of problems that require getting an optimum or near-to-optimum solution. Optimization can be used to solve a lot of different problems such as network design, sets and partitions, storage and retrieval or scheduling. On the other hand, in nature, there exist many processes that seek a stable state. These processes can be seen as natural optimization processes. Over the last 30 years several attempts have been made to develop optimization algorithms, which simulate these natural optimization processes. These attempts have resulted in methods such as Simulated Annealing, based on natural annealing processes or Evolutionary Computation, based on biological evolution processes. Geneti...

The ecological and evolutionary implications of merging different types of networks

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

2011-01-01

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

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

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Funk, W Chris; Murphy, Melanie A

2010-02-01

Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

Evolutionary Developmental Robotics: Improving Morphology and Control of Physical Robots.

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Vujovic, Vuk; Rosendo, Andre; Brodbeck, Luzius; Iida, Fumiya

2017-01-01

Evolutionary algorithms have previously been applied to the design of morphology and control of robots. The design space for such tasks can be very complex, which can prevent evolution from efficiently discovering fit solutions. In this article we introduce an evolutionary-developmental (evo-devo) experiment with real-world robots. It allows robots to grow their leg size to simulate ontogenetic morphological changes, and this is the first time that such an experiment has been performed in the physical world. To test diverse robot morphologies, robot legs of variable shapes were generated during the evolutionary process and autonomously built using additive fabrication. We present two cases with evo-devo experiments and one with evolution, and we hypothesize that the addition of a developmental stage can be used within robotics to improve performance. Moreover, our results show that a nonlinear system-environment interaction exists, which explains the nontrivial locomotion patterns observed. In the future, robots will be present in our daily lives, and this work introduces for the first time physical robots that evolve and grow while interacting with the environment.

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

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Yue, Jia-Xing; Li, Jinpeng; Wang, Dan; Araki, Hitoshi; Tian, Dacheng; Yang, Sihai

2010-11-09

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

Evolutionary games on graphs

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Szabó, György; Fáth, Gábor

2007-07-01

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

A new evolutionary system for evolving artificial neural networks.

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Yao, X; Liu, Y

1997-01-01

This paper presents a new evolutionary system, i.e., EPNet, for evolving artificial neural networks (ANNs). The evolutionary algorithm used in EPNet is based on Fogel's evolutionary programming (EP). Unlike most previous studies on evolving ANN's, this paper puts its emphasis on evolving ANN's behaviors. Five mutation operators proposed in EPNet reflect such an emphasis on evolving behaviors. Close behavioral links between parents and their offspring are maintained by various mutations, such as partial training and node splitting. EPNet evolves ANN's architectures and connection weights (including biases) simultaneously in order to reduce the noise in fitness evaluation. The parsimony of evolved ANN's is encouraged by preferring node/connection deletion to addition. EPNet has been tested on a number of benchmark problems in machine learning and ANNs, such as the parity problem, the medical diagnosis problems, the Australian credit card assessment problem, and the Mackey-Glass time series prediction problem. The experimental results show that EPNet can produce very compact ANNs with good generalization ability in comparison with other algorithms.

A Note on Evolutionary Algorithms and Its Applications

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Bhargava, Shifali

2013-01-01

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

The mixing evolutionary algorithm : indepedent selection and allocation of trials

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C.H.M. van Kemenade

1997-01-01

textabstractWhen using an evolutionary algorithm to solve a problem involving building blocks we have to grow the building blocks and then mix these building blocks to obtain the (optimal) solution. Finding a good balance between the growing and the mixing process is a prerequisite to get a reliable

Recent advances in evolutionary multi-objective optimization

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Datta, Rituparna; Gupta, Abhishek

2017-01-01

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

Including product features in process redesign

DEFF Research Database (Denmark)

Hvam, Lars; Hauksdóttir, Dagný; Mortensen, Niels Henrik

2017-01-01

do not take into account how the product features are applied throughout the process, which makes it difficult to obtain a comprehensive understanding of the activities in the processes and to generate significant improvements. The suggested approach models the product family using the so......This article suggests a visual modelling method for integrating models of product features with business process models for redesigning the business processes involving specifications of customer-tailored products and services. The current methods for redesigning these types of business processes......-called product variant master and the business process modelling notation for modelling the process flow. The product model is combined with the process map by identifying features used in each step of the process flow. Additionally, based on the information absorbed from the integrated model, the value stream...

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...

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

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O'Malley, Maureen A

2012-01-01

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

Evolutionary medicine and its implications for endocrinological issues (e.g. menopause).

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Kirchengast, Sylvia; Rühli, Frank

2013-06-01

Evolutionary medicine, which was formalized in the early 1990s, investigates evolutionary causes of recent human disease, disorders and malfunctions but also the influence of changing living conditions and modernization on health and disease. Evolutionary medicine can also provide insights into endocrinological disorders and in particular in the process of female reproductive senescence. Female reproductive senescence, i.e. menopausal transition is physiologically caused by the decline of estrogen secretion, which is associated with various somatic and psychic discomforts making this stage of life extremely uncomfortable. From the viewpoint of evolutionary medicine, these menopausal symptoms are the result from the sudden decrease of very high lifetime estrogen levels to zero during postmenopause, a situation which is quite new in our evolution and history. While women in recent developed countries experience menarche early, menopause late, few pregnancies, short periods of lactation and consequently low life time estrogen levels. The opposite is true of women living in traditional societies, whose living conditions may be interpreted as a mirror of the situation in our history. From this viewpoint we can conclude that menopausal symptoms may are the result of a mismatch between female reproductive physiology and recent living conditions. Copyright © 2013 Elsevier Inc. All rights reserved.

Phylogenetic inference with weighted codon evolutionary distances.

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Criscuolo, Alexis; Michel, Christian J

2009-04-01

We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.

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

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Pei-ai Zhang

2014-01-01

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

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

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

2001-01-01

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made. PMID:11432813

Artificial intelligence in peer review: How can evolutionary computation support journal editors?

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Mrowinski, Maciej J; Fronczak, Piotr; Fronczak, Agata; Ausloos, Marcel; Nedic, Olgica

2017-01-01

With the volume of manuscripts submitted for publication growing every year, the deficiencies of peer review (e.g. long review times) are becoming more apparent. Editorial strategies, sets of guidelines designed to speed up the process and reduce editors' workloads, are treated as trade secrets by publishing houses and are not shared publicly. To improve the effectiveness of their strategies, editors in small publishing groups are faced with undertaking an iterative trial-and-error approach. We show that Cartesian Genetic Programming, a nature-inspired evolutionary algorithm, can dramatically improve editorial strategies. The artificially evolved strategy reduced the duration of the peer review process by 30%, without increasing the pool of reviewers (in comparison to a typical human-developed strategy). Evolutionary computation has typically been used in technological processes or biological ecosystems. Our results demonstrate that genetic programs can improve real-world social systems that are usually much harder to understand and control than physical systems.

Artificial intelligence in peer review: How can evolutionary computation support journal editors?

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Maciej J Mrowinski

Full Text Available With the volume of manuscripts submitted for publication growing every year, the deficiencies of peer review (e.g. long review times are becoming more apparent. Editorial strategies, sets of guidelines designed to speed up the process and reduce editors' workloads, are treated as trade secrets by publishing houses and are not shared publicly. To improve the effectiveness of their strategies, editors in small publishing groups are faced with undertaking an iterative trial-and-error approach. We show that Cartesian Genetic Programming, a nature-inspired evolutionary algorithm, can dramatically improve editorial strategies. The artificially evolved strategy reduced the duration of the peer review process by 30%, without increasing the pool of reviewers (in comparison to a typical human-developed strategy. Evolutionary computation has typically been used in technological processes or biological ecosystems. Our results demonstrate that genetic programs can improve real-world social systems that are usually much harder to understand and control than physical systems.

Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays.

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Kirchhoff, K N; Hauffe, T; Stelbrink, B; Albrecht, C; Wilke, T

2017-08-01

Species richness in freshwater bony fishes depends on two main processes: the transition into and the diversification within freshwater habitats. In contrast to bony fishes, only few cartilaginous fishes, mostly stingrays (Myliobatoidei), were able to colonize fresh water. Respective transition processes have been mainly assessed from a physiological and morphological perspective, indicating that the freshwater lifestyle is strongly limited by the ability to perform osmoregulatory adaptations. However, the transition history and the effect of physiological constraints on the diversification in stingrays remain poorly understood. Herein, we estimated the geographic pathways of freshwater colonization and inferred the mode of habitat transitions. Further, we assessed habitat-related speciation rates in a time-calibrated phylogenetic framework to understand factors driving the transition of stingrays into and the diversification within fresh water. Using South American and Southeast Asian freshwater taxa as model organisms, we found one independent freshwater colonization event by stingrays in South America and at least three in Southeast Asia. We revealed that vicariant processes most likely caused freshwater transition during the time of major marine incursions. The habitat transition rates indicate that brackish water species switch preferably back into marine than forth into freshwater habitats. Moreover, our results showed significantly lower diversification rates in brackish water lineages, whereas freshwater and marine lineages exhibit similar rates. Thus, brackish water habitats may have functioned as evolutionary bottlenecks for the colonization of fresh water by stingrays, probably because of the higher variability of environmental conditions in brackish water. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

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Michael J Wise

Full Text Available Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED, measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV, dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza, and viroporins agnoprotein (polyomavirus, p7 (hepatitis C and VPU (HIV emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles, PB1/PB2 (influenza and VP1 (rotavirus, and internal serine proteases such as NS3 (dengue and hepatitis C virus emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

Science.gov (United States)

Wise, Michael J

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma

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Whittle Carrie A

2010-07-01

Full Text Available Abstract Background The self-fertile filamentous ascomycete Neurospora tetrasperma contains a large (~7 Mbp and young (mat chromosomes. The objective of the present study is to reveal the evolutionary history, including key genomic events, associated with the various regions of the mat chromosomes among ten strains representing all the nine known species (lineages contained within the N. tetrasperma species complex. Results Comparative analysis of sequence divergence among alleles of 24 mat-linked genes (mat A and mat a indicates that a large region of suppressed recombination exists within the mat chromosome for each of nine lineages of N. tetrasperma sensu latu. The recombinationally suppressed region varies in size and gene composition among lineages, and is flanked on both ends by normally recombining regions. Genealogical analyses among lineages reveals that eight gene conversion events have occurred between homologous mat A and mat a-linked alleles of genes located within the region of restricted recombination during the evolutionary history of N. tetrasperma. Conclusions We conclude that the region of suppressed recombination in the mat chromosomes has likely been subjected to independent contraction and/or expansion during the evolutionary history of the N. tetrasperma species complex. Furthermore, we infer that gene conversion events are likely a common phenomenon within this recombinationally suppressed genomic region. We argue that gene conversions might provide an efficient mechanism of adaptive editing of functional genes, including the removal of deleterious mutations, within the young recombinationally suppressed region of the mat chromosomes.

