Sample records for modeling neutral evolution
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The role of weak selection and high mutation rates in nearly neutral evolution.
Lawson, Daniel John; Jensen, Henrik Jeldtoft
2009-04-21
Neutral dynamics occur in evolution if all types are 'effectively equal' in their reproductive success, where the definition of 'effectively equal' depends on the population size and the details of mutations. Empirically observed neutral genetic evolution in extremely large clonal populations can only be explained under current models if selection is completely absent. Such models typically consider the case where population dynamics occurs on a different timescale to evolution. However, this assumption is invalid when mutations are not rare in a whole population. We show that this has important consequences for the occurrence of neutral evolution in clonal populations. In highly connected type spaces, neutral dynamics can occur for all population sizes despite significant selective differences, via the forming of effectively neutral networks connecting rare neutral types. Biological implications include an explanation for the high diversity of rare types that survive in large clonal populations, and a theoretical justification for the use of neutral null models.
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Neutral null models for diversity in serial transfer evolution experiments.
Harpak, Arbel; Sella, Guy
2014-09-01
Evolution experiments with microorganisms coupled with genome-wide sequencing now allow for the systematic study of population genetic processes under a wide range of conditions. In learning about these processes in natural, sexual populations, neutral models that describe the behavior of diversity and divergence summaries have played a pivotal role. It is therefore natural to ask whether neutral models, suitably modified, could be useful in the context of evolution experiments. Here, we introduce coalescent models for polymorphism and divergence under the most common experimental evolution assay, a serial transfer experiment. This relatively simple setting allows us to address several issues that could affect diversity patterns in evolution experiments, whether selection is operating or not: the transient behavior of neutral polymorphism in an experiment beginning from a single clone, the effects of randomness in the timing of cell division and noisiness in population size in the dilution stage. In our analyses and discussion, we emphasize the implications for experiments aimed at measuring diversity patterns and making inferences about population genetic processes based on these measurements. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.
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NASA Astrophysics Data System (ADS)
Wilds, Roy; Kauffman, Stuart A.; Glass, Leon
2008-09-01
We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.
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Barrier displacement on a neutral landscape: Towards a theory of continental biogeography
Albert, James S.; Schoolmaster, Donald; Tagliacollo, Victor; Duke-Sylvester, Scott M.
2017-01-01
Here we present SEAMLESS (Spatially-Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g. Lagrange, GeoSSE, BayArea, BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here towards the formulation of a general theory of continental biogeography.
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Anomalous diffusion in neutral evolution of model proteins.
Nelson, Erik D; Grishin, Nick V
2015-06-01
Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n. We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.
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Anomalous diffusion in neutral evolution of model proteins
NASA Astrophysics Data System (ADS)
Nelson, Erik D.; Grishin, Nick V.
2015-06-01
Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n . We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.
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Modeling Evolution on Nearly Neutral Network Fitness Landscapes
NASA Astrophysics Data System (ADS)
Yakushkina, Tatiana; Saakian, David B.
2017-08-01
To describe virus evolution, it is necessary to define a fitness landscape. In this article, we consider the microscopic models with the advanced version of neutral network fitness landscapes. In this problem setting, we suppose a fitness difference between one-point mutation neighbors to be small. We construct a modification of the Wright-Fisher model, which is related to ordinary infinite population models with nearly neutral network fitness landscape at the large population limit. From the microscopic models in the realistic sequence space, we derive two versions of nearly neutral network models: with sinks and without sinks. We claim that the suggested model describes the evolutionary dynamics of RNA viruses better than the traditional Wright-Fisher model with few sequences.
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NASA Astrophysics Data System (ADS)
Noirel, Josselin; Simonson, Thomas
2008-11-01
Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate μ and the population size N, the biological population can evolve purely randomly (μN ≪1) or it can evolve in such a way as to select for sequences of higher mutational robustness (μN ≫1). The stringency of the selection depends not only on the product μN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.
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Noirel, Josselin; Simonson, Thomas
2008-11-14
Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate mu and the population size N, the biological population can evolve purely randomly (muN<1) or it can evolve in such a way as to select for sequences of higher mutational robustness (muN>1). The stringency of the selection depends not only on the product muN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.
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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.
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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
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Neutral and Non-Neutral Evolution of Duplicated Genes with Gene Conversion
Fawcett, Jeffrey A.; Innan, Hideki
2011-01-01
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples. PMID:24710144
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Constructive neutral evolution: exploring evolutionary theory's curious disconnect.
Stoltzfus, Arlin
2012-10-13
Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article.
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Constructive neutral evolution: exploring evolutionary theory’s curious disconnect
2012-01-01
Abstract Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the “mutational landscape” model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Reviewers Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article. PMID:23062217
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Fully Bayesian tests of neutrality using genealogical summary statistics.
Drummond, Alexei J; Suchard, Marc A
2008-10-31
Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome. Here we harness posterior predictive simulation to exploit summary statistics of both the data and model parameters to test the goodness-of-fit of standard models of evolution. We apply the method to test the selective neutrality of molecular evolution in non-recombining gene genealogies and we demonstrate the utility of our method on four real data sets, identifying significant departures of neutrality in human influenza A virus, even after controlling for variation in population size. Importantly, by employing a full model-based Bayesian analysis, our method separates the effects of demography from the effects of selection. The method also allows multiple summary statistics to be used in concert, thus potentially increasing sensitivity. Furthermore, our method remains useful in situations where analytical expectations and variances of summary statistics are not available. This aspect has great potential for the analysis of temporally spaced data, an expanding area previously ignored for limited availability of theory and methods.
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Functional versus non-functional intratumor heterogeneity in cancer
Williams, Marc J.; Werner, Benjamin; Graham, Trevor A.; Sottoriva, Andrea
2016-01-01
ABSTRACT Next-generation sequencing data from human cancers are often difficult to interpret within the context of tumor evolution. We developed a mathematical model describing the accumulation of mutations under neutral evolutionary dynamics and showed that 323/904 cancers (∼30%) from multiple types were consistent with the neutral model of tumor evolution. PMID:27652316
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How range shifts induced by climate change affect neutral evolution
McInerny, G.J.; Turner, J.R.G.; Wong, H.Y.; Travis, J.M.J.; Benton, T.G.
2009-01-01
We investigate neutral evolution during range shifts in a strategic model of a metapopulation occupying a climate gradient. Using heritable, neutral markers, we track the spatio-temporal fate of lineages. Owing to iterated founder effects (‘mutation surfing’), survival of lineages derived from the leading range limit is enhanced. At trailing limits, where habitat suitability decreases, survival is reduced (mutations ‘wipe out’). These processes alter (i) the spatial spread of mutations, (ii) origins of persisting mutations and (iii) the generation of diversity. We show that large changes in neutral evolution can be a direct consequence of range shifting. PMID:19324824
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How range shifts induced by climate change affect neutral evolution.
McInerny, G J; Turner, J R G; Wong, H Y; Travis, J M J; Benton, T G
2009-04-22
We investigate neutral evolution during range shifts in a strategic model of a metapopulation occupying a climate gradient. Using heritable, neutral markers, we track the spatio-temporal fate of lineages. Owing to iterated founder effects ('mutation surfing'), survival of lineages derived from the leading range limit is enhanced. At trailing limits, where habitat suitability decreases, survival is reduced (mutations 'wipe out'). These processes alter (i) the spatial spread of mutations, (ii) origins of persisting mutations and (iii) the generation of diversity. We show that large changes in neutral evolution can be a direct consequence of range shifting.
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Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.
Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D
2014-09-12
A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.
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A non-equilibrium neutral model for analysing cultural change.
