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

PubMed Central

Jiang, Xiaowei; Ji, Yanjie; 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. PMID:25610455

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

PubMed

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.

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

PubMed

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.

Pattern and Process in the Comparative Study of Convergent Evolution.

PubMed

Mahler, D Luke; Weber, Marjorie G; Wagner, Catherine E; Ingram, Travis

2017-08-01

Understanding processes that have shaped broad-scale biodiversity patterns is a fundamental goal in evolutionary biology. The development of phylogenetic comparative methods has yielded a tool kit for analyzing contemporary patterns by explicitly modeling processes of change in the past, providing neontologists tools for asking questions previously accessible only for select taxa via the fossil record or laboratory experimentation. The comparative approach, however, differs operationally from alternative approaches to studying convergence in that, for studies of only extant species, convergence must be inferred using evolutionary process models rather than being directly measured. As a result, investigation of evolutionary pattern and process cannot be decoupled in comparative studies of convergence, even though such a decoupling could in theory guard against adaptationist bias. Assumptions about evolutionary process underlying comparative tools can shape the inference of convergent pattern in sometimes profound ways and can color interpretation of such patterns. We discuss these issues and other limitations common to most phylogenetic comparative approaches and suggest ways that they can be avoided in practice. We conclude by promoting a multipronged approach to studying convergence that integrates comparative methods with complementary tests of evolutionary mechanisms and includes ecological and biogeographical perspectives. Carefully employed, the comparative method remains a powerful tool for enriching our understanding of convergence in macroevolution, especially for investigation of why convergence occurs in some settings but not others.

The tangled bank of amino acids

PubMed Central

Pollock, David D.

2016-01-01

Abstract The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. PMID:27028523

Is specialization an evolutionary dead end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists.

PubMed

Day, E H; Hua, X; Bromham, L

2016-06-01

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator-specific plants and host-specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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

NASA Astrophysics Data System (ADS)

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.

Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes).

PubMed

Arbour, J H; López-Fernández, H

2014-11-01

Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The evolution and devolution of cognitive control: The costs of deliberation in a competitive world

PubMed Central

Tomlin, Damon; Rand, David G.; Ludvig, Elliot A.; Cohen, Jonathan D.

2015-01-01

Dual-system theories of human cognition, under which fast automatic processes can complement or compete with slower deliberative processes, have not typically been incorporated into larger scale population models used in evolutionary biology, macroeconomics, or sociology. However, doing so may reveal important phenomena at the population level. Here, we introduce a novel model of the evolution of dual-system agents using a resource-consumption paradigm. By simulating agents with the capacity for both automatic and controlled processing, we illustrate how controlled processing may not always be selected over rigid, but rapid, automatic processing. Furthermore, even when controlled processing is advantageous, frequency-dependent effects may exist whereby the spread of control within the population undermines this advantage. As a result, the level of controlled processing in the population can oscillate persistently, or even go extinct in the long run. Our model illustrates how dual-system psychology can be incorporated into population-level evolutionary models, and how such a framework can be used to examine the dynamics of interaction between automatic and controlled processing that transpire over an evolutionary time scale. PMID:26078086

The evolution and devolution of cognitive control: The costs of deliberation in a competitive world.

PubMed

Tomlin, Damon; Rand, David G; Ludvig, Elliot A; Cohen, Jonathan D

2015-06-16

Dual-system theories of human cognition, under which fast automatic processes can complement or compete with slower deliberative processes, have not typically been incorporated into larger scale population models used in evolutionary biology, macroeconomics, or sociology. However, doing so may reveal important phenomena at the population level. Here, we introduce a novel model of the evolution of dual-system agents using a resource-consumption paradigm. By simulating agents with the capacity for both automatic and controlled processing, we illustrate how controlled processing may not always be selected over rigid, but rapid, automatic processing. Furthermore, even when controlled processing is advantageous, frequency-dependent effects may exist whereby the spread of control within the population undermines this advantage. As a result, the level of controlled processing in the population can oscillate persistently, or even go extinct in the long run. Our model illustrates how dual-system psychology can be incorporated into population-level evolutionary models, and how such a framework can be used to examine the dynamics of interaction between automatic and controlled processing that transpire over an evolutionary time scale.

Structural symmetry in evolutionary games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-10-06

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. © 2015 The Author(s).

Structural symmetry in evolutionary games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

True-Triaxial Experimental Study of the Evolutionary Features of the Acoustic Emissions and Sounds of Rockburst Processes

NASA Astrophysics Data System (ADS)

Su, Guoshao; Shi, Yanjiong; Feng, Xiating; Jiang, Jianqing; Zhang, Jie; Jiang, Quan

2018-02-01

Rockbursts are markedly characterized by the ejection of rock fragments from host rocks at certain speeds. The rockburst process is always accompanied by acoustic signals that include acoustic emissions (AE) and sounds. A deep insight into the evolutionary features of AE and sound signals is important to improve the accuracy of rockburst prediction. To investigate the evolutionary features of AE and sound signals, rockburst tests on granite rock specimens under true-triaxial loading conditions were performed using an improved rockburst testing system, and the AE and sounds during rockburst development were recorded and analyzed. The results show that the evolutionary features of the AE and sound signals were obvious and similar. On the eve of a rockburst, a `quiescent period' could be observed in both the evolutionary process of the AE hits and the sound waveform. Furthermore, the time-dependent fractal dimensions of the AE hits and sound amplitude both showed a tendency to continuously decrease on the eve of the rockbursts. In addition, on the eve of the rockbursts, the main frequency of the AE and sound signals both showed decreasing trends, and the frequency spectrum distributions were both characterized by low amplitudes, wide frequency bands and multiple peak shapes. Thus, the evolutionary features of sound signals on the eve of rockbursts, as well as that of AE signals, can be used as beneficial information for rockburst prediction.

The tangled bank of amino acids.

PubMed

Goldstein, Richard A; Pollock, David D

2016-07-01

The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. © 2016 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Evolutionary Dynamics and Diversity in Microbial Populations

NASA Astrophysics Data System (ADS)

Thompson, Joel; Fisher, Daniel

2013-03-01

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

Differences in the selection response of serially repeated color pattern characters: standing variation, development, and evolution.

PubMed

Allen, Cerisse E; Beldade, Patrícia; Zwaan, Bas J; Brakefield, Paul M

2008-03-26

There is spectacular morphological diversity in nature but lineages typically display a limited range of phenotypes. Because developmental processes generate the phenotypic variation that fuels natural selection, they are a likely source of evolutionary biases, facilitating some changes and limiting others. Although shifts in developmental regulation are associated with morphological differences between taxa, it is unclear how underlying mechanisms affect the rate and direction of evolutionary change within populations under selection. Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters. The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus. Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.

The σ law of evolutionary dynamics in community-structured population.

PubMed

Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

2012-08-07

Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolutionary games on cycles with strong selection

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Evolutionary perspectives on the links between mitochondrial genotype and disease phenotype.

PubMed

Dowling, Damian K

2014-04-01

Disorders of the mitochondrial respiratory chain are heterogeneous in their symptoms and underlying genetics. Simple links between candidate mutations and expression of disease phenotype typically do not exist. It thus remains unclear how the genetic variation in the mitochondrial genome contributes to the phenotypic expression of complex traits and disease phenotypes. I summarize the basic genetic processes known to underpin mitochondrial disease. I highlight other plausible processes, drawn from the evolutionary biological literature, whose contribution to mitochondrial disease expression remains largely empirically unexplored. I highlight recent advances to the field, and discuss common-ground and -goals shared by researchers across medical and evolutionary domains. Mitochondrial genetic variance is linked to phenotypic variance across a variety of traits (e.g. reproductive function, life expectancy) fundamental to the upkeep of good health. Evolutionary theory predicts that mitochondrial genomes are destined to accumulate male-harming (but female-friendly) mutations, and this prediction has received proof-of-principle support. Furthermore, mitochondrial effects on the phenotype are typically manifested via interactions between mitochondrial and nuclear genes. Thus, whether a mitochondrial mutation is pathogenic in effect can depend on the nuclear genotype in which is it expressed. Many disease phenotypes associated with OXPHOS malfunction might be determined by the outcomes of mitochondrial-nuclear interactions, and by the evolutionary forces that historically shaped mitochondrial DNA (mtDNA) sequences. Concepts and results drawn from the evolutionary sciences can have broad, but currently under-utilized, applicability to the medical sciences and provide new insights into understanding the complex genetics of mitochondrial disease. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research. Copyright © 2013. Published by Elsevier B.V.

The study on knowledge transferring incentive for information system requirement development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yang

2015-03-10

Information system requirement development is a process of users’ knowledge sharing and transferring. However the tacit requirements developing is a main problem during requirement development process, for the reason of difficult to encoding, express, and communicate. Knowledge fusion and corporate effort is needed to finding tacit requirements. Under this background, our paper try to find out the rule of effort dynamic evolutionary of software developer and user by building an evolutionary game model on the condition of incentive system. And in addition this paper provides an in depth discussion at the end of this paper.

Neoplastic growth: the consequence of evolutionary malignant resistance to chronic damage for survival of cells (review of a new theory of the origin of cancer).

PubMed

Monceviciūte-Eringiene, E

2005-01-01

In the present review, a new theory that the mechanisms of general evolutionary persistent resistance to damaging factors are closely related to the development of tumour cells is introduced. Evolutionary resistance and its variability have an immense power to drive and control the process of carcinogenesis and the success of microbial and antitumour chemotherapy. First, this phenomenon of adaptation is characteristic of microbial cells whose resistance to antibiotics and other chemotherapeutic drugs is manifested through ATP-dependent transmembrane transporters. The structure and function of some multidrug transporters of resistance are conserved from microorganisms to mammals. When somatic cells are exposed to carcinogens and develop into tumour cells, they also acquire resistance to the toxic effects of carcinogens through these same transmembrane transporters (P-glycoprotein, glutathione S-transferases and other products of evolutionary resistance-related genes arisen for detoxification and exportation of cytotoxic xenobiotics and drugs). Cancerous cells acquire a persistent evolutionary resistance to chemotherapy drugs or irradiation through the same ATP-dependent transporters encountered in prokaryotic and eukaryotic cells. The mechanism of acquired resistance of cells to damaging factors, which becomes manifested during tumorigenic process formation, is a general biological law of primary significance in carcinogenesis. This resistance can be called malignant as, once formed, it does not disappear, as does also a clone of malignant cells. In tumorous cells, the mutagenic processes, morphological and functional modifications are a mechanism of secondary significance in carcinogenesis, contributing to formation of damage-resistant cells. This mechanism characterizes the processes of simplification arising in damage-resistant cells. Such cells acquire parasitic features. To survive under unfavourable conditions, they get adapted as if returning down the evolutionary stairs back to a more primitive stage of atavistic regression, which is characteristic of primitive forms of existence. Therefore they cease obeying the growth-regulating mechanisms in the organism and acquire the potential of unlimited division and accelerated growth (metastases) as do unicellular organisms or their forms resistant to damaging factors in the environment and in the host organism. Thus, cancer is a natural self-protective response of the damaged cells to the biological, physical and chemical damage and oxidative stress. This response has been developed in the process of evolution under the impact of the general biological Darwinian law of nature--to survive through variability and adaptation to the changed environmental conditions. Thus, malignization is the consequence of an evolutionary variety of the general biological resistance of cells to damage and stress in order to survive.

Integrating Evolutionary and Molecular Genetics of Aging

PubMed Central

Flatt, Thomas; Schmidt, Paul S.

2010-01-01

Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940’s and 1950’s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980’s and 1990’s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging. PMID:19619612

Integrating evolutionary and molecular genetics of aging.

PubMed

Flatt, Thomas; Schmidt, Paul S

2009-10-01

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

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

The relative importance of rapid evolution for plant-microbe interactions depends on ecological context.

PubMed

Terhorst, Casey P; Lennon, Jay T; Lau, Jennifer A

2014-06-22

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant-microbe interactions.

Comparison of multiobjective evolutionary algorithms: empirical results.

PubMed

Zitzler, E; Deb, K; Thiele, L

2000-01-01

In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly in converging to the Pareto-optimal front (e.g., multimodality and deception). By investigating these different problem features separately, it is possible to predict the kind of problems to which a certain technique is or is not well suited. However, in contrast to what was suspected beforehand, the experimental results indicate a hierarchy of the algorithms under consideration. Furthermore, the emerging effects are evidence that the suggested test functions provide sufficient complexity to compare multiobjective optimizers. Finally, elitism is shown to be an important factor for improving evolutionary multiobjective search.

An emerging synthesis between community ecology and evolutionary biology.

PubMed

Johnson, Marc T J; Stinchcombe, John R

2007-05-01

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

The composition of genomes with respect to short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. The underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, which we detect in all species across domains of life. We hypothesize that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Alternative contributions may come from interference of protein-DNA binding with replication and mutational repair processes, which operates with similar rates. We conclude that genome-wide word compositions have been molded by DNA binding proteins through tiny evolutionary steps over timescales spanning millions of generations.

A road map for integrating eco-evolutionary processes into biodiversity models.

PubMed

Thuiller, Wilfried; Münkemüller, Tamara; Lavergne, Sébastien; Mouillot, David; Mouquet, Nicolas; Schiffers, Katja; Gravel, Dominique

2013-05-01

The demand for projections of the future distribution of biodiversity has triggered an upsurge in modelling at the crossroads between ecology and evolution. Despite the enthusiasm around these so-called biodiversity models, most approaches are still criticised for not integrating key processes known to shape species ranges and community structure. Developing an integrative modelling framework for biodiversity distribution promises to improve the reliability of predictions and to give a better understanding of the eco-evolutionary dynamics of species and communities under changing environments. In this article, we briefly review some eco-evolutionary processes and interplays among them, which are essential to provide reliable projections of species distributions and community structure. We identify gaps in theory, quantitative knowledge and data availability hampering the development of an integrated modelling framework. We argue that model development relying on a strong theoretical foundation is essential to inspire new models, manage complexity and maintain tractability. We support our argument with an example of a novel integrated model for species distribution modelling, derived from metapopulation theory, which accounts for abiotic constraints, dispersal, biotic interactions and evolution under changing environmental conditions. We hope such a perspective will motivate exciting and novel research, and challenge others to improve on our proposed approach. © 2013 John Wiley & Sons Ltd/CNRS.

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

2016-10-01

The composition of a genome with respect to all possible short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional DNA binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. We demonstrate that the underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, a signal that we detect in all species across domains of life. We consider the possibility that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Likewise, we show that evolutionary mechanisms based on interference of protein-DNA binding with replication and mutational repair processes could yield similar results and operate with similar rates. On the basis of these modeling and bioinformatic results, we conclude that genome-wide word compositions have been molded by DNA binding proteins acting through tiny evolutionary steps over time scales spanning millions of generations.

A model of the hierarchy of behaviour, cognition, and consciousness.

PubMed

Toates, Frederick

2006-03-01

Processes comparable in important respects to those underlying human conscious and non-conscious processing can be identified in a range of species and it is argued that these reflect evolutionary precursors of the human processes. A distinction is drawn between two types of processing: (1) stimulus-based and (2) higher-order. For 'higher-order,' in humans the operations of processing are themselves associated with conscious awareness. Conscious awareness sets the context for stimulus-based processing and its end-point is accessible to conscious awareness. However, the mechanics of the translation between stimulus and response proceeds without conscious control. The paper argues that higher-order processing is an evolutionary addition to stimulus-based processing. The model's value is shown for gaining insight into a range of phenomena and their link with consciousness. These include brain damage, learning, memory, development, vision, emotion, motor control, reasoning, the voluntary versus involuntary debate, and mental disorder.

Nonequivalence of updating rules in evolutionary games under high mutation rates.

PubMed

Kaiping, G A; Jacobs, G S; Cox, S J; Sluckin, T J

2014-10-01

Moran processes are often used to model selection in evolutionary simulations. The updating rule in Moran processes is a birth-death process, i. e., selection according to fitness of an individual to give birth, followed by the death of a random individual. For well-mixed populations with only two strategies this updating rule is known to be equivalent to selecting unfit individuals for death and then selecting randomly for procreation (biased death-birth process). It is, however, known that this equivalence does not hold when considering structured populations. Here we study whether changing the updating rule can also have an effect in well-mixed populations in the presence of more than two strategies and high mutation rates. We find, using three models from different areas of evolutionary simulation, that the choice of updating rule can change model results. We show, e. g., that going from the birth-death process to the death-birth process can change a public goods game with punishment from containing mostly defectors to having a majority of cooperative strategies. From the examples given we derive guidelines indicating when the choice of the updating rule can be expected to have an impact on the results of the model.

Nonequivalence of updating rules in evolutionary games under high mutation rates

NASA Astrophysics Data System (ADS)

Kaiping, G. A.; Jacobs, G. S.; Cox, S. J.; Sluckin, T. J.

2014-10-01

Moran processes are often used to model selection in evolutionary simulations. The updating rule in Moran processes is a birth-death process, i. e., selection according to fitness of an individual to give birth, followed by the death of a random individual. For well-mixed populations with only two strategies this updating rule is known to be equivalent to selecting unfit individuals for death and then selecting randomly for procreation (biased death-birth process). It is, however, known that this equivalence does not hold when considering structured populations. Here we study whether changing the updating rule can also have an effect in well-mixed populations in the presence of more than two strategies and high mutation rates. We find, using three models from different areas of evolutionary simulation, that the choice of updating rule can change model results. We show, e. g., that going from the birth-death process to the death-birth process can change a public goods game with punishment from containing mostly defectors to having a majority of cooperative strategies. From the examples given we derive guidelines indicating when the choice of the updating rule can be expected to have an impact on the results of the model.

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

PubMed

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.

Emergence and dynamics of self-producing information niches as a step towards pre-evolutionary organization

PubMed Central

Carter, Richard J.; Wiesner, Karoline

2018-01-01

As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches. In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions. By determining the information required to generate each niche, we show that niche transitions are only allowed if accompanied by an equal or increased level of information production that arises internally or via environmental perturbations that serve as an exogenous source of population diversification. Overall, our simulations show how proto-autopoietic networks of basic information processors form and compete, and under what conditions they persist over time or go extinct. These findings may be relevant to understanding how inanimate systems such as chemically communicating protocells can initiate the transition to living matter prior to the onset of contemporary evolutionary and genetic mechanisms. PMID:29343630

Aspiration dynamics and the sustainability of resources in the public goods dilemma

NASA Astrophysics Data System (ADS)

Du, Jinming; Wu, Bin; Wang, Long

2016-04-01

How to exploit public non-renewable resources is a public goods dilemma. Individuals can choose to limit the depletion in order to use the resource for a longer time or consume more goods to benefit themselves. When the resource is used up, there is no benefit for the future generations any more, thus the evolutionary process ends. Here we investigate what mechanisms can extend the use of resources in the framework of evolutionary game theory under two updating rules based on imitation and aspiration, respectively. Compared with imitation process, aspiration dynamics may prolong the sustainable time of a public resource.

Evolutionary games under incompetence.

PubMed

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.

Evolutionary fuzzy modeling human diagnostic decisions.

PubMed

Peña-Reyes, Carlos Andrés

2004-05-01

Fuzzy CoCo is a methodology, combining fuzzy logic and evolutionary computation, for constructing systems able to accurately predict the outcome of a human decision-making process, while providing an understandable explanation of the underlying reasoning. Fuzzy logic provides a formal framework for constructing systems exhibiting both good numeric performance (accuracy) and linguistic representation (interpretability). However, fuzzy modeling--meaning the construction of fuzzy systems--is an arduous task, demanding the identification of many parameters. To solve it, we use evolutionary computation techniques (specifically cooperative coevolution), which are widely used to search for adequate solutions in complex spaces. We have successfully applied the algorithm to model the decision processes involved in two breast cancer diagnostic problems, the WBCD problem and the Catalonia mammography interpretation problem, obtaining systems both of high performance and high interpretability. For the Catalonia problem, an evolved system was embedded within a Web-based tool-called COBRA-for aiding radiologists in mammography interpretation.

Evolutionary developmental genetics of fruit morphological variation within the Solanaceae

PubMed Central

Wang, Li; Li, Jing; Zhao, Jing; He, Chaoying

2015-01-01

Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops. PMID:25918515

The evolutionary language game: an orthogonal approach.

PubMed

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

2005-08-21

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

Laboratory evolution of protein conformational dynamics.

PubMed

Campbell, Eleanor C; Correy, Galen J; Mabbitt, Peter D; Buckle, Ashley M; Tokuriki, Nobuhiko; Jackson, Colin J

2017-11-08

This review focuses on recent work that has begun to establish specific functional roles for protein conformational dynamics, specifically how the conformational landscapes that proteins can sample can evolve under laboratory based evolutionary selection. We discuss recent technical advances in computational and biophysical chemistry, which have provided us with new ways to dissect evolutionary processes. Finally, we offer some perspectives on the emerging view of conformational dynamics and evolution, and the challenges that we face in rationally engineering conformational dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantifying selection in evolving populations using time-resolved genetic data

NASA Astrophysics Data System (ADS)

Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

The long-term evolution of multilocus traits under frequency-dependent disruptive selection.

PubMed

van Doorn, G Sander; Dieckmann, Ulf

2006-11-01

Frequency-dependent disruptive selection is widely recognized as an important source of genetic variation. Its evolutionary consequences have been extensively studied using phenotypic evolutionary models, based on quantitative genetics, game theory, or adaptive dynamics. However, the genetic assumptions underlying these approaches are highly idealized and, even worse, predict different consequences of frequency-dependent disruptive selection. Population genetic models, by contrast, enable genotypic evolutionary models, but traditionally assume constant fitness values. Only a minority of these models thus addresses frequency-dependent selection, and only a few of these do so in a multilocus context. An inherent limitation of these remaining studies is that they only investigate the short-term maintenance of genetic variation. Consequently, the long-term evolution of multilocus characters under frequency-dependent disruptive selection remains poorly understood. We aim to bridge this gap between phenotypic and genotypic models by studying a multilocus version of Levene's soft-selection model. Individual-based simulations and deterministic approximations based on adaptive dynamics theory provide insights into the underlying evolutionary dynamics. Our analysis uncovers a general pattern of polymorphism formation and collapse, likely to apply to a wide variety of genetic systems: after convergence to a fitness minimum and the subsequent establishment of genetic polymorphism at multiple loci, genetic variation becomes increasingly concentrated on a few loci, until eventually only a single polymorphic locus remains. This evolutionary process combines features observed in quantitative genetics and adaptive dynamics models, and it can be explained as a consequence of changes in the selection regime that are inherent to frequency-dependent disruptive selection. Our findings demonstrate that the potential of frequency-dependent disruptive selection to maintain polygenic variation is considerably smaller than previously expected.

Towards a mechanistic foundation of evolutionary theory.

PubMed

Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

2017-02-15

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

Scientific Change as AN Evolutionary, Information Process: its Structural, Conceptual and Cultural Elements.

NASA Astrophysics Data System (ADS)

Al-Bustany, Fatin Khalil Ismail

1989-09-01

My aim in this dissertation is to develop an evolutionary conception of science based on recent studies in evolution theory, the thermodynamics of non-equilibrium and information theory, as exemplified in the works of Prigogine, Jantsch, Wicken and Gatlin. The nature of scientific change is of interest to philosophers and historians of science. Some construe it after a revolutionary model (e.g. Kuhn), others adopt an evolutionary view (e.g. Toulmin). It appears to me that it is possible to construct an evolutionary model encompassing the revolutionary mode as well. The following strategies are employed: (1) A distinction is made between two types of growth: one represents gradual change, the other designates radical transformations, and two principles underlying the process of change, one of conservation, the other of innovation. (2) Science in general, and scientific theories in particular, are looked upon as dissipative structures. These are characterised by openness, irreversibility and self-organisation. In terms of these, one may identify a state of "normal" growth and another of violent fluctuations leading to a new order (revolutionary phase). These fluctuations are generated by the flow of information coming from the observable world. The chief merits of this evolutionary model of the development of science lie in the emphasis it puts on the relation of science to its environment, in the description of scientific change as a process of interaction between internal and external elements (structural, conceptual, and cultural), in the enhancement of our understanding progress and rationality in science, and in the post Neo -Darwinian conception of evolution, stressing self-organisation, the innovativeness of the evolutionary process and the trend toward complexification. These features are also manifested in the process of discovery, which is a fundamental part of the scientific enterprise. In addition, a distinction is made between two types of discovery which serves as a criterion for delineating various episodes in the development of science. The evolutionary model further displays a complementarity mode of description on several levels: between science and its milieu, stability and instability, discovery and confirmation.

Software Engineering Guidebook

NASA Technical Reports Server (NTRS)

Connell, John; Wenneson, Greg

1993-01-01

The Software Engineering Guidebook describes SEPG (Software Engineering Process Group) supported processes and techniques for engineering quality software in NASA environments. Three process models are supported: structured, object-oriented, and evolutionary rapid-prototyping. The guidebook covers software life-cycles, engineering, assurance, and configuration management. The guidebook is written for managers and engineers who manage, develop, enhance, and/or maintain software under the Computer Software Services Contract.

Extrapolating Weak Selection in Evolutionary Games

PubMed Central

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

2013-01-01

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

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism.

PubMed

Álvarez-Presas, M; Sánchez-Gracia, A; Carbayo, F; Rozas, J; Riutort, M

2014-06-01

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.

Evolving political science. Biological adaptation, rational action, and symbolism.

PubMed

Tingley, Dustin

2006-01-01

Political science, as a discipline, has been reluctant to adopt theories and methodologies developed in fields studying human behavior from an evolutionary standpoint. I ask whether evolutionary concepts are reconcilable with standard political-science theories and whether those concepts help solve puzzles to which these theories classically are applied. I find that evolutionary concepts readily and simultaneously accommodate theories of rational choice, symbolism, interpretation, and acculturation. Moreover, phenomena perennially hard to explain in standard political science become clearer when human interactions are understood in light of natural selection and evolutionary psychology. These phenomena include the political and economic effects of emotion, status, personal attractiveness, and variations in information-processing and decision-making under uncertainty; exemplary is the use of "focal points" in multiple-equilibrium games. I conclude with an overview of recent research by, and ongoing debates among, scholars analyzing politics in evolutionarily sophisticated terms.

Evolutionary Models for Simple Biosystems

NASA Astrophysics Data System (ADS)

Bagnoli, Franco

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

Evolutionary game dynamics of controlled and automatic decision-making

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

Evolutionary game dynamics of controlled and automatic decision-making.

PubMed

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

2015-07-01

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

The sources of adaptive variation

PubMed Central

2017-01-01

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. PMID:28566483

The sources of adaptive variation.

PubMed

Charlesworth, Deborah; Barton, Nicholas H; Charlesworth, Brian

2017-05-31

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. © 2017 The Author(s).

Intelligent monitoring and diagnosis systems for the Space Station Freedom ECLSS

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, James R.

1991-01-01

Specific activities in NASA's environmental control and life support system (ECLSS) advanced automation project that is designed to minimize the crew and ground manpower needed for operations are discussed. Various analyses and the development of intelligent software for the initial and evolutionary Space Station Freedom (SSF) ECLSS are described. The following are also discussed: (1) intelligent monitoring and diagnostics applications under development for the ECLSS domain; (2) integration into the MSFC ECLSS hardware testbed; and (3) an evolutionary path from the baseline ECLSS automation to the more advanced ECLSS automation processes.

Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future.

PubMed

Dongen, S V

2006-11-01

The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes.

Cooperation in microbial communities and their biotechnological applications

PubMed Central

Cavaliere, Matteo; Feng, Song; Soyer, Orkun S.

2017-01-01

Summary Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross‐feeding, which can be understood in the general framework of ecological and evolutionary (eco‐evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of ‘cheating’ cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications. PMID:28447371

Ecological and evolutionary consequences of niche construction for its agent.

PubMed

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.

Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

PubMed

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

2016-05-03

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

EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

NASA Astrophysics Data System (ADS)

Wagh, Aditi; Wilensky, Uri

2018-04-01

Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience with programming. This paper presents a class of programming environments that we call quickstart: Environments with a negligible threshold for entry into programming and a modest ceiling. We posit that such environments can provide benefits of programming for learning without incurring associated costs for novice programmers. To make this claim, we present a design-based research study conducted to compare programming models of evolutionary processes with a quickstart toolkit with exploring pre-built models of the same processes. The study was conducted in six seventh grade science classes in two schools. Students in the programming condition used EvoBuild, a quickstart toolkit for programming agent-based models of evolutionary processes, to build their NetLogo models. Students in the exploration condition used pre-built NetLogo models. We demonstrate that although students came from a range of academic backgrounds without prior programming experience, and all students spent the same number of class periods on the activities including the time students took to learn programming in this environment, EvoBuild students showed greater learning about evolutionary mechanisms. We discuss the implications of this work for design research on programming environments in K-12 science education.

Mega-evolutionary dynamics of the adaptive radiation of birds.

PubMed

Cooney, Christopher R; Bright, Jen A; Capp, Elliot J R; Chira, Angela M; Hughes, Emma C; Moody, Christopher J A; Nouri, Lara O; Varley, Zoë K; Thomas, Gavin H

2017-02-16

The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin's finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.

Knowledge.

PubMed

Jost, Jürgen

2017-06-01

We investigate the basic principles of structural knowledge. Structural knowledge underlies cognition, and it organizes, selects and assigns meaning to information. It is the result of evolutionary, cultural and developmental processes. Because of its own constraints, it needs to discover and exploit regularities and thereby achieve a complexity reduction.

Developmental mechanisms underlying variation in craniofacial disease and evolution.

PubMed

Fish, Jennifer L

2016-07-15

Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed

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.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

The locus of sexual selection: moving sexual selection studies into the post-genomics era.

PubMed

Wilkinson, G S; Breden, F; Mank, J E; Ritchie, M G; Higginson, A D; Radwan, J; Jaquiery, J; Salzburger, W; Arriero, E; Barribeau, S M; Phillips, P C; Renn, S C P; Rowe, L

2015-04-01

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Deciphering the Interdependence between Ecological and Evolutionary Networks.

PubMed

Melián, Carlos J; Matthews, Blake; de Andreazzi, Cecilia S; Rodríguez, Jorge P; Harmon, Luke J; Fortuna, Miguel A

2018-05-24

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator-prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

EDEN: evolutionary dynamics within environments

PubMed Central

Münch, Philipp C.; Stecher, Bärbel; McHardy, Alice C.

2017-01-01

Abstract Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact alice.mchardy@helmholtz-hzi.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637301

Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California

USDA-ARS?s Scientific Manuscript database

Determining the reproductive mode contributing to dispersal within and between populations of invasive species is essential to understand the ecological and evolutionary processes underlying invasions and to guide management strategies. Ludwigia hexapetala and L. grandiflora are emergent aquatic sp...

JCoDA: a tool for detecting evolutionary selection.

PubMed

Steinway, Steven N; Dannenfelser, Ruth; Laucius, Christopher D; Hayes, James E; Nayak, Sudhir

2010-05-27

The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.

JCoDA: a tool for detecting evolutionary selection

PubMed Central

2010-01-01

Background The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. Conclusions JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda. PMID:20507581

Toward a unifying framework for evolutionary processes.

PubMed

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

2015-10-21

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Resolving the evolutionary paradox of genetic instability: a cost-benefit analysis of DNA repair in changing environments.

PubMed

Breivik, Jarle; Gaudernack, Gustav

2004-04-09

Loss of genetic stability is a critical phenomenon in cancer and antibiotic resistance, and the prevailing dogma is that unstable cells survive because instability provides adaptive mutations. Challenging this view, we have argued that genetic instability arises because DNA repair may be a counterproductive strategy in mutagenic environments. This paradoxical relationship has also been confirmed by explicit experiments, but the underlying evolutionary principles remain controversial. This paper aims to clarify the issue, and presents a model that explains genetic instability from the basic perspective of molecular evolution and information processing.

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.

PubMed

Wünsche, Andrea; Dinh, Duy M; Satterwhite, Rebecca S; Arenas, Carolina Diaz; Stoebel, Daniel M; Cooper, Tim F

2017-03-01

Populations evolving in constant environments exhibit declining adaptability. Understanding the basis of this pattern could reveal underlying processes determining the repeatability of evolutionary outcomes. In principle, declining adaptability can be due to a decrease in the effect size of beneficial mutations, a decrease in the rate at which they occur, or some combination of both. By evolving Escherichia coli populations started from different steps along a single evolutionary trajectory, we show that declining adaptability is best explained by a decrease in the size of available beneficial mutations. This pattern reflected the dominant influence of negative genetic interactions that caused new beneficial mutations to confer smaller benefits in fitter genotypes. Genome sequencing revealed that starting genotypes that were more similar to one another did not exhibit greater similarity in terms of new beneficial mutations, supporting the view that epistasis acts globally, having a greater influence on the effect than on the identity of available mutations along an adaptive trajectory. Our findings provide support for a general mechanism that leads to predictable phenotypic evolutionary trajectories.

Processes of Quantum Associative Memory (QuAM) Through New Maximally Entangled States (Singh-Rajput MES)

NASA Astrophysics Data System (ADS)

Singh, Manu Pratap; Rajput, B. S.