Collective influence in evolutionary social dilemmas

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Szolnoki, Attila; Perc, Matjaž

2016-03-01

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

Socio-technical transition as a co-evolutionary process: Innovation and the role of niche markets in the transition to motor vehicles

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Birky, Alicia K.

2008-10-01

Significant reductions in greenhouse emissions from personal transportation will require a transition to an alternative technology regime based on renewable energy sources. Two bodies of research, the quasi-evolutionary (QE) model and the multi-level perspective (MLP) assert that processes within niches play a fundamental role in such transitions. This research asks whether the description of transitions based on this niche hypothesis and its underlying assumptions is consistent with the historical U.S. transition to motor vehicles at the beginning of the 20th century. Unique to this dissertation is the combination of the perspective of the entrepreneur with co-evolutionary approaches to socio-technical transitions. This approach is augmented with concepts from the industry life-cycle model and with a taxonomy of mechanisms of learning. Using this analytic framework, I examine specifically the role of entrepreneurial behavior and processes within and among firms in the co-evolution of technologies and institutions during the transition to motor vehicles. I find that niche markets played an important role in the development of the technology, institutions, and the industry. However, I also find that the diffusion of the automobile is not consistent with the niche hypothesis in the following ways: (1) product improvements and cost reductions were not realized in niche markets, but were achieved simultaneously with diffusion into mass markets; (2) in addition to learning-by-doing and learning-by-interacting with users, knowledge spillovers and interacting with suppliers were critical in this process; (3) cost reductions were not automatic results of expanding markets, but rather arose from the strategies of entrepreneurs based on personal perspectives and values. This finding supports the use of a behavioral approach with a micro-focus in the analysis of socio-technical change. I also find that the emergence and diffusion of the motor vehicle can only be understood by

Is capitalism in our genes? Competition, cooperation and the idea of homo oeconomicus from an evolutionary perspective

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Portera Mariagrazia

2016-01-01

Full Text Available In the last few years a growing number of academic disciplines in the Humanities and Social Sciences have turned to the evolutionary approach: Evolutionary Economics, among these disciplines, is a thriving subfield of Economics, which adopts Darwin’s evolutionary ideas and concepts for the understanding of economic system and modes of production. Evolutionary hypotheses such as the „selfish gene“ idea, the ideas of „inclusive fitness“, „struggle for life“ and „survival of the fittest“ may suggest - and have indeed suggested - that humans are rational self-interest individuals, doing what they can to increase their own reproductive chances or at least the chances of their close relatives („inclusive fitness“. To put it differently, evolutionary theory seems to suggest that capitalism (in a broad sense is a system that has co-evolved with humans and best fits our evolved psychology. Is this the whole story? Is capitalism „in our genes“? In this paper I argue that conclusions such as „we are born to be rational self-interested agents“ or „capitalism is encoded in our genome“ are the result of a misleading application of Darwin’s evolutionary theory to human socio-economic processes, mainly to justify a (Western society based on selfish principles, but which is not naturally selfish in itself. Evolution seems to be the result of cooperative, not only (or not mainly competitive processes, and the model of Homo oeconomicus, that is the idea that humans are rational self-interested agents always trying to maximize profit, is, also from an bio-evolutionary perspective, nothing more than a fictional exercise.

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

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An-Jiang Lu

2016-03-01

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

Analysis of Knowledge-Sharing Evolutionary Game in University Teacher Team

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Huo, Mingkui

2013-01-01

The knowledge-sharing activity is a major drive force behind the progress and innovation of university teacher team. Based on the evolutionary game theory, this article analyzes the knowledge-sharing process model of this team, studies the influencing mechanism of various factors such as knowledge aggregate gap, incentive coefficient and risk…

Deciding to Cooperate in Northern Ghana: Trust as an Evolutionary Constraint Across Cultural Diversity.

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Acedo-Carmona, Cristina; Gomila, Antoni

2015-11-27

The upper-east and northern regions of Ghana offers a unique opportunity to study the influence of evolutionary social dynamics in making cooperation possible, despite cultural differences. These regions are occupied by several distinct ethnic groups, in interaction, such as the Kussasi, Mamprusi, Bimoba, Konkomba, and Fulani. We will report our fieldwork related to how cooperation takes places there, both within each group and among people from the different groups. Methods included personal networks of cooperation (ego networks), interviews and analysis of group contexts. The most important result is that, while each ethnic group may differ in terms of family and clan structure, a similar pattern can be found in all of them, of cooperation structured around small groups of trust-based close relationships. The study suggests that habitual decisions about cooperation are not strategic or self-interested, but instead are based on unconscious processes sustained by the emotional bonds of trust. These kind of emotional bonds are claimed to be relevant from an evolutionary point of view.

An Evolutionary Game Theoretic Approach to Multi-Sector Coordination and Self-Organization

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Fernando P. Santos

2016-04-01

Full Text Available Coordination games provide ubiquitous interaction paradigms to frame human behavioral features, such as information transmission, conventions and languages as well as socio-economic processes and institutions. By using a dynamical approach, such as Evolutionary Game Theory (EGT, one is able to follow, in detail, the self-organization process by which a population of individuals coordinates into a given behavior. Real socio-economic scenarios, however, often involve the interaction between multiple co-evolving sectors, with specific options of their own, that call for generalized and more sophisticated mathematical frameworks. In this paper, we explore a general EGT approach to deal with coordination dynamics in which individuals from multiple sectors interact. Starting from a two-sector, consumer/producer scenario, we investigate the effects of including a third co-evolving sector that we call public. We explore the changes in the self-organization process of all sectors, given the feedback that this new sector imparts on the other two.

Evolutionary engineering of industrial microorganisms-strategies and applications.

Science.gov (United States)

Zhu, Zhengming; Zhang, Juan; Ji, Xiaomei; Fang, Zhen; Wu, Zhimeng; Chen, Jian; Du, Guocheng

2018-06-01

Microbial cells have been widely used in the industry to obtain various biochemical products, and evolutionary engineering is a common method in biological research to improve their traits, such as high environmental tolerance and improvement of product yield. To obtain better integrate functions of microbial cells, evolutionary engineering combined with other biotechnologies have attracted more attention in recent years. Classical laboratory evolution has been proven effective to letting more beneficial mutations occur in different genes but also has some inherent limitations such as a long evolutionary period and uncontrolled mutation frequencies. However, recent studies showed that some new strategies may gradually overcome these limitations. In this review, we summarize the evolutionary strategies commonly used in industrial microorganisms and discuss the combination of evolutionary engineering with other biotechnologies such as systems biology and inverse metabolic engineering. Finally, we prospect the importance and application prospect of evolutionary engineering as a powerful tool especially in optimization of industrial microbial cell factories.

Evolutionary theory and the naturalist fallacy

DEFF Research Database (Denmark)

Grodal, Torben Kragh

2008-01-01

that great work of art are also automatically fitness-enhancing in the present day environment, at that there are simple correllations between whether a work of art has a high aesthetic value and whether it is fitness-enhancing or not.  Keywords :  Evolutionary aesthetics, film theory, literary theory......The article is an invited response to a target article by Joseph Carroll entitled "An evolutionary paradigm for literary study". It argues that the target article  misuse the fact that works of art are based on adaptations that were fitness-enhancing in the era of evolutionary adaptations to claim...

Evolutionary public health: introducing the concept.

Science.gov (United States)

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

2017-07-29

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

A teleofunctional account of evolutionary mismatch.

Science.gov (United States)

Cofnas, Nathan

When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

The COG database: an updated version includes eukaryotes

Directory of Open Access Journals (Sweden)

Sverdlov Alexander V

2003-09-01

Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.

Science.gov (United States)

de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

2016-11-01

Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. Copyright © 2016 de Villemereuil et al.

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

DEFF Research Database (Denmark)

Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M. M.

2017-01-01

Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions....... Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether...... factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending...

How to Identify and Interpret Evolutionary Tree Diagrams

Science.gov (United States)

Kong, Yi; Anderson, Trevor; Pelaez, Nancy

2016-01-01

Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly…

"Messing with the Mind: Evolutionary Challenges to Human Brain Augmentation

Directory of Open Access Journals (Sweden)

ARTHUR eSANIOTIS

2014-09-01

Full Text Available The issue of brain augmentation has received considerable scientific attention over the last two decades. A key factor to brain augmentation that has been widely overlooked are the complex evolutionary processes which have taken place in evolving the human brain to its current state of functioning. Like other bodily organs, the human brain has been subject to the forces of biological adaptation. The structure and function of the brain, is very complex and only now we are beginning to understand some of the basic concepts of cognition. Therefore, this article proposes that brain-machine interfacing and nootropics are not going to produce augmented brains because we do not understand enough about how evolutionary pressures have informed the neural networks which support human cognitive faculties.

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

Science.gov (United States)

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Embodied Artificial Evolution - Artificial Evolutionary Systems in the 21st Century

NARCIS (Netherlands)

Eiben, A.E.; Haasdijk, E.W.; Kernbach, S

2012-01-01

Evolution is one of the major omnipresent powers in the universe that has been studied for about two centuries. Recent scientific and technical developments make it possible to make the transition from passively understanding to actively using evolutionary processes. Today this is possible in

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...

Evolutionary Regeneration Model of Thought Process

OpenAIRE

Noboru, HOKKYO; Hitachi Energy Research Laboratory

1982-01-01

A preliminary attempt is made to understand the thought process and the evolution of the nervous system on the same footing as regeneration processes obeying certain recursive algebraic rules which possibly economize the information content of the increasingly complex structural-functional correlate of the evolving and thinking nervous system.