Kandler, Anne; Shennan, Stephen
2013-08-07
Neutral evolution is a frequently used model to analyse changes in frequencies of cultural variants over time. Variants are chosen to be copied according to their relative frequency and new variants are introduced by a process of random mutation. Here we present a non-equilibrium neutral model which accounts for temporally varying population sizes and mutation rates and makes it possible to analyse the cultural system under consideration at any point in time. This framework gives an indication whether observed changes in the frequency distributions of a set of cultural variants between two time points are consistent with the random copying hypothesis. We find that the likelihood of the existence of the observed assemblage at the end of the considered time period (expressed by the probability of the observed number of cultural variants present in the population during the whole period under neutral evolution) is a powerful indicator of departures from neutrality. Further, we study the effects of frequency-dependent selection on the evolutionary trajectories and present a case study of change in the decoration of pottery in early Neolithic Central Europe. Based on the framework developed we show that neutral evolution is not an adequate description of the observed changes in frequency. Copyright © 2013 Elsevier Ltd. All rights reserved.
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The Neutral Gas and Ion Mass Spectrometer on the Mars Atmosphere and Volatile Evolution Mission
NASA Technical Reports Server (NTRS)
Mahaffy, Paul R.; Benna, Mehdi; King, Todd; Harpold, Daniel N.; Arvey, Robert; Barciniak, Michael; Bendt, Mirl; Carrigan, Daniel; Errigo, Therese; Holmes, Vincent;
2014-01-01
The Neutral Gas and Ion Mass Spectrometer (NGIMS) of the Mars Atmosphere and Volatile Evolution Mission (MAVEN) is designed to measure the composition, structure, and variability of the upper atmosphere of Mars. The NGIMS complements two other instrument packages on the MAVEN spacecraft designed to characterize the neutral upper atmosphere and ionosphere of Mars and the solar wind input to this region of the atmosphere. The combined measurement set is designed to quantify atmosphere escape rates and provide input to models of the evolution of the martian atmosphere. The NGIMS is designed to measure both surface reactive and inert neutral species and ambient ions along the spacecraft track over the 125-500 km altitude region utilizing a dual ion source and a quadrupole analyzer.
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Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions
NASA Astrophysics Data System (ADS)
Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.
2014-12-01
The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.
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Speciation and Neutral Molecular Evolution in One-Dimensional Closed Population
NASA Astrophysics Data System (ADS)
Semovski, Sergei V.; Bukin, Yuri S.; Sherbakov, Dmitry Yu.
Models are presented suitable for a description of speciation processes arising due to reproductive isolation depending on genetic distance. The main attention is paid to the model of a one-dimensional closed population, which describes the evolution of littoral benthic organisms. In order to correspond the modeling results to the results obtained in the course of experimental phylogenetic studies, all individual-based models described here involve neutrally evolving and maternally inherited DNA sequence. Sub-samples of the resulting sequences were used for a posteriori phylogenetic inferences which then were compared to the "true" evolutionary histories.
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Neutral hydrogen in the post-reionization universe
NASA Astrophysics Data System (ADS)
Padmanabhan, Hamsa
2018-05-01
The evolution of neutral hydrogen (HI) across redshifts is a powerful probe of cosmology, large scale structure in the universe and the intergalactic medium. Using a data-driven halo model to describe the distribution of HI in the post-reionization universe (z ~ 5 to 0), we obtain the best-fitting parameters from a rich sample of observational data: low redshift 21-cm emission line studies, intermediate redshift intensity mapping experiments, and higher redshift Damped Lyman Alpha (DLA) observations. Our model describes the abundance and clustering of neutral hydrogen across redshifts 0 - 5, and is useful for investigating different aspects of galaxy evolution and for comparison with hydrodynamical simulations. The framework can be applied for forecasting future observations with neutral hydrogen, and extended to the case of intensity mapping with molecular and other line transitions at intermediate redshifts.
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Neutral evolution of mutational robustness
van Nimwegen, Erik; Crutchfield, James P.; Huynen, Martijn
1999-01-01
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population’s limit distribution on the neutral network is solely determined by the network topology and given by the principal eigenvector of the network’s adjacency matrix. Moreover, the average number of neutral mutant neighbors per individual is given by the matrix spectral radius. These results quantify the extent to which populations evolve mutational robustness—the insensitivity of the phenotype to mutations—and thus reduce genetic load. Because the average neutrality is independent of evolutionary parameters—such as mutation rate, population size, and selective advantage—one can infer global statistics of neutral network topology by using simple population data available from in vitro or in vivo evolution. Populations evolving on neutral networks of RNA secondary structures show excellent agreement with our theoretical predictions. PMID:10449760
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Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics
NASA Astrophysics Data System (ADS)
Scott, Adam; King, Dawn; Bahar, Sonya
2013-03-01
An evolutionary model was recently introduced for sympatric, phenotypic evolution over a variable fitness landscape with assortative mating (Dees & Bahar 2010). Organisms in the model are described by coordinates in a two-dimensional phenotype space, born at random coordinates with limited variation from their parents as determined by a mutation parameter, mutability. The model has been extended to include both neutral evolution and asexual reproduction in Scott et al (submitted). It has been demonstrated that a second order, non-equilibrium phase transition occurs for the temporal dynamics as the mutability is varied, for both the original model and for neutral conditions. This transition likely belongs to the directed percolation universality class. In contrast, the spatial dynamics of the model shows characteristics of an ordinary percolation phase transition. Here, we characterize the phase transitions exhibited by this model by determining critical exponents for the relaxation times, characteristic lengths, and cluster (species) mass distributions. Missouri Research Board; J.S. McDonnell Foundation
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Feature Profile Evolution of SiO2 Trenches In Fluorocarbon Plasmas
NASA Technical Reports Server (NTRS)
Hwang, Helen; Govindan, T. R.; Meyyappan, M.; Arunachalam, Valli; Rauf, Shahid; Coronell, Dan; Carroll, Carol W. (Technical Monitor)
1999-01-01
Etching of silicon microstructures for semiconductor manufacturing in chlorine plasmas has been well characterized. The etching proceeds in a two-part process, where the chlorine neutrals passivate the Si surface and then the ions etch away SiClx. However, etching in more complicated gas mixtures and materials, such as etching of SiO2 in Ar/C4F8, requires knowledge of the ion and neutral distribution functions as a function of angle and velocity, in addition to modeling the gas surface reactions. In order to address these needs, we have developed and integrated a suite of models to simulate the etching process from the plasma reactor level to the feature profile evolution level. This arrangement allows for a better understanding, control, and prediction of the influence of equipment level process parameters on feature profile evolution. We are currently using the HPEM (Hybrid Plasma Equipment Model) and PCMCM (Plasma Chemistry Monte Carlo Model) to generate plasma properties and ion and neutral distribution functions for argon/fluorocarbon discharges in a GEC Reference Cell. These quantities are then input to the feature scale model, Simulation of Profile Evolution by Level Sets (SPELS). A surface chemistry model is used to determine the interaction of the incoming species with the substrate material and simulate the evolution of the trench profile. The impact of change of gas pressure and inductive power on the relative flux of CFx and F to the wafer, the etch and polymerization rates, and feature profiles will be examined. Comparisons to experimental profiles will also be presented.
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Neutral Theory and Rapidly Evolving Viral Pathogens.
Frost, Simon D W; Magalis, Brittany Rife; Kosakovsky Pond, Sergei L
2018-06-01
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance. We highlight the multiple ways in which the neutral theory has had an impact, which has been accelerated in the age of high-throughput, high-resolution genomics.
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O'Dwyer, James P; Kandler, Anne
2017-12-05
Neutral evolution assumes that there are no selective forces distinguishing different variants in a population. Despite this striking assumption, many recent studies have sought to assess whether neutrality can provide a good description of different episodes of cultural change. One approach has been to test whether neutral predictions are consistent with observed progeny distributions, recording the number of variants that have produced a given number of new instances within a specified time interval: a classic example is the distribution of baby names. Using an overlapping generations model, we show that these distributions consist of two phases: a power-law phase with a constant exponent of [Formula: see text], followed by an exponential cut-off for variants with very large numbers of progeny. Maximum-likelihood estimations of the model parameters provide a direct way to establish whether observed empirical patterns are consistent with neutral evolution. We apply our approach to a complete dataset of baby names from Australia. Crucially, we show that analyses based on only the most popular variants, as is often the case in studies of cultural evolution, can provide misleading evidence for underlying transmission hypotheses. While neutrality provides a plausible description of progeny distributions of abundant variants, rare variants deviate from neutrality. Further, we develop a simulation framework that allows the detection of alternative cultural transmission processes. We show that anti-novelty bias is able to replicate the complete progeny distribution of the Australian dataset.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).