2016-07-01

Using Singh-Rajput MES as memory states in the evolutionary process of pattern storage and the non-evolutionary process of pattern recall (the two fundamental constituents of QuAM), the suitability and superiority of these MES over Bell's MES have been demonstrated in both these processes. It has been shown that, under the operations of all the possible memorization operators for a two-qubit system, the first two states of Singh-Rajput MES are useful for storing the pattern |11> and the last two of these MES are useful in storing the pattern |10> while Bell's MES are not much suitable as memory states in a valid memorization process. The recall operations have also been conducted by separately choosing Singh-Rajput MES and Bell's MES as memory states for possible various queries and it has been shown that in each case the choices of Singh-Rajput MES as valid memory states are much more suitable than those of Bell's MES.

Markov-modulated Markov chains and the covarion process of molecular evolution.

PubMed

Galtier, N; Jean-Marie, A

2004-01-01

The covarion (or site specific rate variation, SSRV) process of biological sequence evolution is a process by which the evolutionary rate of a nucleotide/amino acid/codon position can change in time. In this paper, we introduce time-continuous, space-discrete, Markov-modulated Markov chains as a model for representing SSRV processes, generalizing existing theory to any model of rate change. We propose a fast algorithm for diagonalizing the generator matrix of relevant Markov-modulated Markov processes. This algorithm makes phylogeny likelihood calculation tractable even for a large number of rate classes and a large number of states, so that SSRV models become applicable to amino acid or codon sequence datasets. Using this algorithm, we investigate the accuracy of the discrete approximation to the Gamma distribution of evolutionary rates, widely used in molecular phylogeny. We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models.

Intense natural selection preceded the invasion of new adaptive zones during the radiation of New World leaf-nosed bats.

PubMed

Rossoni, Daniela M; Assis, Ana Paula A; Giannini, Norberto P; Marroig, Gabriel

2017-09-11

The family Phyllostomidae, which evolved in the New World during the last 30 million years, represents one of the largest and most morphologically diverse mammal families. Due to its uniquely diverse functional morphology, the phyllostomid skull is presumed to have evolved under strong directional selection; however, quantitative estimation of the strength of selection in this extraordinary lineage has not been reported. Here, we used comparative quantitative genetics approaches to elucidate the processes that drove cranial evolution in phyllostomids. We also quantified the strength of selection and explored its association with dietary transitions and specialization along the phyllostomid phylogeny. Our results suggest that natural selection was the evolutionary process responsible for cranial diversification in phyllostomid bats. Remarkably, the strongest selection in the phyllostomid phylogeny was associated with dietary specialization and the origination of novel feeding habits, suggesting that the adaptive diversification of phyllostomid bats was triggered by ecological opportunities. These findings are consistent with Simpson's quantum evolutionary model of transitions between adaptive zones. The multivariate analyses used in this study provides a powerful tool for understanding the role of evolutionary processes in shaping phenotypic diversity in any group on both micro- and macroevolutionary scales.

Hybrid zone studies: An interdisciplinary approach for the analysis of evolutionary processes

USGS Publications Warehouse

Scribner, Kim T.

1994-01-01

There has been considerable debate in the ecological and evolutionary literature over the relative importance and rate by which microevolutionary processes operating at the population level result in separation and differentiation of lineages and populations, and ultimately in speciation. Our understanding of evolutionary processes have need greatly enhances through the study of hybridization and hybrid zones. Indeed, hybrid zones have been described as “natural laboratories” (Barton, N. H., and G .M. Hewitt, 189. Adaptation, speciation, and hybrid zones. Nature 341:497-503) or as “windows on the evolutionary processes” (Harrison, R. G. 1990. Hybrid zones: windows on the evolutionary process. Oxford Surveys in Evolutionary Biology 7:69-128). Hybrid zones greatly facilitate analyses of evolutionary dynamics because differences in factors such as mating preference, fertility, and viability are likely to be magnified, making the consequences easier to document over short periods of time.

Iris double recognition based on modified evolutionary neural network

NASA Astrophysics Data System (ADS)

Liu, Shuai; Liu, Yuan-Ning; Zhu, Xiao-Dong; Huo, Guang; Liu, Wen-Tao; Feng, Jia-Kai

2017-11-01

Aiming at multicategory iris recognition under illumination and noise interference, this paper proposes a method of iris double recognition based on a modified evolutionary neural network. An equalization histogram and Laplace of Gaussian operator are used to process the iris to suppress illumination and noise interference and Haar wavelet to convert the iris feature to binary feature encoding. Calculate the Hamming distance for the test iris and template iris , and compare with classification threshold, determine the type of iris. If the iris cannot be identified as a different type, there needs to be a secondary recognition. The connection weights in back-propagation (BP) neural network use modified evolutionary neural network to adaptively train. The modified neural network is composed of particle swarm optimization with mutation operator and BP neural network. According to different iris libraries in different circumstances of experimental results, under illumination and noise interference, the correct recognition rate of this algorithm is higher, the ROC curve is closer to the coordinate axis, the training and recognition time is shorter, and the stability and the robustness are better.

Evolution of an ancient venom: recognition of a novel family of cnidarian toxins and the common evolutionary origin of sodium and potassium neurotoxins in sea anemone.

PubMed

Jouiaei, Mahdokht; Sunagar, Kartik; Federman Gross, Aya; Scheib, Holger; Alewood, Paul F; Moran, Yehu; Fry, Bryan G

2015-06-01

Despite Cnidaria (sea anemones, corals, jellyfish, and hydroids) being the oldest venomous animal lineage, structure-function relationships, phyletic distributions, and the molecular evolutionary regimes of toxins encoded by these intriguing animals are poorly understood. Hence, we have comprehensively elucidated the phylogenetic and molecular evolutionary histories of pharmacologically characterized cnidarian toxin families, including peptide neurotoxins (voltage-gated Na(+) and K(+) channel-targeting toxins: NaTxs and KTxs, respectively), pore-forming toxins (actinoporins, aerolysin-related toxins, and jellyfish toxins), and the newly discovered small cysteine-rich peptides (SCRiPs). We show that despite long evolutionary histories, most cnidarian toxins remain conserved under the strong influence of negative selection-a finding that is in striking contrast to the rapid evolution of toxin families in evolutionarily younger lineages, such as cone snails and advanced snakes. In contrast to the previous suggestions that implicated SCRiPs in the biomineralization process in corals, we demonstrate that they are potent neurotoxins that are likely involved in the envenoming function, and thus represent the first family of neurotoxins from corals. We also demonstrate the common evolutionary origin of type III KTxs and NaTxs in sea anemones. We show that type III KTxs have evolved from NaTxs under the regime of positive selection, and likely represent a unique evolutionary innovation of the Actinioidea lineage. We report a correlation between the accumulation of episodically adaptive sites and the emergence of novel pharmacological activities in this rapidly evolving neurotoxic clade. © The Author 2015. 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.

Simulation of the evolution of root water foraging strategies in dry and shallow soils.

PubMed

Renton, Michael; Poot, Pieter

2014-09-01

The dynamic structural development of plants can be seen as a strategy for exploiting the limited resources available within their environment, and we would expect that evolution would lead to efficient strategies that reduce costs while maximizing resource acquisition. In particular, perennial species endemic to habitats with shallow soils in seasonally dry environments have been shown to have a specialized root system morphology that may enhance access to water resources in the underlying rock. This study aimed to explore these hypotheses by applying evolutionary algorithms to a functional-structural root growth model. A simulation model of a plant's root system was developed, which represents the dynamics of water uptake and structural growth. The model is simple enough for evolutionary optimization to be computationally feasible, yet flexible enough to allow a range of structural development strategies to be explored. The model was combined with an evolutionary algorithm in order to investigate a case study habitat with a highly heterogeneous distribution of resources, both spatially and temporally--the situation of perennial plants occurring on shallow soils in seasonally dry environments. Evolution was simulated under two contrasting fitness criteria: (1) the ability to find wet cracks in underlying rock, and (2) maximizing above-ground biomass. The novel approach successfully resulted in the evolution of more efficient structural development strategies for both fitness criteria. Different rooting strategies evolved when different criteria were applied, and each evolved strategy made ecological sense in terms of the corresponding fitness criterion. Evolution selected for root system morphologies which matched those of real species from corresponding habitats. Specialized root morphology with deeper rather than shallower lateral branching enhances access to water resources in underlying rock. More generally, the approach provides insights into both evolutionary processes and ecological costs and benefits of different plant growth strategies.

Mega-evolutionary dynamics of the adaptive radiation of birds

PubMed Central

Capp, Elliot J. R.; Chira, Angela M.; Hughes, Emma C.; Moody, Christopher J. A.; Nouri, Lara O.; Varley, Zoë K.; Thomas, Gavin H.

2017-01-01

The origin and expansion of biological diversity is regulated by both developmental trajectories1,2 and limits on available ecological niches3–7. As lineages diversify an early, often rapid, phase of species and trait proliferation gives way to evolutionary slowdowns as new species pack into ever more densely occupied regions of ecological niche space6,8. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear9. Here we address this problem on a global scale by analysing a novel crowd-sourced dataset of 3D-scanned bill morphology from >2000 species. We find that bill diversity expanded early in extant avian evolutionary history before transitioning to a phase dominated by morphospace packing. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare but major discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian9 and Simpsonian4 ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks. PMID:28146475

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis

PubMed Central

Chu, Xin-Yi; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-01-01

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information. PMID:28708071

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis.

PubMed

Chu, Xin-Yi; Jiang, Ling-Han; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-07-14

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Evolutionary Computing Methods for Spectral Retrieval

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

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

NASA Astrophysics Data System (ADS)

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 modalities, with students who built models not incorporating slippage explanations in responses. Study 3 compares these modalities with a control using traditional activities. Pre and posttests reveal that the two modalities manifested greater facility with accessing and assembling rules than the control. The dissertation offers implications for the design of learning environments for evolutionary change, design of the two modalities based on their strengths and weaknesses, and teacher training for the same.

Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

PubMed Central

Ferriere, Regis; Legendre, Stéphane

2013-01-01

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

Evolution of cooperation driven by incremental learning

NASA Astrophysics Data System (ADS)

Li, Pei; Duan, Haibin

2015-02-01

It has been shown that the details of microscopic rules in structured populations can have a crucial impact on the ultimate outcome in evolutionary games. So alternative formulations of strategies and their revision processes exploring how strategies are actually adopted and spread within the interaction network need to be studied. In the present work, we formulate the strategy update rule as an incremental learning process, wherein knowledge is refreshed according to one's own experience learned from the past (self-learning) and that gained from social interaction (social-learning). More precisely, we propose a continuous version of strategy update rules, by introducing the willingness to cooperate W, to better capture the flexibility of decision making behavior. Importantly, the newly gained knowledge including self-learning and social learning is weighted by the parameter ω, establishing a strategy update rule involving innovative element. Moreover, we quantify the macroscopic features of the emerging patterns to inspect the underlying mechanisms of the evolutionary process using six cluster characteristics. In order to further support our results, we examine the time evolution course for these characteristics. Our results might provide insights for understanding cooperative behaviors and have several important implications for understanding how individuals adjust their strategies under real-life conditions.

Research and Teaching: Analyzing Upper Level Undergraduate Knowledge of Evolutionary Processes-- Can Class Discussions Help?

ERIC Educational Resources Information Center

Tran, Mark V.; Weigel, Emily G.; Richmond, Gail

2014-01-01

For biologists, a proper understanding of evolutionary processes is fundamentally important. However, undergraduate biology students often struggle to understand evolutionary processes, replacing factual knowledge with misconceptions on the subject. Classroom discussions can be effective active learning tools used to address these misconceptions…

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

On the need for widespread horizontal gene transfers under genome size constraint.

PubMed

Isambert, Hervé; Stein, Richard R

2009-08-25

While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes. This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.

How Can We Study the Evolution of Animal Minds?

PubMed Central

Cauchoix, Maxime; Chaine, Alexis S.

2016-01-01

During the last 50 years, comparative cognition and neurosciences have improved our understanding of animal minds while evolutionary ecology has revealed how selection acts on traits through evolutionary time. We describe how cognition can be subject to natural selection like any other biological trait and how this evolutionary approach can be used to understand the evolution of animal cognition. We recount how comparative and fitness methods have been used to understand the evolution of cognition and outline how these approaches could extend our understanding of cognition. The fitness approach, in particular, offers unprecedented opportunities to study the evolutionary mechanisms responsible for variation in cognition within species and could allow us to investigate both proximate (i.e., neural and developmental) and ultimate (i.e., ecological and evolutionary) underpinnings of animal cognition together. We highlight recent studies that have successfully shown that cognitive traits can be under selection, in particular by linking individual variation in cognition to fitness. To bridge the gap between cognitive variation and fitness consequences and to better understand why and how selection can occur on cognition, we end this review by proposing a more integrative approach to study contemporary selection on cognitive traits combining socio-ecological data, minimally invasive neuroscience methods and measurement of ecologically relevant behaviors linked to fitness. Our overall goal in this review is to build a bridge between cognitive neuroscientists and evolutionary biologists, illustrate how their research could be complementary, and encourage evolutionary ecologists to include explicit attention to cognitive processes in their studies of behavior. PMID:27014163

How much can history constrain adaptive evolution? A real-time evolutionary approach of inversion polymorphisms in Drosophila subobscura.

PubMed

Fragata, I; Lopes-Cunha, M; Bárbaro, M; Kellen, B; Lima, M; Santos, M A; Faria, G S; Santos, M; Matos, M; Simões, P

2014-12-01

Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

ERIC Educational Resources Information Center

Wagh, Aditi; Wilensky, Uri

2018-01-01

Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience…

Exploring the evolutionary ecology of fungal endophyte in agricultural systems: using functional traits to reveal mechanisms in community processes

USDA-ARS?s Scientific Manuscript database

All plants, including crop species, harbor a community of fungal endophyte species, however, we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the...

The elusive constellations of poverty.

PubMed

Breugelmans, Seger M; Plantinga, Arnoud; Zeelenberg, Marcel; Poluektova, Olga; Efremova, Maria

2017-01-01

Pepper & Nettle describe possible processes underlying what they call a behavioral constellation of deprivation (BCD). Although we are certain about the application of evolutionary models to our understanding of poverty, we are less certain about the utility of behavioral constellations. The empirical record on poverty-related behaviors is much more divergent and broad than such constellations suggest.

Conundrums, paradoxes, and surprises: a brave new world of biodiversity conservation

Treesearch

A.E. Lugo

2012-01-01

Anthropogenic activity is altering the global disturbance regime through such processes as urbanization, deforestation, and climate change. These disturbance events alter the environmental conditions under which organisms live and adapt and trigger succession, thus setting the biota in otiion in both ecological and evolutionary space. The result is the mixing of...

Evolutionary principles and their practical application

PubMed Central

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

2011-01-01

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

Evolutionary principles and their practical application.

PubMed

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.

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

PubMed

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

2018-04-01

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

Archaeological data reveal slow rates of evolution during plant domestication.

PubMed

Purugganan, Michael D; Fuller, Dorian Q

2011-01-01

Domestication is an evolutionary process of species divergence in which morphological and physiological changes result from the cultivation/tending of plant or animal species by a mutualistic partner, most prominently humans. Darwin used domestication as an analogy to evolution by natural selection although there is strong debate on whether this process of species evolution by human association is an appropriate model for evolutionary study. There is a presumption that selection under domestication is strong and most models assume rapid evolution of cultivated species. Using archaeological data for 11 species from 60 archaeological sites, we measure rates of evolution in two plant domestication traits--nonshattering and grain/seed size increase. Contrary to previous assumptions, we find the rates of phenotypic evolution during domestication are slow, and significantly lower or comparable to those observed among wild species subjected to natural selection. Our study indicates that the magnitudes of the rates of evolution during the domestication process, including the strength of selection, may be similar to those measured for wild species. This suggests that domestication may be driven by unconscious selection pressures similar to that observed for natural selection, and the study of the domestication process may indeed prove to be a valid model for the study of evolutionary change. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Multi-objective optimization of an arch dam shape under static loads using an evolutionary game method

NASA Astrophysics Data System (ADS)

Meng, Rui; Cheong, Kang Hao; Bao, Wei; Wong, Kelvin Kian Loong; Wang, Lu; Xie, Neng-gang

2018-06-01

This article attempts to evaluate the safety and economic performance of an arch dam under the action of static loads. The geometric description of a crown cantilever section and the horizontal arch ring is presented. A three-objective optimization model of arch dam shape is established based on the arch dam volume, maximum principal tensile stress and total strain energy. The evolutionary game method is then applied to obtain the optimal solution. In the evolutionary game technique, a novel and more efficient exploration method of the game players' strategy space, named the 'sorting partition method under the threshold limit', is presented, with the game profit functions constructed according to both competitive and cooperative behaviour. By way of example, three optimization goals have all shown improvements over the initial solutions. In particular, the evolutionary game method has potentially faster convergence. This demonstrates the preliminary proof of principle of the evolutionary game method.

Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change

PubMed Central

Davis, Jenny; Pavlova, Alexandra; Thompson, Ross; Sunnucks, Paul

2013-01-01

Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refuges based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid-adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater-dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short-range endemics. Ecological refuges can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refuges. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have little thermal or hydrological buffering. Accordingly, conservation planning must focus on maintaining meta-population processes, especially through dynamic connectivity between aquatic habitats at a landscape scale. PMID:23526791

Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change.

PubMed

Davis, Jenny; Pavlova, Alexandra; Thompson, Ross; Sunnucks, Paul

2013-07-01

Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refugees based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid-adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater-dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short-range endemics. Ecological refugees can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refugees. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have little thermal or hydrological buffering. Accordingly, conservation planning must focus on maintaining meta-population processes, especially through dynamic connectivity between aquatic habitats at a landscape scale. © 2013 Blackwell Publishing Ltd.

Evolution of early embryogenesis in rhabditid nematodes

PubMed Central

Brauchle, Michael; Kiontke, Karin; MacMenamin, Philip; Fitch, David H. A.; Piano, Fabio

2009-01-01

The cell biological events that guide early embryonic development occur with great precision within species but can be quite diverse across species. How these cellular processes evolve and which molecular components underlie evolutionary changes is poorly understood. To begin to address these questions, we systematically investigated early embryogenesis, from the one- to the four-cell embryo, in 34 nematode species related to C. elegans. We found 40 cell-biological characters that captured the phenotypic differences between these species. By tracing the evolutionary changes on a molecular phylogeny, we found that these characters evolved multiple times and independently of one another. Strikingly, all these phenotypes are mimicked by single-gene RNAi experiments in C. elegans. We use these comparisons to hypothesize the molecular mechanisms underlying the evolutionary changes. For example, we predict that a cell polarity module was altered during the evolution of the Protorhabditis group and show that PAR-1, a kinase localized asymmetrically in C. elegans early embryos, is symmetrically localized in the one-cell stage of Protorhabditis group species. Our genome-wide approach identifies candidate molecules—and thereby modules—associated with evolutionary changes in cell-biological phenotypes. PMID:19643102

Evolutionary dynamics on graphs

NASA Astrophysics Data System (ADS)

Lieberman, Erez; Hauert, Christoph; Nowak, Martin A.

2005-01-01

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

Decentralized diagnostics based on a distributed micro-genetic algorithm for transducer networks monitoring large experimental systems.

PubMed

Arpaia, P; Cimmino, P; Girone, M; La Commara, G; Maisto, D; Manna, C; Pezzetti, M

2014-09-01

Evolutionary approach to centralized multiple-faults diagnostics is extended to distributed transducer networks monitoring large experimental systems. Given a set of anomalies detected by the transducers, each instance of the multiple-fault problem is formulated as several parallel communicating sub-tasks running on different transducers, and thus solved one-by-one on spatially separated parallel processes. A micro-genetic algorithm merges evaluation time efficiency, arising from a small-size population distributed on parallel-synchronized processors, with the effectiveness of centralized evolutionary techniques due to optimal mix of exploitation and exploration. In this way, holistic view and effectiveness advantages of evolutionary global diagnostics are combined with reliability and efficiency benefits of distributed parallel architectures. The proposed approach was validated both (i) by simulation at CERN, on a case study of a cold box for enhancing the cryogeny diagnostics of the Large Hadron Collider, and (ii) by experiments, under the framework of the industrial research project MONDIEVOB (Building Remote Monitoring and Evolutionary Diagnostics), co-funded by EU and the company Del Bo srl, Napoli, Italy.

Understanding the function of bacterial and eukaryotic thiolases II by integrating evolutionary and functional approaches.

PubMed

Fox, Ana Romina; Soto, Gabriela; Mozzicafreddo, Matteo; Garcia, Araceli Nora; Cuccioloni, Massimiliano; Angeletti, Mauro; Salerno, Juan Carlos; Ayub, Nicolás Daniel

2014-01-01

Acetoacetyl-CoA thiolase (EC 2.3.1.9), commonly named thiolase II, condenses two molecules of acetyl-CoA to give acetoacetyl-CoA and CoA. This enzyme acts in anabolic processes as the first step in the biosynthesis of isoprenoids and polyhydroxybutyrate in eukaryotes and bacteria, respectively. We have recently reported the evolutionary and functional equivalence of these enzymes, suggesting that thiolase II could be the rate limiting enzyme in these pathways and presented evidence indicating that this enzyme modulates the availability of reducing equivalents during abiotic stress adaptation in bacteria and plants. However, these results are not sufficient to clarify why thiolase II was evolutionary selected as a critical enzyme in the production of antioxidant compounds. Regarding this intriguing topic, we propose that thiolase II could sense changes in the acetyl-CoA/CoA ratio induced by the inhibition of the tricarboxylic acid cycle under abiotic stress. Thus, the high level of evolutionary and functional constraint of thiolase II may be due to the connection of this enzyme with an ancient and conserved metabolic route. © 2013.

Winter color polymorphisms identify global hot spots for evolutionary rescue from climate change.

PubMed

Mills, L Scott; Bragina, Eugenia V; Kumar, Alexander V; Zimova, Marketa; Lafferty, Diana J R; Feltner, Jennifer; Davis, Brandon M; Hackländer, Klaus; Alves, Paulo C; Good, Jeffrey M; Melo-Ferreira, José; Dietz, Andreas; Abramov, Alexei V; Lopatina, Natalia; Fay, Kairsten

2018-03-02

Maintenance of biodiversity in a rapidly changing climate will depend on the efficacy of evolutionary rescue, whereby population declines due to abrupt environmental change are reversed by shifts in genetically driven adaptive traits. However, a lack of traits known to be under direct selection by anthropogenic climate change has limited the incorporation of evolutionary processes into global conservation efforts. In 21 vertebrate species, some individuals undergo a seasonal color molt from summer brown to winter white as camouflage against snow, whereas other individuals remain brown. Seasonal snow duration is decreasing globally, and fitness is lower for winter white animals on snowless backgrounds. Based on 2713 georeferenced samples of known winter coat color-from eight species across trophic levels-we identify environmentally driven clinal gradients in winter coat color, including polymorphic zones where winter brown and white morphs co-occur. These polymorphic zones, underrepresented by existing global protected area networks, indicate hot spots for evolutionary rescue in a changing climate. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Lin, Ying-Po

2011-01-01

In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network’s evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective. PMID:22084563

Experimental evolution of protein–protein interaction networks

PubMed Central

Kaçar, Betül; Gaucher, Eric A.

2013-01-01

The modern synthesis of evolutionary theory and genetics has enabled us to discover underlying molecular mechanisms of organismal evolution. We know that in order to maximize an organism's fitness in a particular environment, individual interactions among components of protein and nucleic acid networks need to be optimized by natural selection, or sometimes through random processes, as the organism responds to changes and/or challenges in the environment. Despite the significant role of molecular networks in determining an organism's adaptation to its environment, we still do not know how such inter- and intra-molecular interactions within networks change over time and contribute to an organism's evolvability while maintaining overall network functions. One way to address this challenge is to identify connections between molecular networks and their host organisms, to manipulate these connections, and then attempt to understand how such perturbations influence molecular dynamics of the network and thus influence evolutionary paths and organismal fitness. In the present review, we discuss how integrating evolutionary history with experimental systems that combine tools drawn from molecular evolution, synthetic biology and biochemistry allow us to identify the underlying mechanisms of organismal evolution, particularly from the perspective of protein interaction networks. PMID:23849056

Living on the edge: adaptive and plastic responses of the tree Nothofagus pumilio to a long-term transplant experiment predict rear-edge upward expansion.

PubMed

Mathiasen, Paula; Premoli, Andrea C

2016-06-01

Current climate change affects the competitive ability and reproductive success of many species, leading to local extinctions, adjustment to novel local conditions by phenotypic plasticity or rapid adaptation, or tracking their optima through range shifts. However, many species have limited ability to expand to suitable areas. Altitudinal gradients, with abrupt changes in abiotic conditions over short distances, represent "natural experiments" for the evaluation of ecological and evolutionary responses under scenarios of climate change. Nothofagus pumilio is the tree species which dominates as pure stands the montane forests of Patagonia. We evaluated the adaptive value of variation in quantitative traits of N. pumilio under contrasting conditions of the altitudinal gradient with a long-term reciprocal transplant experimental design. While high-elevation plants show little response in plant, leaf, and phenological traits to the experimental trials, low-elevation ones show greater plasticity in their responses to changing environments, particularly at high elevation. Our results suggest a relatively reduced potential for evolutionary adaptation of high-elevation genotypes, and a greater evolutionary potential of low-elevation ones. Under global warming scenarios of forest upslope migration, high-elevation variants may be outperformed by low-elevation ones during this process, leading to the local extinction and/or replacement of these genotypes. These results challenge previous models and predictions expected under global warming for altitudinal gradients, on which the leading edge is considered to be the upper treeline forests.

Loci under selection during multiple range expansions of an invasive plant are mostly population specific, but patterns are associated with climate.

PubMed

Zenni, Rafael D; Hoban, Sean M

2015-07-01

Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate-related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene-level patterns of evolution may be population specific. © 2015 John Wiley & Sons Ltd.

Experimentally evolved and phenotypically plastic responses to enforced monogamy in a hermaphroditic flatworm.

PubMed

Janicke, T; Sandner, P; Ramm, S A; Vizoso, D B; Schärer, L

2016-09-01

Sexual selection is considered a potent evolutionary force in all sexually reproducing organisms, but direct tests in terms of experimental evolution of sexual traits are still lacking for simultaneously hermaphroditic animals. Here, we tested how evolution under enforced monogamy affected a suite of reproductive traits (including testis area, sex allocation, genital morphology, sperm morphology and mating behaviour) in the outcrossing hermaphroditic flatworm Macrostomum lignano, using an assay that also allowed the assessment of phenotypically plastic responses to group size. The experiment comprised 32 independent selection lines that evolved under either monogamy or polygamy for 20 generations. While we did not observe an evolutionary shift in sex allocation, we detected effects of the selection regime for two male morphological traits. Specifically, worms evolving under enforced monogamy had a distinct shape of the male copulatory organ and produced sperm with shorter appendages. Many traits that did not evolve under enforced monogamy showed phenotypic plasticity in response to group size. Notably, individuals that grew up in larger groups had a more male-biased sex allocation and produced slightly longer sperm than individuals raised in pairs. We conclude that, in this flatworm, enforced monogamy induced moderate evolutionary but substantial phenotypically plastic responses. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Eco-Evo PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

EPA Science Inventory

We synthesize how advances in computational methods and population genomics can be combined within an Ecological-Evolutionary (Eco-Evo) PVA model. Eco-Evo PVA models are powerful new tools for understanding the influence of evolutionary processes on plant and animal population pe...

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

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.

In vivo evolutionary engineering for ethanol-tolerance of Saccharomyces cerevisiae haploid cells triggers diploidization.

PubMed

Turanlı-Yıldız, Burcu; Benbadis, Laurent; Alkım, Ceren; Sezgin, Tuğba; Akşit, Arman; Gökçe, Abdülmecit; Öztürk, Yavuz; Baykal, Ahmet Tarık; Çakar, Zeynep Petek; François, Jean M

2017-09-01

Microbial ethanol production is an important alternative energy resource to replace fossil fuels, but at high level, this product is highly toxic, which hampers its efficient production. Towards increasing ethanol-tolerance of Saccharomyces cerevisiae, the so far best industrial ethanol-producer, we evaluated an in vivo evolutionary engineering strategy based on batch selection under both constant (5%, v v -1 ) and gradually increasing (5-11.4%, v v -1 ) ethanol concentrations. Selection under increasing ethanol levels yielded evolved clones that could tolerate up to 12% (v v -1 ) ethanol and had cross-resistance to other stresses. Quite surprisingly, diploidization of the yeast population took place already at 7% (v v -1 ) ethanol level during evolutionary engineering, and this event was abolished by the loss of MKT1, a gene previously identified as being implicated in ethanol tolerance (Swinnen et al., Genome Res., 22, 975-984, 2012). Transcriptomic analysis confirmed diploidization of the evolved clones with strong down-regulation in mating process, and in several haploid-specific genes. We selected two clones exhibiting the highest viability on 12% ethanol, and found productivity and titer of ethanol significantly higher than those of the reference strain under aerated fed-batch cultivation conditions. This higher fermentation performance could be related with a higher abundance of glycolytic and ribosomal proteins and with a relatively lower respiratory capacity of the evolved strain, as revealed by a comparative transcriptomic and proteomic analysis between the evolved and the reference strains. Altogether, these results emphasize the efficiency of the in vivo evolutionary engineering strategy for improving ethanol tolerance, and the link between ethanol tolerance and diploidization. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Fixism and conservation science.

PubMed

Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

2017-08-01

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

Time to Evolve? Potential Evolutionary Responses of Fraser River Sockeye Salmon to Climate Change and Effects on Persistence

PubMed Central

Reed, Thomas E.; Schindler, Daniel E.; Hague, Merran J.; Patterson, David A.; Meir, Eli; Waples, Robin S.; Hinch, Scott G.

2011-01-01

Evolutionary adaptation affects demographic resilience to climate change but few studies have attempted to project changes in selective pressures or quantify impacts of trait responses on population dynamics and extinction risk. We used a novel individual-based model to explore potential evolutionary changes in migration timing and the consequences for population persistence in sockeye salmon Oncorhynchus nerka in the Fraser River, Canada, under scenarios of future climate warming. Adult sockeye salmon are highly sensitive to increases in water temperature during their arduous upriver migration, raising concerns about the fate of these ecologically, culturally, and commercially important fish in a warmer future. Our results suggest that evolution of upriver migration timing could allow these salmon to avoid increasingly frequent stressful temperatures, with the odds of population persistence increasing in proportion to the trait heritability and phenotypic variance. With a simulated 2°C increase in average summer river temperatures by 2100, adult migration timing from the ocean to the river advanced by ∼10 days when the heritability was 0.5, while the risk of quasi-extinction was only 17% of that faced by populations with zero evolutionary potential (i.e., heritability fixed at zero). The rates of evolution required to maintain persistence under simulated scenarios of moderate to rapid warming are plausible based on estimated heritabilities and rates of microevolution of timing traits in salmon and related species, although further empirical work is required to assess potential genetic and ecophysiological constraints on phenological adaptation. These results highlight the benefits to salmon management of maintaining evolutionary potential within populations, in addition to conserving key habitats and minimizing additional stressors where possible, as a means to build resilience to ongoing climate change. More generally, they demonstrate the importance and feasibility of considering evolutionary processes, in addition to ecology and demography, when projecting population responses to environmental change. PMID:21738573

A case study in evolutionary contingency.

PubMed

Blount, Zachary D

2016-08-01

Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Promotion of cooperation by selective group extinction

NASA Astrophysics Data System (ADS)

Böttcher, Marvin A.; Nagler, Jan

2016-06-01

Multilevel selection is an important organizing principle that crucially underlies evolutionary processes from the emergence of cells to eusociality and the economics of nations. Previous studies on multilevel selection assumed that the effective higher-level selection emerges from lower-level reproduction. This leads to selection among groups, although only individuals reproduce. We introduce selective group extinction, where groups die with a probability inversely proportional to their group fitness. When accounting for this the critical benefit-to-cost ratio is substantially lowered. Because in game theory and evolutionary dynamics the degree of cooperation crucially depends on this ratio above which cooperation emerges, previous studies may have substantially underestimated the establishment and maintenance of cooperation.

THE `IN' AND THE `OUT': An Evolutionary Approach

NASA Astrophysics Data System (ADS)

Medina-Martins, P. R.; Rocha, L.

It is claimed that a great deal of the problems which the mechanist approaches to the emulation/modelling of the human mind are presently facing are due to a host of canons so `readily' accepted and acquainted that some of their underlying processes have not yet been the objective of intensive research. The essay proposes a (possible) solution for some of these problems introducing the tenets of a new paradigm which, based on a reappraisal of the concepts of purposiveness and teleology, lays emphasis on the evolutionary aspects (biological and mental) of alive beings. A complex neuro-fuzzy system which works as the supporting realization of this paradigm is briefly described in the essay.