Regional systems of innovation: an evolutionary perspective

OpenAIRE

P Cooke; M G Uranga; G Etxebarria

1998-01-01

The authors develop the concept of regional systems of innovation and relate it to preexisting research on national systems of innovation. They argue that work conducted in the 'new regional science' field is complementary to systems of innovation approaches. They seek to link new regional work to evolutionary economics, and argue for the development of evolutionary regional science. Common elements of interest to evolutionary innovation research and new regional science are important in unde...

Evolutionary considerations in the development of chronic pelvic pain.

Science.gov (United States)

Jarrell, John; Arendt-Nielsen, Lars

2016-08-01

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

Optimality and stability of symmetric evolutionary games with applications in genetic selection.

Science.gov (United States)

Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

2015-06-01

Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

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

Directory of Open Access Journals (Sweden)

Pradeep Pillai

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

Evolutionary hypothesis for Chiari type I malformation.

Science.gov (United States)

Fernandes, Yvens Barbosa; Ramina, Ricardo; Campos-Herrera, Cynthia Resende; Borges, Guilherme

2013-10-01

Chiari I malformation (CM-I) is classically defined as a cerebellar tonsillar herniation (≥5 mm) through the foramen magnum. A decreased posterior fossa volume, mainly due to basioccipital hypoplasia and sometimes platybasia, leads to posterior fossa overcrowding and consequently cerebellar herniation. Regardless of radiological findings, embryological genetic hypothesis or any other postulations, the real cause behind this malformation is yet not well-elucidated and remains largely unknown. The aim of this paper is to approach CM-I under a broader and new perspective, conjoining anthropology, genetics and neurosurgery, with special focus on the substantial changes that have occurred in the posterior cranial base through human evolution. Important evolutionary allometric changes occurred during brain expansion and genetics studies of human evolution demonstrated an unexpected high rate of gene flow interchange and possibly interbreeding during this process. Based upon this review we hypothesize that CM-I may be the result of an evolutionary anthropological imprint, caused by evolving species populations that eventually met each other and mingled in the last 1.7 million years. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enhancing Evolutionary Optimization in Uncertain Environments by Allocating Evaluations via Multi-armed Bandit Algorithms

OpenAIRE

Qiu, Xin; Miikkulainen, Risto

2018-01-01

Optimization problems with uncertain fitness functions are common in the real world, and present unique challenges for evolutionary optimization approaches. Existing issues include excessively expensive evaluation, lack of solution reliability, and incapability in maintaining high overall fitness during optimization. Using conversion rate optimization as an example, this paper proposes a series of new techniques for addressing these issues. The main innovation is to augment evolutionary algor...

Is the political animal politically ignorant? Applying evolutionary psychology to the study of political attitudes.

Science.gov (United States)

Petersen, Michael Bang; Aarøe, Lene

2012-12-20

As evidenced by research in evolutionary psychology, humans have evolved sophisticated psychological mechanisms tailored to solve enduring adaptive problems of social life. Many of these social problems are political in nature and relate to the distribution of costs and benefits within and between groups. In that sense, evolutionary psychology suggests that humans are, by nature, political animals. By implication, a straightforward application of evolutionary psychology to the study of public opinion seems to entail that modern individuals find politics intrinsically interesting. Yet, as documented by more than fifty years of research in political science, people lack knowledge of basic features of the political process and the ability to form consistent political attitudes. By reviewing and integrating research in evolutionary psychology and public opinion, we describe (1) why modern mass politics often fail to activate evolved mechanisms and (2) the conditions in which these mechanisms are in fact triggered.

Generating minimal living systems from non-living materials and increasing their evolutionary abilities

DEFF Research Database (Denmark)

Rasmussen, Steen; Constantinescu, Adi; Svaneborg, Carsten

2016-01-01

We review lessons learned about evolutionary transitions from a bottom up construction of minimal life. We use a particular systemic protocell design process as a starting point for exploring two fundamental questions: (1) how may minimal living systems emerge from nonliving materials? - and (2......) how may minimal living systems support increasingly more evolutionary richness? Under (1) we present what has been accomplished so far and discuss the remaining open challenges and their possible solutions. Under (2) we present a design principle we have utilized successfully both for our...

Evolutionary robotics

Indian Academy of Sciences (India)

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

The limits of weak selection and large population size in evolutionary game theory.

Science.gov (United States)

Sample, Christine; Allen, Benjamin

2017-11-01

Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed. Formal mathematical definitions of the [Formula: see text] and [Formula: see text] limits are provided. Applying these definitions to the Moran process of evolutionary game theory, we obtain asymptotic expressions for fixation probability and conditions for success in these limits. We find that the asymptotic expressions for fixation probability, and the conditions for a strategy to be favored over a neutral mutation, are different in the [Formula: see text] and [Formula: see text] limits. However, the ordering of limits does not affect the conditions for one strategy to be favored over another.

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).

The use of information theory in evolutionary biology.

Science.gov (United States)

Adami, Christoph

2012-05-01

Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

Context dependent DNA evolutionary models

DEFF Research Database (Denmark)

Jensen, Jens Ledet

This paper is about stochastic models for the evolution of DNA. For a set of aligned DNA sequences, connected in a phylogenetic tree, the models should be able to explain - in probabilistic terms - the differences seen in the sequences. From the estimates of the parameters in the model one can...... start to make biologically interpretations and conclusions concerning the evolutionary forces at work. In parallel with the increase in computing power, models have become more complex. Starting with Markov processes on a space with 4 states, and extended to Markov processes with 64 states, we are today...... studying models on spaces with 4n (or 64n) number of states with n well above one hundred, say. For such models it is no longer possible to calculate the transition probability analytically, and often Markov chain Monte Carlo is used in connection with likelihood analysis. This is also the approach taken...

Packets Distributing Evolutionary Algorithm Based on PSO for Ad Hoc Network

Science.gov (United States)

Xu, Xiao-Feng

2018-03-01

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

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

Science.gov (United States)

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

2014-03-01

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

Consciousness, crosstalk, and the mereological fallacy: An evolutionary perspective

Science.gov (United States)

Wallace, Rodrick

2012-12-01

The cross-sectional decontextualization afflicting contemporary neuroscience - attributing to ‘the brain’ what is the province of the whole organism - is mirrored by an evolutionary decontextualization exceptionalizing consciousness. The living state is characterized by cognitive processes at all scales and levels of organization. Many can be associated with dual information sources that ‘speak’ a ‘language’ of behavior-in-context. Shifting global broadcasts analogous to consciousness, albeit far slower - wound healing, tumor control, immune function, gene expression, etc. - have emerged through repeated evolutionary exaptation of the crosstalk and noise inherent to all information transmission. These recruit ‘unconscious’ cognitive modules into tunable arrays as needed to meet threats and opportunities across multiple frames of reference. The development is straightforward, based on the powerful necessary conditions imposed by the asymptotic limit theorems of communication theory, in the same sense that the Central Limit Theorem constrains sums of stochastic variates. Recognition of information as a form of free energy instantiated by physical processes that consume free energy permits analogs to phase transition and nonequilibrium thermodynamic arguments, leading to ‘dynamic regression models’ useful for data analysis.

An evolutionary perspective on gradual formation of superego in the primal horde

Directory of Open Access Journals (Sweden)

Erdem ePulcu

2014-01-01

Full Text Available Freud proposed that the processes which occurred in the primal horde are essential for understanding superego formation and therefore, the successful dissolution of the Oedipus complex. However, Freud theorized superego formation in the primal horde as if it is an instant, all-or-none achievement. The present paper proposes an alternative model aiming to explain gradual development of superego in the primitive man. The proposed model is built on knowledge from evolutionary and neural sciences as well as anthropology, and it particularly focuses on the evolutionary significance of the acquisition of fire by hominids in the Pleistocene period in the light of archaeological findings. Acquisition of fire is discussed as a form of sublimation which might have helped Prehistoric man to maximise the utility of limited evolutionary biological resources, potentially contributing to the rate and extent of bodily evolution. The limitations of both Freud's original conceptualisation and the present model are discussed accordingly in an interdisciplinary framework.

Ecological and evolutionary influences on body size and shape in the Galápagos marine iguana (Amblyrhynchus cristatus).

Science.gov (United States)

Chiari, Ylenia; Glaberman, Scott; Tarroso, Pedro; Caccone, Adalgisa; Claude, Julien

2016-07-01

Oceanic islands are often inhabited by endemic species that have undergone substantial morphological evolutionary change due to processes of multiple colonizations from various source populations, dispersal, and local adaptation. Galápagos marine iguanas are an example of an island endemic exhibiting high morphological diversity, including substantial body size variation among populations and sexes, but the causes and magnitude of this variation are not well understood. We obtained morphological measurements from marine iguanas throughout their distribution range. These data were combined with genetic and local environmental data from each population to investigate the effects of evolutionary history and environmental conditions on body size and shape variation and sexual dimorphism. Our results indicate that body size and shape are highly variable among populations. Sea surface temperature and island perimeter, but not evolutionary history as depicted by phylogeographic patterns in this species, explain variation in body size among populations. Conversely, evolutionary history, but not environmental parameters or island size, was found to influence variation in body shape among populations. Finally, in all populations except one, we found strong sexual dimorphism in body size and shape in which males are larger, with higher heads than females, while females have longer heads than males. Differences among populations suggest that plasticity and/or genetic adaptation may shape body size and shape variation in marine iguanas. This study will help target future investigations to address the contribution of plasticity versus genetic adaptation on size and shape variation in marine iguanas.

Self-organized modularization in evolutionary algorithms.