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The maintenance of single-locus polymorphism. IV. Models with mutation from existing alleles.
Spencer, H G; Marks, R W
1992-01-01
The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.
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Epistasis increases the rate of conditionally neutral substitution in an adapting population.
Draghi, Jeremy A; Parsons, Todd L; Plotkin, Joshua B
2011-04-01
Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations--i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations--substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations.
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Epistasis Increases the Rate of Conditionally Neutral Substitution in an Adapting Population
Draghi, Jeremy A.; Parsons, Todd L.; Plotkin, Joshua B.
2011-01-01
Kimura observed that the rate of neutral substitution should equal the neutral mutation rate. This classic result is central to our understanding of molecular evolution, and it continues to influence phylogenetics, genomics, and the interpretation of evolution experiments. By demonstrating that neutral mutations substitute at a rate independent of population size and selection at linked sites, Kimura provided an influential justification for the idea of a molecular clock and emphasized the importance of genetic drift in shaping molecular evolution. But when epistasis among sites is common, as numerous empirical studies suggest, do neutral mutations substitute according to Kimura's expectation? Here we study simulated, asexual populations of RNA molecules, and we observe that conditionally neutral mutations—i.e., mutations that do not alter the fitness of the individual in which they arise, but that may alter the fitness effects of subsequent mutations—substitute much more often than expected while a population is adapting. We quantify these effects using a simple population-genetic model that elucidates how the substitution rate at conditionally neutral sites depends on the population size, mutation rate, strength of selection, and prevalence of epistasis. We discuss the implications of these results for our understanding of the molecular clock, and for the interpretation of molecular variation in laboratory and natural populations. PMID:21288876
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Neutral biogeography and the evolution of climatic niches.
Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien
2014-05-01
Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.
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Neutral biogeography and the evolution of climatic niches
Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien
2014-01-01
Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191
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Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L
2017-05-01
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Tumor evolution: Linear, branching, neutral or punctuated?☆
Davis, Alexander; Gao, Ruli; Navin, Nicholas
2017-01-01
Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. PMID:28110020
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Fluctuating Selection in the Moran
Dean, Antony M.; Lehman, Clarence; Yi, Xiao
2017-01-01
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model, we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large, and the variance in selection is big. Lowering the frequency of fluctuations makes selection more directional, and so heterozygosity declines. We also show that fluctuating selection raises dn/ds ratios for polymorphism, not only by sweeping selected alleles into the population, but also by purging the neutral variants of selected alleles as they undergo repeated bottlenecks. Our analysis shows that randomly fluctuating selection increases the rate of evolution by increasing the probability of fixation. The impact is especially noticeable when the selection is strong and mutation is weak. Simulations show the increase in the rate of evolution declines as the rate of new mutations entering the population increases, an effect attributable to clonal interference. Intriguingly, fluctuating selection increases the dn/ds ratios for divergence more than for polymorphism, a pattern commonly seen in comparative genomics. Our model, which extends the classical neutral model of molecular evolution by incorporating random fluctuations in selection, accommodates a wide variety of observations, both neutral and selected, with economy. PMID:28108586
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Stability and Evolution of Supernova Fallback Disks
NASA Astrophysics Data System (ADS)
Menou, Kristen; Perna, Rosalba; Hernquist, Lars
2001-10-01
We show that thin accretion disks made of carbon or oxygen are subject to the same thermal ionization instability as hydrogen and helium disks. We argue that the instability applies to disks of any metal content. The relevance of the instability to supernova fallback disks probably means that their power-law evolution breaks down when they first become neutral. We construct simple analytical models for the viscous evolution of fallback disks to show that it is possible for these disks to become neutral when they are still young (ages of a few 103 to 104 yr), compact in size (a few 109 to 1011 cm) and generally accreting at sub-Eddington rates (M~a few 1014-1018 g s-1). Based on recent results on the nature of viscosity in the disks of close binaries, we argue that this time may also correspond to the end of the disk activity period. Indeed, in the absence of a significant source of viscosity in the neutral phase, the entire disk will likely turn to dust and become passive. We discuss various applications of the evolutionary model, including anomalous X-ray pulsars and young radio pulsars. Our analysis indicates that metal-rich fallback disks around newly born neutron stars and black holes become neutral generally inside the tidal truncation radius (Roche limit) for planets at ~1011 cm. Consequently, the efficiency of the planetary formation process in this context will mostly depend on the ability of the resulting disk of rocks to spread via collisions beyond the Roche limit. It appears easier for the merger product of a doubly degenerate binary, whether it is a massive white dwarf or a neutron star, to harbor planets because its remnant disk has a rather large initial angular momentum, which allows it to spread beyond the Roche limit before becoming neutral. The early super-Eddington phase of accretion is a source of uncertainty for the disk evolution models presented here.
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Applying ecological models to communities of genetic elements: the case of neutral theory.
Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan
2015-07-01
A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.
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The Maintenance of Single-Locus Polymorphism. IV. Models with Mutation from Existing Alleles
Spencer, H. G.; Marks, R. W.
1992-01-01
The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory. PMID:1732162
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Fluctuating Selection in the Moran.
Dean, Antony M; Lehman, Clarence; Yi, Xiao
2017-03-01
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model, we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large, and the variance in selection is big. Lowering the frequency of fluctuations makes selection more directional, and so heterozygosity declines. We also show that fluctuating selection raises d n / d s ratios for polymorphism, not only by sweeping selected alleles into the population, but also by purging the neutral variants of selected alleles as they undergo repeated bottlenecks. Our analysis shows that randomly fluctuating selection increases the rate of evolution by increasing the probability of fixation. The impact is especially noticeable when the selection is strong and mutation is weak. Simulations show the increase in the rate of evolution declines as the rate of new mutations entering the population increases, an effect attributable to clonal interference. Intriguingly, fluctuating selection increases the d n / d s ratios for divergence more than for polymorphism, a pattern commonly seen in comparative genomics. Our model, which extends the classical neutral model of molecular evolution by incorporating random fluctuations in selection, accommodates a wide variety of observations, both neutral and selected, with economy. Copyright © 2017 by the Genetics Society of America.
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McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M
2013-01-01
Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.
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Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing; Gao, Feng; Alam, S. Munir; Boyd, Scott D.; Fire, Andrew Z.; Roskin, Krishna M.; Schramm, Chaim A.; Zhang, Zhenhai; Zhu, Jiang; Shapiro, Lawrence; Mullikin, James C.; Gnanakaran, S.; Hraber, Peter; Wiehe, Kevin; Kelsoe, Garnett; Yang, Guang; Xia, Shi-Mao; Montefiori, David C.; Parks, Robert; Lloyd, Krissey E.; Scearce, Richard M.; Soderberg, Kelly A.; Cohen, Myron; Kaminga, Gift; Louder, Mark K.; Tran, Lillan M.; Chen, Yue; Cai, Fangping; Chen, Sheri; Moquin, Stephanie; Du, Xiulian; Joyce, Gordon M.; Srivatsan, Sanjay; Zhang, Baoshan; Zheng, Anqi; Shaw, George M.; Hahn, Beatrice H.; Kepler, Thomas B.; Korber, Bette T.M.; Kwong, Peter D.; Mascola, John R.; Haynes, Barton F.
2013-01-01
Current HIV-1 vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in ~20% of HIV-1-infected individuals, and details of their generation could provide a roadmap for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from time of infection. The mature antibody, CH103, neutralized ~55% of HIV-1 isolates, and its co-crystal structure with gp120 revealed a novel loop-based mechanism of CD4-binding site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the CH103-lineage unmutated common ancestor avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data elucidate the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies and provide insights into strategies to elicit similar antibodies via vaccination. PMID:23552890
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NASA Astrophysics Data System (ADS)
Stokes, M.; Perron, J. T.