Evolution Model and Simulation of Profit Model of Agricultural Products Logistics Financing

NASA Astrophysics Data System (ADS)

Yang, Bo; Wu, Yan

2018-03-01

Agricultural products logistics financial warehousing business mainly involves agricultural production and processing enterprises, third-party logistics enterprises and financial institutions tripartite, to enable the three parties to achieve win-win situation, the article first gives the replication dynamics and evolutionary stability strategy between the three parties in business participation, and then use NetLogo simulation platform, using the overall modeling and simulation method of Multi-Agent, established the evolutionary game simulation model, and run the model under different revenue parameters, finally, analyzed the simulation results. To achieve the agricultural products logistics financial financing warehouse business to participate in tripartite mutually beneficial win-win situation, thus promoting the smooth flow of agricultural products logistics business.

Transcription as a source of genome instability

PubMed Central

Kim, Nayun; Jinks-Robertson, Sue

2012-01-01

Alterations in genome sequence and structure contribute to somatic disease, affect the fitness of subsequent generations and drive evolutionary processes. The critical roles of highly accurate replication and efficient repair in maintaining overall genome integrity are well known, but the more localized stability costs associated with transcribing DNA into RNA molecules are less appreciated. Here we review the diverse ways that the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape. PMID:22330764

Mutation-selection equilibrium in games with multiple strategies.

PubMed

Antal, Tibor; Traulsen, Arne; Ohtsuki, Hisashi; Tarnita, Corina E; Nowak, Martin A

2009-06-21

In evolutionary games the fitness of individuals is not constant but depends on the relative abundance of the various strategies in the population. Here we study general games among n strategies in populations of large but finite size. We explore stochastic evolutionary dynamics under weak selection, but for any mutation rate. We analyze the frequency dependent Moran process in well-mixed populations, but almost identical results are found for the Wright-Fisher and Pairwise Comparison processes. Surprisingly simple conditions specify whether a strategy is more abundant on average than 1/n, or than another strategy, in the mutation-selection equilibrium. We find one condition that holds for low mutation rate and another condition that holds for high mutation rate. A linear combination of these two conditions holds for any mutation rate. Our results allow a complete characterization of nxn games in the limit of weak selection.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

[The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

PubMed

Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

2010-01-01

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

Simulation of the evolution of root water foraging strategies in dry and shallow soils

PubMed Central

Renton, Michael; Poot, Pieter

2014-01-01

Background and Aims The dynamic structural development of plants can be seen as a strategy for exploiting the limited resources available within their environment, and we would expect that evolution would lead to efficient strategies that reduce costs while maximizing resource acquisition. In particular, perennial species endemic to habitats with shallow soils in seasonally dry environments have been shown to have a specialized root system morphology that may enhance access to water resources in the underlying rock. This study aimed to explore these hypotheses by applying evolutionary algorithms to a functional–structural root growth model. Methods A simulation model of a plant's root system was developed, which represents the dynamics of water uptake and structural growth. The model is simple enough for evolutionary optimization to be computationally feasible, yet flexible enough to allow a range of structural development strategies to be explored. The model was combined with an evolutionary algorithm in order to investigate a case study habitat with a highly heterogeneous distribution of resources, both spatially and temporally – the situation of perennial plants occurring on shallow soils in seasonally dry environments. Evolution was simulated under two contrasting fitness criteria: (1) the ability to find wet cracks in underlying rock, and (2) maximizing above-ground biomass. Key Results The novel approach successfully resulted in the evolution of more efficient structural development strategies for both fitness criteria. Different rooting strategies evolved when different criteria were applied, and each evolved strategy made ecological sense in terms of the corresponding fitness criterion. Evolution selected for root system morphologies which matched those of real species from corresponding habitats. Conclusions Specialized root morphology with deeper rather than shallower lateral branching enhances access to water resources in underlying rock. More generally, the approach provides insights into both evolutionary processes and ecological costs and benefits of different plant growth strategies. PMID:24651371

Passing thoughts on the evolutionary stability of implicit motor behaviour: performance retention under physiological fatigue.

PubMed

Poolton, J M; Masters, R S W; Maxwell, J P

2007-06-01

Heuristics of evolutionary biology (e.g., survival of the fittest) dictate that phylogenetically older processes are inherently more stable and resilient to disruption than younger processes. On the grounds that non-declarative behaviour emerged long before declarative behaviour, Reber (1992) argues that implicit (non-declarative) learning is supported by neural processes that are evolutionarily older than those supporting explicit learning. Reber suggested that implicit learning thus leads to performance that is more robust than explicit learning. Applying this evolutionary framework to motor performance, we examined whether implicit motor learning, relative to explicit motor learning, conferred motor output that was resilient to physiological fatigue and durable over time. In Part One of the study a fatigued state was induced by a double Wingate Anaerobic test protocol. Fatigue had no affect on performance of participants in the implicit condition; whereas, performance of participants in the explicit condition deteriorated significantly. In Part Two of the study a convenience sample of participants was recalled following a one-year hiatus. In both the implicit and the explicit condition retention of performance was seen and, contrary to the findings in Part One, so was resilience to fatigue. The resilient performance in the explicit condition after one year may have resulted from forgetting (the decay of declarative knowledge) or from consolidation of declarative knowledge as implicit memories. In either case, implicit processes were left to more effectively support motor performance.

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

PubMed

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.

Evolutionary rescue from extinction is contingent on a lower rate of environmental change.

PubMed

Lindsey, Haley A; Gallie, Jenna; Taylor, Susan; Kerr, Benjamin

2013-02-28

The extinction rate of populations is predicted to rise under increasing rates of environmental change. If a population experiencing increasingly stressful conditions lacks appropriate phenotypic plasticity or access to more suitable habitats, then genetic change may be the only way to avoid extinction. Evolutionary rescue from extinction occurs when natural selection enriches a population for more stress-tolerant genetic variants. Some experimental studies have shown that lower rates of environmental change lead to more adapted populations or fewer extinctions. However, there has been little focus on the genetic changes that underlie evolutionary rescue. Here we demonstrate that some evolutionary trajectories are contingent on a lower rate of environmental change. We allowed hundreds of populations of Escherichia coli to evolve under variable rates of increase in concentration of the antibiotic rifampicin. We then genetically engineered all combinations of mutations from isolates evolved under lower rates of environmental change. By assessing fitness of these engineered strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change. Rapidly deteriorating environments not only limit mutational opportunities by lowering population size, but they can also eliminate sets of mutations as evolutionary options. As anthropogenic activities are leading to environmental change at unprecedented rapidity, it is critical to understand how the rate of environmental change affects both demographic and genetic underpinnings of evolutionary rescue.

Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution.

PubMed

Smaers, J B; Soligo, C

2013-05-22

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.

Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution

PubMed Central

Smaers, J. B.; Soligo, C.

2013-01-01

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning. PMID:23536600

Evolutionary relevance facilitates visual information processing.

PubMed

Jackson, Russell E; Calvillo, Dusti P

2013-11-03

Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective.

PubMed

Luo, Shiqi; Lu, Jian

2017-06-01

Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established "transposition-selection" population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms. Copyright © 2017 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Production and hosting by Elsevier B.V. All rights reserved.

Crowd-driven Ecosystem for Evolutionary Design

DTIC Science & Technology

2012-07-28

also embeds social media connections to maximize crowd engagement. Within such an environment, experts and non- traditional contributors (crowd) can...process.” The CEED platform also embeds social media connections to maximize crowd engagement. When completed, the software developed under the...track a project of interest online through other social media (namely RSS, Facebook, and Twitter) as well as on the vehicleforge website itself

Facial bone fragmentation in blind cavefish arises through two unusual ossification processes.

PubMed

Powers, Amanda K; Kaplan, Shane A; Boggs, Tyler E; Gross, Joshua B

2018-05-03

The precise mechanisms underlying cranial bone development, evolution and patterning remain incompletely characterised. This poses a challenge to understanding the etiologies of craniofacial malformations evolving in nature. Capitalising on natural variation, "evolutionary model systems" provide unique opportunities to identify underlying causes of aberrant phenotypes as a complement to studies in traditional systems. Mexican blind cavefish are a prime evolutionary model for cranial disorders since they frequently exhibit extreme alterations to the skull and lateral asymmetries. These aberrations occur in stark contrast to the normal cranial architectures of closely related surface-dwelling fish, providing a powerful comparative paradigm for understanding cranial bone formation. Using a longitudinal and in vivo analytical approach, we discovered two unusual ossification processes in cavefish that underlie the development of 'fragmented' and asymmetric cranial bones. The first mechanism involves the sporadic appearance of independent bony elements that fail to fuse together later in development. The second mechanism involves the "carving" of channels in the mature bone, a novel form of post-ossification remodeling. In the extreme cave environment, these novel mechanisms may have evolved to augment sensory input, and may indirectly result in a trade-off between sensory expansion and cranial bone development.

Darwinian evolution in the light of genomics

PubMed Central

Koonin, Eugene V.

2009-01-01

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

How does cognition evolve? Phylogenetic comparative psychology

PubMed Central

Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

2014-01-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

A model of ecological and evolutionary consequences of color polymorphism.

PubMed

Forsman, Anders; Ahnesjö, Jonas; Caesar, Sofia; Karlsson, Magnus

2008-01-01

We summarize direct and indirect effects on fitness components of animal color pattern and present a synthesis of theories concerning the ecological and evolutionary dynamics of chromatic multiple niche polymorphisms. Previous endeavors have aimed primarily at identifying conditions that promote the evolution and maintenance of polymorphisms. We consider in a conceptual model also the reciprocal influence of color polymorphism on population processes and propose that polymorphism entails selective advantages that may promote the ecological success of polymorphic species. The model begins with an evolutionary branching event from mono- to polymorphic condition that, under the influence of correlational selection, is predicted to promote the evolution of physical integration of coloration and other traits (cf. multi-trait coevolution and complex phenotypes). We propose that the coexistence within a population of alternative ecomorphs with coadapted gene complexes promotes utilization of diverse environmental resources, population stability and persistence, colonization success, and range expansions, and enhances the evolutionary potential and speciation. Conversely, we predict polymorphic populations to be less vulnerable to environmental change and at lower risk of range contractions and extinctions compared with monomorphic populations. We offer brief suggestions as to how these falsifiable predictions may be tested.

Evolution of female-specific wingless forms in bagworm moths.

PubMed

Niitsu, Shuhei; Sugawara, Hirotaka; Hayashi, Fumio

2017-01-01

The evolution of winglessness in insects has been typically interpreted as a consequence of developmental and other adaptations to various environments that are secondarily derived from a winged morph. Several species of bagworm moths (Insecta: Lepidoptera, Psychidae) exhibit a case-dwelling larval life style along with one of the most extreme cases of sexual dimorphism: wingless female adults. While the developmental process that led to these wingless females is well known, the origins and evolutionary transitions are not yet understood. To examine the evolutionary patterns of wing reduction in bagworm females, we reconstruct the molecular phylogeny of over 30 Asian species based on both mitochondrial (cytochrome c oxidase subunit I) and nuclear (28S rRNA) DNA sequences. Under a parsimonious assumption, the molecular phylogeny implies that: (i) the evolutionary wing reduction towards wingless females consisted of two steps: (Step I) from functional wings to vestigial wings (nonfunctional) and (Step II) from vestigial wings to the most specialized vermiform adults (lacking wings and legs); and (ii) vermiform morphs evolved independently at least twice. Based on the results of our study, we suggest that the evolutionary changes in the developmental system are essential for the establishment of different wingless forms in insects. © 2016 Wiley Periodicals, Inc.

How does cognition evolve? Phylogenetic comparative psychology.

PubMed

MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

2012-03-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

Clownfishes evolution below and above the species level

PubMed Central

Litsios, Glenn; Faye, Laurélène; Salamin, Nicolas

2018-01-01

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels. PMID:29467260

Constraints, Trade-offs and the Currency of Fitness.

PubMed

Acerenza, Luis

2016-03-01

Understanding evolutionary trajectories remains a difficult task. This is because natural evolutionary processes are simultaneously affected by various types of constraints acting at the different levels of biological organization. Of particular importance are constraints where correlated changes occur in opposite directions, called trade-offs. Here we review and classify the main evolutionary constraints and trade-offs, operating at all levels of trait hierarchy. Special attention is given to life history trade-offs and the conflict between the survival and reproduction components of fitness. Cellular mechanisms underlying fitness trade-offs are described. At the metabolic level, a linear trade-off between growth and flux variability was found, employing bacterial genome-scale metabolic reconstructions. Its analysis indicates that flux variability can be considered as the currency of fitness. This currency is used for fitness transfer between fitness components during adaptations. Finally, a discussion is made regarding the constraints which limit the increase in the amount of fitness currency during evolution, suggesting that occupancy constraints are probably the main restrictions.

Ecological and evolutionary drivers of the elevational gradient of diversity.

PubMed

Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

2018-05-02

Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

Self-extinction through optimizing selection.

PubMed

Parvinen, Kalle; Dieckmann, Ulf

2013-09-21

Evolutionary suicide is a process in which selection drives a viable population to extinction. So far, such selection-driven self-extinction has been demonstrated in models with frequency-dependent selection. This is not surprising, since frequency-dependent selection can disconnect individual-level and population-level interests through environmental feedback. Hence it can lead to situations akin to the tragedy of the commons, with adaptations that serve the selfish interests of individuals ultimately ruining a population. For frequency-dependent selection to play such a role, it must not be optimizing. Together, all published studies of evolutionary suicide have created the impression that evolutionary suicide is not possible with optimizing selection. Here we disprove this misconception by presenting and analyzing an example in which optimizing selection causes self-extinction. We then take this line of argument one step further by showing, in a further example, that selection-driven self-extinction can occur even under frequency-independent selection. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reverse Evolution of Armor Plates in the Threespine Stickleback

USGS Publications Warehouse

Kitano, J.; Bolnick, D.I.; Beauchamp, D.A.; Mazur, M.M.; Mori, S.; Nakano, T.; Peichel, C.L.

2008-01-01

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not??only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution," [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime. ?? 2008 Elsevier Ltd. All rights reserved.

Antagonistic versus non-antagonistic models of balancing selection: Characterizing the relative timescales and hitchhiking effects of partial selective sweeps

PubMed Central

Connallon, Tim; Clark, Andrew G.

2012-01-01

Antagonistically selected alleles -- those with opposing fitness effects between sexes, environments, or fitness components -- represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus non-antagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, non-antagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection. PMID:23461340

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior.

PubMed

Schrader, Lukas; Helanterä, Heikki; Oettler, Jan

2017-03-01

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior-a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

PubMed Central

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

Investigating evolutionary constraints on the detection of threatening stimuli in preschool children.

PubMed

Zsido, Andras N; Deak, Anita; Losonci, Adrienn; Stecina, Diana; Arato, Akos; Bernath, Laszlo

2018-04-01

Numerous objects and animals could be threatening, and thus, children learn to avoid them early. Spiders and syringes are among the most common targets of fears and phobias of the modern word. However, they are of different origins: while the former is evolutionary relevant, the latter is not. We sought to investigate the underlying mechanisms that make the quick detection of such stimuli possible and enable the impulse to avoid them in the future. The respective categories of threatening and non-threatening targets were similar in shape, while low-level visual features were controlled. Our results showed that children found threatening cues faster, irrespective of the evolutionary age of the cues. However, they detected non-threatening evolutionary targets faster than non-evolutionary ones. We suggest that the underlying mechanism may be different: general feature detection can account for finding evolutionary threatening cues quickly, while specific features detection is more appropriate for modern threatening stimuli. Copyright © 2018 Elsevier B.V. All rights reserved.

Experimental evidence that the Ornstein-Uhlenbeck model best describes the evolution of leaf litter decomposability.

PubMed

Pan, Xu; Cornelissen, Johannes H C; Zhao, Wei-Wei; Liu, Guo-Fang; Hu, Yu-Kun; Prinzing, Andreas; Dong, Ming; Cornwell, William K

2014-09-01

Leaf litter decomposability is an important effect trait for ecosystem functioning. However, it is unknown how this effect trait evolved through plant history as a leaf 'afterlife' integrator of the evolution of multiple underlying traits upon which adaptive selection must have acted. Did decomposability evolve in a Brownian fashion without any constraints? Was evolution rapid at first and then slowed? Or was there an underlying mean-reverting process that makes the evolution of extreme trait values unlikely? Here, we test the hypothesis that the evolution of decomposability has undergone certain mean-reverting forces due to strong constraints and trade-offs in the leaf traits that have afterlife effects on litter quality to decomposers. In order to test this, we examined the leaf litter decomposability and seven key leaf traits of 48 tree species in the temperate area of China and fitted them to three evolutionary models: Brownian motion model (BM), Early burst model (EB), and Ornstein-Uhlenbeck model (OU). The OU model, which does not allow unlimited trait divergence through time, was the best fit model for leaf litter decomposability and all seven leaf traits. These results support the hypothesis that neither decomposability nor the underlying traits has been able to diverge toward progressively extreme values through evolutionary time. These results have reinforced our understanding of the relationships between leaf litter decomposability and leaf traits in an evolutionary perspective and may be a helpful step toward reconstructing deep-time carbon cycling based on taxonomic composition with more confidence.

Let the social sciences evolve.

PubMed

Smaldino, Paul E; Waring, Timothy M

2014-08-01

We agree that evolutionary perspectives may help us organize many divergent realms of the science of human behavior. Nevertheless, an imperative to unite all social science under an evolutionary framework risks turning off researchers who have their own theoretical perspectives that can be informed by evolutionary theory without being exclusively defined by it. We propose a few considerations for scholars interested in joining the evolutionary and social sciences.

Estimating true evolutionary distances under the DCJ model.

PubMed

Lin, Yu; Moret, Bernard M E

2008-07-01

Modern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of organisms. The evolutionary mechanisms through which the set of the genes of an organism is altered and reordered are of great interest to systematists, evolutionary biologists, comparative genomicists and biomedical researchers. Perhaps the most basic concept in this area is that of evolutionary distance between two genomes: under a given model of genomic evolution, how many events most likely took place to account for the difference between the two genomes? We present a method to estimate the true evolutionary distance between two genomes under the 'double-cut-and-join' (DCJ) model of genome rearrangement, a model under which a single multichromosomal operation accounts for all genomic rearrangement events: inversion, transposition, translocation, block interchange and chromosomal fusion and fission. Our method relies on a simple structural characterization of a genome pair and is both analytically and computationally tractable. We provide analytical results to describe the asymptotic behavior of genomes under the DCJ model, as well as experimental results on a wide variety of genome structures to exemplify the very high accuracy (and low variance) of our estimator. Our results provide a tool for accurate phylogenetic reconstruction from multichromosomal gene rearrangement data as well as a theoretical basis for refinements of the DCJ model to account for biological constraints. All of our software is available in source form under GPL at http://lcbb.epfl.ch.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

PubMed Central

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M.; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel

2017-01-01

Abstract Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. PMID:28204787

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Interpreting Evolutionary Diagrams: When Topology and Process Conflict

ERIC Educational Resources Information Center

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

2010-01-01

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

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

PubMed

Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A

2012-06-01

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.

The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity

PubMed Central

Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A.

2012-01-01

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population’s phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models. PMID:22426879

Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.

PubMed

Kane, Nolan C; Barker, Michael S; Zhan, Shing H; Rieseberg, Loren H

2011-12-01

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

The link between flowering time and stress tolerance.

PubMed

Kazan, Kemal; Lyons, Rebecca

2016-01-01

Evolutionary success in plants is largely dependent on the successful transition from vegetative to reproductive growth. In the lifetime of a plant, flowering is not only an essential part of the reproductive process but also a critical developmental stage that can be vulnerable to environmental stresses. Exposure to stress during this period can cause substantial yield losses in seed-producing plants. However, it is becoming increasingly evident that altering flowering time is an evolutionary strategy adopted by plants to maximize the chances of reproduction under diverse stress conditions, ranging from pathogen infection to heat, salinity, and drought. Here, recent studies that have revealed new insights into how biotic and abiotic stress signals can be integrated into floral pathways are reviewed. A better understanding of how complex environmental variables affect plant phenology is important for future genetic manipulation of crops to increase productivity under the changing climate. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

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

ERIC Educational Resources Information Center

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…

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

PubMed

Duchêne, D A; Hua, X; Bromham, L

2017-10-01

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Estimating the ratios of the stationary distribution values for Markov chains modeling evolutionary algorithms.

PubMed

Mitavskiy, Boris; Cannings, Chris

2009-01-01

The evolutionary algorithm stochastic process is well-known to be Markovian. These have been under investigation in much of the theoretical evolutionary computing research. When the mutation rate is positive, the Markov chain modeling of an evolutionary algorithm is irreducible and, therefore, has a unique stationary distribution. Rather little is known about the stationary distribution. In fact, the only quantitative facts established so far tell us that the stationary distributions of Markov chains modeling evolutionary algorithms concentrate on uniform populations (i.e., those populations consisting of a repeated copy of the same individual). At the same time, knowing the stationary distribution may provide some information about the expected time it takes for the algorithm to reach a certain solution, assessment of the biases due to recombination and selection, and is of importance in population genetics to assess what is called a "genetic load" (see the introduction for more details). In the recent joint works of the first author, some bounds have been established on the rates at which the stationary distribution concentrates on the uniform populations. The primary tool used in these papers is the "quotient construction" method. It turns out that the quotient construction method can be exploited to derive much more informative bounds on ratios of the stationary distribution values of various subsets of the state space. In fact, some of the bounds obtained in the current work are expressed in terms of the parameters involved in all the three main stages of an evolutionary algorithm: namely, selection, recombination, and mutation.

Inherit the policy: A sociocultural approach to understanding evolutionary biology policy in South Carolina

NASA Astrophysics Data System (ADS)

Moore, Gregory D.

South Carolina biology Indicator 5.6 calls for students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory" (South Carolina Department of Education, 2006). Levinson and Sutton (2001) offered a sociocultural approach to policy that considers cultural and historical influences at all levels of the policy process. Lipsky (1980/2010) and others have identified teachers as de facto policy makers, exercising broad discretion in the execution of their work. This study looks to Ajzen's Theory of Planned Behavior as an initial framework to inform how evolutionary biology policy in South Carolina is conceptualized and understood at different levels of the policy process. The results of this study indicate that actors in the state's evolutionary biology policy process draw upon a myriad of Discourses (Gee, 1999/2005). These Discourses shape cultural dynamics and the agency of the policy actors as they navigate conflicting messages between testing mandates and evolutionary biology policy. There indeed exist gaps between how evolutionary biology policy in South Carolina is conceptualized and understood at the different levels of the policy process. Evidence from this study suggests that appropriation-level policy actors must be brought into the Discourse related to the critical analysis of evolutionary biology and academic freedom legislation must be enacted if South Carolina biology Indicator 5.6 is to realize practical significance in educational policy.

Are hotspots of evolutionary potential adequately protected in southern California?

USGS Publications Warehouse

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.

Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

PubMed Central

Woese, Carl R.; Olsen, Gary J.; Ibba, Michael; Söll, Dieter

2000-01-01

The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense. PMID:10704480

Feedbacks between geomorphology and biota controlling Earth surface processes and landforms: A review of foundation concepts and current understandings

NASA Astrophysics Data System (ADS)

Corenblit, Dov; Baas, Andreas C. W.; Bornette, Gudrun; Darrozes, José; Delmotte, Sébastien; Francis, Robert A.; Gurnell, Angela M.; Julien, Frédéric; Naiman, Robert J.; Steiger, Johannes

2011-06-01

This review article presents recent advances in the field of biogeomorphology related to the reciprocal coupling between Earth surface processes and landforms, and ecological and evolutionary processes. The aim is to present to the Earth Science community ecological and evolutionary concepts and associated recent conceptual developments for linking geomorphology and biota. The novelty of the proposed perspective is that (1) in the presence of geomorphologic-engineer species, which modify sediment and landform dynamics, natural selection operating at the scale of organisms may have consequences for the physical components of ecosystems, and particularly Earth surface processes and landforms; and (2) in return, these modifications of geomorphologic processes and landforms often feed back to the ecological characteristics of the ecosystem (structure and function) and thus to biological characteristics of engineer species and/or other species (adaptation and speciation). The main foundation concepts from ecology and evolutionary biology which have led only recently to an improved conception of landform dynamics in geomorphology are reviewed and discussed. The biogeomorphologic macroevolutionary insights proposed explicitly integrate geomorphologic niche-dimensions and processes within an ecosystem framework and reflect current theories of eco-evolutionary and ecological processes. Collectively, these lead to the definition of an integrated model describing the overall functioning of biogeomorphologic systems over ecological and evolutionary timescales.

The Evolution of Consciousness in the Novel in English

NASA Astrophysics Data System (ADS)

Gojkovic, Zorica

This dissertation examines how the novel in English reflects the evolution of human consciousness. Characters in novels express a level of consciousness through their world view, which reflects the level of consciousness of the author and his/her period. Over time the world view evolves from a perception of physical reality as ultimate reality, to physical reality as illusion, in contrast to primary reality, which is spirit, or energy, or God, or the holistic frequency realm. Great mystics and sages all over the world, and throughout history, have had this understanding about the nature of reality. What is new is that different investigative currents are coming together and sharing this new vision of reality. The underlying unity, or enfolded order, is a broader realm where fragmentation is united by a deeper truth. This oneness is analogized to a hologram, where each part is in the whole and the whole in each part. The process of the evolution of consciousness in the novel is examined in three parts. In part one, Chapter One, connections are established between some of the pertinent developments in quantum physics, mysticism and Erich Neumann's theory of the evolution of consciousness. This information sets the stage for the exploration of the evolutionary process in the novel. Part two, chapters two to seven, explore various themes that demonstrate the evolutionary process in the novel. Novels that most effectively demonstrate the evolution are used. Part three, Chapter Eight, summarizes the evolutionary process and demonstrates the way in which wholeness is achieved from the initial separateness. Part three also explores some implications for the novel in light of this analysis.

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

PubMed

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

2017-07-01

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

An evolutionary perspective on health psychology: new approaches and applications.

PubMed

Tybur, Joshua M; Bryan, Angela D; Hooper, Ann E Caldwell

2012-12-20

Although health psychologists' efforts to understand and promote health are most effective when guided by theory, health psychology has not taken full advantage of theoretical insights provided by evolutionary psychology. Here, we argue that evolutionary perspectives can fruitfully inform strategies for addressing some of the challenges facing health psychologists. Evolutionary psychology's emphasis on modular, functionally specialized psychological systems can inform approaches to understanding the myriad behaviors grouped under the umbrella of "health," as can theoretical perspectives used by evolutionary anthropologists, biologists, and psychologists (e.g., Life History Theory). We detail some early investigations into evolutionary health psychology, and we provide suggestions for directions for future research.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

PubMed

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel; Wegmann, Daniel

2017-11-01

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

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

NASA Astrophysics Data System (ADS)

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

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

Sex-ratio control erodes sexual selection, revealing evolutionary feedback from adaptive plasticity.

PubMed

Fawcett, Tim W; Kuijper, Bram; Weissing, Franz J; Pen, Ido

2011-09-20

Female choice is a powerful selective force, driving the elaboration of conspicuous male ornaments. This process of sexual selection has profound implications for many life-history decisions, including sex allocation. For example, females with attractive partners should produce more sons, because these sons will inherit their father's attractiveness and enjoy high mating success, thereby yielding greater fitness returns than daughters. However, previous research has overlooked the fact that there is a reciprocal feedback from life-history strategies to sexual selection. Here, using a simple mathematical model, we show that if mothers adaptively control offspring sex in relation to their partner's attractiveness, sexual selection is weakened and male ornamentation declines. This weakening occurs because the ability to determine offspring sex reduces the fitness difference between females with attractive and unattractive partners. We use individual-based, evolutionary simulations to show that this result holds under more biologically realistic conditions. Sexual selection and sex allocation thus interact in a dynamic fashion: The evolution of conspicuous male ornaments favors sex-ratio adjustment, but this conditional strategy then undermines the very same process that generated it, eroding sexual selection. We predict that, all else being equal, the most elaborate sexual displays should be seen in species with little or no control over offspring sex. The feedback process we have described points to a more general evolutionary principle, in which a conditional strategy weakens directional selection on another trait by reducing fitness differences.

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

PubMed

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

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

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

PubMed

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.

"Conceptual Change" as both Revolutionary and Evolutionary Process

ERIC Educational Resources Information Center

Keiny, Shoshana

2008-01-01

Our argument concerning the debate around the process of "conceptual change" is that it is both an evolutionary learning process and a revolutionary paradigm change. To gain a deeper understanding of the process, the article focuses on the discourse of educational facilitators participating in a community of learners. Applying the methodology of…

Cascading failures and the emergence of cooperation in evolutionary-game based models of social and economical networks.

PubMed

Wang, Wen-Xu; Lai, Ying-Cheng; Armbruster, Dieter

2011-09-01

We study catastrophic behaviors in large networked systems in the paradigm of evolutionary games by incorporating a realistic "death" or "bankruptcy" mechanism. We find that a cascading bankruptcy process can arise when defection strategies exist and individuals are vulnerable to deficit. Strikingly, we observe that, after the catastrophic cascading process terminates, cooperators are the sole survivors, regardless of the game types and of the connection patterns among individuals as determined by the topology of the underlying network. It is necessary that individuals cooperate with each other to survive the catastrophic failures. Cooperation thus becomes the optimal strategy and absolutely outperforms defection in the game evolution with respect to the "death" mechanism. Our results can be useful for understanding large-scale catastrophe in real-world systems and in particular, they may yield insights into significant social and economical phenomena such as large-scale failures of financial institutions and corporations during an economic recession.

Cascading failures and the emergence of cooperation in evolutionary-game based models of social and economical networks

NASA Astrophysics Data System (ADS)

Wang, Wen-Xu; Lai, Ying-Cheng; Armbruster, Dieter

2011-09-01

We study catastrophic behaviors in large networked systems in the paradigm of evolutionary games by incorporating a realistic "death" or "bankruptcy" mechanism. We find that a cascading bankruptcy process can arise when defection strategies exist and individuals are vulnerable to deficit. Strikingly, we observe that, after the catastrophic cascading process terminates, cooperators are the sole survivors, regardless of the game types and of the connection patterns among individuals as determined by the topology of the underlying network. It is necessary that individuals cooperate with each other to survive the catastrophic failures. Cooperation thus becomes the optimal strategy and absolutely outperforms defection in the game evolution with respect to the "death" mechanism. Our results can be useful for understanding large-scale catastrophe in real-world systems and in particular, they may yield insights into significant social and economical phenomena such as large-scale failures of financial institutions and corporations during an economic recession.

Putting together phylogenetic and ontogenetic perspectives on empathy.

PubMed

Decety, Jean; Svetlova, Margarita

2012-01-01

The ontogeny of human empathy is better understood with reference to the evolutionary history of the social brain. Empathy has deep evolutionary, biochemical, and neurological underpinnings. Even the most advanced forms of empathy in humans are built on more basic forms and remain connected to core mechanisms associated with affective communication, social attachment, and parental care. In this paper, we argue that it is essential to consider empathy within a neurodevelopmental framework that recognizes both the continuities and changes in socioemotional understanding from infancy to adulthood. We bring together neuroevolutionary and developmental perspectives on the information processing and neural mechanisms underlying empathy and caring, and show that they are grounded in multiple interacting systems and processes. Moreover, empathy in humans is assisted by other abstract and domain-general high-level cognitive abilities such as executive functions, mentalizing and language, as well as the ability to differentiate another's mental states from one's own, which expand the range of behaviors that can be driven by empathy. Copyright © 2011 Elsevier Ltd. All rights reserved.

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

PubMed

Tago, Damian; Meyer, Damien F

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium

PubMed Central

Tago, Damian; Meyer, Damien F.

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria. PMID:27610355

Evolutionary Explanations for Antibiotic Resistance in Daily Press, Online Websites and Biology Textbooks in Sweden

ERIC Educational Resources Information Center

Bohlin, Gustav; Höst, Gunnar E.

2015-01-01

The present study explores the extent and precision of evolutionary explanations for antibiotic resistance in communication directed toward the Swedish public. Bacterial resistance develops through evolutionary mechanisms and knowledge of these helps to explain causes underlying the growing prevalence of resistant strains, as well as important…

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

PubMed

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.

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

PubMed

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.

Evolutionary change in physiological phenotypes along the human lineage

PubMed Central

Vining, Alexander Q.; Nunn, Charles L.

2016-01-01

Background and Objectives: 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. Methodology: 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. Results: 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. Conclusions and Implications: 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. PMID:27615376

Climate change and timing of avian breeding and migration: evolutionary versus plastic changes

PubMed Central

Charmantier, Anne; Gienapp, Phillip

2014-01-01

There are multiple observations around the globe showing that in many avian species, both the timing of migration and breeding have advanced, due to warmer springs. Here, we review the literature to disentangle the actions of evolutionary changes in response to selection induced by climate change versus changes due to individual plasticity, that is, the capacity of an individual to adjust its phenology to environmental variables. Within the abundant literature on climate change effects on bird phenology, only a small fraction of studies are based on individual data, yet individual data are required to quantify the relative importance of plastic versus evolutionary responses. While plasticity seems common and often adaptive, no study so far has provided direct evidence for an evolutionary response of bird phenology to current climate change. This assessment leads us to notice the alarming lack of tests for microevolutionary changes in bird phenology in response to climate change, in contrast with the abundant claims on this issue. In short, at present we cannot draw reliable conclusions on the processes underlying the observed patterns of advanced phenology in birds. Rapid improvements in techniques for gathering and analysing individual data offer exciting possibilities that should encourage research activity to fill this knowledge gap. PMID:24454545

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

von der Heyden, Sophie

2017-03-01

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

Can Evolution Supply What Ecology Demands?