Science.gov (United States)

Dauscher, Peter; Uthmann, Thomas

2005-01-01

The principle of modularization has proven to be extremely successful in the field of technical applications and particularly for Software Engineering purposes. The question to be answered within the present article is whether mechanisms can also be identified within the framework of Evolutionary Computation that cause a modularization of solutions. We will concentrate on processes, where modularization results only from the typical evolutionary operators, i.e. selection and variation by recombination and mutation (and not, e.g., from special modularization operators). This is what we call Self-Organized Modularization. Based on a combination of two formalizations by Radcliffe and Altenberg, some quantitative measures of modularity are introduced. Particularly, we distinguish Built-in Modularity as an inherent property of a genotype and Effective Modularity, which depends on the rest of the population. These measures can easily be applied to a wide range of present Evolutionary Computation models. It will be shown, both theoretically and by simulation, that under certain conditions, Effective Modularity (as defined within this paper) can be a selection factor. This causes Self-Organized Modularization to take place. The experimental observations emphasize the importance of Effective Modularity in comparison with Built-in Modularity. Although the experimental results have been obtained using a minimalist toy model, they can lead to a number of consequences for existing models as well as for future approaches. Furthermore, the results suggest a complex self-amplification of highly modular equivalence classes in the case of respected relations. Since the well-known Holland schemata are just the equivalence classes of respected relations in most Simple Genetic Algorithms, this observation emphasizes the role of schemata as Building Blocks (in comparison with arbitrary subsets of the search space).

Multipurpose Water Reservoir Management: An Evolutionary Multiobjective Optimization Approach

Directory of Open Access Journals (Sweden)

Luís A. Scola

2014-01-01

Full Text Available The reservoirs that feed large hydropower plants should be managed in order to provide other uses for the water resources. Those uses include, for instance, flood control and avoidance, irrigation, navigability in the rivers, and other ones. This work presents an evolutionary multiobjective optimization approach for the study of multiple water usages in multiple interlinked reservoirs, including both power generation objectives and other objectives not related to energy generation. The classical evolutionary algorithm NSGA-II is employed as the basic multiobjective optimization machinery, being modified in order to cope with specific problem features. The case studies, which include the analysis of a problem which involves an objective of navigability on the river, are tailored in order to illustrate the usefulness of the data generated by the proposed methodology for decision-making on the problem of operation planning of multiple reservoirs with multiple usages. It is shown that it is even possible to use the generated data in order to determine the cost of any new usage of the water, in terms of the opportunity cost that can be measured on the revenues related to electric energy sales.

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

Science.gov (United States)

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

2014-01-01

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

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

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Peña, Jorge; Rochat, Yannick

2012-01-01

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

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

Directory of Open Access Journals (Sweden)

Evert Haasdijk

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

Genetic Process Mining: Alignment-based Process Model Mutation

NARCIS (Netherlands)

Eck, van M.L.; Buijs, J.C.A.M.; Dongen, van B.F.; Fournier, F.; Mendling, J.

2015-01-01

The Evolutionary Tree Miner (ETM) is a genetic process discovery algorithm that enables the user to guide the discovery process based on preferences with respect to four process model quality dimensions: replay fitness, precision, generalization and simplicity. Traditionally, the ETM algorithm uses

Evolutionary analysis of hepatitis C virus gene sequences from 1953

Science.gov (United States)

Gray, Rebecca R.; Tanaka, Yasuhito; Takebe, Yutaka; Magiorkinis, Gkikas; Buskell, Zelma; Seeff, Leonard; Alter, Harvey J.; Pybus, Oliver G.

2013-01-01

Reconstructing the transmission history of infectious diseases in the absence of medical or epidemiological records often relies on the evolutionary analysis of pathogen genetic sequences. The precision of evolutionary estimates of epidemic history can be increased by the inclusion of sequences derived from ‘archived’ samples that are genetically distinct from contemporary strains. Historical sequences are especially valuable for viral pathogens that circulated for many years before being formally identified, including HIV and the hepatitis C virus (HCV). However, surprisingly few HCV isolates sampled before discovery of the virus in 1989 are currently available. Here, we report and analyse two HCV subgenomic sequences obtained from infected individuals in 1953, which represent the oldest genetic evidence of HCV infection. The pairwise genetic diversity between the two sequences indicates a substantial period of HCV transmission prior to the 1950s, and their inclusion in evolutionary analyses provides new estimates of the common ancestor of HCV in the USA. To explore and validate the evolutionary information provided by these sequences, we used a new phylogenetic molecular clock method to estimate the date of sampling of the archived strains, plus the dates of four more contemporary reference genomes. Despite the short fragments available, we conclude that the archived sequences are consistent with a proposed sampling date of 1953, although statistical uncertainty is large. Our cross-validation analyses suggest that the bias and low statistical power observed here likely arise from a combination of high evolutionary rate heterogeneity and an unstructured, star-like phylogeny. We expect that attempts to date other historical viruses under similar circumstances will meet similar problems. PMID:23938759

Evolutionary-Simulative Methodology in the Management of Social and Economic Systems

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Konyavskiy V.A.

2017-01-01

Full Text Available The article outlines the main provisions of the evolutionary-simulative methodology (ESM which is a methodology of mathematical modeling of equilibrium random processes (CPR, widely used in the economy. It discusses the basic directions of use of ESM solutions for social problems and economic management systems.

Evolutionary Algorithms for Boolean Functions in Diverse Domains of Cryptography.

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

2016-01-01

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

Computational Modeling of Teaching and Learning through Application of Evolutionary Algorithms

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Richard Lamb

2015-09-01

Full Text Available Within the mind, there are a myriad of ideas that make sense within the bounds of everyday experience, but are not reflective of how the world actually exists; this is particularly true in the domain of science. Classroom learning with teacher explanation are a bridge through which these naive understandings can be brought in line with scientific reality. The purpose of this paper is to examine how the application of a Multiobjective Evolutionary Algorithm (MOEA can work in concert with an existing computational-model to effectively model critical-thinking in the science classroom. An evolutionary algorithm is an algorithm that iteratively optimizes machine learning based computational models. The research question is, does the application of an evolutionary algorithm provide a means to optimize the Student Task and Cognition Model (STAC-M and does the optimized model sufficiently represent and predict teaching and learning outcomes in the science classroom? Within this computational study, the authors outline and simulate the effect of teaching on the ability of a “virtual” student to solve a Piagetian task. Using the Student Task and Cognition Model (STAC-M a computational model of student cognitive processing in science class developed in 2013, the authors complete a computational experiment which examines the role of cognitive retraining on student learning. Comparison of the STAC-M and the STAC-M with inclusion of the Multiobjective Evolutionary Algorithm shows greater success in solving the Piagetian science-tasks post cognitive retraining with the Multiobjective Evolutionary Algorithm. This illustrates the potential uses of cognitive and neuropsychological computational modeling in educational research. The authors also outline the limitations and assumptions of computational modeling.

Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (mammalia, carnivora).

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Finarelli, John A; Goswami, Anjali

2013-12-01

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead-up to extant taxa; they represent now-extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC-based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant-only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep-time organismal evolution in the absence of deep-time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies. © 2013 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

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

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David Lee Erickson

2014-11-01

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

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 a pe...... tests. The presented algorithm is applied to urban traffic signal timing optimization and the effect is satisfied....

Evolutionary modeling-based approach for model errors correction

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S. Q. Wan

2012-08-01

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

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

AN EVOLUTIONARY ALGORITHM FOR FAST INTENSITY BASED IMAGE MATCHING BETWEEN OPTICAL AND SAR SATELLITE IMAGERY

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P. Fischer

2018-04-01

Full Text Available This paper presents a hybrid evolutionary algorithm for fast intensity based matching between satellite imagery from SAR and very high-resolution (VHR optical sensor systems. The precise and accurate co-registration of image time series and images of different sensors is a key task in multi-sensor image processing scenarios. The necessary preprocessing step of image matching and tie-point detection is divided into a search problem and a similarity measurement. Within this paper we evaluate the use of an evolutionary search strategy for establishing the spatial correspondence between satellite imagery of optical and radar sensors. The aim of the proposed algorithm is to decrease the computational costs during the search process by formulating the search as an optimization problem. Based upon the canonical evolutionary algorithm, the proposed algorithm is adapted for SAR/optical imagery intensity based matching. Extensions are drawn using techniques like hybridization (e.g. local search and others to lower the number of objective function calls and refine the result. The algorithm significantely decreases the computational costs whilst finding the optimal solution in a reliable way.

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

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Kauffman, Rick, Jr.

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

Evolutionary quantum game theory in the context of socio-economic systems

International Nuclear Information System (INIS)

Hanauske, Matthias

2011-01-01

The evolution of socio-economic systems depend on the interdependent decision processes of its underlying system components. The mathematical model to describe the strategic decision of players within a socio-economic game is ''game theory''. ''Quantum game theory'' is a mathematical and conceptual amplification of classical game theory. The space of all conceivable decision paths is extended from the purely rational, measurable space in the Hilbert-space of complex numbers - which is the mathematical space where quantum theory is formulated. By the concept of a potential entanglement of the imaginary quantum strategy parts, it is possible to include cooperate decision path, caused by cultural or moral standards. If this strategy entanglement is large enough, then additional Nash equilibria can occur, previously present dominant strategies could become nonexistent and new evolutionary stable strategies do appear for some game classes. Within this PhD thesis the main results of classical and quantum games are summarized and all of the possible game classes of evolutionary (2 player)-(2 strategy) games are extended to quantum games. It is shown that the quantum extension of classical games with an underlying dilemma-like structure give different results, if the strength of strategic entanglement is above a certain barrier. After the German summary and the introduction paper, five different applications of the theory are discussed within the thesis. (orig.)

Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans

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K.D. Klepzig; A.S. Adams; J. Handelsman; K.F. Raffa

2009-01-01

Symbiosis is receiving increased attention among all aspects of biology because of the unifying themes it helps construct across ecological,evolutionary, developmental, semiochemical, and pest management theory. Insects show a vast array of symbiotic relationships with a wide diversity of microorganisms. These relationships may confer a variety of benefits to the host...

Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

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Huang, Bing-Hong; Liao, Pei-Chun

2015-07-01

Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

What to expect from an evolutionary hypothesis for a human disease: The case of type 2 diabetes.