2017-12-01
Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.
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On the Overdispersed Molecular Clock
Takahata, Naoyuki
1987-01-01
Rates of molecular evolution at some loci are more irregular than described by simple Poisson processes. Three situations under which molecular evolution would not follow simple Poisson processes are reevaluated from the viewpoint of the neutrality hypothesis: (i) concomitant or multiple substitutions in a gene, (ii) fluctuating substitution rates in time caused by coupled effects of deleterious mutations and bottlenecks, and (iii) changes in the degree of selective constraints against a gene (neutral space) caused by successive substitutions. The common underlying assumption that these causes are lineage nonspecific excludes the case where mutation rates themselves change systematically among lineages or taxonomic groups, and severely limits the extent of variation in the number of substitutions among lineages. Even under this stringent condition, however, the third hypothesis, the fluctuating neutral space model, can generate fairly large variation. This is described by a time-dependent renewal process, which does not exhibit any episodic nature of molecular evolution. It is argued that the observed elevated variances in the number of nucleotide or amino acid substitutions do not immediately call for positive Darwinian selection in molecular evolution. PMID:3596230
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McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.
2013-01-01
Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801
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The response of plasma density to breaking inertial gravity wave in the lower regions of ionosphere
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tang, Wenbo, E-mail: Wenbo.Tang@asu.edu; Mahalov, Alex, E-mail: Alex.Mahalov@asu.edu
2014-04-15
We present a three-dimensional numerical study for the E and lower F region ionosphere coupled with the neutral atmosphere dynamics. This model is developed based on a previous ionospheric model that examines the transport patterns of plasma density given a prescribed neutral atmospheric flow. Inclusion of neutral dynamics in the model allows us to examine the charge-neutral interactions over the full evolution cycle of an inertial gravity wave when the background flow spins up from rest, saturates and eventually breaks. Using Lagrangian analyses, we show the mixing patterns of the ionospheric responses and the formation of ionospheric layers. The correspondingmore » plasma density in this flow develops complex wave structures and small-scale patches during the gravity wave breaking event.« less
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Pascoal, Sonia; Mendrok, Magdalena; Wilson, Alastair J; Hunt, John; Bailey, Nathan W
2017-06-01
Sexual selection can target many different types of traits. However, the relative influence of different sexually selected traits during evolutionary divergence is poorly understood. We used the field cricket Teleogryllus oceanicus to quantify and compare how five traits from each of three sexual signal modalities and components diverge among allopatric populations: male advertisement song, cuticular hydrocarbon (CHC) profiles and forewing morphology. Population divergence was unexpectedly consistent: we estimated the among-population (genetic) variance-covariance matrix, D, for all 15 traits, and D max explained nearly two-thirds of its variation. CHC and wing traits were most tightly integrated, whereas song varied more independently. We modeled the dependence of among-population trait divergence on genetic distance estimated from neutral markers to test for signatures of selection versus neutral divergence. For all three sexual trait types, phenotypic variation among populations was largely explained by a neutral model of divergence. Our findings illustrate how phenotypic integration across different types of sexual traits might impose constraints on the evolution of mating isolation and divergence via sexual selection. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Emergent Neutrality in Adaptive Asexual Evolution
Schiffels, Stephan; Szöllősi, Gergely J.; Mustonen, Ville; Lässig, Michael
2011-01-01
In nonrecombining genomes, genetic linkage can be an important evolutionary force. Linkage generates interference interactions, by which simultaneously occurring mutations affect each other’s chance of fixation. Here, we develop a comprehensive model of adaptive evolution in linked genomes, which integrates interference interactions between multiple beneficial and deleterious mutations into a unified framework. By an approximate analytical solution, we predict the fixation rates of these mutations, as well as the probabilities of beneficial and deleterious alleles at fixed genomic sites. We find that interference interactions generate a regime of emergent neutrality: all genomic sites with selection coefficients smaller in magnitude than a characteristic threshold have nearly random fixed alleles, and both beneficial and deleterious mutations at these sites have nearly neutral fixation rates. We show that this dynamic limits not only the speed of adaptation, but also a population’s degree of adaptation in its current environment. We apply the model to different scenarios: stationary adaptation in a time-dependent environment and approach to equilibrium in a fixed environment. In both cases, the analytical predictions are in good agreement with numerical simulations. Our results suggest that interference can severely compromise biological functions in an adapting population, which sets viability limits on adaptive evolution under linkage. PMID:21926305
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Reduced model (SOLT) simulations of neutral-plasma interaction
NASA Astrophysics Data System (ADS)
Russell, David; Myra, James
2017-10-01
The 2D scrape-off-layer turbulence (SOLT) code has been enhanced by the addition of kinetic-neutral physics. Plasma-neutral interactions include charge exchange (CX) and ionization (IZ). Under the assumption that the CX and IZ collision rates are independent of the ion-neutral relative velocity, a 1D (radial: x) Boltzmann equation has been derived for the evolution of the (vy,vz) -averaged neutral distribution function (G), and that evolution has been added to SOLT. The CX and IZ rates are determined by the poloidally (y) averaged plasma density and temperatures, and G = G(x,vx,t). Results from 1D simulations that use diffusion as a proxy for turbulent transport are presented to illustrate the capability, including the approach to a steady state driven by sustained neutral injection in the far-SOL and source-driven heating in the core. Neutral density and energy profiles are obtained for the resulting self-consistent equilibrium plasma profiles. The effect of neutral drag on poloidal ExB mean flow and shearing rate is illustrated. Progress on 2D turbulence (blob) simulations is reported. Work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences, under Award Number DE-FG02-97ER54392.
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Frequency Spectrum Neutrality Tests: One for All and All for One
Achaz, Guillaume
2009-01-01
Neutrality tests based on the frequency spectrum (e.g., Tajima's D or Fu and Li's F) are commonly used by population geneticists as routine tests to assess the goodness-of-fit of the standard neutral model on their data sets. Here, I show that these neutrality tests are specific instances of a general model that encompasses them all. I illustrate how this general framework can be taken advantage of to devise new more powerful tests that better detect deviations from the standard model. Finally, I exemplify the usefulness of the framework on SNP data by showing how it supports the selection hypothesis in the lactase human gene by overcoming the ascertainment bias. The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution. PMID:19546320
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Valenzuela, Carlos Y
2013-01-01
The Neutral Theory of Evolution (NTE) proposes mutation and random genetic drift as the most important evolutionary factors. The most conspicuous feature of evolution is the genomic stability during paleontological eras and lack of variation among taxa; 98% or more of nucleotide sites are monomorphic within a species. NTE explains this homology by random fixation of neutral bases and negative selection (purifying selection) that does not contribute either to evolution or polymorphisms. Purifying selection is insufficient to account for this evolutionary feature and the Nearly-Neutral Theory of Evolution (N-NTE) included negative selection with coefficients as low as mutation rate. These NTE and N-NTE propositions are thermodynamically (tendency to random distributions, second law), biotically (recurrent mutation), logically and mathematically (resilient equilibria instead of fixation by drift) untenable. Recurrent forward and backward mutation and random fluctuations of base frequencies alone in a site make life organization and fixations impossible. Drift is not a directional evolutionary factor, but a directional tendency of matter-energy processes (second law) which threatens the biotic organization. Drift cannot drive evolution. In a site, the mutation rates among bases and selection coefficients determine the resilient equilibrium frequency of bases that genetic drift cannot change. The expected neutral random interaction among nucleotides is zero; however, huge interactions and periodicities were found between bases of dinucleotides separated by 1, 2... and more than 1,000 sites. Every base is co-adapted with the whole genome. Neutralists found that neutral evolution is independent of population size (N); thus neutral evolution should be independent of drift, because drift effect is dependent upon N. Also, chromosome size and shape as well as protein size are far from random.