PubMed

Kokko, Hanna; Chaturvedi, Anurag; Croll, Daniel; Fischer, Martin C; Guillaume, Frédéric; Karrenberg, Sophie; Kerr, Ben; Rolshausen, Gregor; Stapley, Jessica

2017-03-01

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation. Copyright © 2016 Elsevier Ltd. All rights reserved.

An Evolutionary Perspective on Family Studies: Differential Susceptibility to Environmental Influences.

PubMed

Hartman, Sarah; Belsky, Jay

2016-12-01

An evolutionary perspective of human development provides the basis for the differential-susceptibility hypothesis which stipulates that individuals should differ in their susceptibility to environmental influences, with some being more affected than others by both positive and negative developmental experiences and environmental exposures. This paper reviews evidence consistent with this claim while revealing that temperamental and genetic characteristics play a role in distinguishing more and less susceptible individuals. The differential-susceptibility framework under consideration is contrasted to the traditional diathesis-stress view that "vulnerability" traits predispose some to being disproportionately affected by (only) adverse experiences. We raise several issues stimulated by the literature that need to be clarified in further research. Lastly, we suggest that therapy may differ in its effects depending on an individual's susceptibility. © 2015 Family Process Institute.

Chasing the Rainbow: The Non-conscious Nature of Being.

PubMed

Oakley, David A; Halligan, Peter W

2017-01-01

Despite the compelling subjective experience of executive self-control, we argue that "consciousness" contains no top-down control processes and that "consciousness" involves no executive, causal, or controlling relationship with any of the familiar psychological processes conventionally attributed to it. In our view, psychological processing and psychological products are not under the control of consciousness. In particular, we argue that all "contents of consciousness" are generated by and within non-conscious brain systems in the form of a continuous self-referential personal narrative that is not directed or influenced in any way by the "experience of consciousness." This continuously updated personal narrative arises from selective "internal broadcasting" of outputs from non-conscious executive systems that have access to all forms of cognitive processing, sensory information, and motor control. The personal narrative provides information for storage in autobiographical memory and is underpinned by constructs of self and agency, also created in non-conscious systems. The experience of consciousness is a passive accompaniment to the non-conscious processes of internal broadcasting and the creation of the personal narrative. In this sense, personal awareness is analogous to the rainbow which accompanies physical processes in the atmosphere but exerts no influence over them. Though it is an end-product created by non-conscious executive systems, the personal narrative serves the powerful evolutionary function of enabling individuals to communicate (externally broadcast) the contents of internal broadcasting. This in turn allows recipients to generate potentially adaptive strategies, such as predicting the behavior of others and underlies the development of social and cultural structures, that promote species survival. Consequently, it is the capacity to communicate to others the contents of the personal narrative that confers an evolutionary advantage-not the experience of consciousness (personal awareness) itself.

Chasing the Rainbow: The Non-conscious Nature of Being

PubMed Central

Oakley, David A.; Halligan, Peter W.

2017-01-01

Despite the compelling subjective experience of executive self-control, we argue that “consciousness” contains no top-down control processes and that “consciousness” involves no executive, causal, or controlling relationship with any of the familiar psychological processes conventionally attributed to it. In our view, psychological processing and psychological products are not under the control of consciousness. In particular, we argue that all “contents of consciousness” are generated by and within non-conscious brain systems in the form of a continuous self-referential personal narrative that is not directed or influenced in any way by the “experience of consciousness.” This continuously updated personal narrative arises from selective “internal broadcasting” of outputs from non-conscious executive systems that have access to all forms of cognitive processing, sensory information, and motor control. The personal narrative provides information for storage in autobiographical memory and is underpinned by constructs of self and agency, also created in non-conscious systems. The experience of consciousness is a passive accompaniment to the non-conscious processes of internal broadcasting and the creation of the personal narrative. In this sense, personal awareness is analogous to the rainbow which accompanies physical processes in the atmosphere but exerts no influence over them. Though it is an end-product created by non-conscious executive systems, the personal narrative serves the powerful evolutionary function of enabling individuals to communicate (externally broadcast) the contents of internal broadcasting. This in turn allows recipients to generate potentially adaptive strategies, such as predicting the behavior of others and underlies the development of social and cultural structures, that promote species survival. Consequently, it is the capacity to communicate to others the contents of the personal narrative that confers an evolutionary advantage—not the experience of consciousness (personal awareness) itself. PMID:29184516

Understanding phylogenetic incongruence: lessons from phyllostomid bats

PubMed Central

Dávalos, Liliana M; Cirranello, Andrea L; Geisler, Jonathan H; Simmons, Nancy B

2012-01-01

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats. PMID:22891620

GRC-2006-C-01252

NASA Image and Video Library

2002-08-09

Performance Acceptance Test of a prototype-model NEXT (NASA Evolutionary Xenon Thruster) ion engine that was delivered to NASA Glenn Research Center by Aerojet. The test dates were May 10 - May 17, 2006. The test was conducted in the Vacuum Facility 6 test facility located in the Electric Power Laboratory. The test successfully demonstrated the PM manufacturing process carried out by Aerojet under the guidance of NASA Glenn Research Center and PM1 acceptable functionality

Adiabatic model of field reversal by fast ions in an axisymmetric open trap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsidulko, Yu. A., E-mail: tsidulko@mail.ru

2016-06-15

A model of field reversal by fast ions has been developed under the assumption of preservation of fast-ion adiabatic invariants. Analytical solutions obtained in the approximation of a narrow fast-ion layer and numerical solutions to the evolutionary problem are presented. The solutions demonstrate the process of formation of a field reversed configuration with parameters close to those of the planned experiment.

Using connectivity to identify climatic drivers of local adaptation: a response to Macdonald et al.

PubMed

Prunier, Jérôme G; Blanchet, Simon

2018-04-30

Macdonald et al. (Ecol. Lett., 21, 2018, 207-216) proposed an analytical framework for identifying evolutionary processes underlying trait-environment relationships observed in natural populations. Here, we propose an expanded and refined framework based on simulations and bootstrap-based approaches, and we elaborate on an important statistical caveat common to most datasets. © 2018 John Wiley & Sons Ltd/CNRS.

Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines.

PubMed

Santangelo, James S; Johnson, Marc T J; Ness, Rob W

2018-05-16

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover ( Trifolium repens ) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation. © 2018 The Author(s).

Neoblasts and the evolution of whole-body regeneration.

PubMed

Gehrke, Andrew R; Srivastava, Mansi

2016-10-01

The molecular mechanisms underlying whole-body regeneration are best understood in the planarian flatworm Schmidtea mediterranea, where a heterogeneous population of somatic stem cells called neoblasts provides new tissue for regeneration of essentially any missing body part. Studies on Schmidtea have provided a detailed description of neoblasts and their role in regeneration, but comparatively little is known about the evolutionary history of these cells and their underlying developmental programs. Acoels, an understudied group of aquatic worms that are also capable of extensive whole-body regeneration, have arisen as an attractive group to study the evolution of regenerative processes due to their phylogenetically distant position relative to flatworms. Here, we review the phylogenetic distribution of neoblast cells and compare their anatomical locations, transcriptional profiles, and roles during regeneration in flatworms and acoels to understand the evolution of whole-body regeneration. While the general role of neoblasts appears conserved in species separated by 550 million years of evolution, the extrinsic inputs they receive during regeneration can vary, making the distinction between homology and convergence of mechanism unclear. A more detailed understanding of the precise mechanisms behind whole-body regeneration in diverse phyla is necessary to understand the evolutionary history of this powerful process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Theoretical studies in interstellar cloud chemistry

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Prasad, S. S.

1993-01-01

This final report represents the completion of the three tasks under the purchase order no. SCPDE5620,1,2F. Chemical composition of gravitationally contracting, but otherwise quiescent, interstellar clouds and of interstellar clouds traversed by high velocity shocks, were modeled in a comprehensive manner that represents a significant progress in modeling these objects. The evolutionary chemical modeling, done under this NASA contract, represents a notable advance over the 'classical' fixed condition equilibrium models because the evolutionary models consider not only the chemical processes but also the dynamical processes by which the dark interstellar clouds may have assumed their present state. The shock calculations, being reported here, are important because they extend the limited chemical composition derivable from dynamical calculations for the total density and temperature structures behind the shock front. In order to be tractable, the dynamical calculations must severely simplify the chemistry. The present shock calculations take the shock profiles from the dynamical calculations and derive chemical composition in a comprehensive manner. The results of the present modeling study are still to be analyzed with reference to astronomical observational data and other contemporary model predictions. As far as humanly possible, this analysis will be continued with CRE's (Creative Research Enterprises's) IR&D resources, until a sponsor is found.

Non-cooperative game theory in biology and cooperative reasoning in humans.

PubMed

Kabalak, Alihan; Smirnova, Elena; Jost, Jürgen

2015-06-01

The readiness for spontaneous cooperation together with the assumptions that others share this cooperativity has been identified as a fundamental feature that distinguishes humans from other animals, including the great apes. At the same time, cooperativity presents an evolutionary puzzle because non-cooperators do better in a group of cooperators. We develop here an analysis of the process leading to cooperation in terms of rationality concepts, game theory and epistemic logic. We are, however, not attempting to reconstruct the actual evolutionary process. We rather want to provide the logical structure underlying cooperation in order to understand why cooperation is possible and what kind of reasoning and beliefs would lead to cooperative decision-making. Game theory depends on an underlying common belief in non-cooperative rationality of the players, and cooperativity similarly can utilize a common belief in cooperative rationality as its basis. We suggest a weaker concept of rational decision-making in games that encompasses both types of decision-making. We build this up in stages, starting from simple optimization, then using anticipation of the reaction of others, to finally arrive at reflexive and cooperative reasoning. While each stage is more difficult than the preceding, importantly, we also identify a reduction of complexity achieved by the consistent application of higher stage reasoning.

Dynamic evolution and biogenesis of small RNAs during sex reversal.

PubMed

Liu, Jie; Luo, Majing; Sheng, Yue; Hong, Qiang; Cheng, Hanhua; Zhou, Rongjia

2015-05-06

Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.

Functional and evolutionary trade-offs co-occur between two consolidated memory phases in Drosophila melanogaster

PubMed Central

Lagasse, Fabrice; Moreno, Celine; Preat, Thomas; Mery, Frederic

2012-01-01

Memory is a complex and dynamic process that is composed of different phases. Its evolution under natural selection probably depends on a balance between fitness benefits and costs. In Drosophila, two separate forms of consolidated memory phases can be generated experimentally: anaesthesia-resistant memory (ARM) and long-term memory (LTM). In recent years, several studies have focused on the differences between these long-lasting memory types and have found that, at the functional level, ARM and LTM are antagonistic. How this functional relationship will affect their evolutionary dynamics remains unknown. We selected for flies with either improved ARM or improved LTM over several generations, and found that flies selected specifically for improvement of one consolidated memory phase show reduced performance in the other memory phase. We also found that improved LTM was linked to decreased longevity in male flies but not in females. Conversely, males with improved ARM had increased longevity. We found no correlation between either improved ARM or LTM and other phenotypic traits. This is, to our knowledge, the first evidence of a symmetrical evolutionary trade-off between two memory phases for the same learning task. Such trade-offs may have an important impact on the evolution of cognitive capacities. On a neural level, these results support the hypothesis that mechanisms underlying these forms of consolidated memory are, to some degree, antagonistic. PMID:22859595

Genetic architecture and balancing selection: the life and death of differentiated variants.

PubMed

Llaurens, Violaine; Whibley, Annabel; Joron, Mathieu

2017-05-01

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems. © 2017 John Wiley & Sons Ltd.

Experimental evidence that the Ornstein-Uhlenbeck model best describes the evolution of leaf litter decomposability

PubMed Central

Pan, Xu; Cornelissen, Johannes H C; Zhao, Wei-Wei; Liu, Guo-Fang; Hu, Yu-Kun; Prinzing, Andreas; Dong, Ming; Cornwell, William K

2014-01-01

Leaf litter decomposability is an important effect trait for ecosystem functioning. However, it is unknown how this effect trait evolved through plant history as a leaf ‘afterlife’ integrator of the evolution of multiple underlying traits upon which adaptive selection must have acted. Did decomposability evolve in a Brownian fashion without any constraints? Was evolution rapid at first and then slowed? Or was there an underlying mean-reverting process that makes the evolution of extreme trait values unlikely? Here, we test the hypothesis that the evolution of decomposability has undergone certain mean-reverting forces due to strong constraints and trade-offs in the leaf traits that have afterlife effects on litter quality to decomposers. In order to test this, we examined the leaf litter decomposability and seven key leaf traits of 48 tree species in the temperate area of China and fitted them to three evolutionary models: Brownian motion model (BM), Early burst model (EB), and Ornstein-Uhlenbeck model (OU). The OU model, which does not allow unlimited trait divergence through time, was the best fit model for leaf litter decomposability and all seven leaf traits. These results support the hypothesis that neither decomposability nor the underlying traits has been able to diverge toward progressively extreme values through evolutionary time. These results have reinforced our understanding of the relationships between leaf litter decomposability and leaf traits in an evolutionary perspective and may be a helpful step toward reconstructing deep-time carbon cycling based on taxonomic composition with more confidence. PMID:25535551

Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model.

PubMed

Mossel, Elchanan; Steel, Mike

2014-11-07

Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique - majority rule - estimates the root state by the most frequently occurring state at the leaves. Alternative methods - such as maximum parsimony - explicitly take the tree structure into account. Since either method can outperform the other on particular trees, it is useful to consider the accuracy of the methods on trees generated under some evolutionary null model, such as a Yule pure-birth model. In this short note, we answer a recently posed question concerning the performance of majority rule on Yule trees under a symmetric 2-state Markovian substitution model of character state change. We show that majority rule is accurate precisely when the ratio of the birth (speciation) rate of the Yule process to the substitution rate exceeds the value 4. By contrast, maximum parsimony has been shown to be accurate only when this ratio is at least 6. Our proof relies on a second moment calculation, coupling, and a novel application of a reflection principle. Copyright © 2014 Elsevier Ltd. All rights reserved.

Expected utility violations evolve under status-based selection mechanisms.

PubMed

Dickson, Eric S

2008-10-07

The expected utility theory of decision making under uncertainty, a cornerstone of modern economics, assumes that humans linearly weight "utilities" for different possible outcomes by the probabilities with which these outcomes occur. Despite the theory's intuitive appeal, both from normative and from evolutionary perspectives, many experiments demonstrate systematic, though poorly understood, patterns of deviation from EU predictions. This paper offers a novel theoretical account of such patterns of deviation by demonstrating that EU violations can emerge from evolutionary selection when individual "status" affects inclusive fitness. In humans, battles for resources and social standing involve high-stakes decision making, and assortative mating ensures that status matters for fitness outcomes. The paper therefore proposes grounding the study of decision making under uncertainty in an evolutionary game-theoretic framework.

Incorporating evolutionary processes into population viability models.

PubMed

Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

2015-06-01

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees.

PubMed

Rabosky, Daniel L

2014-01-01

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

PubMed Central

Rabosky, Daniel L.

2014-01-01

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes. PMID:24586858

Juvenile skeletogenesis in anciently diverged sea urchin clades.

PubMed

Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

2015-04-01

Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in situ hybridization was adapted. This method displays current gene expression in the developing test and perignathic girdle skeletal elements of both Sp and Et juveniles. Active, specific expression of the sm37 biomineralization gene in these muscle attachment structures accompanies morphogenetic development of these clade-specific features in juveniles of both species. Skeletogenesis at these clade-specific muscle attachment structures displays molecular earmarks of the well understood embryonic skeletogenic GRN: thus the upstream regulatory gene alx1 and the gene encoding the vegfR signaling receptor are both expressed at the sites where they are formed. This work opens the way to analysis of the alternative spatial specification processes that were installed at the evolutionary divergence of the two extant subclasses of sea urchins. Copyright © 2015 Elsevier Inc. All rights reserved.

The evolution of cooperation by negotiation in a noisy world.

PubMed

Ito, K; McNamara, J M; Yamauchi, A; Higginson, A D

2017-03-01

Cooperative interactions among individuals are ubiquitous despite the possibility of exploitation by selfish free riders. One mechanism that may promote cooperation is 'negotiation': individuals altering their behaviour in response to the behaviour of others. Negotiating individuals decide their actions through a recursive process of reciprocal observation, thereby reducing the possibility of free riding. Evolutionary games with response rules have shown that infinitely many forms of the rule can be evolutionarily stable simultaneously, unless there is variation in individual quality. This potentially restricts the conditions under which negotiation could maintain cooperation. Organisms interact with one another in a noisy world in which cooperative effort and the assessment of effort may be subject to error. Here, we show that such noise can make the number of evolutionarily stable rules finite, even without quality variation, and so noise could help maintain cooperative behaviour. We show that the curvature of the benefit function is the key factor determining whether individuals invest more or less as their partner's investment increases, investing less when the benefit to investment has diminishing returns. If the benefits of low investment are very small then behavioural flexibility tends to promote cooperation, because negotiation enables cooperators to reach large benefits. Under some conditions, this leads to a repeating cycle in which cooperative behaviour rises and falls over time, which may explain between-population differences in cooperative behaviour. In other conditions, negotiation leads to extremely high levels of cooperative behaviour, suggesting that behavioural flexibility could facilitate the evolution of eusociality in the absence of high relatedness. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

The Design and Transformation of Biofundamentals: A Nonsurvey Introductory Evolutionary and Molecular Biology Course.

PubMed

Klymkowsky, Michael W; Rentsch, Jeremy D; Begovic, Emina; Cooper, Melanie M

2016-01-01

Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master. The original Web-based course's design presaged many of the recommendations of the Vision and Change report; in particular, a focus on social evolutionary mechanisms, stochastic (evolutionary and molecular) processes, and core ideas (cellular continuity, evolutionary homology, molecular interactions, coupled chemical reactions, and molecular machines). Inspired by insights from the Chemistry, Life, the Universe & Everything general chemistry project, we transformed the original Web version into a (freely available) book with a more unified narrative flow and a set of formative assessments delivered through the beSocratic system. We outline how student responses to course materials are guiding future course modifications, in particular a more concerted effort at helping students to construct logical, empirically based arguments, explanations, and models. © 2016 M. W. Klymkowsky et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Evolution of fairness and coalition formation in three-person ultimatum games.

PubMed

Nishimura, Takeshi; Okada, Akira; Shirata, Yasuhiro

2017-05-07

We consider the evolution of fairness and coalition formation in a three-person ultimatum game in which the coalition value depends on its size. Traditional game theory, which assumes selfish and rational players, predicts the largest and efficient coalition with a proposer exploiting most of the total value. In a stochastic evolutionary model (the frequency-dependent Moran process with mutations) where players make errors in estimating the payoffs and strategies of others, evolutionary selection favors the formation of a two-person subcoalition under weak selection and in the low mutation limit if and only if its coalition value exceeds a high proportion (0.7) of that of the largest coalition. Proposers offer 30-35% of the subcoalition value to a coalition member, excluding a non-member. Multilateral bargaining is critically different from the bilateral one. Coalition-forming behavior may cause economic inefficiency and social exclusion. Stochastic evolutionary game theory thus provides theoretical support to explain the behavior of human subjects in economic experiments of a three-person ultimatum game. Copyright © 2017 Elsevier Ltd. All rights reserved.

Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system.

PubMed

Solbakken, Monica Hongrø; Voje, Kjetil Lysne; Jakobsen, Kjetill Sigurd; Jentoft, Sissel

2017-04-26

Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor ( TLR ) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions. In the order of Gadiformes, expansions correlate with the loss of major histocompatibility complex class II ( MHCII ) and diversifying selection analyses support that this has fostered new immunological innovations in TLR s within this lineage. In teleosts overall, TLRs expansions correlate with species latitudinal distributions and maximum depth. By contrast, lineage-specific gene losses overlap with well-described changes in palaeoclimate (global ocean anoxia) and past Atlantic Ocean geography. In conclusion, we suggest that the evolvability of the teleost immune system has most likely played a prominent role in the survival and successful radiation of this lineage. © 2017 The Authors.

Head shape evolution in Gymnophthalmidae: does habitat use constrain the evolution of cranial design in fossorial lizards?

PubMed

Barros, F C; Herrel, A; Kohlsdorf, T

2011-11-01

Habitat usage comprises interactions between ecological parameters and organismal capacities, and the selective pressures that ultimately determine the outcome of such processes in an evolutionary scale may be conflicting when the same morphological structure is recruited for different activities. Here, we investigate the roles of diet and locomotion in the evolution of cranial design in gymnophthalmid lizards and test the hypothesis that microhabitat use drives head shape evolution, particularly in head-first burrowers. Morphological factors were analysed in relation to continuous ecological indexes (prey hardness and substrate compactness) using conventional and phylogenetic approaches. Results suggest that the evolution of head morphology in Gymnophthalmidae was shaped under the influence of microhabitat use rather than diet: burrowers have shorter heads with lower rostral angulation, independently of the prey consumed. Food preferences appear to be relatively conserved throughout the phylogeny of the group, which may have permitted the extensive radiation of gymnophthalmids into fossorial microhabitats. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Universal scaling in the branching of the tree of life.

PubMed

Herrada, E Alejandro; Tessone, Claudio J; Klemm, Konstantin; Eguíluz, Víctor M; Hernández-García, Emilio; Duarte, Carlos M

2008-07-23

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants1[W][OA

PubMed Central

Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua; Gao, Li-zhi

2013-01-01

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs. PMID:23396833

Squamate hatchling size and the evolutionary causes of negative offspring size allometry.

PubMed

Meiri, S; Feldman, A; Kratochvíl, L

2015-02-01

Although fecundity selection is ubiquitous, in an overwhelming majority of animal lineages, small species produce smaller number of offspring per clutch. In this context, egg, hatchling and neonate sizes are absolutely larger, but smaller relative to adult body size in larger species. The evolutionary causes of this widespread phenomenon are not fully explored. The negative offspring size allometry can result from processes limiting maximal egg/offspring size forcing larger species to produce relatively smaller offspring ('upper limit'), or from a limit on minimal egg/offspring size forcing smaller species to produce relatively larger offspring ('lower limit'). Several reptile lineages have invariant clutch sizes, where females always lay either one or two eggs per clutch. These lineages offer an interesting perspective on the general evolutionary forces driving negative offspring size allometry, because an important selective factor, fecundity selection in a single clutch, is eliminated here. Under the upper limit hypotheses, large offspring should be selected against in lineages with invariant clutch sizes as well, and these lineages should therefore exhibit the same, or shallower, offspring size allometry as lineages with variable clutch size. On the other hand, the lower limit hypotheses would allow lineages with invariant clutch sizes to have steeper offspring size allometries. Using an extensive data set on the hatchling and female sizes of > 1800 species of squamates, we document that negative offspring size allometry is widespread in lizards and snakes with variable clutch sizes and that some lineages with invariant clutch sizes have unusually steep offspring size allometries. These findings suggest that the negative offspring size allometry is driven by a constraint on minimal offspring size, which scales with a negative allometry. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Algorithmic Mechanism Design of Evolutionary Computation.

PubMed

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.

Algorithmic Mechanism Design of Evolutionary Computation

PubMed Central

2015-01-01

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

THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL*

PubMed Central

Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

2014-01-01

Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

Evolutionary change in physiological phenotypes along the human lineage.

PubMed

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.

Niche construction theory: a practical guide for ecologists.

PubMed

Odling-Smee, John; Erwin, Douglas H; Palkovacs, Eric P; Feldman, Marcus W; Laland, Kevin N

2013-03-01

Niche construction theory (NCT) explicitly recognizes environmental modication by organisms ("niche construction") and their legacy overtime ("ecological inheritance") to be evolutionary processes in their own right. Here we illustrate how niche construction theory provides usedl conceptual tools and theoretical insights for integrating ecosystem ecology and evolutionary theory. We begin by briefly describing NCT, and illustrating how it deifers from conventional evolutionary approaches. We then distinguish between two aspects ofniche construction--environment alteration and subsequent evolution in response to constructed environments--equating the first of these with "ecosystem engineering." We describe some of the ecological and evolutionary impacts on ecosystems of niche construction, ecosystem engineering and ecological inheritance, and illustrate how these processes trigger ecological and evolutionary feedbacks and leave detectable ecological signatures that are open to investigation. FIinally, we provide a practical guide to how NCT could be deployed by ecologists and evolutionary biologists to aeplore ecoeoolutionay dynamics. We suggest that, by highlighting the ecological and evolutionay ramifications of changes that organisms bring about in ecosystems, NCT helps link ecosystem ecology to evolutionary biology, potentially leading to a deeper understanding of how ecosystems change over time.

Commentary: Should Gender Differences Be Included in the Evolutionary Upgrade to Cognitive Load Theory?

ERIC Educational Resources Information Center

Bevilacqua, Andy

2017-01-01

Recent upgrades to cognitive load theory suggest that evolutionary processes have shaped the way that working memory processes cultural and social information. According to evolutionarily educational psychologists, some forms of information are processed with lower working memory loads than other forms. The former are evolutionarily salient and…

Using Loop Heat Pipes to Minimize Survival Heater Power for NASA's Evolutionary Xenon Thruster Power Processing Units

NASA Technical Reports Server (NTRS)

Choi, Michael K.

2017-01-01

A thermal design concept of using propylene loop heat pipes to minimize survival heater power for NASA's Evolutionary Xenon Thruster power processing units is presented. It reduces the survival heater power from 183 W to 35 W per power processing unit. The reduction is 81%.

The Evolutionary Process of Secondary Innovation in the Context of Globalization: A Case Study

ERIC Educational Resources Information Center

Wu, Xiaobo; Xu, Guannan; Ma, Rufei; Du, Jian

2008-01-01

This paper examines the evolutionary process of secondary innovation in a typical Chinese equipment manufacturing firm in the context of globalization and elaborates how to achieve latecomer's advantage from imitation to innovation. Four stages are identified in the process of international manufacturing: the equipment import stage, the production…

Barnacle cement: a polymerization model based on evolutionary concepts

PubMed Central

Dickinson, Gary H.; Vega, Irving E.; Wahl, Kathryn J.; Orihuela, Beatriz; Beyley, Veronica; Rodriguez, Eva N.; Everett, Richard K.; Bonaventura, Joseph; Rittschof, Daniel

2009-01-01

Summary Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. PMID:19837892

Advanced evolutionary molecular engineering to produce thermostable cellulase by using a small but efficient library.

PubMed

Ito, Y; Ikeuchi, A; Imamura, C

2013-01-01

We aimed at constructing thermostable cellulase variants of cellobiohydrolase II, derived from the mesophilic fungus Phanerochaete chrysosporium, by using an advanced evolutionary molecular engineering method. By aligning the amino acid sequences of the catalytic domains of five thermophilic fungal CBH2 and PcCBH2 proteins, we identified 45 positions where the PcCBH2 genes differ from the consensus sequence of two to five thermophilic fungal CBH2s. PcCBH2 variants with the consensus mutations were obtained by a cell-free translation system that was chosen for easy evaluation of thermostability. From the small library of consensus mutations, advantageous mutations for improving thermostability were found to occur with much higher frequency relative to a random library. To further improve thermostability, advantageous mutations were accumulated within the wild-type gene. Finally, we obtained the most thermostable variant Mall4, which contained all 15 advantageous mutations found in this study. This variant had the same specific cellulase activity as the wild type and retained sufficient activity at 50°C for >72 h, whereas wild-type PcCBH2 retained much less activity under the same conditions. The history of the accumulation process indicated that evolution of PcCBH2 toward improved thermostability was ideally and rapidly accomplished through the evolutionary process employed in this study.

Incorporating Eco-Evolutionary Processes into Population Models:Design and Applications

EPA Science Inventory

Eco-evolutionary population models are powerful new tools for exploring howevolutionary processes influence plant and animal population dynamics andvice-versa. The need to manage for climate change and other dynamicdisturbance regimes is creating a demand for the incorporation of...

NexGen PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

EPA Science Inventory

We examine how the integration of evolutionary and ecological processes in population dynamics – an emerging framework in ecology – could be incorporated into population viability analysis (PVA). Driven by parallel, complementary advances in population genomics and computational ...

Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

PubMed

McNamara, K B; Simmons, L W

2017-09-01

Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Why an extended evolutionary synthesis is necessary

PubMed Central

2017-01-01

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology. PMID:28839929

Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage

PubMed Central

2011-01-01

Background Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura) and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei) exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage. Results A phylogeny was constructed for Trichomycterus areolatus under the following best-fit molecular models of evolution GTR + I + R, HKY + I, and HKY for cytochrome b, growth hormone, and rag 1 respectively. A GTR + I + R model provided the best fit for both 28S and mitochondrial loci and was used to construct both Aegla phylogenies. Three different diversification models were observed and the three groups arose during different time periods, from 2.25 to 5.05 million years ago (Ma). Cladogenesis within Trichomycterus areolatus was initiated roughly 2.25 Ma (Late Pliocene - Early Pleistocene) some 1.7 - 2.8 million years after the basal divergences observed in both Aegla clades. These results reject the hypothesis of codivergence. Conclusions The similar genetic distances between terminal sister-lineages observed in these select taxa from the freshwater Chilean species assemblage were formed by different processes occurring over the last ~5.0 Ma. Dramatic changes in historic sea levels documented in the region appear to have independently shaped the evolutionary history of each group. Our study illustrates the important role that history plays in shaping a species assemblage and argues against assuming similar patterns equal a shared evolutionary history. PMID:22118288

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

PubMed Central

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

2014-01-01

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation. PMID:24699231

Evolutionary innovation and diversification of carotenoid-based pigmentation in finches.

PubMed

Ligon, Russell A; Simpson, Richard K; Mason, Nicholas A; Hill, Geoffrey E; McGraw, Kevin J

2016-12-01

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary "innovation" that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes-where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved-supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Hybridization affects life-history traits and host specificity in Diorhabda spp

USDA-ARS?s Scientific Manuscript database

Hybridization is an influential evolutionary process that has been viewed alternatively as an evolutionary dead-end or as an important creative evolutionary force. In colonizing species, such as introduced biological control agents, hybridization can negate the effects of bottlenecks and genetic dri...

Simulating natural selection in landscape genetics

Treesearch

E. L. Landguth; S. A. Cushman; N. Johnson

2012-01-01

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

PubMed

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Macro-evolutionary studies of cultural diversity: a review of empirical studies of cultural transmission and cultural adaptation.

PubMed

Mace, Ruth; Jordan, Fiona M

2011-02-12

A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity.

Tropical grassy biomes: misunderstood, neglected, and under threat.

PubMed

Parr, Catherine L; Lehmann, Caroline E R; Bond, William J; Hoffmann, William A; Andersen, Alan N

2014-04-01

Tropical grassy biomes (TGBs) are globally extensive, provide critical ecosystem services, and influence the earth-atmosphere system. Yet, globally applied biome definitions ignore vegetation characteristics that are critical to their functioning and evolutionary history. Hence, TGB identification is inconsistent and misinterprets the ecological processes governing vegetation structure, with cascading negative consequences for biodiversity. Here, we discuss threats linked to the definition of TGB, the Clean Development Mechanism (CDM) and Reducing Emissions from Deforestation and Forest Degradation schemes (REDD+), and enhanced atmospheric CO2, which may facilitate future state shifts. TGB degradation is insidious and less visible than in forested biomes. With human reliance on TGBs and their propensity for woody change, ecology and evolutionary history are fundamental to not only the identification of TGBs, but also their management for future persistence. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessing the benefits and risks of translocations in changing environments: a genetic perspective

PubMed Central

Weeks, Andrew R; Sgro, Carla M; Young, Andrew G; Frankham, Richard; Mitchell, Nicki J; Miller, Kim A; Byrne, Margaret; Coates, David J; Eldridge, Mark D B; Sunnucks, Paul; Breed, Martin F; James, Elizabeth A; Hoffmann, Ary A

2011-01-01

Translocations are being increasingly proposed as a way of conserving biodiversity, particularly in the management of threatened and keystone species, with the aims of maintaining biodiversity and ecosystem function under the combined pressures of habitat fragmentation and climate change. Evolutionary genetic considerations should be an important part of translocation strategies, but there is often confusion about concepts and goals. Here, we provide a classification of translocations based on specific genetic goals for both threatened species and ecological restoration, separating targets based on ‘genetic rescue’ of current population fitness from those focused on maintaining adaptive potential. We then provide a framework for assessing the genetic benefits and risks associated with translocations and provide guidelines for managers focused on conserving biodiversity and evolutionary processes. Case studies are developed to illustrate the framework. PMID:22287981

Macro-evolutionary studies of cultural diversity: a review of empirical studies of cultural transmission and cultural adaptation

PubMed Central

Mace, Ruth; Jordan, Fiona M.

2011-01-01

A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity. PMID:21199844

Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

PubMed

Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

2016-07-29

Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions. Copyright © 2016, American Association for the Advancement of Science.

Metabolic rate and climatic fluctuations shape continental wide pattern of genetic divergence and biodiversity in fishes.