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Watve, Milind; Diwekar-Joshi, Manawa

2016-10-01

Evolutionary medicine has a promise to bring in a conceptual revolution in medicine. However, as yet the field does not have the same theoretical rigour as that of many other fields in evolutionary studies. We discuss here with reference to type 2 diabetes mellitus (T2DM) what role an evolutionary hypothesis should play in the development of thinking in medicine. Starting with the thrifty gene hypothesis, evolutionary thinking in T2DM has undergone several transitions, modifications and refinements of the thrift family of hypotheses. In addition alternative hypotheses independent of thrift are also suggested. However, most hypotheses look at partial pictures; make selective use of supportive data ignoring inconvenient truths. Most hypotheses look at a superficial picture and avoid getting into the intricacies of underlying molecular, neuronal and physiological processes. Very few hypotheses have suggested clinical implications and none of them have been tested with randomized clinical trials. In the meanwhile the concepts in the pathophysiology of T2DM are undergoing radical changes and evolutionary hypotheses need to take them into account. We suggest an approach and a set of criteria to evaluate the relative merits of the alternative hypotheses. A number of hypotheses are likely to fail when critically evaluated against these criteria. It is possible that more than one selective process are at work in the evolution of propensity to T2DM, but the intercompatibility of the alternative selective forces and their relative contribution needs to be examined. The approach we describe could potentially lead to a sound evolutionary theory that is clinically useful and testable by randomized controlled clinical trials. Copyright © 2016 Elsevier GmbH. All rights reserved.

Evolutionary Game Theory: A Renaissance

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Jonathan Newton

2018-05-01

Full Text Available Economic agents are not always rational or farsighted and can make decisions according to simple behavioral rules that vary according to situation and can be studied using the tools of evolutionary game theory. Furthermore, such behavioral rules are themselves subject to evolutionary forces. Paying particular attention to the work of young researchers, this essay surveys the progress made over the last decade towards understanding these phenomena, and discusses open research topics of importance to economics and the broader social sciences.

Evolutionary paths of streptococcal and staphylococcal superantigens

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Okumura Kayo

2012-08-01

Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

Codon usage is associated with the evolutionary age of genes in metazoan genomes

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Linial Nathan

2009-12-01

Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.

Evaluating and Improving Automatic Sleep Spindle Detection by Using Multi-Objective Evolutionary Algorithms

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Min-Yin Liu

2017-05-01

Full Text Available Sleep spindles are brief bursts of brain activity in the sigma frequency range (11–16 Hz measured by electroencephalography (EEG mostly during non-rapid eye movement (NREM stage 2 sleep. These oscillations are of great biological and clinical interests because they potentially play an important role in identifying and characterizing the processes of various neurological disorders. Conventionally, sleep spindles are identified by expert sleep clinicians via visual inspection of EEG signals. The process is laborious and the results are inconsistent among different experts. To resolve the problem, numerous computerized methods have been developed to automate the process of sleep spindle identification. Still, the performance of these automated sleep spindle detection methods varies inconsistently from study to study. There are two reasons: (1 the lack of common benchmark databases, and (2 the lack of commonly accepted evaluation metrics. In this study, we focus on tackling the second problem by proposing to evaluate the performance of a spindle detector in a multi-objective optimization context and hypothesize that using the resultant Pareto fronts for deriving evaluation metrics will improve automatic sleep spindle detection. We use a popular multi-objective evolutionary algorithm (MOEA, the Strength Pareto Evolutionary Algorithm (SPEA2, to optimize six existing frequency-based sleep spindle detection algorithms. They include three Fourier, one continuous wavelet transform (CWT, and two Hilbert-Huang transform (HHT based algorithms. We also explore three hybrid approaches. Trained and tested on open-access DREAMS and MASS databases, two new hybrid methods of combining Fourier with HHT algorithms show significant performance improvement with F1-scores of 0.726–0.737.

Revising the recent evolutionary history of equids using ancient DNA.

Science.gov (United States)

Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

2009-12-22

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

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

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Yuki Furuse

2016-11-01

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

Evolutionary Computation and Its Applications in Neural and Fuzzy Systems

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Biaobiao Zhang

2011-01-01

Full Text Available Neural networks and fuzzy systems are two soft-computing paradigms for system modelling. Adapting a neural or fuzzy system requires to solve two optimization problems: structural optimization and parametric optimization. Structural optimization is a discrete optimization problem which is very hard to solve using conventional optimization techniques. Parametric optimization can be solved using conventional optimization techniques, but the solution may be easily trapped at a bad local optimum. Evolutionary computation is a general-purpose stochastic global optimization approach under the universally accepted neo-Darwinian paradigm, which is a combination of the classical Darwinian evolutionary theory, the selectionism of Weismann, and the genetics of Mendel. Evolutionary algorithms are a major approach to adaptation and optimization. In this paper, we first introduce evolutionary algorithms with emphasis on genetic algorithms and evolutionary strategies. Other evolutionary algorithms such as genetic programming, evolutionary programming, particle swarm optimization, immune algorithm, and ant colony optimization are also described. Some topics pertaining to evolutionary algorithms are also discussed, and a comparison between evolutionary algorithms and simulated annealing is made. Finally, the application of EAs to the learning of neural networks as well as to the structural and parametric adaptations of fuzzy systems is also detailed.

The integration of Darwinism and evolutionary morphology: Alexej Nikolajevich Sewertzoff (1866-1936) and the developmental basis of evolutionary change.

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

2004-07-15

The growth of evolutionary morphology in the late 19th and early 20th centuries was inspired by the work of Carl Gegenbaur (1826-1903) and his protégé and friend Ernst Haeckel (1834-1919). However, neither of them succeeded in creating and applying a strictly Darwinian (selectionist) methodology. This task was left to the next generation of evolutionary morphologists. In this paper we present a relatively unknown researcher, Alexej Nikolajevich Sewertzoff (1866-1936) who made important contributions towards a synthesis of Darwinism and evolutionary morphology. Copyright 2004 Wiley-Liss, Inc.

Islamic medicine and evolutionary medicine: a comparative analysis.

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Saniotis, Arthur

2012-01-01

The advent of evolutionary medicine in the last two decades has provided new insights into the causes of human disease and possible preventative strategies. One of the strengths of evolutionary medicine is that it follows a multi-disciplinary approach. Such an approach is vital to future biomedicine as it enables for the infiltration of new ideas. Although evolutionary medicine uses Darwinian evolution as a heuristic for understanding human beings' susceptibility to disease, this is not necessarily in conflict with Islamic medicine. It should be noted that current evolutionary theory was first expounded by various Muslim scientists such as al-Jāḥiẓ, al-Ṭūsī, Ibn Khaldūn and Ibn Maskawayh centuries before Darwin and Wallace. In this way, evolution should not be viewed as being totally antithetical to Islam. This article provides a comparative overview of Islamic medicine and Evolutionary medicine as well as drawing points of comparison between the two approaches which enables their possible future integration.

Handbook of differential equations evolutionary equations

CERN Document Server

Dafermos, CM

2008-01-01

The material collected in this volume discusses the present as well as expected future directions of development of the field with particular emphasis on applications. The seven survey articles present different topics in Evolutionary PDE's, written by leading experts.- Review of new results in the area- Continuation of previous volumes in the handbook series covering Evolutionary PDEs- Written by leading experts

Research on Evolutionary Mechanism of Agile Supply Chain Network via Complex Network Theory

Directory of Open Access Journals (Sweden)

Nai-Ru Xu

2016-01-01

Full Text Available The paper establishes the evolutionary mechanism model of agile supply chain network by means of complex network theory which can be used to describe the growth process of the agile supply chain network and analyze the complexity of the agile supply chain network. After introducing the process and the suitability of taking complex network theory into supply chain network research, the paper applies complex network theory into the agile supply chain network research, analyzes the complexity of agile supply chain network, presents the evolutionary mechanism of agile supply chain network based on complex network theory, and uses Matlab to simulate degree distribution, average path length, clustering coefficient, and node betweenness. Simulation results show that the evolution result displays the scale-free property. It lays the foundations of further research on agile supply chain network based on complex network theory.

First insights into the evolutionary history of the Davallia repens complex

NARCIS (Netherlands)

Chen, C.-W.; Ngan, L.T.; Hidayat, A.; Evangelista, L.; Nooteboom, H.P.; Chiou, W.-L.

2014-01-01

Davallia repens and its close relatives have been identified as a species complex in this study because of the existence of continuously morphological variation. To decipher its evolutionary history, integrated methodologies were applied in this study including morphology, cytology, reproductive

Evolutionary algorithms for mobile ad hoc networks

CERN Document Server

Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal

2014-01-01

Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...

Classifying the evolutionary and ecological features of neoplasms

Science.gov (United States)

Maley, Carlo C.; Aktipis, Athena; Graham, Trevor A.; Sottoriva, Andrea; Boddy, Amy M.; Janiszewska, Michalina; Silva, Ariosto S.; Gerlinger, Marco; Yuan, Yinyin; Pienta, Kenneth J.; Anderson, Karen S.; Gatenby, Robert; Swanton, Charles; Posada, David; Wu, Chung-I; Schiffman, Joshua D.; Hwang, E. Shelley; Polyak, Kornelia; Anderson, Alexander R. A.; Brown, Joel S.; Greaves, Mel; Shibata, Darryl

2018-01-01

Neoplasms change over time through a process of cell-level evolution, driven by genetic and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic cell determines which changes provide adaptive benefits. There is widespread recognition of the importance of these evolutionary and ecological processes in cancer, but to date, no system has been proposed for drawing clinically relevant distinctions between how different tumours are evolving. On the basis of a consensus conference of experts in the fields of cancer evolution and cancer ecology, we propose a framework for classifying tumours that is based on four relevant components. These are the diversity of neoplastic cells (intratumoural heterogeneity) and changes over time in that diversity, which make up an evolutionary index (Evo-index), as well as the hazards to neoplastic cell survival and the resources available to neoplastic cells, which make up an ecological index (Eco-index). We review evidence demonstrating the importance of each of these factors and describe multiple methods that can be used to measure them. Development of this classification system holds promise for enabling clinicians to personalize optimal interventions based on the evolvability of the patient’s tumour. The Evo- and Eco-indices provide a common lexicon for communicating about how neoplasms change in response to interventions, with potential implications for clinical trials, personalized medicine and basic cancer research. PMID:28912577

Animal egg as evolutionary innovation: a solution to the "embryonic hourglass" puzzle.