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Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process
Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya
2015-01-01
The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution. PMID:26177190
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Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.
Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya
2015-07-01
The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.
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IslandFAST: A Semi-numerical Tool for Simulating the Late Epoch of Reionization
DOE Office of Scientific and Technical Information (OSTI.GOV)
Xu, Yidong; Chen, Xuelei; Yue, Bin
2017-08-01
We present the algorithm and main results of our semi-numerical simulation, islandFAST, which was developed from 21cmFAST and designed for the late stage of reionization. The islandFAST simulation predicts the evolution and size distribution of the large-scale underdense neutral regions (neutral islands), and we find that the late Epoch of Reionization proceeds very fast, showing a characteristic scale of the neutral islands at each redshift. Using islandFAST, we compare the impact of two types of absorption systems, i.e., the large-scale underdense neutral islands versus small-scale overdense absorbers, in regulating the reionization process. The neutral islands dominate the morphology of themore » ionization field, while the small-scale absorbers dominate the mean-free path of ionizing photons, and also delay and prolong the reionization process. With our semi-numerical simulation, the evolution of the ionizing background can be derived self-consistently given a model for the small absorbers. The hydrogen ionization rate of the ionizing background is reduced by an order of magnitude in the presence of dense absorbers.« less
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Random genetic drift, natural selection, and noise in human cranial evolution.
Roseman, Charles C
2016-08-01
This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C.; Paoletti, Christopher; Nowak, Martin A.
2015-01-01
Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a “molecular clock” to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution. PMID:25719560
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Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A
2015-02-01
Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.
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Lawson, Daniel John; Jensen, Henrik Jeldtoft
2007-03-02
The process of "evolutionary diffusion," i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.
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Dvornyk, Volodymyr; Jahan, Akhee Sabiha
2012-01-01
Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across the globe. Despite high haplotype diversity (0.774), nucleotide diversity of cpmA is very low (π = 0.0034): the gene appears to be even more conserved than housekeeping genes. Even though the populations were sampled thousands kilometers apart, they manifested virtually no genetic differentiation at this locus (FST = 0.0228). Using various tests for neutrality, we determined that evolution of cpmA significantly departures from the neutral model and is governed by episodic positive selection. PMID:22844070
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Dynamic Evolution Model Based on Social Network Services
NASA Astrophysics Data System (ADS)
Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen
2013-11-01
Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.
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Hidden long evolutionary memory in a model biochemical network
NASA Astrophysics Data System (ADS)
Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan
2018-04-01
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.
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Physics-based Control-oriented Modeling of the Current Profile Evolution in NSTX-Upgrade
NASA Astrophysics Data System (ADS)
Ilhan, Zeki; Barton, Justin; Shi, Wenyu; Schuster, Eugenio; Gates, David; Gerhardt, Stefan; Kolemen, Egemen; Menard, Jonathan
2013-10-01
The operational goals for the NSTX-Upgrade device include non-inductive sustainment of high- β plasmas, realization of the high performance equilibrium scenarios with neutral beam heating, and achievement of longer pulse durations. Active feedback control of the current profile is proposed to enable these goals. Motivated by the coupled, nonlinear, multivariable, distributed-parameter plasma dynamics, the first step towards feedback control design is the development of a physics-based, control-oriented model for the current profile evolution in response to non-inductive current drives and heating systems. For this purpose, the nonlinear magnetic-diffusion equation is coupled with empirical models for the electron density, electron temperature, and non-inductive current drives (neutral beams). The resulting first-principles-driven, control-oriented model is tailored for NSTX-U based on the PTRANSP predictions. Main objectives and possible challenges associated with the use of the developed model for control design are discussed. This work was supported by PPPL.
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Neutral Community Dynamics and the Evolution of Species Interactions.
Coelho, Marco Túlio P; Rangel, Thiago F
2018-04-01
A contemporary goal in ecology is to determine the ecological and evolutionary processes that generate recurring structural patterns in mutualistic networks. One of the great challenges is testing the capacity of neutral processes to replicate observed patterns in ecological networks, since the original formulation of the neutral theory lacks trophic interactions. Here, we develop a stochastic-simulation neutral model adding trophic interactions to the neutral theory of biodiversity. Without invoking ecological differences among individuals of different species, and assuming that ecological interactions emerge randomly, we demonstrate that a spatially explicit multitrophic neutral model is able to capture the recurrent structural patterns of mutualistic networks (i.e., degree distribution, connectance, nestedness, and phylogenetic signal of species interactions). Nonrandom species distribution, caused by probabilistic events of migration and speciation, create nonrandom network patterns. These findings have broad implications for the interpretation of niche-based processes as drivers of ecological networks, as well as for the integration of network structures with demographic stochasticity.
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Etching in Chlorine Discharges Using an Integrated Feature Evolution-Plasma Model
NASA Technical Reports Server (NTRS)
Hwang, Helen H.; Bose, Deepak; Govindan, T. R.; Meyyappan, M.; Biegel, Bryan (Technical Monitor)
2001-01-01
Etching of semiconductor materials is reliant on plasma properties. Quantities such as ion and neutral fluxes, both in magnitude and in direction, are often determined by reactor geometry (height, radius, position of the coils, etc.) In order to obtain accurate etching profiles, one must also model the plasma as a whole to obtain local fluxes and distributions. We have developed a set of three models that simulates C12 plasmas for etching of silicon, ion and neutral trajectories in the plasma, and feature profile evolution. We have found that the location of the peak in the ion densities in the reactor plays a major role in determining etching uniformity across the wafer. For a stove top coil inductively coupled plasma (ICP), the ion density is peaked at the top of the reactor. This leads to nearly uniform neutral and ion fluxes across the wafer. A side coil configuration causes the ion density to peak near the sidewalls. Ion fluxes are thus greater toward the wall's and decrease toward the center. In addition, the ions bombard the wafer at a slight angle. This angle is sufficient to cause slanted profiles, which is highly undesirable.
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Biological evolution and statistical physics
NASA Astrophysics Data System (ADS)
Drossel, Barbara
2001-03-01
This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.
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NASA Astrophysics Data System (ADS)
Tewari, Brij
2016-07-01
Insoluble metal hexacyanoferrate(II) complexes could have concentrated biomonomers from dilute prebiotic soup during course of chemical evolution and origin of life or primitive earth. In the light of above hypothesis, adsorption of tryptophane and phenylalanine was studied on cadmium and molybdenum ferrocyanides at neutral pH (7.0 ± 0.01) and at a temperature of 30 ± 1º C. Interaction of amino acids with metal ferrocyanides are found to be maximum at neutral pH. Neutral pH is chosen for the adsorption studies because most of the reactions in biological systems taken place at neutral pH range. Adsorption trend follow Langmuir isotherm model. The Langmuir constants b and Qo were calculated at neutral pH, tryptophane was found to more adsorbed than phenylalanine on both metal ferrocyanides studied. Molybdenum ferrocyanides studied. Molybdenum ferrocyanides was found to have more uptake capacity for both adsorbates than cadmium ferrocyanides. The present study suggests that metal ferrocyanides might have played a role in the stabilization of biomolecules through their surface activity during course of chemical solution and origins of life on primitive earth.
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NASA Astrophysics Data System (ADS)
Lawson, Daniel John; Jensen, Henrik Jeldtoft
2007-03-01
The process of “evolutionary diffusion,” i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.
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The early universe history from contraction-deformation of the Standard Model
NASA Astrophysics Data System (ADS)
Gromov, N. A.
2017-03-01
The elementary particles evolution in the early Universe from Plank time up to several milliseconds is presented. The developed theory is based on the high-temperature (high-energy) limit of the Standard Model which is generated by the contractions of its gauge groups. At the infinite temperature all particles lose masses. Only massless neutral -bosons, massless Z-quarks, neutrinos and photons are survived in this limit. The weak interactions become long-range and are mediated by neutral currents, quarks have only one color degree of freedom.
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New paradigms in clonal evolution: punctuated equilibrium in cancer.