PubMed

April, Julien; Hanner, Robert H; Mayden, Richard L; Bernatchez, Louis

2013-01-01

Taxonomically exhaustive and continent wide patterns of genetic divergence within and between species have rarely been described and the underlying evolutionary causes shaping biodiversity distribution remain contentious. Here, we show that geographic patterns of intraspecific and interspecific genetic divergence among nearly all of the North American freshwater fish species (>750 species) support a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence and very likely influencing speciation rates. Results indicate that the recurrent glacial cycles caused global reduction in intraspecific diversity, interspecific genetic divergence, and species richness at higher latitudes. At the opposite, longer geographic isolation, higher metabolic rate increasing substitution rate and possibly the rapid accumulation of genetic incompatibilities, led to an increasing biodiversity towards lower latitudes. This indicates that both intrinsic and extrinsic factors similarly affect micro and macro evolutionary processes shaping global patterns of biodiversity distribution. These results also indicate that factors favouring allopatric speciation are the main drivers underlying the diversification of North American freshwater fishes.

Metabolic Rate and Climatic Fluctuations Shape Continental Wide Pattern of Genetic Divergence and Biodiversity in Fishes

PubMed Central

April, Julien; Hanner, Robert H.; Mayden, Richard L.; Bernatchez, Louis

2013-01-01

Taxonomically exhaustive and continent wide patterns of genetic divergence within and between species have rarely been described and the underlying evolutionary causes shaping biodiversity distribution remain contentious. Here, we show that geographic patterns of intraspecific and interspecific genetic divergence among nearly all of the North American freshwater fish species (>750 species) support a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence and very likely influencing speciation rates. Results indicate that the recurrent glacial cycles caused global reduction in intraspecific diversity, interspecific genetic divergence, and species richness at higher latitudes. At the opposite, longer geographic isolation, higher metabolic rate increasing substitution rate and possibly the rapid accumulation of genetic incompatibilities, led to an increasing biodiversity towards lower latitudes. This indicates that both intrinsic and extrinsic factors similarly affect micro and macro evolutionary processes shaping global patterns of biodiversity distribution. These results also indicate that factors favouring allopatric speciation are the main drivers underlying the diversification of North American freshwater fishes. PMID:23922969

Towards a richer evolutionary game theory

PubMed Central

McNamara, John M.

2013-01-01

Most examples of the application of evolutionary game theory to problems in biology involve highly simplified models. I contend that it is time to move on and include much more richness in models. In particular, more thought needs to be given to the importance of (i) between-individual variation; (ii) the interaction between individuals, and hence the process by which decisions are reached; (iii) the ecological and life-history context of the situation; (iv) the traits that are under selection, and (v) the underlying psychological mechanisms that lead to behaviour. I give examples where including variation between individuals fundamentally changes predicted outcomes of a game. Variation also selects for real-time responses, again resulting in changed outcomes. Variation can select for other traits, such as choosiness and social sensitivity. More generally, many problems involve coevolution of more than one trait. I identify situations where a reductionist approach, in which a game is isolated from is ecological setting, can be misleading. I also highlight the need to consider flexibility of behaviour, mental states and other issues concerned with the evolution of mechanism. PMID:23966616

Mosaic evolution and adaptive brain component alteration under domestication seen on the background of evolutionary theory.

PubMed

Rehkämper, Gerd; Frahm, Heiko D; Cnotka, Julia

2008-01-01

Brain sizes and brain component sizes of five domesticated pigeon breeds including homing (racing) pigeons are compared with rock doves (Columba livia) based on an allometric approach to test the influence of domestication on brain and brain component size. Net brain volume, the volumes of cerebellum and telencephalon as a whole are significantly smaller in almost all domestic pigeons. Inside the telencephalon, mesopallium, nidopallium (+ entopallium + arcopallium) and septum are smaller as well. The hippocampus is significantly larger, particularly in homing pigeons. This finding is in contrast to the predictions of the 'regression hypothesis' of brain alteration under domestication. Among the domestic pigeons homing pigeons have significantly larger olfactory bulbs. These data are interpreted as representing a functional adaptation to homing that is based on spatial cognition and sensory integration. We argue that domestication as seen in domestic pigeons is not principally different from evolution in the wild, but represents a heuristic model to understand the evolutionary process in terms of adaptation and optimization. Copyright 2007 S. Karger AG, Basel.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

PubMed

Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

2012-09-15

Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

Evolutionary Nephrology.

PubMed

Chevalier, Robert L

2017-05-01

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

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

The Growth of Developmental Thought: Implications for a New Evolutionary Psychology

PubMed Central

Lickliter, Robert

2009-01-01

Evolution has come to be increasingly discussed in terms of changes in developmental processes rather than simply in terms of changes in gene frequencies. This shift is based in large part on the recognition that since all phenotypic traits arise during ontogeny as products of individual development, a primary basis for evolutionary change must be variations in the patterns and processes of development. Further, the products of development are epigenetic, not just genetic, and this is the case even when considering the evolutionary process. These insights have led investigators to reconsider the established notion of genes as the primary cause of development, opening the door to research programs focused on identifying how genetic and non-genetic factors coact to guide and constrain the process of development and its outcomes. I explore this growth of developmental thought and its implications for the achievement of a unified theory of heredity, development, and evolution and consider its implications for the realization of a new, developmentally-based evolutionary psychology. PMID:19956346

Testing for Independence between Evolutionary Processes.

PubMed

Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

2016-09-01

Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bottleneck Effect on Evolutionary Rate in the Nearly Neutral Mutation Model

PubMed Central

Araki, H.; Tachida, H.

1997-01-01

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N(1) and N(2) (N(1) > N(2)), in the simulations. The overdispersion is observed if 2N(2)σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock. PMID:9335622

Temperature-Dependent Sex Determination under Rapid Anthropogenic Environmental Change: Evolution at a Turtle's Pace?

PubMed

Refsnider, Jeanine M; Janzen, Fredric J

2016-01-01

Organisms become adapted to their environment by evolving through natural selection, a process that generally transpires over many generations. Currently, anthropogenically driven environmental changes are occurring orders of magnitude faster than they did prior to human influence, which could potentially outpace the ability of some organisms to adapt. Here, we focus on traits associated with temperature-dependent sex determination (TSD), a classic polyphenism, in a model turtle species to address the evolutionary potential of species with TSD to respond to rapid climate change. We show, first, that sex-ratio outcomes in species with TSD are sensitive to climatic variation. We then identify the evolutionary potential, in terms of heritability, of TSD and quantify the evolutionary potential of 3 key traits involved in TSD: pivotal temperature, maternal nest-site choice, and nesting phenology. We find that these traits display different patterns of adaptive potential: pivotal temperature exhibits moderate heritable variation, whereas nest-site choice and nesting phenology, with considerable phenotypic plasticity, have only modest evolutionary potential to alter sex ratios. Therefore, the most likely response of species with TSD to anthropogenically induced climate change may be a combination of microevolution in thermal sensitivity of the sex-determining pathway and of plasticity in maternal nesting behavior. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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.

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

PubMed Central

Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

2016-01-01

The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

The niche construction perspective: a critical appraisal.

PubMed

Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

2014-05-01

Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). © 2013 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Evolutionary Theory under Fire.

ERIC Educational Resources Information Center

Lewin, Roger

1980-01-01

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

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

PubMed

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

2018-04-01

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

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

PubMed

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.

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

PubMed

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.

Environmental quality and evolutionary potential: lessons from wild populations

PubMed Central

Charmantier, Anne; Garant, Dany

2005-01-01

An essential requirement to determine a population's potential for evolutionary change is to quantify the amount of genetic variability expressed for traits under selection. Early investigations in laboratory conditions showed that the magnitude of the genetic and environmental components of phenotypic variation can change with environmental conditions. However, there is no consensus as to how the expression of genetic variation is sensitive to different environmental conditions. Recently, the study of quantitative genetics in the wild has been revitalized by new pedigree analyses based on restricted maximum likelihood, resulting in a number of studies investigating these questions in wild populations. Experimental manipulation of environmental quality in the wild, as well as the use of naturally occurring favourable or stressful environments, has broadened the treatment of different taxa and traits. Here, we conduct a meta-analysis on recent studies comparing heritability in favourable versus unfavourable conditions in non-domestic and non-laboratory animals. The results provide evidence for increased heritability in more favourable conditions, significantly so for morphometric traits but not for traits more closely related to fitness. We discuss how these results are explained by underlying changes in variance components, and how they represent a major step in our understanding of evolutionary processes in wild populations. We also show how these trends contrast with the prevailing view resulting mainly from laboratory experiments on Drosophila. Finally, we underline the importance of taking into account the environmental variation in models predicting quantitative trait evolution. PMID:16011915

Rooting phylogenetic trees under the coalescent model using site pattern probabilities.

PubMed

Tian, Yuan; Kubatko, Laura

2017-12-19

Phylogenetic tree inference is a fundamental tool to estimate ancestor-descendant relationships among different species. In phylogenetic studies, identification of the root - the most recent common ancestor of all sampled organisms - is essential for complete understanding of the evolutionary relationships. Rooted trees benefit most downstream application of phylogenies such as species classification or study of adaptation. Often, trees can be rooted by using outgroups, which are species that are known to be more distantly related to the sampled organisms than any other species in the phylogeny. However, outgroups are not always available in evolutionary research. In this study, we develop a new method for rooting species tree under the coalescent model, by developing a series of hypothesis tests for rooting quartet phylogenies using site pattern probabilities. The power of this method is examined by simulation studies and by application to an empirical North American rattlesnake data set. The method shows high accuracy across the simulation conditions considered, and performs well for the rattlesnake data. Thus, it provides a computationally efficient way to accurately root species-level phylogenies that incorporates the coalescent process. The method is robust to variation in substitution model, but is sensitive to the assumption of a molecular clock. Our study establishes a computationally practical method for rooting species trees that is more efficient than traditional methods. The method will benefit numerous evolutionary studies that require rooting a phylogenetic tree without having to specify outgroups.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

PubMed

Badyaev, Alexander V; Morrison, Erin S; Belloni, Virginia; Sanderson, Michael J

2015-08-20

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness - the ability to synthesize the same carotenoid from an additional dietary starting point. We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage's metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration. The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

A theoretical comparison of evolutionary algorithms and simulated annealing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, W.E.

1995-08-28

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

Allostatic load and comorbidities: A mitochondrial, epigenetic, and evolutionary perspective.

PubMed

Juster, Robert-Paul; Russell, Jennifer J; Almeida, Daniel; Picard, Martin

2016-11-01

Stress-related pathophysiology drives comorbid trajectories that elude precise prediction. Allostatic load algorithms that quantify biological "wear and tear" represent a comprehensive approach to detect multisystemic disease processes of the mind and body. However, the multiple morbidities directly or indirectly related to stress physiology remain enigmatic. Our aim in this article is to propose that biological comorbidities represent discrete pathophysiological processes captured by measuring allostatic load. This has applications in research and clinical settings to predict physical and psychiatric comorbidities alike. The reader will be introduced to the concepts of allostasis, allostasic states, allostatic load, and allostatic overload as they relate to stress-related diseases and the proposed prediction of biological comorbidities that extend rather to understanding psychopathologies. In our transdisciplinary discussion, we will integrate perspectives related to (a) mitochondrial biology as a key player in the allostatic load time course toward diseases that "get under the skin and skull"; (b) epigenetics related to child maltreatment and biological embedding that shapes stress perception throughout lifespan development; and (c) evolutionary drivers of distinct personality profiles and biobehavioral patterns that are linked to dimensions of psychopathology.

Tinkering: a conceptual and historical evaluation.

PubMed

Laubichler, Manfred D

2007-01-01

Francois Jacob's article 'Evolution and Tinkering' published in Science in 1977 is still the locus classicus for the concept of tinkering in biology. It first introduced the notion of tinkering to a wide audience of scientists. Jacob drew on a variety of different sources ranging from molecular biology to evolutionary biology and cultural anthropology. The notion of tinkering, or more accurately, the concept of bricolage, are conceptual abstractions that allow for the theoretical analysis of a wide range of phenomena that are united by a shared underlying process--tinkering, or the opportunistic rearrangement and recombination of existing elements. This paper looks at Jacob's analysis as itself an example of conceptual tinkering. It traces the history of some of its elements and sketches how it has become part of an inclusive discourse of theoretical biology and evolutionary developmental biology that emerged over the last 30 years. I will argue that the theoretical power of Jacob's analysis lies in the fact that he captured a widespread phenomenon. His conceptual analysis is thus an example of an interdisciplinary synthesis that is based on a shared process rather than a shared object.

Ecological and evolutionary processes at expanding range margins.

PubMed

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.

Open Issues in Evolutionary Robotics.

PubMed

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

2016-01-01

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

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

PubMed

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.

Stochastic eco-evolutionary model of a prey-predator community.

PubMed

Costa, Manon; Hauzy, Céline; Loeuille, Nicolas; Méléard, Sylvie

2016-02-01

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.

The major synthetic evolutionary transitions.

PubMed

Solé, Ricard

2016-08-19

Evolution is marked by well-defined events involving profound innovations that are known as 'major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These 'synthetic' transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Author(s).

The major synthetic evolutionary transitions

PubMed Central

Solé, Ricard

2016-01-01

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

Mouse Models as Predictors of Human Responses: Evolutionary Medicine.

PubMed

Uhl, Elizabeth W; Warner, Natalie J

Mice offer a number of advantages and are extensively used to model human diseases and drug responses. Selective breeding and genetic manipulation of mice have made many different genotypes and phenotypes available for research. However, in many cases, mouse models have failed to be predictive. Important sources of the prediction problem have been the failure to consider the evolutionary basis for species differences, especially in drug metabolism, and disease definitions that do not reflect the complexity of gene expression underlying disease phenotypes. Incorporating evolutionary insights into mouse models allow for unique opportunities to characterize the effects of diet, different gene expression profiles, and microbiomics underlying human drug responses and disease phenotypes.

Historical change and evolutionary theory.

PubMed

Masters, Roger D

2007-09-01

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

Theories of Evolution, Science (Experimental): 5315.42.

ERIC Educational Resources Information Center

Adams, Joseph P.

This is an in-depth course of study of the historical attempts to explain the evolutionary process and of recent developments pertinent to the study of biomedical evolution. Topics included in the module are: (1) ancient concepts of the evolutionary process; (2) various aspects of Lamarckism, Darwinism and neo-Darwinism, including substantiating…

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

NASA Astrophysics Data System (ADS)

Lin, XuXun; Yuan, PengCheng

2018-01-01

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

How Cultural Evolutionary Theory Can Inform Social Psychology and Vice Versa

ERIC Educational Resources Information Center

Mesoudi, Alex

2009-01-01

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…

Match Fitness: Development, Evolution, and Behavior--Comment on Frankenhuis and Del Giudice (2012)

ERIC Educational Resources Information Center

Gluckman, Peter D.; Beedle, Alan S.

2012-01-01

The application of evolutionary thinking to human physical and psychological medicine suggests several pathways through which evolutionary processes affect risk of disease. Among these is the concept of mismatch between an individual and its environment, either because the environment has changed for the whole species ("evolutionary novelty") or…

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

ERIC Educational Resources Information Center

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…

Genetics of dispersal.

PubMed

Saastamoinen, Marjo; Bocedi, Greta; Cote, Julien; Legrand, Delphine; Guillaume, Frédéric; Wheat, Christopher W; Fronhofer, Emanuel A; Garcia, Cristina; Henry, Roslyn; Husby, Arild; Baguette, Michel; Bonte, Dries; Coulon, Aurélie; Kokko, Hanna; Matthysen, Erik; Niitepõld, Kristjan; Nonaka, Etsuko; Stevens, Virginie M; Travis, Justin M J; Donohue, Kathleen; Bullock, James M; Del Mar Delgado, Maria

2018-02-01

Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Genetics of dispersal

PubMed Central

Bocedi, Greta; Cote, Julien; Legrand, Delphine; Guillaume, Frédéric; Wheat, Christopher W.; Fronhofer, Emanuel A.; Garcia, Cristina; Henry, Roslyn; Husby, Arild; Baguette, Michel; Bonte, Dries; Coulon, Aurélie; Kokko, Hanna; Matthysen, Erik; Niitepõld, Kristjan; Nonaka, Etsuko; Stevens, Virginie M.; Travis, Justin M. J.; Donohue, Kathleen; Bullock, James M.; del Mar Delgado, Maria

2017-01-01

ABSTRACT Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits. PMID:28776950

Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples

PubMed Central

Koch, Marcus A.; German, Dmitry A.

2013-01-01

Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella. PMID:23914192

Empirical verification of evolutionary theories of aging.

PubMed

Kyryakov, Pavlo; Gomez-Perez, Alejandra; Glebov, Anastasia; Asbah, Nimara; Bruno, Luigi; Meunier, Carolynne; Iouk, Tatiana; Titorenko, Vladimir I

2016-10-25

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

Evolution and behavioural responses to human-induced rapid environmental change

PubMed Central

Sih, Andrew; Ferrari, Maud C O; Harris, David J

2011-01-01

Almost all organisms live in environments that have been altered, to some degree, by human activities. Because behaviour mediates interactions between an individual and its environment, the ability of organisms to behave appropriately under these new conditions is crucial for determining their immediate success or failure in these modified environments. While hundreds of species are suffering dramatically from these environmental changes, others, such as urbanized and pest species, are doing better than ever. Our goal is to provide insights into explaining such variation. We first summarize the responses of some species to novel situations, including novel risks and resources, habitat loss/fragmentation, pollutants and climate change. Using a sensory ecology approach, we present a mechanistic framework for predicting variation in behavioural responses to environmental change, drawing from models of decision-making processes and an understanding of the selective background against which they evolved. Where immediate behavioural responses are inadequate, learning or evolutionary adaptation may prove useful, although these mechanisms are also constrained by evolutionary history. Although predicting the responses of species to environmental change is difficult, we highlight the need for a better understanding of the role of evolutionary history in shaping individuals’ responses to their environment and provide suggestion for future work. PMID:25567979

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Evolution and behavioural responses to human-induced rapid environmental change.

PubMed

Sih, Andrew; Ferrari, Maud C O; Harris, David J

2011-03-01

Almost all organisms live in environments that have been altered, to some degree, by human activities. Because behaviour mediates interactions between an individual and its environment, the ability of organisms to behave appropriately under these new conditions is crucial for determining their immediate success or failure in these modified environments. While hundreds of species are suffering dramatically from these environmental changes, others, such as urbanized and pest species, are doing better than ever. Our goal is to provide insights into explaining such variation. We first summarize the responses of some species to novel situations, including novel risks and resources, habitat loss/fragmentation, pollutants and climate change. Using a sensory ecology approach, we present a mechanistic framework for predicting variation in behavioural responses to environmental change, drawing from models of decision-making processes and an understanding of the selective background against which they evolved. Where immediate behavioural responses are inadequate, learning or evolutionary adaptation may prove useful, although these mechanisms are also constrained by evolutionary history. Although predicting the responses of species to environmental change is difficult, we highlight the need for a better understanding of the role of evolutionary history in shaping individuals' responses to their environment and provide suggestion for future work.

Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy.

PubMed

Bowen, B W

1999-12-01

The scientific foundations of conservation policy are the subject of a recent tripolar debate, with systematists arguing for the primacy of phylogenetic rankings, ecologists arguing for protection at the level of populations or ecosystems, and evolutionary biologists urging more attention for the factors that enhance adaptation and biodiversity. In the field of conservation genetics, this controversy is manifested in the diverse viewpoints of molecular systematists, population biologists, and evolutionary (and quantitative) geneticists. A resolution of these viewpoints is proposed here, based on the premise that preserving particular objects (genes, species, or ecosystems) is not the ultimate goal of conservation. In order to be successful, conservation efforts must preserve the processes of life. This task requires the identification and protection of diverse branches in the tree of life (phylogenetics), the maintenance of life-support systems for organisms (ecology), and the continued adaptation of organisms to changing environments (evolution). None of these objectives alone is sufficient to preserve the threads of life across time. Under this temporal perspective, molecular genetic technologies have applications in all three conservation agendas; DNA sequence comparisons serve the phylogenetic goals, population genetic markers serve the ecological goals, quantitative genetics and genome explorations serve the evolutionary goals.

Evolutionary response of landraces to climate change in centers of crop diversity

PubMed Central

Mercer, Kristin L; Perales, Hugo R

2010-01-01

Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource. PMID:25567941

Evolutionary response of landraces to climate change in centers of crop diversity.

PubMed

Mercer, Kristin L; Perales, Hugo R

2010-09-01

Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource.

Sixty-Five Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders.

PubMed

Barnes, Richard; Clark, Adam Thomas

2017-07-01

For many taxa and systems, species richness peaks at midelevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary midelevation regions. To test this hypothesis, we use records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to midelevation bands by using the model to predict plethodontid evolutionary history and contemporary geographic distributions. Our results show that models that incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.

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

PubMed

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

2015-07-01

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

Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses.

PubMed

Pedersen, Casper-Emil T; Frandsen, Peter; Wekesa, Sabenzia N; Heller, Rasmus; Sangula, Abraham K; Wadsworth, Jemma; Knowles, Nick J; Muwanika, Vincent B; Siegismund, Hans R

2015-01-01

With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined.

PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees

PubMed Central

Lee, Bongshin; Nachmanson, Lev; Robertson, George; Carlson, Jonathan M.; Heckerman, David

2009-01-01

Summary: Evolutionary biologists are often interested in finding correlations among biological traits across a number of species, as such correlations may lead to testable hypotheses about the underlying function. Because some species are more closely related than others, computing and visualizing these correlations must be done in the context of the evolutionary tree that relates species. In this note, we introduce PhyloDet (short for PhyloDetective), an evolutionary tree visualization tool that enables biologists to visualize multiple traits mapped to the tree. Availability: http://research.microsoft.com/cue/phylodet/ Contact: bongshin@microsoft.com. PMID:19633096

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

DOE PAGES

Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.; ...

2017-10-27

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. The progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Therefore, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. We introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration,more » biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.« less

Functional Interdependence Theory: An Evolutionary Account of Social Situations.

PubMed

Balliet, Daniel; Tybur, Joshua M; Van Lange, Paul A M

2017-11-01

Social interactions are characterized by distinct forms of interdependence, each of which has unique effects on how behavior unfolds within the interaction. Despite this, little is known about the psychological mechanisms that allow people to detect and respond to the nature of interdependence in any given interaction. We propose that interdependence theory provides clues regarding the structure of interdependence in the human ancestral past. In turn, evolutionary psychology offers a framework for understanding the types of information processing mechanisms that could have been shaped under these recurring conditions. We synthesize and extend these two perspectives to introduce a new theory: functional interdependence theory (FIT). FIT can generate testable hypotheses about the function and structure of the psychological mechanisms for inferring interdependence. This new perspective offers insight into how people initiate and maintain cooperative relationships, select social partners and allies, and identify opportunities to signal social motives.

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. The progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Therefore, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. We introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration,more » biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.« less

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project.

PubMed

Weston, David J; Turetsky, Merritt R; Johnson, Matthew G; Granath, Gustaf; Lindo, Zoë; Belyea, Lisa R; Rice, Steven K; Hanson, David T; Engelhardt, Katharina A M; Schmutz, Jeremy; Dorrepaal, Ellen; Euskirchen, Eugénie S; Stenøien, Hans K; Szövényi, Péter; Jackson, Michelle; Piatkowski, Bryan T; Muchero, Wellington; Norby, Richard J; Kostka, Joel E; Glass, Jennifer B; Rydin, Håkan; Limpens, Juul; Tuittila, Eeva-Stiina; Ullrich, Kristian K; Carrell, Alyssa; Benscoter, Brian W; Chen, Jin-Gui; Oke, Tobi A; Nilsson, Mats B; Ranjan, Priya; Jacobson, Daniel; Lilleskov, Erik A; Clymo, R S; Shaw, A Jonathan

2018-01-01

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses. © 2017 UT-Battelle New Phytologist © 2017 New Phytologist Trust.

Hyper-heuristic Evolution of Dispatching Rules: A Comparison of Rule Representations.

PubMed

Branke, Jürgen; Hildebrandt, Torsten; Scholz-Reiter, Bernd

2015-01-01

Dispatching rules are frequently used for real-time, online scheduling in complex manufacturing systems. Design of such rules is usually done by experts in a time consuming trial-and-error process. Recently, evolutionary algorithms have been proposed to automate the design process. There are several possibilities to represent rules for this hyper-heuristic search. Because the representation determines the search neighborhood and the complexity of the rules that can be evolved, a suitable choice of representation is key for a successful evolutionary algorithm. In this paper we empirically compare three different representations, both numeric and symbolic, for automated rule design: A linear combination of attributes, a representation based on artificial neural networks, and a tree representation. Using appropriate evolutionary algorithms (CMA-ES for the neural network and linear representations, genetic programming for the tree representation), we empirically investigate the suitability of each representation in a dynamic stochastic job shop scenario. We also examine the robustness of the evolved dispatching rules against variations in the underlying job shop scenario, and visualize what the rules do, in order to get an intuitive understanding of their inner workings. Results indicate that the tree representation using an improved version of genetic programming gives the best results if many candidate rules can be evaluated, closely followed by the neural network representation that already leads to good results for small to moderate computational budgets. The linear representation is found to be competitive only for extremely small computational budgets.

Multi-target drugs to address multiple checkpoints in complex inflammatory pathologies: evolutionary cues for novel "first-in-class" anti-inflammatory drug candidates: a reviewer's perspective.

PubMed

Mathew, Geetha; Unnikrishnan, M K

2015-10-01

Inflammation is a complex, metabolically expensive process involving multiple signaling pathways and regulatory mechanisms which have evolved over evolutionary timescale. Addressing multiple targets of inflammation holistically, in moderation, is probably a more evolutionarily viable strategy, as compared to current therapy which addresses drug targets in isolation. Polypharmacology, addressing multiple targets, is commonly used in complex ailments, suggesting the superior safety and efficacy profile of multi-target (MT) drugs. Phenotypic drug discovery, which generated successful MT and first-in-class drugs in the past, is now re-emerging. A multi-pronged approach, which modulates the evolutionarily conserved, robust and pervasive cellular mechanisms of tissue repair, with AMPK at the helm, regulating the complex metabolic/immune/redox pathways underlying inflammation, is perhaps a more viable strategy than addressing single targets in isolation. Molecules that modulate multiple molecular mechanisms of inflammation in moderation (modulating TH cells toward the anti-inflammatory phenotype, activating AMPK, stimulating Nrf2 and inhibiting NFκB) might serve as a model for a novel Darwinian "first-in-class" therapeutic category that holistically addresses immune, redox and metabolic processes associated with inflammatory repair. Such a multimodal biological activity is supported by the fact that several non-calorific pleiotropic natural products with anti-inflammatory action have been incorporated into diet (chiefly guided by the adaptive development of olfacto-gustatory preferences over evolutionary timescales) rendering such molecules, endowed with evolutionarily privileged molecular scaffolds, naturally oriented toward multiple targets.

The Mechanisms of Psychedelic Visionary Experiences: Hypotheses from Evolutionary Psychology

PubMed Central

Winkelman, Michael J.

2017-01-01

Neuropharmacological effects of psychedelics have profound cognitive, emotional, and social effects that inspired the development of cultures and religions worldwide. Findings that psychedelics objectively and reliably produce mystical experiences press the question of the neuropharmacological mechanisms by which these highly significant experiences are produced by exogenous neurotransmitter analogs. Humans have a long evolutionary relationship with psychedelics, a consequence of psychedelics' selective effects for human cognitive abilities, exemplified in the information rich visionary experiences. Objective evidence that psychedelics produce classic mystical experiences, coupled with the finding that hallucinatory experiences can be induced by many non-drug mechanisms, illustrates the need for a common model of visionary effects. Several models implicate disturbances of normal regulatory processes in the brain as the underlying mechanisms responsible for the similarities of visionary experiences produced by psychedelic and other methods for altering consciousness. Similarities in psychedelic-induced visionary experiences and those produced by practices such as meditation and hypnosis and pathological conditions such as epilepsy indicate the need for a general model explaining visionary experiences. Common mechanisms underlying diverse alterations of consciousness involve the disruption of normal functions of the prefrontal cortex and default mode network (DMN). This interruption of ordinary control mechanisms allows for the release of thalamic and other lower brain discharges that stimulate a visual information representation system and release the effects of innate cognitive functions and operators. Converging forms of evidence support the hypothesis that the source of psychedelic experiences involves the emergence of these innate cognitive processes of lower brain systems, with visionary experiences resulting from the activation of innate processes based in the mirror neuron system (MNS). PMID:29033783

The extended evolutionary synthesis: its structure, assumptions and predictions

PubMed Central

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

2015-01-01

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

Phylogenetic diversity of macromycetes and woody plants along an elevational gradient in Eastern Mexico

Treesearch

Marko Gomez-Hernandez; Guadalupe Williams-Linera; D. Jean Lodge; Roger Guevara; Eduardo Ruiz-Sanchez; Etelvina Gandara

2016-01-01

Phylogenetic information provides insight into the ecological and evolutionary processes that organize species assemblages. We compared patterns of phylogenetic diversity among macromycete and woody plant communities along a steep elevational gradient in eastern Mexico to better understand the evolutionary processes that structure their communities. Macrofungi and...

Preliminary Evolutionary Explanations: A Basic Framework for Conceptual Change and Explanatory Coherence in Evolution

ERIC Educational Resources Information Center

Kampourakis, Kostas; Zogza, Vasso

2009-01-01

This study aimed to explore secondary students' explanations of evolutionary processes, and to determine how consistent these were, after a specific evolution instruction. In a previous study it was found that before instruction students provided different explanations for similar processes to tasks with different content. Hence, it seemed that…

The effects of stress and sex on selection, genetic covariance, and the evolutionary response.

PubMed

Holman, L; Jacomb, F

2017-10-01

The capacity of a population to adapt to selection (evolvability) depends on whether the structure of genetic variation permits the evolution of fitter trait combinations. Selection, genetic variance and genetic covariance can change under environmental stress, and males and females are not genetically independent, yet the combined effects of stress and dioecy on evolvability are not well understood. Here, we estimate selection, genetic (co)variance and evolvability in both sexes of Tribolium castaneum flour beetles under stressful and benign conditions, using a half-sib breeding design. Although stress uncovered substantial latent heritability, stress also affected genetic covariance, such that evolvability remained low under stress. Sexual selection on males and natural selection on females favoured a similar phenotype, and there was positive intersex genetic covariance. Consequently, sexual selection on males augmented adaptation in females, and intralocus sexual conflict was weak or absent. This study highlights that increased heritability does not necessarily increase evolvability, suggests that selection can deplete genetic variance for multivariate trait combinations with strong effects on fitness, and tests the recent hypothesis that sexual conflict is weaker in stressful or novel environments. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes

PubMed Central

Sethi, Isha; Gluck, Christian; Zhou, Huiqing

2017-01-01

Abstract Although epidermal keratinocyte development and differentiation proceeds in similar fashion between humans and mice, evolutionary pressures have also wrought significant species-specific physiological differences. These differences between species could arise in part, by the rewiring of regulatory network due to changes in the global targets of lineage-specific transcriptional master regulators such as p63. Here we have performed a systematic and comparative analysis of the p63 target gene network within the integrated framework of the transcriptomic and epigenomic landscape of mouse and human keratinocytes. We determined that there exists a core set of ∼1600 genomic regions distributed among enhancers and super-enhancers, which are conserved and occupied by p63 in keratinocytes from both species. Notably, these DNA segments are typified by consensus p63 binding motifs under purifying selection and are associated with genes involved in key keratinocyte and skin-centric biological processes. However, the majority of the p63-bound mouse target regions consist of either murine-specific DNA elements that are not alignable to the human genome or exhibit no p63 binding in the orthologous syntenic regions, typifying an occupancy lost subset. Our results suggest that these evolutionarily divergent regions have undergone significant turnover of p63 binding sites and are associated with an underlying inactive and inaccessible chromatin state, indicative of their selective functional activity in the transcriptional regulatory network in mouse but not human. Furthermore, we demonstrate that this selective targeting of genes by p63 correlates with subtle, but measurable transcriptional differences in mouse and human keratinocytes that converges on major metabolic processes, which often exhibit species-specific trends. Collectively our study offers possible molecular explanation for the observable phenotypic differences between the mouse and human skin and broadly informs on the prevailing principles that govern the tug-of-war between evolutionary forces of rigidity and plasticity over transcriptional regulatory programs. PMID:28505376

Evolutionary cell biology: two origins, one objective.