Science.gov (United States)

Newman, Stuart A

2011-11-15

The evolutionary origin of the egg stage of animal development presents several difficulties for conventional developmental and evolutionary narratives. If the egg's internal organization represents a template for key features of the developed organism, why can taxa within a given phylum exhibit very different egg types, pass through a common intermediate morphology (the so-called "phylotypic stage"), only to diverge again, thus exemplifying the embryonic "hourglass"? Moreover, if different egg types typically represent adaptations to different environmental conditions, why do birds and mammals, for example, have such vastly different eggs with respect to size, shape, and postfertilization dynamics, whereas all these features are more similar for ascidians and mammals? Here, I consider the possibility that different body plans had their origin in self-organizing physical processes in ancient clusters of cells, and suggest that eggs represented a set of independent evolutionary innovations subsequently inserted into the developmental trajectories of such aggregates. I first describe how "dynamical patterning modules" (DPMs) associations between components of the metazoan developmental-genetic toolkit and certain physical processes and effects may have organized primitive animal body plans independently of an egg stage. Next, I describe how adaptive specialization of cells released from such aggregates could have become "proto-eggs," which regenerated the parental cell clusters by cleavage, conserving the characteristic DPMs available to a lineage. Then, I show how known processes of cytoplasmic reorganization following fertilization are often based on spontaneous, self-organizing physical effects ("egg-patterning processes": EPPs). I suggest that rather than acting as developmental blueprints or prepatterns, the EPPs refine the phylotypic body plans determined by the DPMs by setting the boundary and initial conditions under which these multicellular patterning

Evolutionary change in physiological phenotypes along the human lineage.

Science.gov (United States)

Vining, Alexander Q; Nunn, Charles L

2016-01-01

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

Comparing Evolutionary Strategies on a Biobjective Cultural Algorithm

Directory of Open Access Journals (Sweden)

Carolina Lagos

2014-01-01

Full Text Available Evolutionary algorithms have been widely used to solve large and complex optimisation problems. Cultural algorithms (CAs are evolutionary algorithms that have been used to solve both single and, to a less extent, multiobjective optimisation problems. In order to solve these optimisation problems, CAs make use of different strategies such as normative knowledge, historical knowledge, circumstantial knowledge, and among others. In this paper we present a comparison among CAs that make use of different evolutionary strategies; the first one implements a historical knowledge, the second one considers a circumstantial knowledge, and the third one implements a normative knowledge. These CAs are applied on a biobjective uncapacitated facility location problem (BOUFLP, the biobjective version of the well-known uncapacitated facility location problem. To the best of our knowledge, only few articles have applied evolutionary multiobjective algorithms on the BOUFLP and none of those has focused on the impact of the evolutionary strategy on the algorithm performance. Our biobjective cultural algorithm, called BOCA, obtains important improvements when compared to other well-known evolutionary biobjective optimisation algorithms such as PAES and NSGA-II. The conflicting objective functions considered in this study are cost minimisation and coverage maximisation. Solutions obtained by each algorithm are compared using a hypervolume S metric.

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

Science.gov (United States)

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

2015-11-01

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

An Evolutionary Psychology Approach to Consumer Choice

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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.

Geography and major host evolutionary transitions shape the resource use of plant parasites.

Science.gov (United States)

Calatayud, Joaquín; Hórreo, José Luis; Madrigal-González, Jaime; Migeon, Alain; Rodríguez, Miguel Á; Magalhães, Sara; Hortal, Joaquín

2016-08-30

The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore-plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites.

Evolutionary fuzzy ARTMAP neural networks for classification of semiconductor defects.

Science.gov (United States)

Tan, Shing Chiang; Watada, Junzo; Ibrahim, Zuwairie; Khalid, Marzuki

2015-05-01

Wafer defect detection using an intelligent system is an approach of quality improvement in semiconductor manufacturing that aims to enhance its process stability, increase production capacity, and improve yields. Occasionally, only few records that indicate defective units are available and they are classified as a minority group in a large database. Such a situation leads to an imbalanced data set problem, wherein it engenders a great challenge to deal with by applying machine-learning techniques for obtaining effective solution. In addition, the database may comprise overlapping samples of different classes. This paper introduces two models of evolutionary fuzzy ARTMAP (FAM) neural networks to deal with the imbalanced data set problems in a semiconductor manufacturing operations. In particular, both the FAM models and hybrid genetic algorithms are integrated in the proposed evolutionary artificial neural networks (EANNs) to classify an imbalanced data set. In addition, one of the proposed EANNs incorporates a facility to learn overlapping samples of different classes from the imbalanced data environment. The classification results of the proposed evolutionary FAM neural networks are presented, compared, and analyzed using several classification metrics. The outcomes positively indicate the effectiveness of the proposed networks in handling classification problems with imbalanced data sets.

Evolutionary analysis of groundwater flow: Application of multivariate statistical analysis to hydrochemical data in the Densu Basin, Ghana

Science.gov (United States)

Yidana, Sandow Mark; Bawoyobie, Patrick; Sakyi, Patrick; Fynn, Obed Fiifi

2018-02-01

An evolutionary trend has been postulated through the analysis of hydrochemical data of a crystalline rock aquifer system in the Densu Basin, Southern Ghana. Hydrochemcial data from 63 groundwater samples, taken from two main groundwater outlets (Boreholes and hand dug wells) were used to postulate an evolutionary theory for the basin. Sequential factor and hierarchical cluster analysis were used to disintegrate the data into three factors and five clusters (spatial associations). These were used to characterize the controls on groundwater hydrochemistry and its evolution in the terrain. The dissolution of soluble salts and cation exchange processes are the dominant processes controlling groundwater hydrochemistry in the terrain. The trend of evolution of this set of processes follows the pattern of groundwater flow predicted by a calibrated transient groundwater model in the area. The data suggest that anthropogenic activities represent the second most important process in the hydrochemistry. Silicate mineral weathering is the third most important set of processes. Groundwater associations resulting from Q-mode hierarchical cluster analysis indicate an evolutionary pattern consistent with the general groundwater flow pattern in the basin. These key findings are at variance with results of previous investigations and indicate that when carefully done, groundwater hydrochemical data can be very useful for conceptualizing groundwater flow in basins.

Quantifying evolutionary dynamics from variant-frequency time series

Science.gov (United States)

Khatri, Bhavin S.

2016-09-01

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

Limitations of Evolutionary Theory in Explaining Marital Satisfaction and Stability of Couple Relationships

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Victoria Cabrera García

2014-01-01

Full Text Available The explanation of marital satisfaction and stability in trajectories of couple relationships has been the central interest in different studies (Karney, Bradbury. & Johnson, 1999; Sabatelli & Ripoll, 2004; Schoebi, Karney & Bradbury, 2012. However, there are still several questions and unknown aspects surrounding the topic. Within this context, the present reflection seeks to analyze whether the principles of Evolutionary Theory suffice to explain three marital trajectories in terms of satisfaction and stability. With this in mind, we have included other explanations proposed by the Psychosocial Theory that Evolutionary Theory does not refer to in order to better understand mating behavior. Moreover, other factors that could account for satisfied and stable relationships were analyzed. Suggestions for future investigations include the analysis of other marital trajectories that may or may not end in separation or divorce but are not included in this article.

On economic applications of evolutionary game theory

OpenAIRE

Daniel Friedman

1998-01-01

Evolutionary games have considerable unrealized potential for modeling substantive economic issues. They promise richer predictions than orthodox game models but often require more extensive specifications. This paper exposits the specification of evolutionary game models and classifies the possible asymptotic behavior for one and two dimensional models.

On the Evolutionary Stability of Bargaining Inefficiency

DEFF Research Database (Denmark)

Poulsen, Anders

This paper investigates whether 'tough' bargaining behavior, which gives rise to inefficiency, can be evolutionary stable. We show that in a two-stage Nash Demand Game tough behavior survives. Indeed, almost all the surplus may be wasted. We also study the Ultimatum Game. Here evolutionary select...

Can an Evolutionary Analysis Dissolve the Paradox of Horror?

DEFF Research Database (Denmark)

Kjeldgaard-Christiansen, Jens; Clasen, Mathias; Johnson, John

The paradox of horror” is the problem of why so many people are motivated to experience the negative emotions induced by horror media. In this talk, we argue that an evolutionary analysis may dissolve the paradox of horror. From an evolutionary perspective, horror may be analyzed as a simulation...... technology that allows users to attain adaptive experience with perceived threat and negative emotion in a safe environment. The argument is supported by results from a comprehensive MTurk survey of American users of horror media (n=1,071). Results include findings on the personal details (e.g., sex......), supernatural beliefs (e.g., paranormal beliefs), personality traits (e.g., Big Five), horror genre preferences (e.g., supernatural versus natural horror), and horror-induced emotional responses of users of horror media. The strongest individual predictors of horror media enjoyment are sex (male preference...

Evolutionary Robotics: What, Why, and Where to

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Stephane eDoncieux

2015-03-01

Full Text Available Evolutionary robotics applies the selection, variation, and heredity principles of natural evolution to the design of robots with embodied intelligence. It can be considered as a subfield of robotics that aims to create more robust and adaptive robots. A pivotal feature of the evolutionary approach is that it considers the whole robot at once, and enables the exploitation of robot features in a holistic manner. Evolutionary robotics can also be seen as an innovative approach to the study of evolution based on a new kind of experimentalism. The use of robots as a substrate can help address questions that are difficult, if not impossible, to investigate through computer simulations or biological studies. In this paper we consider the main achievements of evolutionary robotics, focusing particularly on its contributions to both engineering and biology. We briefly elaborate on methodological issues, review some of the most interesting findings, and discuss important open issues and promising avenues for future work.

Evolutionary ethics from Darwin to Moore.

Science.gov (United States)

Allhoff, Fritz

2003-01-01

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

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

Science.gov (United States)

Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

2009-01-01

Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

Directory of Open Access Journals (Sweden)

Green Eric D

2009-07-01

Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

[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.

Comparison of evolutionary algorithms in gene regulatory network model inference.

LENUS (Irish Health Repository)

2010-01-01

ABSTRACT: BACKGROUND: The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. RESULTS: This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. CONCLUSIONS: Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established.

Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

Science.gov (United States)

Fostervold, Knut Inge; Watten, Reidulf G; Volden, Frode

2014-01-01

The literature discussing visual ergonomics often mention that human vision is adapted to light emitted by the sun. However, theoretical and practical implications of this viewpoint is seldom discussed or taken into account. The paper discusses some of the main theoretical implications of an evolutionary approach to visual ergonomics. Based on interactional theory and ideas from ecological psychology an evolutionary stress model is proposed as a theoretical framework for future research in ergonomics and human factors. The model stresses the importance of developing work environments that fits with our evolutionary adaptations. In accordance with evolutionary psychology, the environment of evolutionary adaptedness (EEA) and evolutionarily-novel environments (EN) are used as key concepts. Using work with visual display units (VDU) as an example, the paper discusses how this knowledge can be utilized in an ergonomic analysis of risk factors in the work environment. The paper emphasises the importance of incorporating evolutionary theory in the field of ergonomics. Further, the paper encourages scientific practices that further our understanding of any phenomena beyond the borders of traditional proximal explanations.

What can other animals tell us about human social cognition?An evolutionary perspective on reflective and reflexive processing

Directory of Open Access Journals (Sweden)

Erin E Hecht

2012-07-01

Full Text Available Human neuroscience has seen a recent boom in studies on reflective, controlled, explicit social cognitive functions like imitation, perspective‐taking, and empathy. The relationship of these higher‐level functions to lower‐level, reflexive, automatic, implicit functions is an area of current research. As the field continues to address this relationship, we suggest that an evolutionary, comparative approach will be useful, even essential. There is a large body of research on reflexive, automatic, implicit processes in animals. A growing perspective sees social cognitive processes as phylogenically continuous, making findings in other species relevant for understanding our own. One of these phylogenically continuous processes appears to be self‐other matching or simulation. Mice are more sensitive to pain after watching other mice experience pain; geese experience heart rate increases when seeing their mate in conflict; and infant macaques, chimpanzees, and humans automatically mimic adult facial expressions. In this article, we review findings in different species that illustrate how such reflexive processes are related to (higher order reflexive processes, such as cognitive empathy, theory of mind, and learning by imitation. We do so in the context of self‐other matching in three different domains – in the motor domain (somatomotor movements, in the perceptual domain (eye movements and cognition about visual perception, and in the autonomic/emotional domain. We also review research on the developmental origin of these processes and their neural bases across species. We highlight gaps in existing knowledge and point out some questions for future research. We conclude that our understanding of the psychological and neural mechanisms of self‐other mapping and other functions in our own species can be informed by considering the layered complexity these functions in other species.

Human Behavior and Cognition in Evolutionary Economics.

Science.gov (United States)

Nelson, Richard R

2011-12-01

My brand of evolutionary economics recognizes, highlights, that modern economies are always in the process of changing, never fully at rest, with much of the energy coming from innovation. This perspective obviously draws a lot from Schumpeter. Continuing innovation, and the creative destruction that innovation engenders, is driving the system. There are winners and losers in the process, but generally the changes can be regarded as progress. The processes through which economic activity and performance evolve has a lot in common with evolution in biology. In particular, at any time the economy is marked by considerable variety, there are selection forces winnowing on that variety, but also continuing emergence of new ways of doing things and often economic actors. But there also are important differences from biological evolution. In particular, both innovation and selection are to a considerable degree purposive activities, often undertaken on the basis of relatively strong knowledge.

Evolutionary Biology Today

Indian Academy of Sciences (India)

Hindi and English. Port 1. Resonance, Vo1.7 ... they use. Of course, many evolutionary biologists do work with fossils or DNA, or both, but there are also large numbers of ... The first major division that I like to make is between studies focussed ...

Genome size as a key to evolutionary complex aquatic plants: polyploidy and hybridization in Callitriche (Plantaginaceae.

Directory of Open Access Journals (Sweden)

Jan Prančl

Full Text Available Despite their complex evolutionary histories, aquatic plants are highly underrepresented in contemporary biosystematic studies. Of them, the genus Callitriche is particularly interesting because of such evolutionary features as wide variation in chromosome numbers and pollination systems. However, taxonomic difficulties have prevented broader investigation of this genus. In this study we applied flow cytometry to Callitriche for the first time in order to gain an insight into evolutionary processes and genome size differentiation in the genus. Flow cytometry complemented by confirmation of chromosome counts was applied to an extensive dataset of 1077 Callitriche individuals from 495 localities in 11 European countries and the USA. Genome size was determined for 12 taxa. The results suggest that many important processes have interacted in the evolution of the genus, including polyploidization and hybridization. Incongruence between genome size and ploidy level, intraspecific variation in genome size, formation of autotriploid and hybridization between species with different pollination systems were also detected. Hybridization takes place particularly in the diploid-tetraploid complex C. cophocarpa-C. platycarpa, for which the triploid hybrids were frequently recorded in the area of co-occurrence of its parents. A hitherto unknown hybrid (probably C. hamulata × C. cophocarpa with a unique chromosome number was discovered in the Czech Republic. However, hybridization occurs very rarely among most of the studied species. The main ecological preferences were also compared among the taxa collected. Although Callitriche taxa often grow in mixed populations, the ecological preferences of individual species are distinctly different in some cases. Anyway, flow cytometry is a very efficient method for taxonomic delimitation, determination and investigation of Callitriche species, and is even able to distinguish homoploid taxa and identify introduced

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

OpenAIRE

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

2009-01-01

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

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

Energy Technology Data Exchange (ETDEWEB)

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

2009-01-01

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

Understanding variation in human fertility: what can we learn from evolutionary demography?

Science.gov (United States)

Sear, Rebecca; Lawson, David W; Kaplan, Hillard; Shenk, Mary K

2016-04-19

Decades of research on human fertility has presented a clear picture of how fertility varies, including its dramatic decline over the last two centuries in most parts of the world. Why fertility varies, both between and within populations, is not nearly so well understood. Fertility is a complex phenomenon, partly physiologically and partly behaviourally determined, thus an interdisciplinary approach is required to understand it. Evolutionary demographers have focused on human fertility since the 1980s. The first wave of evolutionary demographic research made major theoretical and empirical advances, investigating variation in fertility primarily in terms of fitness maximization. Research focused particularly on variation within high-fertility populations and small-scale subsistence societies and also yielded a number of hypotheses for why fitness maximization seems to break down as fertility declines during the demographic transition. A second wave of evolutionary demography research on fertility is now underway, paying much more attention to the cultural and psychological mechanisms underpinning fertility. It is also engaging with the complex, multi-causal nature of fertility variation, and with understanding fertility in complex modern and transitioning societies. Here, we summarize the history of evolutionary demographic work on human fertility, describe the current state of the field, and suggest future directions. © 2016 The Author(s).

The First Joke: Exploring the Evolutionary Origins of Humor

Directory of Open Access Journals (Sweden)

Joseph Polimeni

2006-01-01

Full Text Available Humor is a complex cognitive function which often leads to laughter. Contemporary humor theorists have begun to formulate hypotheses outlining the possible innate cognitive structures underlying humor. Humor's conspicuous presence in the behavioral repertoire of humankind invites adaptive explanations. This article explores the possible adaptive features of humor and ponders its evolutionary path through hominid history. Current humor theories and previous evolutionary ideas on humor are reviewed. In addition, scientific fields germane to the evolutionary study of humor are examined: animal models, genetics, children's humor, humor in pathological conditions, neurobiology, humor in traditional societies and cognitive archeology. Candidate selection pressures and associated evolutionary mechanisms are considered. The authors conclude that several evolutionary-related topics such as the origins of language, cognition underlying spiritual feelings, hominid group size, and primate teasing could have special relevance to the origins of humor.

Predicting loss of evolutionary history: Where are we?

Science.gov (United States)

Veron, Simon; Davies, T Jonathan; Cadotte, Marc W; Clergeau, Philippe; Pavoine, Sandrine

2017-02-01

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic

Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

Science.gov (United States)

Miklós, István; Zádori, Zoltán

2012-02-01

HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ) and on the carboxy-terminal region of the extracellular domain (CAED) of the human amyloid precursor protein (APP) and a taxonomically well defined group of APP orthologues (APPOs). In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (pHD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1) and Amyloid-like protein 2 (APLP2). Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N) and English (H6R) mutations) in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

What Is Sexual Orientation All About? Explaining an Evolutionary Paradox

OpenAIRE

Brad Bowins

2015-01-01

Numerous psychological, biological, and evolutionary theories have been proposed to explain sexual orientation. For a theory to be valid it must account for the evolutionary or Darwinian paradox of how homosexual behavior seemingly blocking evolutionary fitness could have evolved. Typically it is only evolutionary based theories that attempt to address this issue. All theories proposed to date have limitations, a major one being that they tend to be specific for male or female sexual orientat...

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

KAUST Repository

Ishikawa, Masakazu

2016-06-19

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

KAUST Repository

Ishikawa, Masakazu; Yuyama, Ikuko; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-01-01

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

The evolutionary implications of epigenetic inheritance.

Science.gov (United States)

Jablonka, Eva

2017-10-06

The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.

Evolutionary Computing for Intelligent Power System Optimization and Control

DEFF Research Database (Denmark)

This new book focuses on how evolutionary computing techniques benefit engineering research and development tasks by converting practical problems of growing complexities into simple formulations, thus largely reducing development efforts. This book begins with an overview of the optimization the...... theory and modern evolutionary computing techniques, and goes on to cover specific applications of evolutionary computing to power system optimization and control problems....

Spore: Spawning Evolutionary Misconceptions?

Science.gov (United States)

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

2010-10-01

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

Using Process Mining to Learn from Process Changes in Evolutionary Systems

NARCIS (Netherlands)

Günther, Christian W.; Rinderle, S.B.; Reichert, M.U.; van der Aalst, Wil M.P.; Recker, Jan

2008-01-01

Traditional information systems struggle with the requirement to provide flexibility and process support while still enforcing some degree of control. Accordingly, adaptive process management systems (PMSs) have emerged that provide some flexibility by enabling dynamic process changes during

Evolutionary changes of Hox genes and relevant regulatory factors provide novel insights into mammalian morphological modifications.