Cross, William Ch; Graham, Trevor A; Wright, Nicholas A
2016-10-01
Evolutionary theories are themselves subject to evolution. Clonal evolution - the model that describes the initiation and progression of cancer - is entering a period of profound change, brought about largely by technological developments in genome analysis. A flurry of recent publications, using modern mathematical and bioinformatics techniques, have revealed both punctuated and neutral evolution phenomena that are poorly explained by the conventional graduated perspectives. In this review, we propose that a hybrid model, inspired by the evolutionary model of punctuated equilibrium, could better explain these recent observations. We also discuss the conceptual changes and clinical implications of variable evolutionary tempos. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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An adaptive radiation model for the origin of new genefunctions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Francino, M. Pilar
2004-10-18
The evolution of new gene functions is one of the keys to evolutionary innovation. Most novel functions result from gene duplication followed by divergence. However, the models hitherto proposed to account for this process are not fully satisfactory. The classic model of neofunctionalization holds that the two paralogous gene copies resulting from a duplication are functionally redundant, such that one of them can evolve under no functional constraints and occasionally acquire a new function. This model lacks a convincing mechanism for the new gene copies to increase in frequency in the population and survive the mutational load expected to accumulatemore » under neutrality, before the acquisition of the rare beneficial mutations that would confer new functionality. The subfunctionalization model has been proposed as an alternative way to generate genes with altered functions. This model also assumes that new paralogous gene copies are functionally redundant and therefore neutral, but it predicts that relaxed selection will affect both gene copies such that some of the capabilities of the parent gene will disappear in one of the copies and be retained in the other. Thus, the functions originally present in a single gene will be partitioned between the two descendant copies. However, although this model can explain increases in gene number, it does not really address the main evolutionary question, which is the development of new biochemical capabilities. Recently, a new concept has been introduced into the gene evolution literature which is most likely to help solve this dilemma. The key point is to allow for a period of natural selection for the duplication per se, before new function evolves, rather than considering gene duplication to be neutral as in the previous models. Here, I suggest a new model that draws on the advantage of postulating selection for gene duplication, and proposes that bursts of adaptive gene amplification in response to specific selection pressures provide the raw material for the evolution of new function.« less
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Speijer, Dave
2011-05-01
Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.
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Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.
Gu, Xun; Ruan, Hang; Su, Zhixi; Zou, Yangyun
2017-09-01
While phylogenetic analysis of transcriptomes of the same tissue is usually congruent with the species tree, the controversy emerges when multiple tissues are included, that is, whether species from the same tissue are clustered together, or different tissues from the same species are clustered together. Recent studies have suggested that phylogenetic network approach may shed some lights on our understanding of multi-tissue transcriptome evolution; yet the underlying evolutionary mechanism remains unclear. In this paper we develop a Brownian-based model of transcriptome evolution under the phylogenetic network that can statistically distinguish between the patterns of species-clustering and tissue-clustering. Our model can be used as a null hypothesis (neutral transcriptome evolution) for testing any correlation in tissue evolution, can be applied to cancer transcriptome evolution to study whether two tumors of an individual appeared independently or via metastasis, and can be useful to detect convergent evolution at the transcriptional level. Copyright © 2017. Published by Elsevier Inc.
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Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria
Christie, Joshua R.; Schaerf, Timothy M.; Beekman, Madeleine
2015-01-01
Why are mitochondria almost always inherited from one parent during sexual reproduction? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes, clearing of deleterious mutations, and optimization of mitochondrial-nuclear coadaptation. Mathematical models, however, fail to show that uniparental inheritance can replace biparental inheritance under any existing hypothesis. Recent empirical evidence indicates that mixing two different but normal mitochondrial haplotypes within a cell (heteroplasmy) can cause cell and organism dysfunction. Using a mathematical model, we test if selection against heteroplasmy can lead to the evolution of uniparental inheritance. When we assume selection against heteroplasmy and mutations are neither advantageous nor deleterious (neutral mutations), uniparental inheritance replaces biparental inheritance for all tested parameter values. When heteroplasmy involves mutations that are advantageous or deleterious (non-neutral mutations), uniparental inheritance can still replace biparental inheritance. We show that uniparental inheritance can evolve with or without pre-existing mating types. Finally, we show that selection against heteroplasmy can explain why some organisms deviate from strict uniparental inheritance. Thus, we suggest that selection against heteroplasmy explains the evolution of uniparental inheritance. PMID:25880558
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NASA Astrophysics Data System (ADS)
Reddy, A.; Sonwalkar, V. S.; Huba, J. D.
2018-02-01
Knowledge of field-aligned electron and ion distributions is necessary for understanding the physical processes causing variations in field-aligned electron and ion densities. Using whistler mode sounding by Radio Plasma Imager/Imager for Magnetopause-to-Aurora Global Exploration (RPI/IMAGE), we determined the evolution of dayside electron and ion densities along L ˜ 2 and L ˜ 3 (90-4,000 km) during a 7 day (21-27 November 2005) geomagnetically quiet to moderately active period. Over this period the O+/H+ transition height was ˜880 ± 60 km and ˜1000 ± 100 km, respectively, at L ˜ 2 and L ˜ 3. The electron density varied in a complex manner; it was different at L ˜ 2 and L ˜ 3 and below and above the O+/H+ transition height. The measured electron and ion densities are consistent with those from Challenging Minisatellite Payload (CHAMP) and Defense Meteorological Satellite Program (DMSP) and other past measurements, but they deviated from bottomside sounding and International Reference Ionosphere (IRI) 2012 empirical model results. Using SAMI2 (Naval Research Laboratory (NRL) ionosphere model) with reasonably adjusted values of inputs (neutral densities, winds, electric fields, and photoelectron heating), we simulated the evolution of O+/H+ transition height and field-aligned electron and ion densities so that a fair agreement was obtained between the simulation results and observations. Simulation studies indicated that reduced neutral densities (H and/or O) with time limited O+-H charge exchange process. This reduction in neutral densities combined with changes in neutral winds and plasma temperature led to the observed variations in the electron and ion densities. The observation/simulation method presented here can be extended to investigate the role of neutral densities and composition, disturbed winds, and prompt penetration electric fields in the storm time ionosphere/plasmasphere dynamics.
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NASA Astrophysics Data System (ADS)
Massip, Florian; Arndt, Peter F.
2013-04-01
Recently, an enrichment of identical matching sequences has been found in many eukaryotic genomes. Their length distribution exhibits a power law tail raising the question of what evolutionary mechanism or functional constraints would be able to shape this distribution. Here we introduce a simple and evolutionarily neutral model, which involves only point mutations and segmental duplications, and produces the same statistical features as observed for genomic data. Further, we extend a mathematical model for random stick breaking to analytically show that the exponent of the power law tail is -3 and universal as it does not depend on the microscopic details of the model.
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Adaptation and colonization history affect the evolution of clines in two introduced species.
Keller, Stephen R; Sowell, Dexter R; Neiman, Maurine; Wolfe, Lorne M; Taylor, Douglas R
2009-08-01
Phenotypic and genetic clines have long been synonymous with adaptive evolution. However, other processes (for example, migration, range expansion, invasion) may generate clines in traits or loci across geographical and environmental gradients. It is therefore important to distinguish between clines that represent adaptive evolution and those that result from selectively neutral demographic or genetic processes. We tested for the differentiation of phenotypic traits along environmental gradients using two species in the genus Silene, whilst statistically controlling for colonization history and founder effects. We sampled seed families from across the native and introduced ranges, genotyped individuals and estimated phenotypic differentiation in replicated common gardens. The results suggest that post-glacial expansion of S. vulgaris and S. latifolia involved both neutral and adaptive genetic differentiation (clines) of life history traits along major axes of environmental variation in Europe and North America. Phenotypic clines generally persisted when tested against the neutral expectation, although some clines disappeared (and one cline emerged) when the effects of genetic ancestry were statistically removed. Colonization history, estimated using genetic markers, is a useful null model for tests of adaptive trait divergence, especially during range expansion and invasion when selection and gene flow may not have reached equilibrium.