PubMed

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

2014-12-02

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

Evolutionary cell biology: Two origins, one objective

PubMed Central

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

2014-01-01

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

Longevity and ageing: appraising the evolutionary consequences of growing old

PubMed Central

Bonsall, Michael B

2005-01-01

Senescence or ageing is an increase in mortality and/or decline in fertility with increasing age. Evolutionary theories predict that ageing or longevity evolves in response to patterns of extrinsic mortality or intrinsic damage. If ageing is viewed as the outcome of the processes of behaviour, growth and reproduction then it should be possible to predict mortality rate. Recent developments have shown that it is now possible to integrate these ecological and physiological processes and predict the shape of mortality trajectories. By drawing on the key exciting developments in the cellular, physiological and ecological process of longevity the evolutionary consequences of ageing are reviewed. In presenting these ideas an evolutionary demographic framework is used to argue how trade-offs in life-history strategies are important in the maintenance of variation in longevity within and between species. Evolutionary processes associated with longevity have an important role in explaining levels of biological diversity and speciation. In particular, the effects of life-history trait trade-offs in maintaining and promoting species diversity are explored. Such trade-offs can alleviate the effects of intense competition between species and promote species coexistence and diversification. These results have important implications for understanding a number of core ecological processes such as how species are divided among niches, how closely related species co-occur and the rules by which species assemble into food-webs. Theoretical work reveals that the proximate physiological processes are as important as the ecological factors in explaining the variation in the evolution of longevity. Possible future research challenges integrating work on the evolution and mechanisms of growing old are briefly discussed. PMID:16553312

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

PubMed

O'Malley, Maureen A

2018-06-01

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

From genes to ecosystems: Measuring evolutionary diversity and community structure with Forest Inventory and Analysis (FIA) data

Treesearch

Kevin M. Potter

2009-01-01

Forest genetic sustainability is an important component of forest health because genetic diversity and evolutionary processes allow for the adaptation of species and for the maintenance of ecosystem functionality and resilience. Phylogenetic community analyses, a set of new statistical methods for describing the evolutionary relationships among species, offer an...

On Cellular Darwinism: Mitochondria.

PubMed

Bull, Larry

2016-01-01

The significant role of mitochondria within cells is becoming increasingly clear. This letter uses the NKCS model of coupled fitness landscapes to explore aspects of organelle-nucleus coevolution. The phenomenon of mitochondrial diversity is allowed to emerge under a simple intracellular evolutionary process, including varying the relative rate of evolution by the organelle. It is shown how the conditions for the maintenance of more than one genetic variant of mitochondria are similar to those previously suggested as needed for the original symbiotic origins of the relationship using the NKCS model.

ITO-based evolutionary algorithm to solve traveling salesman problem

NASA Astrophysics Data System (ADS)

Dong, Wenyong; Sheng, Kang; Yang, Chuanhua; Yi, Yunfei

2014-03-01

In this paper, a ITO algorithm inspired by ITO stochastic process is proposed for Traveling Salesmen Problems (TSP), so far, many meta-heuristic methods have been successfully applied to TSP, however, as a member of them, ITO needs further demonstration for TSP. So starting from designing the key operators, which include the move operator, wave operator, etc, the method based on ITO for TSP is presented, and moreover, the ITO algorithm performance under different parameter sets and the maintenance of population diversity information are also studied.

Population delimitation across contrasting evolutionary clines in deer mice (Peromyscus maniculatus)

PubMed Central

Yang, D-S; Kenagy, G

2011-01-01

Despite current interest in population genetics, a concrete definition of a “population” remains elusive. Multiple ecologically and evolutionarily based definitions of population are in current use, which focus, respectively, on demographic and genetic interactions. Accurate population delimitation is crucial for not only evolutionary and ecological population biology, but also for conservation of threatened populations. Along the Pacific Coast of North America, two contrasting patterns of geographic variation in deer mice (Peromyscus maniculatus) converge within the state of Oregon. Populations of these mice diverge morphologically across an east–west axis, and they diverge in mitochondrial DNA haplotypes across a north–south axis. In this study, we investigate these geographically contrasting patterns of differentiation in the context of ecological and evolutionary definitions (paradigms) of populations. We investigate these patterns using a new and geographically expansive sample that integrates data on morphology, mitochondrial DNA, and nuclear DNA. We found no evidence of nuclear genetic differentiation between the morphologically and mitochondrially distinct populations, thus indicating the occurrence of gene flow across Oregon. Under the evolutionary paradigm, Oregon populations can be considered a single population, whereas morphological and mitochondrial differentiations do not indicate distinct populations. In contrast, under the ecological paradigm morphological differentiation indicates distinct populations based on the low likelihood of demographic interactions between geographically distant individuals. The two sympatric but mitochondrially distinct haplogroups form a single population under the ecological paradigm. Hence, we find that the difference between evolutionary and ecological paradigms is the time-scale of interest, and we believe that the more chronologically inclusive evolutionary paradigm may be preferable except in cases where only a single generation is of interest. PMID:22393480

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

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

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

PubMed

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

2017-04-01

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

Genetic basis and fitness correlates of dynamic carotenoid-based ornamental coloration in male and female common kestrels Falco tinnunculus.

PubMed

Vergara, P; Fargallo, J A; Martínez-Padilla, J

2015-01-01

Knowledge of the genetic basis of sexual ornaments is essential to understand their evolution through sexual selection. Although carotenoid-based ornaments have been instrumental in the study of sexual selection, given the inability of animals to synthesize carotenoids de novo, they are generally assumed to be influenced solely by environmental variation. However, very few studies have directly estimated the role of genes and the environment in shaping variation in carotenoid-based traits. Using long-term individual-based data, we here explore the evolutionary potential of a dynamic, carotenoid-based ornament (namely skin coloration), in male and female common kestrels. We first estimate the amount of genetic variation underlying variation in hue, chroma and brightness. After correcting for sex differences, the chroma of the orange-yellow eye ring coloration was significantly heritable (h2±SE=0.40±0.17), whereas neither hue (h2=0) nor brightness (h2=0.02) was heritable. Second, we estimate the strength and shape of selection acting upon chromatic (hue and chroma) and achromatic (brightness) variation and show positive and negative directional selection on female but not male chroma and hue, respectively, whereas brightness was unrelated to fitness in both sexes. This suggests that different components of carotenoid-based signals traits may show different evolutionary dynamics. Overall, we show that carotenoid-based coloration is a complex and multifaceted trait. If we are to gain a better understanding of the processes responsible for the generation and maintenance of variation in carotenoid-based coloration, these complexities need to be taken into account. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Eco-Evolutionary Genomics of Chromosomal Inversions.

PubMed

Wellenreuther, Maren; Bernatchez, Louis

2018-05-03

Chromosomal inversions have long fascinated evolutionary biologists due to their suppression of recombination, which can protect co-adapted alleles. Emerging research documents that inversions are commonly linked to spectacular phenotypes and have a pervasive role in eco-evolutionary processes, from mating systems, social organisation, environmental adaptation, and reproductive isolation to speciation. Studies also reveal that inversions are taxonomically widespread, with many being old and large, and that balancing selection is commonly facilitating their maintenance. This challenges the traditional view that the role of balancing selection in maintaining variation is relatively minor. The ubiquitous importance of inversions in ecological and evolutionary processes suggests that structural variation should be better acknowledged and integrated in studies pertaining to the molecular basis of adaptation and speciation. Copyright © 2018 Elsevier Ltd. All rights reserved.

America and the Containment of Arab Radical Nationalism: The Eisenhower Years

DTIC Science & Technology

1994-05-01

evolutionary process in the transformation and defense of the Arab East. 4 The emergence of Nasser and radical nationalism throughout the area required a... processes were evolutionary and optimistic. It would require decades to accomplish what had 10 taken centuries in their own societies. It also required...numerous foreign teohnicians and progressive political leaders, the latter being excluded from the political process by the conservatives. Many of these

[Genetic mechanism and evolutionary significance of the origin of parthenogenetic insects].

PubMed

Wang, Cheng-Ye

2011-12-01

There is a high proportion of parthenogenesis in insecta, and the parthenogenetic potential of insects is an important but often ignored threaten factor for the agricultural and forestry production. The maintenance of parthenogenetic species is a puzzling issue in evolutionary biology. In recent years, although the cellular mechanisms during parthenogenesis in some species have been well studied, the underlying genetic mechanisms that cause the switch from sexual reproduction to parthenogenesis have not been defined. While, understanding the genetic mechanism and evolutionary significance of the origin of parthenogenetic insects is crucial for preventing the pests in agricultural and forestry production. Here we summarized recent studies aimed at identifying the underlying genetic mechanism of parthenogenesis in insects, and briefly discussed its potential application in this filed.

System Design under Uncertainty: Evolutionary Optimization of the Gravity Probe-B Spacecraft

NASA Technical Reports Server (NTRS)

Pullen, Samuel P.; Parkinson, Bradford W.

1994-01-01

This paper discusses the application of evolutionary random-search algorithms (Simulated Annealing and Genetic Algorithms) to the problem of spacecraft design under performance uncertainty. Traditionally, spacecraft performance uncertainty has been measured by reliability. Published algorithms for reliability optimization are seldom used in practice because they oversimplify reality. The algorithm developed here uses random-search optimization to allow us to model the problem more realistically. Monte Carlo simulations are used to evaluate the objective function for each trial design solution. These methods have been applied to the Gravity Probe-B (GP-B) spacecraft being developed at Stanford University for launch in 1999, Results of the algorithm developed here for GP-13 are shown, and their implications for design optimization by evolutionary algorithms are discussed.

Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee Apis mellifera.

PubMed

Lechner, Sarah; Ferretti, Luca; Schöning, Caspar; Kinuthia, Wanja; Willemsen, David; Hasselmann, Martin

2014-02-01

Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116-145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene.

Nucleotide Variability at Its Limit? Insights into the Number and Evolutionary Dynamics of the Sex-Determining Specificities of the Honey Bee Apis mellifera

PubMed Central

Lechner, Sarah; Ferretti, Luca; Schöning, Caspar; Kinuthia, Wanja; Willemsen, David; Hasselmann, Martin

2014-01-01

Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116–145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene. PMID:24170493

Evolutionary process of deep-sea bathymodiolus mussels.

PubMed

Miyazaki, Jun-Ichi; de Oliveira Martins, Leonardo; Fujita, Yuko; Matsumoto, Hiroto; Fujiwara, Yoshihiro

2010-04-27

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. 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. 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 symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular to intracellular symbiotic states in whale carcasses. The estimated evolutionary time suggests that the mytilid ancestors were able to exploit whales during adaptation to the deep sea.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Stationary stability for evolutionary dynamics in finite populations

DOE PAGES

Harper, Marc; Fryer, Dashiell

2016-08-25

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISSmore » candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.« less

Stored Carbon Dynamics are Controlled by a Combination of Evolutionary, Physiological, and Ecological Pressures

NASA Astrophysics Data System (ADS)

Aubrey, D. P.; Mims, J. T.; Oswald, S. W.; Teskey, R. O.; Mitchell, R. J.

2016-12-01

Allocation of assimilated carbon to storage provides a critical carbohydrate buffer when metabolic demands exceed current photosynthetic supply; however, our process-level understanding of controls on carbon storage pools and fluxes remains relatively poor. Recent studies have shifted the paradigm from the concept that stored carbon pools are a sink of low priority that accumulate passively when photosynthetic inputs exceed demand toward the concept that these pools are active sinks of high priority. It follows that allocation toward storage—at the expense of growth—is a trait that would be under selective pressure since species that allocate toward storage should be more resilient to disturbance. Using fire-dependent longleaf pine in a series of manipulative and observational studies, we explore how stored carbon dynamics are controlled by a combination of evolutionary, physiological, and ecological pressures. Our manipulative studies revealed large stored carbon pools in roots that maintained belowground metabolism for a year after current photosynthetic supply was restricted. Likewise, the concentration of stored carbon in the smallest, most metabolically active roots was not influenced until nearly one year later. Our observational studies indicated that stored carbon pools differ among closely related species with overlapping natural distributions, but evolutionary histories of different disturbance frequencies and thus, different selective pressures on carbon storage. Our comparisons of stored carbon pools between longleaf trees growing under xeric or mesic soil moisture regimes indicated that allocation toward storage exhibits plasticity through space and time in response to both short- and long-term variations in resource availability. We expect a continuum of responses to disturbances related to ecological niche and evolutionary adaptation that influence the availability of carbohydrates for metabolic demands. We also expect a continuum in stored carbon pools and metabolic buffering capacity among species as well as spatially, temporally, and developmentally within individual species.

Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

2016-09-01

A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be restricted to uniform time scales associated with the game interaction and strategy adaption evolution. In this study, we remove this restricting assumption by dividing the population into fast and slow groups according to the players' strategy updating frequencies and investigate how different strategy compositions of one group influence the evolutionary outcome of the other's fixation probabilities of strategies within its own group. Analytical analysis and numerical calculations are performed to study the evolutionary dynamics of strategies in typical classes of two-player games (prisoner's dilemma game, snowdrift game, and stag-hunt game). The introduction of the heterogeneity in strategy-update time scales leads to substantial changes in the evolution dynamics of strategies. We provide an approximation formula for the fixation probability of mutant types in finite populations and study the outcome of strategy evolution under the weak selection. We find that although heterogeneity in time scales makes the collective evolutionary dynamics more complicated, the possible long-run evolutionary outcome can be effectively predicted under technical assumptions when knowing the population composition and payoff parameters.

Deep evolutionary origins of neurobiology

PubMed Central

Mancuso, Stefano

2009-01-01

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

Natural History of Innate Host Defense Peptides.

PubMed

Linde, A; Wachter, B; Höner, O P; Dib, L; Ross, C; Tamayo, A R; Blecha, F; Melgarejo, T

2009-12-01

Host defense peptides act on the forefront of innate immunity, thus playing a central role in the survival of animals and plants. Despite vast morphological changes in species through evolutionary history, all animals examined to date share common features in their innate immune defense strategies, hereunder expression of host defense peptides (HDPs). Most studies on HDPs have focused on humans, domestic and laboratory animals. More than a thousand different sequences have been identified, yet data on HDPs in wild-living animals are sparse. The biological functions of HDPs include broad-spectrum antimicrobial activity and immunomodulation. Natural selection and coevolutionary host-pathogen arms race theory suggest that the extent and specificity of the microbial load influences the spectrum and potency of HDPs in different species. Individuals of extant species-that have lived for an extended period in evolutionary history amid populations with intact processes of natural selection-likely possess the most powerful and well-adapted "natural antibiotics". Research on the evolutionary history of the innate defense system and the host in context of the consequences of challenges as well as the efficacy of the innate immune system under natural conditions is therefore of immediate interest. This review focuses on evolutionary aspects of immunophysiology, with emphasis on innate effector molecules. Studies on host defense in wild-living animals may significantly enhance our understanding of inborn immune mechanisms, and help identify molecules that may assist us to cope better with the increasing microbial challenges that likely follow from the continuous amplification of biodiversity levels on Earth.

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

PubMed

Lewnard, Joseph A; Townsend, Jeffrey P

2016-12-20

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

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

PubMed Central

Lewnard, Joseph A.

2016-01-01

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference. PMID:27791071

The capture of heritable variation for genetic quality through social competition.

PubMed

Wolf, Jason B; Harris, W Edwin; Royle, Nick J

2008-09-01

In theory, females of many species choose mates based on traits that are indicators of male genetic quality. A fundamental question in evolutionary biology is why genetic variation for such indicator traits persists despite strong persistent selection imposed by female preference, which is known as the lek paradox. One potential solution to the lek paradox suggests that the traits that are targets of mate choice should evolve condition-dependent expression and that condition should have a large genetic variance. Condition is expected to exhibit high genetic variance because it is affected by a large number of physiological processes and hence, condition-dependent traits should 'capture' variation contributed by a large number of loci. We suggest that a potentially important cause of variation in condition is competition for limited resources. Here, we discuss a pair of models to analyze the evolutionary genetics of traits affected by success in social competition for resources. We show that competition can contribute to genetic variation of 'competition-dependent' traits that have fundamentally different evolutionary properties than other sources of variation. Competition dependence can make traits honest indicators of genetic quality by revealing the relative competitive ability of males, can provide a component of heritable variation that does not contribute to trait evolution, and can help maintain heritable variation under directional selection. Here we provide a general introduction to the concept of competition dependence and briefly introduce two models to demonstrate the potential evolutionary consequences of competition-dependent trait expression.

The predictability of evolution: glimpses into a post-Darwinian world.

PubMed

Conway Morris, Simon

2009-11-01

The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard's walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as "molecules of choice"? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

PubMed

Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence.

PubMed

Berdan, Emma L; Mazzoni, Camila J; Waurick, Isabelle; Roehr, Johannes T; Mayer, Frieder

2015-08-01

Understanding the genetics of speciation and the processes that drive it is a central goal of evolutionary biology. Grasshoppers of the Chorthippus species group differ strongly in calling song (and corresponding female preferences) but are exceedingly similar in other characteristics such as morphology. Here, we performed a population genomic scan on three Chorthippus species (Chorthippus biguttulus, C. mollis and C. brunneus) to gain insight into the genes and processes involved in divergence and speciation in this group. Using an RNA-seq approach, we examined functional variation between the species by calling SNPs for each of the three species pairs and using FST -based approaches to identify outliers. We found approximately 1% of SNPs in each comparison to be outliers. Between 37% and 40% of these outliers were nonsynonymous SNPs (as opposed to a global level of 17%) indicating that we recovered loci under selection. Among the outliers were several genes that may be involved in song production and hearing as well as genes involved in other traits such as food preferences and metabolism. Differences in food preferences between species were confirmed with a behavioural experiment. This indicates that multiple phenotypic differences implicating multiple evolutionary processes (sexual selection and natural selection) are present between the species. © 2015 John Wiley & Sons Ltd.

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution.

PubMed

Vigueira, C C; Olsen, K M; Caicedo, A L

2013-04-01

Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world.

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

PubMed Central

Vigueira, C C; Olsen, K M; Caicedo, A L

2013-01-01

Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world. PMID:23188175

Probabilistic models of eukaryotic evolution: time for integration

PubMed Central

Lartillot, Nicolas

2015-01-01

In spite of substantial work and recent progress, a global and fully resolved picture of the macroevolutionary history of eukaryotes is still under construction. This concerns not only the phylogenetic relations among major groups, but also the general characteristics of the underlying macroevolutionary processes, including the patterns of gene family evolution associated with endosymbioses, as well as their impact on the sequence evolutionary process. All these questions raise formidable methodological challenges, calling for a more powerful statistical paradigm. In this direction, model-based probabilistic approaches have played an increasingly important role. In particular, improved models of sequence evolution accounting for heterogeneities across sites and across lineages have led to significant, although insufficient, improvement in phylogenetic accuracy. More recently, one main trend has been to move away from simple parametric models and stepwise approaches, towards integrative models explicitly considering the intricate interplay between multiple levels of macroevolutionary processes. Such integrative models are in their infancy, and their application to the phylogeny of eukaryotes still requires substantial improvement of the underlying models, as well as additional computational developments. PMID:26323768

Boltzmann, Darwin and Directionality theory

NASA Astrophysics Data System (ADS)

Demetrius, Lloyd A.

2013-09-01

Boltzmann’s statistical thermodynamics is a mathematical theory which relates the macroscopic properties of aggregates of interacting molecules with the laws of their interaction. The theory is based on the concept thermodynamic entropy, a statistical measure of the extent to which energy is spread throughout macroscopic matter. Macroscopic evolution of material aggregates is quantitatively explained in terms of the principle: Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision. Darwin’s theory of evolution is a qualitative theory of the origin of species and the adaptation of populations to their environment. A central concept in the theory is fitness, a qualitative measure of the capacity of an organism to contribute to the ancestry of future generations. Macroscopic evolution of populations of living organisms can be qualitatively explained in terms of a neo-Darwinian principle: Fitness increases as the composition of the population changes under variation and natural selection. Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. This report reviews the analytical and empirical support for directionality theory, and invokes the microevolutionary dynamics of variation and selection to delineate the principles which govern macroevolutionary dynamics of speciation and extinction. We also elucidate the relation between thermodynamic entropy, which pertains to the extent of energy spreading and sharing within inanimate matter, and evolutionary entropy, which refers to the rate of energy appropriation from the environment and allocation within living systems. We show that the entropic principle of thermodynamics is the limit as R→0, M→∞, (where R denote the resource production rate, and M denote population size) of the entropic principle of evolution. We exploit this relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. Life history variation and the evolution of senescence The evolutionary dynamics of speciation and extinction Evolutionary trends in body size. The origin of sporadic forms of cancer and neurological diseases, and the evolution of cooperation are important recent applications of directionality theory. These applications, which draw from the medical sciences and sociobiology, appeal to methods which lie outside the formalism described in this report. A companion review, Demetrius and Gundlach (submitted for publication), gives an account of these applications.An important aspect of this report pertains to the connection between statistical mechanics and evolutionary theory and its implications towards understanding the processes which underlie the emergence of living systems from inanimate matter-a problem which has recently attracted considerable attention, Morowitz (1992), Eigen (1992), Dyson (2000), Pross (2012).The connection between the two disciplines can be addressed by appealing to certain extremal principles which are considered the mainstay of the respective theories.The extremal principle in statistical mechanics can be stated as follows:

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

ERIC Educational Resources Information Center

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

2013-01-01

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

J.A. Schumpeter and T.B. Veblen on economic evolution: the dichotomy between statics and dynamics

PubMed Central

Schütz, Marlies; Rainer, Andreas

2016-01-01

Abstract At present, the discussion on the dichotomy between statics and dynamics is resolved by concentrating on its mathematical meaning. Yet, a simple formalisation masks the underlying methodological discussion. Overcoming this limitation, the paper discusses Schumpeter's and Veblen's viewpoint on dynamic economic systems as systems generating change from within. It contributes to an understanding on their ideas of how economics could become an evolutionary science and on their contributions to elaborate an evolutionary economics. It confronts Schumpeter's with Veblen's perspective on evolutionary economics and provides insight into their evolutionary economic theorising by discussing their ideas on the evolution of capitalism. PMID:28057981

Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication.

PubMed

Hagman, Arne; Säll, Torbjörn; Compagno, Concetta; Piskur, Jure

2013-01-01

When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker's yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined.

Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication

PubMed Central

Hagman, Arne; Säll, Torbjörn; Compagno, Concetta; Piskur, Jure

2013-01-01

When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker’s yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined. PMID:23869229

Brazilian and Mexican experiences in the study of incipient domestication.

PubMed

Lins Neto, Ernani Machado de Freitas; Peroni, Nivaldo; Casas, Alejandro; Parra, Fabiola; Aguirre, Xitlali; Guillén, Susana; Albuquerque, Ulysses Paulino

2014-04-02

Studies of domestication enables a better understanding of human cultures, landscape changes according to peoples' purposes, and evolutionary consequences of human actions on biodiversity. This review aimed at discussing concepts, hypotheses, and current trends in studies of domestication of plants, using examples of cases studied in regions of Mesoamerica and Brazil. We analyzed trends of ethnobiological studies contributing to document processes of domestication and to establish criteria for biodiversity conservation based on traditional ecological knowledge. Based on reviewing our own and other authors' studies we analyzed management patterns and evolutionary trends associated to domestication occurring at plant populations and landscape levels. Particularly, we systematized information documenting: ethnobotanical aspects about plant management and artificial selection mechanisms, morphological consequences of plant management, population genetics of wild and managed plant populations, trends of change in reproduction systems of plants associated to management, and other ecological and physiological aspects influenced by management and domestication. Based on the analysis of study cases of 20 native species of herbs, shrubs and trees we identified similar criteria of artificial selection in different cultural contexts of Mexico and Brazil. Similar evolutionary trends were also identified in morphology (selection in favor of gigantism of useful and correlated parts); organoleptic characteristics such as taste, toxicity, color, texture; reproductive biology, mainly breeding system, phenological changes, and population genetics aspects, maintenance or increasing of genetic diversity in managed populations, high gene flow with wild relatives and low structure maintained by artificial selection. Our review is a first attempt to unify research methods for analyzing a high diversity of processes. Further research should emphasize deeper analyses of contrasting and diverse cultural and ecological contexts for a better understanding of evolution under incipient processes of domestication. Higher research effort is particularly required in Brazil, where studies on this topic are scarcer than in Mexico but where diversity of human cultures managing their also high plant resources diversity offer high potential for documenting the diversity of mechanisms of artificial selection and evolutionary trends. Comparisons and evaluations of incipient domestication in the regions studied as well as the Andean area would significantly contribute to understanding origins and diffusion of the experience of managing and domesticating plants.

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

Treesearch

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...

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Investigating Undergraduate Students' Use of Intuitive Reasoning and Evolutionary Knowledge in Explanations of Antibiotic Resistance.

PubMed

Richard, Melissa; Coley, John D; Tanner, Kimberly D

2017-01-01

Natural selection is a central concept throughout biology; however, it is a process frequently misunderstood. Bacterial resistance to antibiotic medications provides a contextual example of the relevance of evolutionary theory and is also commonly misunderstood. While research has shed light on student misconceptions of natural selection, minimal study has focused on misconceptions of antibiotic resistance. Additionally, research has focused on the degree to which misconceptions may be based in the complexity of biological information or in pedagogical choices, rather than in deep-seated cognitive patterns. Cognitive psychology research has established that humans develop early intuitive assumptions to make sense of the world. In this study, we used a written assessment tool to investigate undergraduate students' misconceptions of antibiotic resistance, use of intuitive reasoning, and application of evolutionary knowledge to antibiotic resistance. We found a majority of students produced and agreed with misconceptions, and intuitive reasoning was present in nearly all students' written explanations. Acceptance of a misconception was significantly associated with production of a hypothesized form of intuitive thinking (all p ≤ 0.05). Intuitive reasoning may represent a subtle but innately appealing linguistic shorthand, and instructor awareness of intuitive reasoning's relation to student misunderstandings has potential for addressing persistent misconceptions. © 2017 M. Richard et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Genetic Diversity and Hybridisation between Native and Introduced Salmonidae Fishes in a Swedish Alpine Lake.

PubMed

Faulks, Leanne; Östman, Örjan

2016-01-01

Understanding the processes underlying diversification can aid in formulating appropriate conservation management plans that help maintain the evolutionary potential of taxa, particularly under human-induced activities and climate change. Here we assessed the microsatellite genetic diversity and structure of three salmonid species, two native (Arctic charr, Salvelinus alpinus and brown trout, Salmo trutta) and one introduced (brook charr, Salvelinus fontinalis), from an alpine lake in sub-arctic Sweden, Lake Ånn. The genetic diversity of the three species was similar and sufficiently high from a conservation genetics perspective: corrected total heterozygosity, H'T = 0.54, 0.66, 0.60 and allelic richness, AR = 4.93, 5.53 and 5.26 for Arctic charr, brown trout and brook charr, respectively. There were indications of elevated inbreeding coefficients in brown trout (GIS = 0.144) and brook charr (GIS = 0.129) although sibling relationships were likely a confounding factor, as a high proportion of siblings were observed in all species within and among sampling locations. Overall genetic structure differed between species, Fst = 0.01, 0.02 and 0.04 in Arctic charr, brown trout and brook charr respectively, and there was differentiation at only a few specific locations. There was clear evidence of hybridisation between the native Arctic charr and the introduced brook charr, with 6% of individuals being hybrids, all of which were sampled in tributary streams. The ecological and evolutionary consequences of the observed hybridisation are priorities for further research and the conservation of the evolutionary potential of native salmonid species.

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

Kramers problem in evolutionary strategies

NASA Astrophysics Data System (ADS)

Dunkel, J.; Ebeling, W.; Schimansky-Geier, L.; Hänggi, P.

2003-06-01

We calculate the escape rates of different dynamical processes for the case of a one-dimensional symmetric double-well potential. In particular, we compare the escape rates of a Smoluchowski process, i.e., a corresponding overdamped Brownian motion dynamics in a metastable potential landscape, with the escape rates obtained for a biologically motivated model known as the Fisher-Eigen process. The main difference between the two models is that the dynamics of the Smoluchowski process is determined by local quantities, whereas the Fisher-Eigen process is based on a global coupling (nonlocal interaction). If considered in the context of numerical optimization algorithms, both processes can be interpreted as archetypes of physically or biologically inspired evolutionary strategies. In this sense, the results discussed in this work are utile in order to evaluate the efficiency of such strategies with regard to the problem of surmounting various barriers. We find that a combination of both scenarios, starting with the Fisher-Eigen strategy, provides a most effective evolutionary strategy.

New Insight into the Colonization Processes of Common Voles: Inferences from Molecular and Fossil Evidence

PubMed Central

Tougard, Christelle; Renvoisé, Elodie; Petitjean, Amélie; Quéré, Jean-Pierre

2008-01-01

Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity. PMID:18958287

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

PubMed

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 complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines. This article was reviewed by W. Ford Doolittle and Eugene V. Koonin.

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

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

NASA Astrophysics Data System (ADS)

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.

Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes.

PubMed

Beres, Stephen B; Kachroo, Priyanka; Nasser, Waleed; Olsen, Randall J; Zhu, Luchang; Flores, Anthony R; de la Riva, Ivan; Paez-Mayorga, Jesus; Jimenez, Francisco E; Cantu, Concepcion; Vuopio, Jaana; Jalava, Jari; Kristinsson, Karl G; Gottfredsson, Magnus; Corander, Jukka; Fittipaldi, Nahuel; Di Luca, Maria Chiara; Petrelli, Dezemona; Vitali, Luca A; Raiford, Annessa; Jenkins, Leslie; Musser, James M

2016-05-31

For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects. The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease. Copyright © 2016 Beres et al.

When mothering goes awry: Challenges and opportunities for utilizing evidence across rodent, nonhuman primate and human studies to better define the biological consequences of negative early caregiving☆

PubMed Central

Sánchez, Mar M.; Gonzalez, Andrea

2016-01-01

Across mammalian species, mothers shape socio-emotional development and serve as essential external regulators of infant physiology, brain development, behavior patterns, and emotional regulation. Caregiving quality, consistency and predictability shape the infant's underlying neurobiological processes. Although the requirements for “optimal” caregiving differ across species, the negative long-term consequences of the absence of needed caregiving (e.g. neglect) or the presence of harmful/aversive caregiving (e.g. physical abuse), are translatable across species. Recognizing the significant potential of cross species comparisons in terms of defining underlying mechanisms, effective translation requires consideration of the evolutionary, ecological, and fundamental biological and developmental differences between and among species. This review provides both an overview of several success stories of cross-species translations in relation to negative caregiving and a template for future studies seeking to most effectively define the underlying biological processes and advance research dedicated to mitigating the lasting negative health consequences of child maltreatment. PMID:26506032

Coevolutionary dynamics in large, but finite populations

NASA Astrophysics Data System (ADS)

Traulsen, Arne; Claussen, Jens Christian; Hauert, Christoph

2006-07-01

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate uc is obtained separating two scenarios: above uc the population predominantly consists of a mixture of strategies whereas below uc the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

The topology of evolutionary novelty and innovation in macroevolution

PubMed Central

2017-01-01

Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’. PMID:29061895

Radial Domany-Kinzel models with mutation and selection

NASA Astrophysics Data System (ADS)

Lavrentovich, Maxim O.; Korolev, Kirill S.; Nelson, David R.

2013-01-01

We study the effect of spatial structure, genetic drift, mutation, and selective pressure on the evolutionary dynamics in a simplified model of asexual organisms colonizing a new territory. Under an appropriate coarse-graining, the evolutionary dynamics is related to the directed percolation processes that arise in voter models, the Domany-Kinzel (DK) model, contact process, and so on. We explore the differences between linear (flat front) expansions and the much less familiar radial (curved front) range expansions. For the radial expansion, we develop a generalized, off-lattice DK model that minimizes otherwise persistent lattice artifacts. With both simulations and analytical techniques, we study the survival probability of advantageous mutants, the spatial correlations between domains of neutral strains, and the dynamics of populations with deleterious mutations. “Inflation” at the frontier leads to striking differences between radial and linear expansions. For a colony with initial radius R0 expanding at velocity v, significant genetic demixing, caused by local genetic drift, occurs only up to a finite time t*=R0/v, after which portions of the colony become causally disconnected due to the inflating perimeter of the expanding front. As a result, the effect of a selective advantage is amplified relative to genetic drift, increasing the survival probability of advantageous mutants. Inflation also modifies the underlying directed percolation transition, introducing novel scaling functions and modifications similar to a finite-size effect. Finally, we consider radial range expansions with deflating perimeters, as might arise from colonization initiated along the shores of an island.

Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

PubMed

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph

2011-02-10

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

PubMed Central

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C.; Dehio, Christoph

2011-01-01

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment. PMID:21347280

Evolutionary adaptation of the sensitivity of connexin26 hemichannels to CO2.

PubMed

de Wolf, Elizabeth; Cook, Jonathan; Dale, Nicholas

2017-02-08

CO 2 readily combines with H 2 O to form [Formula: see text] and H + Because an increase of only 100 nM in the concentration of H + (a decrease of 0.1 unit of pH) in blood can prove fatal, the regulated excretion of CO 2 during breathing is an essential life-preserving process. In rodents and humans, this vital process is mediated in part via the direct sensing of CO 2 via connexin26 (Cx26). CO 2 binds to hemichannels of Cx26 causing them to open and allow release of the neurotransmitter ATP. If Cx26 were to be a universal and important CO 2 sensor across all homeothermic animals, then a simple hypothesis would posit that it should exhibit evolutionary adaptation in animals with different homeostatic set points for the regulation of partial pressure of arterial CO 2 (PaCO 2 ). In humans and rats, PaCO 2 is regulated around a set point of 40 mmHg. By contrast, birds are able to maintain cerebral blood flow and breathing at much lower levels of PaCO 2 Fossorial mammals, such as the mole rat, live exclusively underground in burrows that are both hypoxic and hypercapnic and can thrive under very hypercapnic conditions. We have therefore compared the CO 2 sensitivity of Cx26 from human, chicken, rat and mole rat (Heterocephalus glaber). We find that both the affinity and cooperativity of CO 2 binding to Cx26 have been subjected to evolutionary adaption in a manner consistent with the homeostatic requirements of these four species. This is analogous to the evolutionary adaptation of haemoglobin to the needs of O 2 transport across the animal kingdom and supports the hypothesis that Cx26 is an important and universal CO 2 sensor in homeotherms. © 2017 The Authors.

Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems

PubMed Central

Thrall, Peter H; Oakeshott, John G; Fitt, Gary; Southerton, Simon; Burdon, Jeremy J; Sheppard, Andy; Russell, Robyn J; Zalucki, Myron; Heino, Mikko; Ford Denison, R

2011-01-01

Anthropogenic impacts increasingly drive ecological and evolutionary processes at many spatio-temporal scales, demanding greater capacity to predict and manage their consequences. This is particularly true for agro-ecosystems, which not only comprise a significant proportion of land use, but which also involve conflicting imperatives to expand or intensify production while simultaneously reducing environmental impacts. These imperatives reinforce the likelihood of further major changes in agriculture over the next 30–40 years. Key transformations include genetic technologies as well as changes in land use. The use of evolutionary principles is not new in agriculture (e.g. crop breeding, domestication of animals, management of selection for pest resistance), but given land-use trends and other transformative processes in production landscapes, ecological and evolutionary research in agro-ecosystems must consider such issues in a broader systems context. Here, we focus on biotic interactions involving pests and pathogens as exemplars of situations where integration of agronomic, ecological and evolutionary perspectives has practical value. Although their presence in agro-ecosystems may be new, many traits involved in these associations evolved in natural settings. We advocate the use of predictive frameworks based on evolutionary models as pre-emptive management tools and identify some specific research opportunities to facilitate this. We conclude with a brief discussion of multidisciplinary approaches in applied evolutionary problems. PMID:25567968

Can Evolutionary Principles Explain Patterns of Family Violence?

ERIC Educational Resources Information Center

Archer, John

2013-01-01

The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated…

Unto Others: Illustrating the Human Capacity for Cooperation

ERIC Educational Resources Information Center

Morris, J. Andrew; Urbanski, John; Hunt, Jason

2011-01-01

Research in both evolutionary economics and evolutionary psychology provides strong evidence that human behavior can be, and is, a complex mix of hedonism and altruism with a strong inclination toward cooperation under certain conditions. In this article, behavioral assumptions made in mainstream business theory are compared and contrasted with…

What have humans done for evolutionary biology? Contributions from genes to populations.

PubMed

Briga, Michael; Griffin, Robert M; Berger, Vérane; Pettay, Jenni E; Lummaa, Virpi

2017-11-15

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. © 2017 The Author(s).

What have humans done for evolutionary biology? Contributions from genes to populations

PubMed Central

Briga, Michael; Griffin, Robert M.; Berger, Vérane; Pettay, Jenni E.

2017-01-01

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. PMID:29118130

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

Lyman, R Lee

2009-02-01

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

P97/CDC-48: proteostasis control in tumor cell biology.

PubMed

Fessart, Delphine; Marza, Esther; Taouji, Saïd; Delom, Frédéric; Chevet, Eric

2013-08-28

P97/CDC-48 is a prominent member of a highly evolutionary conserved Walker cassette - containing AAA+ATPases. It has been involved in numerous cellular processes ranging from the control of protein homeostasis to membrane trafficking through the intervention of specific accessory proteins. Expression of p97/CDC-48 in cancers has been correlated with tumor aggressiveness and prognosis, however the precise underlying molecular mechanisms remain to be characterized. Moreover p97/CDC-48 inhibitors were developed and are currently under intense investigation as anticancer drugs. Herein, we discuss the role of p97/CDC-48 in cancer development and its therapeutic potential in tumor cell biology. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

PubMed

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

The automaticity of emotion recognition.

PubMed

Tracy, Jessica L; Robins, Richard W

2008-02-01

Evolutionary accounts of emotion typically assume that humans evolved to quickly and efficiently recognize emotion expressions because these expressions convey fitness-enhancing messages. The present research tested this assumption in 2 studies. Specifically, the authors examined (a) how quickly perceivers could recognize expressions of anger, contempt, disgust, embarrassment, fear, happiness, pride, sadness, shame, and surprise; (b) whether accuracy is improved when perceivers deliberate about each expression's meaning (vs. respond as quickly as possible); and (c) whether accurate recognition can occur under cognitive load. Across both studies, perceivers quickly and efficiently (i.e., under cognitive load) recognized most emotion expressions, including the self-conscious emotions of pride, embarrassment, and shame. Deliberation improved accuracy in some cases, but these improvements were relatively small. Discussion focuses on the implications of these findings for the cognitive processes underlying emotion recognition.

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

PubMed

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.

How evolutionary principles improve the understanding of human health and disease

PubMed Central

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

2011-01-01

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. PMID:25567971

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

PubMed

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.

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

PubMed

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.

Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages.

PubMed

Ying, Bei-Wen; Honda, Tomoya; Tsuru, Saburo; Seno, Shigeto; Matsuda, Hideo; Kazuta, Yasuaki; Yomo, Tetsuya

2015-01-01

Microorganisms in nature are constantly subjected to a limited availability of resources and experience repeated starvation and nutrition. Therefore, microbial life may evolve for both growth fitness and sustainability. By contrast, experimental evolution, as a powerful approach to investigate microbial evolutionary strategies, often targets the increased growth fitness in controlled, steady-state conditions. Here, we address evolutionary changes balanced between growth and maintenance while taking nutritional fluctuations into account. We performed a 290-day-long evolution experiment with a histidine-requiring Escherichia coli strain that encountered repeated histidine-rich and histidine-starved conditions. The cells that experienced seven rounds of starvation and re-feed grew more sustainably under prolonged starvation but dramatically lost growth fitness under rich conditions. The improved sustainability arose from the evolved capability to use a trace amount of histidine for cell propagation. The reduced growth rate was attributed to mutations genetically disturbing the translation machinery, that is, the ribosome, ultimately slowing protein translation. This study provides the experimental demonstration of slow growth accompanied by an enhanced affinity to resources as an evolutionary adaptation to oscillated environments and verifies that it is possible to evolve for reduced growth fitness. Growth economics favored for population increase under extreme resource limitations is most likely a common survival strategy adopted by natural microbes.

Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

PubMed

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.

Quantitative food web analysis supports the energy-limitation hypothesis in cave stream ecosystems.

PubMed

Venarsky, Michael P; Huntsman, Brock M; Huryn, Alexander D; Benstead, Jonathan P; Kuhajda, Bernard R

2014-11-01

Energy limitation has long been the primary assumption underlying conceptual models of evolutionary and ecological processes in cave ecosystems. However, the prediction that cave communities are actually energy-limited in the sense that constituent populations are consuming all or most of their resource supply is untested. We assessed the energy-limitation hypothesis in three cave streams in northeastern Alabama (USA) by combining measurements of animal production, demand, and resource supplies (detritus, primarily decomposing wood particles). Comparisons of animal consumption and detritus supply rates in each cave showed that all, or nearly all, available detritus was required to support macroinvertebrate production. Furthermore, only a small amount of macroinvertebrate prey production remained to support other predatory taxa (i.e., cave fish and salamanders) after accounting for crayfish consumption. Placing the energy demands of a cave community within the context of resource supply rates provided quantitative support for the energy-limitation hypothesis, confirming the mechanism (limited energy surpluses) that likely influences the evolutionary processes and population dynamics that shape cave communities. Detritus-based surface ecosystems often have large detrital surpluses. Thus, cave ecosystems, which show minimal surpluses, occupy the extreme oligotrophic end of the spectrum of detritus-based food webs.

Unconstrained cranial evolution in Neandertals and modern humans compared to common chimpanzees

PubMed Central

Weaver, Timothy D.; Stringer, Chris B.

2015-01-01

A variety of lines of evidence support the idea that neutral evolutionary processes (genetic drift, mutation) have been important in generating cranial differences between Neandertals and modern humans. But how do Neandertals and modern humans compare with other species? And how do these comparisons illuminate the evolutionary processes underlying cranial diversification? To address these questions, we used 27 standard cranial measurements collected on 2524 recent modern humans, 20 Neandertals and 237 common chimpanzees to estimate split times between Neandertals and modern humans, and between Pan troglodytes verus and two other subspecies of common chimpanzee. Consistent with a neutral divergence, the Neandertal versus modern human split-time estimates based on cranial measurements are similar to those based on DNA sequences. By contrast, the common chimpanzee cranial estimates are much lower than DNA-sequence estimates. Apparently, cranial evolution has been unconstrained in Neandertals and modern humans compared with common chimpanzees. Based on these and additional analyses, it appears that cranial differentiation in common chimpanzees has been restricted by stabilizing natural selection. Alternatively, this restriction could be due to genetic and/or developmental constraints on the amount of within-group variance (relative to effective population size) available for genetic drift to act on. PMID:26468243

Genetic erosion impedes adaptive responses to stressful environments

PubMed Central

Bijlsma, R; Loeschcke, Volker

2012-01-01

Biodiversity is increasingly subjected to human-induced changes of the environment. To persist, populations continually have to adapt to these often stressful changes including pollution and climate change. Genetic erosion in small populations, owing to fragmentation of natural habitats, is expected to obstruct such adaptive responses: (i) genetic drift will cause a decrease in the level of adaptive genetic variation, thereby limiting evolutionary responses; (ii) inbreeding and the concomitant inbreeding depression will reduce individual fitness and, consequently, the tolerance of populations to environmental stress. Importantly, inbreeding generally increases the sensitivity of a population to stress, thereby increasing the amount of inbreeding depression. As adaptation to stress is most often accompanied by increased mortality (cost of selection), the increase in the ‘cost of inbreeding’ under stress is expected to severely hamper evolutionary adaptive processes. Inbreeding thus plays a pivotal role in this process and is expected to limit the probability of genetically eroded populations to successfully adapt to stressful environmental conditions. Consequently, the dynamics of small fragmented populations may differ considerably from large nonfragmented populations. The resilience of fragmented populations to changing and deteriorating environments is expected to be greatly decreased. Alleviating inbreeding depression, therefore, is crucial to ensure population persistence. PMID:25568035

Why don’t you use Evolutionary Algorithms in Big Data?

NASA Astrophysics Data System (ADS)

Stanovov, Vladimir; Brester, Christina; Kolehmainen, Mikko; Semenkina, Olga

2017-02-01

In this paper we raise the question of using evolutionary algorithms in the area of Big Data processing. We show that evolutionary algorithms provide evident advantages due to their high scalability and flexibility, their ability to solve global optimization problems and optimize several criteria at the same time for feature selection, instance selection and other data reduction problems. In particular, we consider the usage of evolutionary algorithms with all kinds of machine learning tools, such as neural networks and fuzzy systems. All our examples prove that Evolutionary Machine Learning is becoming more and more important in data analysis and we expect to see the further development of this field especially in respect to Big Data.

Genomic variation associated with local adaptation of weedy rice during de-domestication

PubMed Central

Qiu, Jie; Zhou, Yongjun; Mao, Lingfeng; Ye, Chuyu; Wang, Weidi; Zhang, Jianping; Yu, Yongyi; Fu, Fei; Wang, Yunfei; Qian, Feijian; Qi, Ting; Wu, Sanling; Sultana, Most Humaira; Cao, Ya-Nan; Wang, Yu; Timko, Michael P.; Ge, Song; Fan, Longjiang; Lu, Yongliang

2017-01-01

De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. PMID:28537247

SHARP's systems engineering challenge: rectifying integrated product team requirements with performance issues in an evolutionary spiral development acquisition

NASA Astrophysics Data System (ADS)

Kuehl, C. Stephen

2003-08-01

Completing its final development and early deployment on the Navy's multi-role aircraft, the F/A-18 E/F Super Hornet, the SHAred Reconnaissance Pod (SHARP) provides the war fighter with the latest digital tactical reconnaissance (TAC Recce) Electro-Optical/Infrared (EO/IR) sensor system. The SHARP program is an evolutionary acquisition that used a spiral development process across a prototype development phase tightly coupled into overlapping Engineering and Manufacturing Development (EMD) and Low Rate Initial Production (LRIP) phases. Under a tight budget environment with a highly compressed schedule, SHARP challenged traditional acquisition strategies and systems engineering (SE) processes. Adopting tailored state-of-the-art systems engineering process models allowd the SHARP program to overcome the technical knowledge transition challenges imposed by a compressed program schedule. The program's original goal was the deployment of digital TAC Recce mission capabilities to the fleet customer by summer of 2003. Hardware and software integration technical challenges resulted from requirements definition and analysis activities performed across a government-industry led Integrated Product Team (IPT) involving Navy engineering and test sites, Boeing, and RTSC-EPS (with its subcontracted hardware and government furnished equipment vendors). Requirements development from a bottoms-up approach was adopted using an electronic requirements capture environment to clarify and establish the SHARP EMD product baseline specifications as relevant technical data became available. Applying Earned-Value Management (EVM) against an Integrated Master Schedule (IMS) resulted in efficiently managing SE task assignments and product deliveries in a dynamically evolving customer requirements environment. Application of Six Sigma improvement methodologies resulted in the uncovering of root causes of errors in wiring interconnectivity drawings, pod manufacturing processes, and avionics requirements specifications. Utilizing the draft NAVAIR SE guideline handbook and the ANSI/EIA-632 standard: Processes for Engineering a System, a systems engineering tailored process approach was adopted for the accelerated SHARP EMD prgram. Tailoring SE processes in this accelerated product delivery environment provided unique opportunities to be technically creative in the establishment of a product performance baseline. This paper provides an historical overview of the systems engineering activities spanning the prototype phase through the EMD SHARP program phase, the performance requirement capture activities and refinement process challenges, and what SE process improvements can be applied to future SHARP-like programs adopting a compressed, evolutionary spiral development acquisition paradigm.

Maximizing Submodular Functions under Matroid Constraints by Evolutionary Algorithms.

PubMed

Friedrich, Tobias; Neumann, Frank

2015-01-01

Many combinatorial optimization problems have underlying goal functions that are submodular. The classical goal is to find a good solution for a given submodular function f under a given set of constraints. In this paper, we investigate the runtime of a simple single objective evolutionary algorithm called (1 + 1) EA and a multiobjective evolutionary algorithm called GSEMO until they have obtained a good approximation for submodular functions. For the case of monotone submodular functions and uniform cardinality constraints, we show that the GSEMO achieves a (1 - 1/e)-approximation in expected polynomial time. For the case of monotone functions where the constraints are given by the intersection of K ≥ 2 matroids, we show that the (1 + 1) EA achieves a (1/k + δ)-approximation in expected polynomial time for any constant δ > 0. Turning to nonmonotone symmetric submodular functions with k ≥ 1 matroid intersection constraints, we show that the GSEMO achieves a 1/((k + 2)(1 + ε))-approximation in expected time O(n(k + 6)log(n)/ε.

An Agent-based Model for Groundwater Allocation and Management at the Bakken Shale in Western North Dakota

NASA Astrophysics Data System (ADS)

Lin, T.; Lin, Z.; Lim, S.

2017-12-01

We present an integrated modeling framework to simulate groundwater level change under the dramatic increase of hydraulic fracturing water use in the Bakken Shale oil production area. The framework combines the agent-based model (ABM) with the Fox Hills-Hell Creek (FH-HC) groundwater model. In development of the ABM, institution theory is used to model the regulation policies from the North Dakota State Water Commission, while evolutionary programming and cognitive maps are used to model the social structure that emerges from the behavior of competing individual water businesses. Evolutionary programming allows individuals to select an appropriate strategy when annually applying for potential water use permits; whereas cognitive maps endow agent's ability and willingness to compete for more water sales. All agents have their own influence boundaries that inhibit their competitive behavior toward their neighbors but not to non-neighbors. The decision-making process is constructed and parameterized with both quantitative and qualitative information, i.e., empirical water use data and knowledge gained from surveys with stakeholders. By linking institution theory, evolutionary programming, and cognitive maps, our approach addresses a higher complexity of the real decision making process. Furthermore, this approach is a new exploration for modeling the dynamics of Coupled Human and Natural System. After integrating ABM with the FH-HC model, drought and limited water accessibility scenarios are simulated to predict FH-HC ground water level changes in the future. The integrated modeling framework of ABM and FH-HC model can be used to support making scientifically sound policies in water allocation and management.

BIRDS AS A MODEL TO STUDY ADULT NEUROGENESIS: BRIDGING EVOLUTIONARY, COMPARATIVE AND NEUROETHOLOGICAL APPROCHES

PubMed Central

BARNEA, ANAT; PRAVOSUDOV, VLADIMIR

2011-01-01

During the last few decades evidence has demonstrated that adult neurogenesis is a well-preserved feature throughout the animal kingdom. In birds, ongoing neuronal addition occurs rather broadly, to a number of brain regions. This review describes adult avian neurogenesis and neuronal recruitment, discusses factors that regulate these processes, and touches upon the question of their genetic control. Several attributes make birds an extremely advantageous model to study neurogenesis. First, song learning exhibits seasonal variation that is associated with seasonal variation in neuronal turnover in some song control brain nuclei, which seems to be regulated via adult neurogenesis. Second, food-caching birds naturally use memory-dependent behavior in learning locations of thousands of food caches scattered over their home ranges. In comparison with other birds, food-caching species have relatively enlarged hippocampi with more neurons and intense neurogenesis, which appears to be related to spatial learning. Finally, migratory behavior and naturally occurring social systems in birds also provide opportunities to investigate neurogenesis. Such diversity of naturally-occurring memory-based behaviors, combined with the fact that birds can be studied both in the wild and in the laboratory, make them ideal for investigation of neural processes underlying learning. This can be done by using various approaches, from evolutionary and comparative to neuroethological and molecular. Finally, we connect the avian arena to a broader view by providing a brief comparative and evolutionary overview of adult neurogenesis and by discussing the possible functional role of the new neurons. We conclude by indicating future directions and possible medical applications. PMID:21929623

Modelling and strategy optimisation for a kind of networked evolutionary games with memories under the bankruptcy mechanism

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

This paper investigates the evolutionary dynamic and strategy optimisation for a kind of networked evolutionary games whose strategy updating rules incorporate 'bankruptcy' mechanism, and the situation that each player's bankruptcy is due to the previous continuous low profits gaining from the game is considered. First, by using semi-tensor product of matrices method, the evolutionary dynamic of this kind of games is expressed as a higher order logical dynamic system and then converted into its algebraic form, based on which, the evolutionary dynamic of the given games can be discussed. Second, the strategy optimisation problem is investigated, and some free-type control sequences are designed to maximise the total payoff of the whole game. Finally, an illustrative example is given to show that our new results are very effective.

Invisible hand effect in an evolutionary minority game model

NASA Astrophysics Data System (ADS)

Sysi-Aho, Marko; Saramäki, Jari; Kaski, Kimmo

2005-03-01

In this paper, we study the properties of a minority game with evolution realized by using genetic crossover to modify fixed-length decision-making strategies of agents. Although the agents in this evolutionary game act selfishly by trying to maximize their own performances only, it turns out that the whole society will eventually be rewarded optimally. This “invisible hand” effect is what Adam Smith over two centuries ago expected to take place in the context of free market mechanism. However, this behaviour of the society of agents is realized only under idealized conditions, where all agents are utilizing the same efficient evolutionary mechanism. If on the other hand part of the agents are adaptive, but not evolutionary, the system does not reach optimum performance, which is also the case if part of the evolutionary agents form a uniformly acting “cartel”.

Applying NASA Imaging Radar Datasets to Investigate the Geomorphology of the Amazon's Planalto

NASA Astrophysics Data System (ADS)

McDonald, K. C.; Campbell, K.; Islam, R.; Alexander, P. M.; Cracraft, J.

2016-12-01

The Amazon basin is a biodiversity rich biome and plays a significant role into shaping Earth's climate, ocean and atmospheric gases. Understanding the history of the formation of this basin is essential to our understanding of the region's biodiversity and its response to climate change. During March 2013, the NASA/JPL L-band polarimetric airborne imaging radar, UAVSAR, conducted airborne studies over regions of South America including portions of the western Amazon basin. We utilize UAVSAR imagery acquired during that time over the Planalto, in the Madre de Dios region of southeastern Peru in an assessment of the underlying geomorphology, its relationship to the current distribution of vegetation, and its relationship to geologic processes through deep time. We employ UAVSAR data collections to assess the utility of these high quality imaging radar data for use in identifying geomorphologic features and vegetation communities within the context of improving the understanding of evolutionary processes, and their utility in aiding interpretation of datasets from Earth-orbiting satellites to support a basin-wide characterization across the Amazon. We derive maps of landcover and river branching structure from UAVSAR imagery. We compare these maps to those derived using imaging radar datasets from the Japanese Space Agency's ALOS PALSAR and Digital Elevation Models (DEMs) from NASA's Shuttle Radar Topography Mission (SRTM). Results provide an understanding of the underlying geomorphology of the Amazon planalto as well as its relationship to geologic processes and will support interpretation of the evolutionary history of the Amazon Basin. Portions of this work have been carried out within the framework of the ALOS Kyoto & Carbon Initiative. PALSAR data were provided by JAXA/EORC and the Alaska Satellite Facility.This work is carried out with support from the NASA Biodiversity Program and the NSF DIMENSIONS of Biodiversity Program.

Body shape transformation along a shared axis of anatomical evolution in labyrinth fishes (Anabantoidei).

PubMed

Collar, David C; Quintero, Michelle; Buttler, Bernardo; Ward, Andrea B; Mehta, Rita S

2016-03-01

Major morphological transformations, such as the evolution of elongate body shape in vertebrates, punctuate evolutionary history. A fundamental step in understanding the processes that give rise to such transformations is identification of the underlying anatomical changes. But as we demonstrate in this study, important insights can also be gained by comparing these changes to those that occur in ancestral and closely related lineages. In labyrinth fishes (Anabantoidei), rapid evolution of a highly derived torpedo-shaped body in the common ancestor of the pikehead (Luciocephalus aura and L. pulcher) occurred primarily through exceptional elongation of the head, with secondary contributions involving reduction in body depth and lengthening of the precaudal vertebral region. This combination of changes aligns closely with the primary axis of anatomical diversification in other anabantoids, revealing that pikehead evolution involved extraordinarily rapid change in structures that were ancestrally labile. Finer-scale examination of the anatomical components that determine head elongation also shows alignment between the pikehead evolutionary trajectory and the primary axis of cranial diversification in anabantoids, with much higher evolutionary rates leading to the pikehead. Altogether, our results show major morphological transformation stemming from extreme change along a shared morphological axis in labyrinth fishes. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

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

PubMed Central

Van Holle, Sofie; De Schutter, Kristof; Eggermont, Lore; Tsaneva, Mariya; Dang, Liuyi; Van Damme, Els J. M.

2017-01-01

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins. PMID:28587095

What is a vector?

PubMed Central

Morgan, Eric René; Booth, Mark; Norman, Rachel; Mideo, Nicole; McCallum, Hamish; Fenton, Andy

2017-01-01

Many important and rapidly emerging pathogens of humans, livestock and wildlife are ‘vector-borne’. However, the term ‘vector’ has been applied to diverse agents in a broad range of epidemiological systems. In this perspective, we briefly review some common definitions, identify the strengths and weaknesses of each and consider the functional differences between vectors and other hosts from a range of ecological, evolutionary and public health perspectives. We then consider how the use of designations can afford insights into our understanding of epidemiological and evolutionary processes that are not otherwise apparent. We conclude that from a medical and veterinary perspective, a combination of the ‘haematophagous arthropod’ and ‘mobility’ definitions is most useful because it offers important insights into contact structure and control and emphasizes the opportunities for pathogen shifts among taxonomically similar species with similar feeding modes and internal environments. From a population dynamics and evolutionary perspective, we suggest that a combination of the ‘micropredator’ and ‘sequential’ definition is most appropriate because it captures the key aspects of transmission biology and fitness consequences for the pathogen and vector itself. However, we explicitly recognize that the value of a definition always depends on the research question under study. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289253

Meta-analysis reveals evolution in invasive plant species but little support for Evolution of Increased Competitive Ability (EICA).

PubMed

Felker-Quinn, Emmi; Schweitzer, Jennifer A; Bailey, Joseph K

2013-03-01

Ecological explanations for the success and persistence of invasive species vastly outnumber evolutionary hypotheses, yet evolution is a fundamental process in the success of any species. The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey and Nötzold 1995) proposes that evolutionary change in response to release from coevolved herbivores is responsible for the success of many invasive plant species. Studies that evaluate this hypothesis have used different approaches to test whether invasive populations allocate fewer resources to defense and more to growth and competitive ability than do source populations, with mixed results. We conducted a meta-analysis of experimental tests of evolutionary change in the context of EICA. In contrast to previous reviews, there was no support across invasive species for EICA's predictions regarding defense or competitive ability, although invasive populations were more productive than conspecific native populations under noncompetitive conditions. We found broad support for genetically based changes in defense and competitive plant traits after introduction into new ranges, but not in the manner suggested by EICA. This review suggests that evolution occurs as a result of plant introduction and population expansion in invasive plant species, and may contribute to the invasiveness and persistence of some introduced species.

Meta-analysis reveals evolution in invasive plant species but little support for Evolution of Increased Competitive Ability (EICA)

PubMed Central

Felker-Quinn, Emmi; Schweitzer, Jennifer A; Bailey, Joseph K

2013-01-01

Ecological explanations for the success and persistence of invasive species vastly outnumber evolutionary hypotheses, yet evolution is a fundamental process in the success of any species. The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey and Nötzold 1995) proposes that evolutionary change in response to release from coevolved herbivores is responsible for the success of many invasive plant species. Studies that evaluate this hypothesis have used different approaches to test whether invasive populations allocate fewer resources to defense and more to growth and competitive ability than do source populations, with mixed results. We conducted a meta-analysis of experimental tests of evolutionary change in the context of EICA. In contrast to previous reviews, there was no support across invasive species for EICA's predictions regarding defense or competitive ability, although invasive populations were more productive than conspecific native populations under noncompetitive conditions. We found broad support for genetically based changes in defense and competitive plant traits after introduction into new ranges, but not in the manner suggested by EICA. This review suggests that evolution occurs as a result of plant introduction and population expansion in invasive plant species, and may contribute to the invasiveness and persistence of some introduced species. PMID:23531703

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.

PubMed

Hindersin, Laura; Traulsen, Arne

2015-11-01

We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

PubMed

Raherison, Elie S M; Giguère, Isabelle; Caron, Sébastien; Lamara, Mebarek; MacKay, John J

2015-07-01

Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population.

PubMed

Pulido, Francisco; Berthold, Peter

2010-04-20

Global warming is impacting biodiversity by altering the distribution, abundance, and phenology of a wide range of animal and plant species. One of the best documented responses to recent climate change is alterations in the migratory behavior of birds, but the mechanisms underlying these phenotypic adjustments are largely unknown. This knowledge is still crucial to predict whether populations of migratory birds will adapt to a rapid increase in temperature. We monitored migratory behavior in a population of blackcaps (Sylvia atricapilla) to test for evolutionary responses to recent climate change. Using a common garden experiment in time and captive breeding we demonstrated a genetic reduction in migratory activity and evolutionary change in phenotypic plasticity of migration onset. An artificial selection experiment further revealed that residency will rapidly evolve in completely migratory bird populations if selection for shorter migration distance persists. Our findings suggest that current alterations of the environment are favoring birds wintering closer to the breeding grounds and that populations of migratory birds have strongly responded to these changes in selection. The reduction of migratory activity is probably an important evolutionary process in the adaptation of migratory birds to climate change, because it reduces migration costs and facilitates the rapid adjustment to the shifts in the timing of food availability during reproduction.

Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus

NASA Technical Reports Server (NTRS)

Miller, S. R.; Castenholz, R. W.

2000-01-01

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.

Evolutionary history of Pacific salmon in dynamic environments

PubMed Central

Waples, Robin S; Pess, George R; Beechie, Tim

2008-01-01

Contemporary evolution of Pacific salmon (Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forged during recurrent episodes of Pleistocene glaciation. In northwestern North America, dominant habitat features have been relatively stable for the past 5000 years, but salmon ecosystems remain dynamic because of disturbance regimes (volcanic eruptions, landslides, wildfires, floods, variations in marine and freshwater productivity) that occur on a variety of temporal and spatial scales. These disturbances both create selective pressures for adaptive responses by salmon and inhibit long-term divergence by periodically extirpating local populations and creating episodic dispersal events that erode emerging differences. Recent anthropogenic changes are replicated pervasively across the landscape and interrupt processes that allow natural habitat recovery. If anthropogenic changes can be shaped to produce disturbance regimes that more closely mimic (in both space and time) those under which the species evolved, Pacific salmon should be well-equipped to deal with future challenges, just as they have throughout their evolutionary history. PMID:25567626

A field reciprocal transplant experiment reveals asymmetric costs of migration between lake and river ecotypes of three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Kaufmann, J; Lenz, T L; Kalbe, M; Milinski, M; Eizaguirre, C

2017-05-01

Theory of local adaptation predicts that nonadapted migrants will suffer increased costs compared to local residents. Ultimately this process can result in the reduction of gene flow and culminate in speciation. Here, we experimentally investigated the relative fitness of migrants in foreign habitats, focusing on diverging lake and river ecotypes of three-spined sticklebacks. A reciprocal transplant experiment performed in the field revealed asymmetric costs of migration: whereas mortality of river fish was increased under lake conditions, lake migrants suffered from reduced growth relative to river residents. Selection against migrants thus involved different traits in each habitat but generally contributed to bidirectional reduction in gene flow. Focusing particularly on the parasitic environments, migrant fish differed from resident fish in the parasite community they harboured. This pattern correlated with both cellular phenotypes of innate immunity as well as with allelic variation at the genes of the major histocompatibility complex. In addition to showing the costs of migration in three-spined sticklebacks, this study highlights the role of asymmetric selection particularly from parasitism in genotype sorting and in the emergence of local adaptation. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

PubMed

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.

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

PubMed

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.

The semaphorontic view of homology.

PubMed

Havstad, Joyce C; Assis, Leandro C S; Rieppel, Olivier

2015-11-01

The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra-organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter-species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity--ontogenetic (through development) and phylogenetic (via shared evolutionary history)--break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (-state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (-states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Fewer invited talks by women in evolutionary biology symposia.

PubMed

Schroeder, J; Dugdale, H L; Radersma, R; Hinsch, M; Buehler, D M; Saul, J; Porter, L; Liker, A; De Cauwer, I; Johnson, P J; Santure, A W; Griffin, A S; Bolund, E; Ross, L; Webb, T J; Feulner, P G D; Winney, I; Szulkin, M; Komdeur, J; Versteegh, M A; Hemelrijk, C K; Svensson, E I; Edwards, H; Karlsson, M; West, S A; Barrett, E L B; Richardson, D S; van den Brink, V; Wimpenny, J H; Ellwood, S A; Rees, M; Matson, K D; Charmantier, A; Dos Remedios, N; Schneider, N A; Teplitsky, C; Laurance, W F; Butlin, R K; Horrocks, N P C

2013-09-01

Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001-2011, 9-23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Genes under weaker stabilizing selection increase network evolvability and rapid regulatory adaptation to an environmental shift.

PubMed

Laarits, T; Bordalo, P; Lemos, B

2016-08-01

Regulatory networks play a central role in the modulation of gene expression, the control of cellular differentiation, and the emergence of complex phenotypes. Regulatory networks could constrain or facilitate evolutionary adaptation in gene expression levels. Here, we model the adaptation of regulatory networks and gene expression levels to a shift in the environment that alters the optimal expression level of a single gene. Our analyses show signatures of natural selection on regulatory networks that both constrain and facilitate rapid evolution of gene expression level towards new optima. The analyses are interpreted from the standpoint of neutral expectations and illustrate the challenge to making inferences about network adaptation. Furthermore, we examine the consequence of variable stabilizing selection across genes on the strength and direction of interactions in regulatory networks and in their subsequent adaptation. We observe that directional selection on a highly constrained gene previously under strong stabilizing selection was more efficient when the gene was embedded within a network of partners under relaxed stabilizing selection pressure. The observation leads to the expectation that evolutionarily resilient regulatory networks will contain optimal ratios of genes whose expression is under weak and strong stabilizing selection. Altogether, our results suggest that the variable strengths of stabilizing selection across genes within regulatory networks might itself contribute to the long-term adaptation of complex phenotypes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolutionary engineering for industrial microbiology.

PubMed

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

2012-01-01

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

Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

PubMed Central

Bryson, David M.; Ofria, Charles

2013-01-01

We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a broad range of challenges. PMID:24376669

Adaptive memory: young children show enhanced retention of fitness-related information.