Science.gov (United States)

Li, Kui; Sun, Xiaohui; Chen, Meixiu; Sun, Yingying; Tian, Ran; Wang, Zhengfei; Xu, Shixia; Yang, Guang

2018-01-01

The diversity of body plans of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial and aquatic habitats. However, the genetic basis of those phenotypic modifications, which have occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head-tail axis of animal embryos and the main regulatory factors (Mll, Bmi1 and E2f6) that control the expression of Hox genes. A deflected density of repetitive elements and lineage-specific radical mutations of Mll have been determined in marine mammals with morphological changes, suggesting that evolutionary changes may alter Hox gene expression in these lineages, leading to the morphological modification of these lineages. Although no positive selection was detected at certain ancestor nodes of lineages, the increased ω values of Hox genes implied the relaxation of functional constraints of these genes during the mammalian evolutionary process. More importantly, 49 positively-selected sites were identified in mammalian lineages with phenotypic modifications, indicating adaptive evolution acting on Hox genes and regulatory factors. In addition, 3 parallel amino acid substitutions in some Hox genes were examined in marine mammals, which might be responsible for their streamlined body. © 2017 The Authors. Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

Science.gov (United States)

Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

2015-11-01

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

The great opportunity: Evolutionary applications to medicine and public health.

Science.gov (United States)

Nesse, Randolph M; Stearns, Stephen C

2008-02-01

Evolutionary biology is an essential basic science for medicine, but few doctors and medical researchers are familiar with its most relevant principles. Most medical schools have geneticists who understand evolution, but few have even one evolutionary biologist to suggest other possible applications. The canyon between evolutionary biology and medicine is wide. The question is whether they offer each other enough to make bridge building worthwhile. What benefits could be expected if evolution were brought fully to bear on the problems of medicine? How would studying medical problems advance evolutionary research? Do doctors need to learn evolution, or is it valuable mainly for researchers? What practical steps will promote the application of evolutionary biology in the areas of medicine where it offers the most? To address these questions, we review current and potential applications of evolutionary biology to medicine and public health. Some evolutionary technologies, such as population genetics, serial transfer production of live vaccines, and phylogenetic analysis, have been widely applied. Other areas, such as infectious disease and aging research, illustrate the dramatic recent progress made possible by evolutionary insights. In still other areas, such as epidemiology, psychiatry, and understanding the regulation of bodily defenses, applying evolutionary principles remains an open opportunity. In addition to the utility of specific applications, an evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease - and remarkably resilient - precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for

Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives.

Science.gov (United States)

Iriondo, J M; Milla, R; Volis, S; Rubio de Casas, R

2018-01-01

Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Evolutionary adaptations to dietary changes.

Science.gov (United States)

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

2010-08-21

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

The method of separation for evolutionary spectral density estimation of multi-variate and multi-dimensional non-stationary stochastic processes

KAUST Repository

Schillinger, Dominik

2013-07-01

The method of separation can be used as a non-parametric estimation technique, especially suitable for evolutionary spectral density functions of uniformly modulated and strongly narrow-band stochastic processes. The paper at hand provides a consistent derivation of method of separation based spectrum estimation for the general multi-variate and multi-dimensional case. The validity of the method is demonstrated by benchmark tests with uniformly modulated spectra, for which convergence to the analytical solution is demonstrated. The key advantage of the method of separation is the minimization of spectral dispersion due to optimum time- or space-frequency localization. This is illustrated by the calibration of multi-dimensional and multi-variate geometric imperfection models from strongly narrow-band measurements in I-beams and cylindrical shells. Finally, the application of the method of separation based estimates for the stochastic buckling analysis of the example structures is briefly discussed. © 2013 Elsevier Ltd.

Advanced Reactor Licensing: Experience with Digital I&C Technology in Evolutionary Plants

Energy Technology Data Exchange (ETDEWEB)

Wood, RT

2004-09-27

This report presents the findings from a study of experience with digital instrumentation and controls (I&C) technology in evolutionary nuclear power plants. In particular, this study evaluated regulatory approaches employed by the international nuclear power community for licensing advanced l&C systems and identified lessons learned. The report (1) gives an overview of the modern l&C technologies employed at numerous evolutionary nuclear power plants, (2) identifies performance experience derived from those applications, (3) discusses regulatory processes employed and issues that have arisen, (4) captures lessons learned from performance and regulatory experience, (5) suggests anticipated issues that may arise from international near-term deployment of reactor concepts, and (6) offers conclusions and recommendations for potential activities to support advanced reactor licensing in the United States.

Evolutionary Medicine and Future of Humanity: Will Evolution Have the Final Word?

Directory of Open Access Journals (Sweden)

Maciej Henneberg

2013-06-01

Full Text Available Evolutionary medicine in its classical form assumes that since cultural evolution is faster than biological evolution, ailments of modern people are a result of mismatch between adaptations to the past environments and current situations. A core principle is that we, humans, having evolved for millions of years in a specific natural environment (environment of evolutionary adaptation EEA are biologically adapted to this past environment and the ancient lifestyle. This adaptation to the past produces major mismatch of our bodies with the present, highly anthropic and thus “artificial” living conditions. This article provides two areas of possible future evolution, diet and physical activity levels which have been dramatically altered in industrialised societies. Consequently, micro-evolution is an on-going process.

Development process of muzzle flows including a gun-launched missile

Directory of Open Access Journals (Sweden)

Zhuo Changfei

2015-04-01

Full Text Available Numerical investigations on the launch process of a gun-launched missile from the muzzle of a cannon to the free-flight stage have been performed in this paper. The dynamic overlapped grids approach are applied to dealing with the problems of a moving gun-launched missile. The high-resolution upwind scheme (AUSMPW+ and the detailed reaction kinetics model are adopted to solve the chemical non-equilibrium Euler equations for dynamic grids. The development process and flow field structure of muzzle flows including a gun-launched missile are discussed in detail. This present numerical study confirms that complicated transient phenomena exist in the shortly launching stages when the gun-launched missile moves from the muzzle of a cannon to the free-flight stage. The propellant gas flows, the initial environmental ambient air flows and the moving missile mutually couple and interact. A complete structure of flow field is formed at the launching stages, including the blast wave, base shock, reflected shock, incident shock, shear layer, primary vortex ring and triple point.

Collisional-radiative model including recombination processes for W27+ ion★

Science.gov (United States)

Murakami, Izumi; Sasaki, Akira; Kato, Daiji; Koike, Fumihiro

2017-10-01

We have constructed a collisional-radiative (CR) model for W27+ ions including 226 configurations with n ≤ 9 and ł ≤ 5 for spectroscopic diagnostics. We newly include recombination processes in the model and this is the first result of extreme ultraviolet spectrum calculated for recombining plasma component. Calculated spectra in 40-70 Å range in ionizing and recombining plasma components show similar 3 strong lines and 1 line weak in recombining plasma component at 45-50 Å and many weak lines at 50-65 Å for both components. Recombination processes do not contribute much to the spectrum at around 60 Å for W27+ ion. Dielectronic satellite lines are also minor contribution to the spectrum of recombining plasma component. Dielectronic recombination (DR) rate coefficient from W28+ to W27+ ions is also calculated with the same atomic data in the CR model. We found that larger set of energy levels including many autoionizing states gave larger DR rate coefficients but our rate agree within factor 6 with other works at electron temperature around 1 keV in which W27+ and W28+ ions are usually observed in plasmas. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

Kant and Hegel's Responses to Hume's Skepticism Concerning Causality: An Evolutionary Epistemological Perspective

Directory of Open Access Journals (Sweden)

Adam Christian Scarfe

2012-05-01

Full Text Available According to Hume, determinations of necessary causal connection are without empirical warrant, but, as he maintains, the concept of causality qua necessary connection is indispensable to human beings, having survival value for them, a claim which points to the biological significance of this concept. In contrast to Hume, Kant argues that the causal principle qua necessary connection belongs to the a priori conceptual framework by which rational beings constitute their experience and render the world intelligible. In “Kant’s Doctrine of the A Priori in Light of Contemporary Biology” (1941 / 1962 evolutionary epistemologist Konrad Lorenz sought to adapt Kant’s philosophy to contemporary biology by arguing that the a priori concepts of the understanding can be interpreted as comprising a biologically inherited framework, yet one that is provisional and in flux. Such an evolutionary interpretation of both Hume and Kant’s perspectives of the lacuna concerning causality brings the ideas of these thinkers closer together. Kant himself used suggestive analogies between the major epistemological positions concerning the origin of the a priori concepts of the understanding and the major biological theories of his time concerning the generation and development of organisms. Nevertheless, Kant would probably be reluctant to embrace such an evolutionarily-oriented conception of the categories, given his descriptions of them as self-thought, a priori first principles having a purely intellectual origin, belonging as a very condition for the possibility of the experience of rational beings in general, and as neither the product of a process of development, nor subject to one. This paper shows how Hegel’s emphasis on the dialectical progression of the logical Concept (Begriff can help to ground Lorenz’s evolutionary neo-Kantianism. Toward the end of the paper, I discuss the evolutionary relevance of skepticism and critical thinking in this

Evolutionary Effect on the Embodied Beauty of Landscape Architectures.

Science.gov (United States)

Zhang, Wei; Tang, Xiaoxiang; He, Xianyou; Chen, Guangyao

2018-01-01

According to the framework of evolutionary aesthetics, a sense of beauty is related to environmental adaptation and plasticity of human beings, which has adaptive value and biological foundations. Prior studies have demonstrated that organisms derive benefits from the landscape. In this study, we investigated whether the benefits of landscape might elicit a stronger sense of beauty and what the nature of this sense of beauty is. In two experiments, when viewing classical landscape and nonlandscape architectures photographs, participants rated the aesthetic scores (Experiment 1) and had a two-alternative forced choice aesthetic judgment by pressing the reaction button located near to (15 cm) or far from (45 cm) the presenting stimuli (Experiment 2). The results showed that reaction of aesthetic ratings for classical landscape architectures was faster than those of classical nonlandscape architectures. Furthermore, only the reaction of beautiful judgment of classical landscape architecture photograph was significantly faster when the reaction button was in the near position to the presenting photograph than those in the position of far away from the presenting photograph. This finding suggests a facilitated effect for the aesthetic perception of classical landscape architectures due to their corresponding components including water and green plants with strong evolutionary implications. Furthermore, this sense of beauty for classical landscape architectures might be the embodied approach to beauty based on the viewpoint of evolutionary aesthetics and embodied cognition.

Molluscan Evolutionary Development

DEFF Research Database (Denmark)

Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

2008-01-01

Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.