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Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.
Wernegreen, Jennifer J; Funk, Daniel J
2004-12-01
The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.
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Limits of neutral drift: lessons from the in vitro evolution of two ribozymes.
Petrie, Katherine L; Joyce, Gerald F
2014-10-01
The relative contributions of adaptive selection and neutral drift to genetic change are unknown but likely depend on the inherent abundance of functional genotypes in sequence space and how accessible those genotypes are to one another. To better understand the relative roles of selection and drift in evolution, local fitness landscapes for two different RNA ligase ribozymes were examined using a continuous in vitro evolution system under conditions that foster the capacity for neutral drift to mediate genetic change. The exploration of sequence space was accelerated by increasing the mutation rate using mutagenic nucleotide analogs. Drift was encouraged by carrying out evolution within millions of separate compartments to exploit the founder effect. Deep sequencing of individuals from the evolved populations revealed that the distribution of genotypes did not escape the starting local fitness peak, remaining clustered around the sequence used to initiate evolution. This is consistent with a fitness landscape where high-fitness genotypes are sparse and well isolated, and suggests, at least in this context, that neutral drift alone is not a primary driver of genetic change. Neutral drift does, however, provide a repository of genetic variation upon which adaptive selection can act.
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Identification of neutral tumor evolution across cancer types
Barnes, Chris P; Graham, Trevor A; Sottoriva, Andrea
2016-01-01
Despite extraordinary efforts to profile cancer genomes, interpreting the vast amount of genomic data in the light of cancer evolution remains challenging. Here we demonstrate that neutral tumor evolution results in a power-law distribution of the mutant allele frequencies reported by next-generation sequencing of tumor bulk samples. We find that the neutral power-law fits with high precision 323 of 904 cancers from 14 types, selected from different cohorts. In malignancies identified as neutral, all clonal selection occurred prior to the onset of cancer growth and not in later-arising subclones, resulting in numerous passenger mutations that are responsible for intra-tumor heterogeneity. Reanalyzing cancer sequencing data within the neutral framework allowed the measurement, in each patient, of both the in vivo mutation rate and the order and timing of mutations. This result provides a new way to interpret existing cancer genomic data and to discriminate between functional and non-functional intra-tumor heterogeneity. PMID:26780609
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Rocha, Cheila; Calado, Rita; Borrego, Pedro; ...
2013-10-24
Background: therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4 + T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected atmore » birth. As a result, CD4 + T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4 + T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Finally, our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rocha, Cheila; Calado, Rita; Borrego, Pedro
Background: therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4 + T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected atmore » birth. As a result, CD4 + T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4 + T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Finally, our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.« less
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Siddappa, Nagadenahalli B; Watkins, Jennifer D; Wassermann, Klemens J; Song, Ruijiang; Wang, Wendy; Kramer, Victor G; Lakhashe, Samir; Santosuosso, Michael; Poznansky, Mark C; Novembre, Francis J; Villinger, François; Else, James G; Montefiori, David C; Rasmussen, Robert A; Ruprecht, Ruth M
2010-07-21
HIV-1 clade C (HIV-C) predominates worldwide, and anti-HIV-C vaccines are urgently needed. Neutralizing antibody (nAb) responses are considered important but have proved difficult to elicit. Although some current immunogens elicit antibodies that neutralize highly neutralization-sensitive (tier 1) HIV strains, most circulating HIVs exhibiting a less sensitive (tier 2) phenotype are not neutralized. Thus, both tier 1 and 2 viruses are needed for vaccine discovery in nonhuman primate models. We constructed a tier 1 simian-human immunodeficiency virus, SHIV-1157ipEL, by inserting an "early," recently transmitted HIV-C env into the SHIV-1157ipd3N4 backbone [1] encoding a "late" form of the same env, which had evolved in a SHIV-infected rhesus monkey (RM) with AIDS. SHIV-1157ipEL was rapidly passaged to yield SHIV-1157ipEL-p, which remained exclusively R5-tropic and had a tier 1 phenotype, in contrast to "late" SHIV-1157ipd3N4 (tier 2). After 5 weekly low-dose intrarectal exposures, SHIV-1157ipEL-p systemically infected 16 out of 17 RM with high peak viral RNA loads and depleted gut CD4+ T cells. SHIV-1157ipEL-p and SHIV-1157ipd3N4 env genes diverge mostly in V1/V2. Molecular modeling revealed a possible mechanism for the increased neutralization resistance of SHIV-1157ipd3N4 Env: V2 loops hindering access to the CD4 binding site, shown experimentally with nAb b12. Similar mutations have been linked to decreased neutralization sensitivity in HIV-C strains isolated from humans over time, indicating parallel HIV-C Env evolution in humans and RM. SHIV-1157ipEL-p, the first tier 1 R5 clade C SHIV, and SHIV-1157ipd3N4, its tier 2 counterpart, represent biologically relevant tools for anti-HIV-C vaccine development in primates.
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What Can Galaxies Tell Us About The Epoch of Reionization?
NASA Astrophysics Data System (ADS)
Mason, Charlotte; GLASS, BoRG
2018-01-01
The reionization of neutral hydrogen in the intergalactic medium (IGM) in the universe's first billion years (z>6) was likely driven by the first stars and galaxies, and its history encodes information about their properties. But the timeline of reionization is not well-measured and it is still unclear whether galaxies alone can produce the required ionizing photons. I will describe two key ways in which galaxies at our current observational frontiers can constrain reionization.One tool is the UV luminosity function (LF), which traces the evolution of star-forming galaxies and their ionizing photons. I will describe a Bayesian technique to account for gravitational lensing magnification bias in galaxy surveys to produce accurate LFs. I will then describe a simple, but powerful, model for LF evolution and its implications for reionization and z>10 galaxy surveys with JWST. Secondly, Lyman alpha (Lya) emission from galaxies is a potential probe of the IGM ionization state as Lya photons are strongly attenuated by neutral hydrogen, but requires disentangling physics on pc to Gpc scales. I will introduce a new forward-modeling Bayesian framework which combines cosmological IGM simulations with models of interstellar medium conditions to infer the IGM neutral fraction from observations of Lya emission. I will present our new measurement of the neutral fraction at z~7 and place it in the context of other constraints of the reionization history. I will describe ongoing efforts to build larger samples of Lya emitting galaxies for more accurate measurements with the HST survey GLASS, and will describe future prospects with JWST.
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Effects of convincing power and neutrality on minority opinion spreading
NASA Astrophysics Data System (ADS)
Wu, Yue; Xiong, Xi; Zhang, Yi
2017-02-01
The dynamics evolution of the minority opinion in public debates is studied using a convincing power (CP) model with neutrality. In a given group, an agent with a definite standpoint (yes or no) can be persuaded to be a neutral agent, if its capacity of persuasion is lower than the average CP of its opponents. Besides that a neutral agent will change its state and follow a more persuasive opinion. Starting from two opposite opinions with different rates, repeated local discussions are found to drive the minority reversal. It reveals that in addition to the initial minority, the number of neutral agents is also an important factor to the eventual winners. During the process of consensus, there exists a threshold of initial fraction to guarantee one side win. The results have a guiding significance for designing strategies to win a public debate.
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Decoherence and discrete symmetries in deformed relativistic kinematics
NASA Astrophysics Data System (ADS)
Arzano, Michele
2018-01-01
Models of deformed Poincaré symmetries based on group valued momenta have long been studied as effective modifications of relativistic kinematics possibly capturing quantum gravity effects. In this contribution we show how they naturally lead to a generalized quantum time evolution of the type proposed to model fundamental decoherence for quantum systems in the presence of an evaporating black hole. The same structures which determine such generalized evolution also lead to a modification of the action of discrete symmetries and of the CPT operator. These features can in principle be used to put phenomenological constraints on models of deformed relativistic symmetries using precision measurements of neutral kaons.