PubMed

Aslan, Alp; Bäuml, Karl-Heinz T

2012-01-01

Evolutionary psychologists propose that human cognition evolved through natural selection to solve adaptive problems related to survival and reproduction, with its ultimate function being the enhancement of reproductive fitness. Following this proposal and the evolutionary-developmental view that ancestral selection pressures operated not only on reproductive adults, but also on pre-reproductive children, the present study examined whether young children show superior memory for information that is processed in terms of its survival value. In two experiments, we found such survival processing to enhance retention in 4- to 10-year-old children, relative to various control conditions that also required deep, meaningful processing but were not related to survival. These results suggest that, already in very young children, survival processing is a special and extraordinarily effective form of memory encoding. The results support the functional-evolutionary proposal that young children's memory is "tuned" to process and retain fitness-related information. Copyright © 2011 Elsevier B.V. All rights reserved.

Evolutionary perspectives on learning: conceptual and methodological issues in the study of adaptive specializations.

PubMed

Krause, Mark A

2015-07-01

Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.

Cultural Adaptations to Environmental Variability: An Evolutionary Account of East-West Differences

ERIC Educational Resources Information Center

Chang, Lei; Mak, Miranda C. K.; Li, Tong; Wu, Bao Pei; Chen, Bin Bin; Lu, Hui Jing

2011-01-01

Much research has been conducted to document and sometimes to provide proximate explanations (e.g., Confucianism vs. Western philosophy) for East-West cultural differences. The ultimate evolutionary mechanisms underlying these cross-cultural differences have not been addressed. We propose in this review that East-West cultural differences (e.g.,…

Informations in Models of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Rivoire, Olivier

2016-03-01

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

Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation.

PubMed

López-Malo, María; García-Rios, Estéfani; Melgar, Bruno; Sanchez, Monica R; Dunham, Maitreya J; Guillamón, José Manuel

2015-07-22

Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted at low temperature is interesting for future biotechnological applications. This study aimed to select and develop wine yeast strains that well adapt to ferment at low temperature through evolutionary engineering, and to decipher the process underlying the obtained phenotypes. We used a pool of 27 commercial yeast strains and set up batch serial dilution experiments to mimic wine fermentation conditions at 12 °C. Evolutionary engineering was accomplished by using the natural yeast mutation rate and mutagenesis procedures. One strain (P5) outcompeted the others under both experimental conditions and was able to impose after 200 generations. The evolved strains showed improved growth and low-temperature fermentation performance compared to the ancestral strain. This improvement was acquired only under inositol limitation. The transcriptomic comparison between the evolved and parental strains showed the greatest up-regulation in four mannoprotein coding genes, which belong to the DAN/TIR family (DAN1, TIR1, TIR4 and TIR3). Genome sequencing of the evolved strain revealed the presence of a SNP in the GAA1 gene and the construction of a site-directed mutant (GAA1 (Thr108)) in a derivative haploid of the ancestral strain resulted in improved fermentation performance. GAA1 encodes a GPI transamidase complex subunit that adds GPI, which is required for inositol synthesis, to newly synthesized proteins, including mannoproteins. In this study we demonstrate the importance of inositol and mannoproteins in yeast adaptation at low temperature and the central role of the GAA1 gene by linking both metabolisms.

Probabilistic and Evolutionary Early Warning System: concepts, performances, and case-studies

NASA Astrophysics Data System (ADS)

Zollo, A.; Emolo, A.; Colombelli, S.; Elia, L.; Festa, G.; Martino, C.; Picozzi, M.

2013-12-01

PRESTo (PRobabilistic and Evolutionary early warning SysTem) is a software platform for Earthquake Early Warning that integrates algorithms for real-time earthquake location, magnitude estimation and damage assessment into a highly configurable and easily portable package. In its regional configuration, the software processes, in real-time, the 3-component acceleration data streams coming from seismic stations, for P-waves arrival detection and, in the case a quite large event is occurring, can promptly performs event detection and location, magnitude estimation and peak ground-motion prediction at target sites. The regional approach has been integrated with a threshold-based early warning method that allows, in the very first seconds after a moderate-to-large earthquake, to identify the most Probable Damaged Zone starting from the real-time measurement at near-source stations located at increasing distances from the earthquake epicenter, of the peak displacement (Pd) and predominant period of P-waves (τc), over a few-second long window after the P-wave arrival. Thus, each recording site independently provides an evolutionary alert level, according to the Pd and τc it measured, through a decisional table. Since 2009, PRESTo has been under continuous real-time testing using data streaming from the Iripinia Seismic Network (Southern Italy) and has produced a bulletin of some hundreds low magnitude events, including all the M≥2.5 earthquakes occurred in that period in Irpinia. Recently, PRESTo has been also implemented at the accelerometric network and broad-band networks in South Korea and in Romania, and off-line tested in Iberian Peninsula, in Turkey, in Israel, and in Japan. The feasibility of an Early Warning System at national scale, is currently under testing by studying the performances of the PRESTo platform for the Italian Accelerometric Network. Moreover, PRESTo is under experimentation in order to provide alert in a high-school located in the neighborhood of Naples at about 100 km from the Irpinia region.

Genomic signatures of evolutionary transitions from solitary to group living

USDA-ARS?s Scientific Manuscript database

Eusociality has evolved rarely, but repeatedly, in vertebrates and invertebrates, and resulted inconvergent morphological, physiological, and behavioural innovations. It is unknown whether similar evolutionary processes are responsible for the repeated origins and further elaborations of eusociality...

XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

DOE PAGES

Falls, Zackary; Lonie, David C.; Avery, Patrick; ...

2015-10-23

This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction available for download from the CPC library or the XtalOpt website, http://xtalopt.github.io. XtalOpt is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

The evolutionary psychology of violence.

PubMed

Goetz, Aaron T

2010-02-01

This paper reviews theory and research on the evolutionary psychology of violence. First, I examine evidence suggesting that humans have experienced an evolutionary history of violence. Next, I discuss violence as a context-sensitive strategy that might have provided benefits to our ancestors under certain circumstances. I then focus on the two most common forms of violence that plague humans -violence over status contests and intimate partner violence- outlining psychological mechanisms involved in each. Finally, I suggest that greater progress will be made by shifting the study from contexts to mechanisms.

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

PubMed

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.

Evolutionary origins of a novel host plant detoxification gene in butterflies.

PubMed

Fischer, Hanna M; Wheat, Christopher W; Heckel, David G; Vogel, Heiko

2008-05-01

Chemical interactions between plants and their insect herbivores provide an excellent opportunity to study the evolution of species interactions on a molecular level. Here, we investigate the molecular evolutionary events that gave rise to a novel detoxifying enzyme (nitrile-specifier protein [NSP]) in the butterfly family Pieridae, previously identified as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries, and screening databases we found NSP to be a member of an insect-specific gene family, which we characterized and named the NSP-like gene family. Members consist of variable tandem repeats, are gut expressed, and are found across Insecta evolving in a dynamic, ongoing birth-death process. In the Lepidoptera, multiple copies of single-domain major allergen genes are present and originate via tandem duplications. Multiple domain genes are found solely within the brassicaceous-feeding Pieridae butterflies, one of them being NSP and another called major allergen (MA). Analyses suggest that NSP and its paralog MA have a unique single-domain evolutionary origin, being formed by intragenic domain duplication followed by tandem whole-gene duplication. Duplicates subsequently experienced a period of relaxed constraint followed by an increase in constraint, perhaps after neofunctionalization. NSP and its ortholog MA are still experiencing high rates of change, reflecting a dynamic evolution consistent with the known role of NSP in plant-insect interactions. Our results provide direct evidence to the hypothesis that gene duplication is one of the driving forces for speciation and adaptation, showing that both within- and whole-gene tandem duplications are a powerful force underlying evolutionary adaptation.

Rapid evolution of larval life history, adult immune function and flight muscles in a poleward-moving damselfly.

PubMed

Therry, L; Nilsson-Örtman, V; Bonte, D; Stoks, R

2014-01-01

Although a growing number of studies have documented the evolution of adult dispersal-related traits at the range edge of poleward-expanding species, we know little about evolutionary changes in immune function or traits expressed by nondispersing larvae. We investigated differentiation in larval (growth and development) and adult traits (immune function and flight-related traits) between replicated core and edge populations of the poleward-moving damselfly Coenagrion scitulum. These traits were measured on individuals reared in a common garden experiment at two different food levels, as allocation trade-offs may be easier to detect under energy shortage. Edge individuals had a faster larval life history (growth and development rates), a higher adult immune function and a nearly significant higher relative flight muscle mass. Most of the differentiation between core and edge populations remained and edge populations had a higher relative flight muscle mass when corrected for latitude-specific thermal regimes, and hence could likely be attributed to the range expansion process per se. We here for the first time document a higher immune function in individuals at the expansion front of a poleward-expanding species and documented the rarely investigated evolution of faster life histories during range expansion. The rapid multivariate evolution in these ecological relevant traits between edge and core populations is expected to translate into changed ecological interactions and therefore has the potential to generate novel eco-evolutionary dynamics at the expansion front. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

PubMed

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.

Introduction to the special issue: Tree invasions: towards a better understanding of their complex evolutionary dynamics.

PubMed

Hirsch, Heidi; Richardson, David M; Le Roux, Johannes J

2017-05-01

Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees. The main outcome of this workshop is this Special Issue of AoB PLANTS . The collection of papers in this issue has helped to identify and assess the evolutionary mechanisms that are likely to influence tree invasions. It also facilitated expansion of the unified framework for biological invasions to incorporate key evolutionary processes. The papers cover a wide range of evolutionary mechanisms in tree genomes (adaptation), epigenomes (phenotypic plasticity) and their second genomes (mutualists), and show how such mechanisms can impact tree invasion processes and management. The special issue provides a comprehensive overview of the factors that promote and mitigate the invasive success of tree species in many parts of the world. It also shows that incorporating evolutionary concepts is crucial for understanding the complex drivers of tree invasions and has much potential to improve management. The contributions of the special issue also highlight many priorities for further work in the face of ever-increasing tree invasions; the complexity of this research needs calls for expanded interdisciplinary research collaborations.

Cancer Evolution: Mathematical Models and Computational Inference

PubMed Central

Beerenwinkel, Niko; Schwarz, Roland F.; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. PMID:25293804

Why flying dogs are rare: A general theory of luck in evolutionary transitions.

PubMed

Fleming, Leonore; Brandon, Robert

2015-02-01

There is a worry that the 'major transitions in evolution' represent an arbitrary group of events. This worry is warranted, and we show why. We argue that the transition to a new level of hierarchy necessarily involves a nonselectionist chance process. Thus any unified theory of evolutionary transitions must be more like a general theory of fortuitous luck, rather than a rigid formulation of expected events. We provide a systematic account of evolutionary transitions based on a second-order regularity of chance events, as stipulated by the ZFEL (Zero Force Evolutionary Law). And in doing so, we make evolutionary transitions explainable and predictable, and so not entirely contingent after all. Copyright © 2014 Elsevier Ltd. All rights reserved.

Research traditions and evolutionary explanations in medicine.

PubMed

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'.

Evolution: Language Use and the Evolution of Languages

NASA Astrophysics Data System (ADS)

Croft, William

Language change can be understood as an evolutionary process. Language change occurs at two different timescales, corresponding to the two steps of the evolutionary process. The first timescale is very short, namely, the production of an utterance: this is where linguistic structures are replicated and language variation is generated. The second timescale is (or can be) very long, namely, the propagation of linguistic variants in the speech community: this is where certain variants are selected over others. At both timescales, the evolutionary process is driven by social interaction and the role language plays in it. An understanding of social interaction at the micro-level—face-to-face interactions—and at the macro-level—the structure of speech communities—gives us the basis for understanding the generation and propagation of language structures, and understanding the nature of language itself.

An evolutionary approach to financial history.

PubMed

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."

Clonal evolution of colorectal cancer in IBD.

PubMed

Choi, Chang-Ho R; Bakir, Ibrahim Al; Hart, Ailsa L; Graham, Trevor A

2017-04-01

Optimizing the management of colorectal cancer (CRC) risk in IBD requires a fundamental understanding of the evolutionary process underpinning tumorigenesis. In IBD, clonal evolution begins long before the development of overt neoplasia, and is probably accelerated by the repeated cycles of epithelial wounding and repair that are characteristic of the condition. Here, we review the biological drivers of mutant clone selection in IBD with particular reference to the unique histological architecture of the intestinal epithelium coupled with the inflammatory microenvironment in IBD, and the unique mutation patterns seen in IBD-driven neoplasia when compared with sporadic adenomas and CRC. How these data can be leveraged as evolutionary-based biomarkers to predict cancer risk is discussed, as well as how the efficacy of CRC surveillance programmes and the management of dysplasia can be improved. From a research perspective, the longitudinal surveillance of patients with IBD provides an under-exploited opportunity to investigate the biology of the human gastrointestinal tract over space and time.

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies.

PubMed

Organ, Chris L; Cooper, Lisa Noelle; Hieronymus, Tobin L

2015-10-01

The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization. © 2015 Wiley Periodicals, Inc.

Modalities of gene action predicted by the classical evolutionary biological theory of aging.

PubMed

Martin, George M

2007-04-01

What might now be referred to as the "classical" evolutionary biological theory of why we age has had a number of serious challenges in recent years. While the theory might therefore have to be modified under certain circumstances, in the author's opinion, it still provides the soundest theoretical basis for thinking about how we age. Nine modalities of gene action that have the potential to modulate processes of aging are reviewed, including the two most widely reviewed and accepted concepts ("antagonistic pleiotropy" and "mutation accumulation"). While several of these nine mechanisms can be regarded as derivatives of the antagonistic pleiotropic concept, they frame more specific questions for future research. Such research should pursue what appears to be the dominant factor in the determination of intraspecific variations in longevity-stochastic mechanisms, most likely based upon epigenetics. This contrasts with the dominant factor in the determination of interspecific variations in longevity-the constitutional genome, most likely based upon variations in regulatory loci.

Morphomechanics and Developmental Constraints in the Evolution of Ammonites Shell Form.

PubMed

Erlich, Alexander; Moulton, Derek E; Goriely, Alain; Chirat, Regis

2016-11-01

The idea that physical processes involved in biological development underlie morphogenetic rules and channel morphological evolution has been central to the rise of evolutionary developmental biology. Here, we explore this idea in the context of seashell morphogenesis. We show that a morphomechanical model predicts the effects of variations in shell shape on the ornamental pattern in ammonites, a now extinct group of cephalopods with external chambered shell. Our model shows that several seemingly unrelated characteristics of synchronous, ontogenetic, intraspecific, and evolutionary variations in ornamental patterns among various ammonite species may all be understood from the fact that the mechanical forces underlying the oscillatory behavior of the shell secreting system scale with the cross-sectional curvature of the shell aperture. This simple morphogenetic rule, emerging from biophysical interactions during shell formation, introduced a non-random component in the production of phenotypic variation and channeled the morphological evolution of ammonites over millions of years. As such, it provides a paradigm for the concept of "developmental constraints." © 2016 Wiley Periodicals, Inc.

Integrated Controls-Structures Design Methodology: Redesign of an Evolutionary Test Structure

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Gupta, Sandeep; Elliot, Kenny B.; Joshi, Suresh M.

1997-01-01

An optimization-based integrated controls-structures design methodology for a class of flexible space structures is described, and the phase-0 Controls-Structures-Integration evolutionary model, a laboratory testbed at NASA Langley, is redesigned using this integrated design methodology. The integrated controls-structures design is posed as a nonlinear programming problem to minimize the control effort required to maintain a specified line-of-sight pointing performance, under persistent white noise disturbance. Static and dynamic dissipative control strategies are employed for feedback control, and parameters of these controllers are considered as the control design variables. Sizes of strut elements in various sections of the CEM are used as the structural design variables. Design guides for the struts are developed and employed in the integrated design process, to ensure that the redesigned structure can be effectively fabricated. The superiority of the integrated design methodology over the conventional design approach is demonstrated analytically by observing a significant reduction in the average control power needed to maintain specified pointing performance with the integrated design approach.

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

PubMed

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.

Landscape community genomics: understanding eco-evolutionary processes in complex environments

USGS Publications Warehouse

Hand, Brian K.; Lowe, Winsor H.; Kovach, Ryan P.; Muhlfeld, Clint C.; Luikart, Gordon

2015-01-01

Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Evolutionary grinding model for nanometric control of surface roughness for aspheric optical surfaces.

PubMed

Han, Jeong-Yeol; Kim, Sug-Whan; Han, Inwoo; Kim, Geon-Hee

2008-03-17

A new evolutionary grinding process model has been developed for nanometric control of material removal from an aspheric surface of Zerodur substrate. The model incorporates novel control features such as i) a growing database; ii) an evolving, multi-variable regression equation; and iii) an adaptive correction factor for target surface roughness (Ra) for the next machine run. This process model demonstrated a unique evolutionary controllability of machining performance resulting in the final grinding accuracy (i.e. averaged difference between target and measured surface roughness) of -0.2+/-2.3(sigma) nm Ra over seven trial machine runs for the target surface roughness ranging from 115 nm to 64 nm Ra.

Evolutionary disarmament in interspecific competition.

PubMed

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 disarmament in interspecific competition.

PubMed Central

Kisdi, E.; Geritz, S. A.

2001-01-01

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. PMID:11749715

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

EPA Science Inventory

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 ...

The Genomic Basis for Evolved Pollution Tolerance in Killifish (Fundulus heterclitus).

EPA Science Inventory

Uncovering the molecular mechanisms of adaptive variation is a leading challenge in evolutionary biology. Identifying genes that influence ecological traits can provide insight into the evolutionary processes behind genomic responses to environmental change. Here, we examine the...

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

PubMed Central

Baele, Guy; Lemey, Philippe; Suchard, Marc A.

2016-01-01

Marginal likelihood estimates to compare models using Bayes factors frequently accompany Bayesian phylogenetic inference. Approaches to estimate marginal likelihoods have garnered increased attention over the past decade. In particular, the introduction of path sampling (PS) and stepping-stone sampling (SS) into Bayesian phylogenetics has tremendously improved the accuracy of model selection. These sampling techniques are now used to evaluate complex evolutionary and population genetic models on empirical data sets, but considerable computational demands hamper their widespread adoption. Further, when very diffuse, but proper priors are specified for model parameters, numerical issues complicate the exploration of the priors, a necessary step in marginal likelihood estimation using PS or SS. To avoid such instabilities, generalized SS (GSS) has recently been proposed, introducing the concept of “working distributions” to facilitate—or shorten—the integration process that underlies marginal likelihood estimation. However, the need to fix the tree topology currently limits GSS in a coalescent-based framework. Here, we extend GSS by relaxing the fixed underlying tree topology assumption. To this purpose, we introduce a “working” distribution on the space of genealogies, which enables estimating marginal likelihoods while accommodating phylogenetic uncertainty. We propose two different “working” distributions that help GSS to outperform PS and SS in terms of accuracy when comparing demographic and evolutionary models applied to synthetic data and real-world examples. Further, we show that the use of very diffuse priors can lead to a considerable overestimation in marginal likelihood when using PS and SS, while still retrieving the correct marginal likelihood using both GSS approaches. The methods used in this article are available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses. PMID:26526428

Linking micro- and macro-evolution at the cell type level: a view from the lophotrochozoan Platynereis dumerilii.

PubMed

Simakov, Oleg; Larsson, Tomas A; Arendt, Detlev

2013-09-01

Ever since the origin of the first metazoans over 600 million years ago, cell type diversification has been driven by micro-evolutionary processes at population level, leading to macro-evolution changes above species level. In this review, we introduce the marine annelid Platynereis dumerilii, a member of the lophotrochozoan clade (a key yet most understudied superphylum of bilaterians), as a suitable model system for the simultaneous study, at cellular resolution, of macro-evolutionary processes across phyla and of micro-evolutionary processes across highly polymorphic populations collected worldwide. Recent advances in molecular and experimental techniques, easy maintenance and breeding, and the fast, synchronous and stereotypical development have facilitated the establishment of Platynereis as one of the leading model species in the eco-evo-devo field. Most importantly, Platynereis allows the combination of expression profiling, morphological and physiological characterization at the single cell level. Here, we discuss recent advances in the collection of -omics data for the lab strain and for natural populations collected world-wide that can be integrated with population-specific cellular analyses to result in a cellular atlas integrating genetic, phenotypic and ecological variation. This makes Platynereis a tractable system to begin understanding the interplay between macro- and micro-evolutionary processes and cell type diversity.

Biological and geophysical feedbacks with fire in the Earth system

NASA Astrophysics Data System (ADS)

Archibald, S.; Lehmann, C. E. R.; Belcher, C. M.; Bond, W. J.; Bradstock, R. A.; Daniau, A.-L.; Dexter, K. G.; Forrestel, E. J.; Greve, M.; He, T.; Higgins, S. I.; Hoffmann, W. A.; Lamont, B. B.; McGlinn, D. J.; Moncrieff, G. R.; Osborne, C. P.; Pausas, J. G.; Price, O.; Ripley, B. S.; Rogers, B. M.; Schwilk, D. W.; Simon, M. F.; Turetsky, M. R.; Van der Werf, G. R.; Zanne, A. E.

2018-03-01

Roughly 3% of the Earth’s land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

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

PubMed

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.

Polymorphic Evolutionary Games.

PubMed

Fishman, Michael A

2016-06-07

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

Magnetoreception in birds: different physical processes for two types of directional responses

PubMed Central

Wiltschko, Roswitha; Stapput, Katrin; Ritz, Thorsten; Thalau, Peter; Wiltschko, Wolfgang

2007-01-01

Migratory orientation in birds involves an inclination compass based on radical-pair processes. Under certain light regimes, however, “fixed-direction” responses are observed that do not undergo the seasonal change between spring and autumn typical for migratory orientation. To identify the underlying transduction mechanisms, we analyzed a fixed-direction response under a combination of 502 nm turquoise and 590 nm yellow light, with migratory orientation under 565 nm green light serving as the control. High-frequency fields, diagnostic for a radical-pair mechanism, disrupted migratory orientation without affecting fixed-direction responses. Local anaesthesia of the upper beak where magnetite is found in birds, in contrast, disrupted the fixed-direction response without affecting migratory orientation. The two types of responses are thus based on different physical principles, with the compass response based on a radical pair mechanism and the fixed-direction responses probably originating in magnetite-based receptors in the upper beak. Directional input from these receptors seems to affect the behavior only when the regular inclination compass does not work properly. Evolutionary considerations suggest that magnetite-based receptors may represent an ancient mechanism that, in birds, has been replaced by the modern inclination compass based on radical-pair processes now used for directional orientation. PMID:19404459

Enhanced Memory for both Threat and Neutral Information Under Conditions of Intergroup Threat

PubMed Central

Zhu, Yong; Zhao, Yufang; Ybarra, Oscar; Stephan, Walter G.; Yang, Qing

2015-01-01

Few studies have examined the effect of intergroup threat on cognitive outcomes such as memory. Different theoretical perspectives can inform how intergroup threat should affect memory for threat-relevant and neutral information, such as the mood-congruency approach, Yerkes–Dodson law, Easterbrook’s theory, and also evolutionary perspectives. To test among these, we conducted two experiments to examine how exposure to intergroup threats affected memory compared to control conditions. In study 1, we manipulated symbolic threat and examined participants’ memory for threat and neutral words. In study 2, memory performance was assessed following the induction of realistic threat. Across the studies, in the control condition participants showed better memory for threat-related than neutral information. However, participants under threat remembered neutral information as well as threat-related information. In addition, participants in the threat condition remembered threat-related information as well as participants in the control condition. The findings are discussed in terms of automatic vigilance processes but also the effects of threat on arousal and its effect on information processing. This latter perspective, suggests paradoxically, that under some circumstances involving an outgroup threat, non-threatening information about outgroups can be extensively processed. PMID:26635669

What affects the predictability of evolutionary constraints using a G-matrix? The relative effects of modular pleiotropy and mutational correlation.

PubMed

Chebib, Jobran; Guillaume, Frédéric

2017-10-01

Phenotypic traits do not always respond to selection independently from each other and often show correlated responses to selection. The structure of a genotype-phenotype map (GP map) determines trait covariation, which involves variation in the degree and strength of the pleiotropic effects of the underlying genes. It is still unclear, and debated, how much of that structure can be deduced from variational properties of quantitative traits that are inferred from their genetic (co) variance matrix (G-matrix). Here we aim to clarify how the extent of pleiotropy and the correlation among the pleiotropic effects of mutations differentially affect the structure of a G-matrix and our ability to detect genetic constraints from its eigen decomposition. We show that the eigenvectors of a G-matrix can be predictive of evolutionary constraints when they map to underlying pleiotropic modules with correlated mutational effects. Without mutational correlation, evolutionary constraints caused by the fitness costs associated with increased pleiotropy are harder to infer from evolutionary metrics based on a G-matrix's geometric properties because uncorrelated pleiotropic effects do not affect traits' genetic correlations. Correlational selection induces much weaker modular partitioning of traits' genetic correlations in absence then in presence of underlying modular pleiotropy. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Controlled recovery of phylogenetic communities from an evolutionary model using a network approach

NASA Astrophysics Data System (ADS)

Sousa, Arthur M. Y. R.; Vieira, André P.; Prado, Carmen P. C.; Andrade, Roberto F. S.

2016-04-01

This works reports the use of a complex network approach to produce a phylogenetic classification tree of a simple evolutionary model. This approach has already been used to treat proteomic data of actual extant organisms, but an investigation of its reliability to retrieve a traceable evolutionary history is missing. The used evolutionary model includes key ingredients for the emergence of groups of related organisms by differentiation through random mutations and population growth, but purposefully omits other realistic ingredients that are not strictly necessary to originate an evolutionary history. This choice causes the model to depend only on a small set of parameters, controlling the mutation probability and the population of different species. Our results indicate that for a set of parameter values, the phylogenetic classification produced by the used framework reproduces the actual evolutionary history with a very high average degree of accuracy. This includes parameter values where the species originated by the evolutionary dynamics have modular structures. In the more general context of community identification in complex networks, our model offers a simple setting for evaluating the effects, on the efficiency of community formation and identification, of the underlying dynamics generating the network itself.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification.

PubMed

Robertson, Fiona M; Gundappa, Manu Kumar; Grammes, Fabian; Hvidsten, Torgeir R; Redmond, Anthony K; Lien, Sigbjørn; Martin, Samuel A M; Holland, Peter W H; Sandve, Simen R; Macqueen, Daniel J

2017-06-14

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.

Emergence of life: Physical chemistry changes the paradigm.

PubMed

Spitzer, Jan; Pielak, Gary J; Poolman, Bert

2015-06-10

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Evolutionary Analysis of Structural Protein Gene VP1 of Foot-and-Mouth Disease Virus Serotype Asia 1

PubMed Central

Zhang, Qingxun; Liu, Xinsheng; Fang, Yuzhen; Pan, Li; Lv, Jianliang; Zhang, Zhongwang; Zhou, Peng; Ding, Yaozhong; Chen, Haotai; Shao, Junjun; Zhao, Furong; Lin, Tong; Chang, Huiyun; Zhang, Jie; Wang, Yonglu; Zhang, Yongguang

2015-01-01

Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I–VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10−3 substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown. PMID:25793223

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

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

NASA Astrophysics Data System (ADS)

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 important in explaining recruitment. Overall, through integration of ecological and evolutionary techniques, and using multiple spatial scales, our study offers a unique perspective on factors determining coral-reef fish assemblages.

Bigger testes increase paternity in a simultaneous hermaphrodite, independently of the sperm competition level.

PubMed

Vellnow, N; Marie-Orleach, L; Zadesenets, K S; Schärer, L

2018-02-01

Hermaphroditic animals face the fundamental evolutionary optimization problem of allocating their resources to their male vs. female reproductive function (e.g. testes and sperm vs. ovaries and eggs), and this optimal sex allocation can be affected by both pre- and post-copulatory sexual selection. For example, local sperm competition (LSC) - the competition between related sperm for the fertilization of a partner's ova - occurs in small mating groups and can favour a female-biased sex allocation, because, under LSC, investment into sperm production is predicted to show diminishing fitness returns. Here, we test whether higher testis investment increases an individual's paternity success under sperm competition, and whether the strength of this effect diminishes when LSC is stronger, as predicted by sex allocation theory. We created two subsets of individuals of the simultaneously hermaphroditic flatworm Macrostomum lignano - by sampling worms from either the highest or lowest quartile of the testis investment distribution - and estimated their paternity success in group sizes of either three (strong LSC) or eight individuals (weak LSC). Specifically, using transgenic focal individuals expressing a dominant green-fluorescent protein marker, we showed that worms with high testis investment sired 22% more offspring relative to those with low investment, corroborating previous findings in M. lignano and other species. However, the strength of this effect was not significantly modulated by the experienced group size, contrasting theoretical expectations of more strongly diminishing fitness returns under strong LSC. We discuss the possible implications for the evolutionary maintenance of hermaphroditism in M. lignano. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The semaphorontic view of homology

PubMed Central

Assis, Leandro C.S.; Rieppel, Olivier

2015-01-01

ABSTRACT The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra‐organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter‐species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity—ontogenetic (through development) and phylogenetic (via shared evolutionary history)—break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (‐state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (‐states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 578–587, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26175214

Prospectus

PubMed Central

Parsons, Peter A.

2009-01-01

Free living organisms typically occur in harsh environments challenged by abiotic stresses of varying intensities. Taking ionizing radiation and caloric restriction as examples, environmental variation from benign to extreme gives a fitness-stress continuum where energetic efficiency, a measure of fitness, is inversely related to stress level. Hormesis occurs in benign regions for these examples. In contrast aging emphasizes survival towards the limits of survival under accumulating stress from Reactive Oxygen Species, ROS. An energetic evolutionary approach underlies an ecological aging theory based principally upon survival, which incorporates hormesis. Multiple environmental agents contributing to hormesis should be considered by those attempting to improve the quality of life by delaying the onset of senescence, so enhancing survival. Caloric restriction has wider acceptance in this process than ionizing radiation. PMID:20221282

Climbing Mount Probable

ERIC Educational Resources Information Center

Harper, Marc Allen

2009-01-01

This work attempts to explain the relationships between natural selection, information theory, and statistical inference. In particular, a geometric formulation of information theory known as information geometry and its deep connections to evolutionary game theory inform the role of natural selection in evolutionary processes. The goals of this…

Evolutionary trade-offs in kidney injury and repair.

PubMed

Lei, Yutian; Anders, Hans-Joachim

2017-11-01

Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.

Common evolutionary trends underlie the four-bar linkage systems of sunfish and mantis shrimp.

PubMed

Hu, Yinan; Nelson-Maney, Nathan; Anderson, Philip S L

2017-05-01

Comparative biomechanics offers an opportunity to explore the evolution of disparate biological systems that share common underlying mechanics. Four-bar linkage modeling has been applied to various biological systems such as fish jaws and crustacean appendages to explore the relationship between biomechanics and evolutionary diversification. Mechanical sensitivity states that the functional output of a mechanical system will show differential sensitivity to changes in specific morphological components. We document similar patterns of mechanical sensitivity in two disparate four-bar systems from different phyla: the opercular four-bar system in centrarchid fishes and the raptorial appendage of stomatopods. We built dynamic linkage models of 19 centrarchid and 36 stomatopod species and used phylogenetic generalized least squares regression (PGLS) to compare evolutionary shifts in linkage morphology and mechanical outputs derived from the models. In both systems, the kinematics of the four-bar mechanism show significant evolutionary correlation with the output link, while travel distance of the output arm is correlated with the coupler link. This common evolutionary pattern seen in both fish and crustacean taxa is a potential consequence of the mechanical principles underlying four-bar systems. Our results illustrate the potential influence of physical principles on morphological evolution across biological systems with different structures, behaviors, and ecologies. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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

PubMed

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.

Biological causal links on physiological and evolutionary time scales.

PubMed

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.

Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

PubMed Central

Matz, Mikhail V.; Bayer, Till; Aranda, Manuel; Buschiazzo, Emmanuel; DeSalvo, Michael K.; Lindquist, Erika; Szmant, Alina M.; Coffroth, Mary Alice; Medina, Mónica

2011-01-01

Background Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably. Methodology/Principal Findings We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium. Conclusion/Relevance This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change. PMID:21633702

Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voolstra, Christian R.; Sunagawa, Shinichi; Matz, Mikhail V.

Background: Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably. Methodology/Principal Findings: We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experiencemore » adaptive evolution. 7percent of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineagespecific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium. Conclusion/Relevance: This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals? evolutionary response to global climate change.« less

Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes

PubMed Central

Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

2016-01-01

Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success. PMID:26784357

Evolutionary Multiobjective Design Targeting a Field Programmable Transistor Array

NASA Technical Reports Server (NTRS)

Aguirre, Arturo Hernandez; Zebulum, Ricardo S.; Coello, Carlos Coello

2004-01-01

This paper introduces the ISPAES algorithm for circuit design targeting a Field Programmable Transistor Array (FPTA). The use of evolutionary algorithms is common in circuit design problems, where a single fitness function drives the evolution process. Frequently, the design problem is subject to several goals or operating constraints, thus, designing a suitable fitness function catching all requirements becomes an issue. Such a problem is amenable for multi-objective optimization, however, evolutionary algorithms lack an inherent mechanism for constraint handling. This paper introduces ISPAES, an evolutionary optimization algorithm enhanced with a constraint handling technique. Several design problems targeting a FPTA show the potential of our approach.