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Propagation of Interplanetary Disturbances in the Outer Heliosphere
NASA Technical Reports Server (NTRS)
Wang, Chi
2002-01-01
Work finished during 2002 included: (1) Finished a multi-fluid solar wind model; (2) Determined the solar wind slowdown and interstellar neutral density; (3) Studied shock propagation and evolution in the outer heliosphere; (4) Investigated statistical properties of the solar wind in the outer heliosphere.
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Phase Transition Behavior in a Neutral Evolution Model
NASA Astrophysics Data System (ADS)
King, Dawn; Scott, Adam; Maric, Nevena; Bahar, Sonya
2014-03-01
The complexity of interactions among individuals and between individuals and the environment make agent based modeling ideal for studying emergent speciation. This is a dynamically complex problem that can be characterized via the critical behavior of a continuous phase transition. Concomitant with the main tenets of natural selection, we allow organisms to reproduce, mutate, and die within a neutral phenotype space. Previous work has shown phase transition behavior in an assortative mating model with variable fitness landscapes as the maximum mutation size (μ) was varied (Dees and Bahar, 2010). Similarly, this behavior was recently presented in the work of Scott et al. (2013), even on a completely neutral landscape, for bacterial-like fission as well as for assortative mating. Here we present another neutral model to investigate the `critical' phase transition behavior of three mating types - assortative, bacterial, and random - in a phenotype space as a function of the percentage of random death. Results show two types of phase transitions occurring for the parameters of the population size and the number of clusters (an analogue of species), indicating different evolutionary dynamics for system survival and clustering. This research was supported by funding from: University of Missouri Research Board and James S. McDonnell Foundation.
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Sazatornil, Federico D; Moré, Marcela; Benitez-Vieyra, Santiago; Cocucci, Andrea A; Kitching, Ian J; Schlumpberger, Boris O; Oliveira, Paulo E; Sazima, Marlies; Amorim, Felipe W
2016-11-01
A major challenge in evolutionary ecology is to understand how co-evolutionary processes shape patterns of interactions between species at community level. Pollination of flowers with long corolla tubes by long-tongued hawkmoths has been invoked as a showcase model of co-evolution. Recently, optimal foraging models have predicted that there might be a close association between mouthparts' length and the corolla depth of the visited flowers, thus favouring trait convergence and specialization at community level. Here, we assessed whether hawkmoths more frequently pollinate plants with floral tube lengths similar to their proboscis lengths (morphological match hypothesis) against abundance-based processes (neutral hypothesis) and ecological trait mismatches constraints (forbidden links hypothesis), and how these processes structure hawkmoth-plant mutualistic networks from five communities in four biogeographical regions of South America. We found convergence in morphological traits across the five communities and that the distribution of morphological differences between hawkmoths and plants is consistent with expectations under the morphological match hypothesis in three of the five communities. In the two remaining communities, which are ecotones between two distinct biogeographical areas, interactions are better predicted by the neutral hypothesis. Our findings are consistent with the idea that diffuse co-evolution drives the evolution of extremely long proboscises and flower tubes, and highlight the importance of morphological traits, beyond the forbidden links hypothesis, in structuring interactions between mutualistic partners, revealing that the role of niche-based processes can be much more complex than previously known. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.
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Ruths, Troy; Nakhleh, Luay
2013-05-07
Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels. We leverage our model against experimentally derived data from Escherichia coli. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in origin--degree distribution, clustering coefficient, and motifs--within the E. coli CRN. Our model captures the tightly coupled genome-interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs.
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NASA Astrophysics Data System (ADS)
Karim, Rezwanul
1999-10-01
This article discusses the development of a code where diagnostic neutral helium beam can be used as a probe. The code solves numerically the evolution of the population densities of helium atoms at their several different energy levels as the beam propagates through the plasma. The collisional radiative model has been utilized in this numerical calculation. The spatial dependence of the metastable states of neutral helium atom, as obtained in this numerical analysis, offers a possible diagnostic tool for tokamak plasma. The spatial evolution for several hypothetical plasma conditions was tested. Simulation routines were also run with the plasma parameters (density and temperature profiles) similar to a shot in the Princeton beta experiment modified (PBX-M) tokamak and a shot in Tokamak Fusion Test Reactor tokamak. A comparison between the simulation result and the experimentally obtained data (for each of these two shots) is presented. A good correlation in such comparisons for a number of such shots can establish the accurateness and usefulness of this probe. The result can possibly be extended for other plasma machines and for various plasma conditions in those machines.
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In silico evolution of biochemical networks
NASA Astrophysics Data System (ADS)
Francois, Paul
2010-03-01
We use computational evolution to select models of genetic networks that can be built from a predefined set of parts to achieve a certain behavior. Selection is made with the help of a fitness defining biological functions in a quantitative way. This fitness has to be specific to a process, but general enough to find processes common to many species. Computational evolution favors models that can be built by incremental improvements in fitness rather than via multiple neutral steps or transitions through less fit intermediates. With the help of these simulations, we propose a kinetic view of evolution, where networks are rapidly selected along a fitness gradient. This mathematics recapitulates Darwin's original insight that small changes in fitness can rapidly lead to the evolution of complex structures such as the eye, and explain the phenomenon of convergent/parallel evolution of similar structures in independent lineages. We will illustrate these ideas with networks implicated in embryonic development and patterning of vertebrates and primitive insects.
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New insights on the collisional escape of light neutrals from Mars
NASA Astrophysics Data System (ADS)
Gacesa, Marko; Zahnle, Kevin
2017-04-01
Photodissociative recombination (PDR) of atmospheric molecules on Mars is a major mechanism of production of hot (suprathermal) atoms with sufficient kinetic energy to either directly escape to space or to eject other atmospheric species. This collisional ejection mechanism is important for evaluating the escape rates of all light neutrals that are too heavy to escape via Jeans escape. In particular, it plays a role in estimating the total volume of escaped water constituents (i.e., O and H) from Mars, as well as influences evolution of the atmospheric [D]/[H] ratio1. We present revised estimates of total collisional escape rates of neutral light elements including H, He, and H2, based on recent (years 2015-2016) atmospheric density profiles obtained from the NASA Mars Atmosphere and Volatile Evolution (MAVEN) mission. We also estimate the contribution to the collisional escape from Energetic Neutral Atoms (ENAs) produced in charge-exchange of solar wind H+ and He+ ions with atmospheric gases2,3. Scattering of hot oxygen and atmospheric species of interest is modeled using fully-quantum reactive scattering formalism1,3. The escape rates are evaluated using a 1D model of the atmosphere supplemented with MAVEN measurements of the neutrals. Finally, new estimates of contributions of these non-thermal mechanisms to the estimated PDR escape rates from young Mars4 are presented. [1] M. Gacesa and V. Kharchenko, "Non-thermal escape of molecular hydrogen from Mars", Geophys. Res. Lett., 39, L10203 (2012). [2] N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere", Astroph. J., 790, 98 (2014). [3] M. Gacesa, N. Lewkow, and V. Kharchenko, "Non-thermal production and escape of OH from the upper atmosphere of Mars", Icarus 284, 90 (2017). [4] J. Zhao, F. Tian, Y. Ni, and X. Huang, "DR-induced escape of O and C from early Mars", Icarus 284, 305 (2017).
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Two-fluid Numerical Simulations of Solar Spicules
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kuźma, Błażej; Murawski, Kris; Kayshap, Pradeep
2017-11-10
We aim to study the formation and evolution of solar spicules by means of numerical simulations of the solar atmosphere. With the use of newly developed JOANNA code, we numerically solve two-fluid (for ions + electrons and neutrals) equations in 2D Cartesian geometry. We follow the evolution of a spicule triggered by the time-dependent signal in ion and neutral components of gas pressure launched in the upper chromosphere. We use the potential magnetic field, which evolves self-consistently, but mainly plays a passive role in the dynamics. Our numerical results reveal that the signal is steepened into a shock that propagatesmore » upward into the corona. The chromospheric cold and dense plasma lags behind this shock and rises into the corona with a mean speed of 20–25 km s{sup −1}. The formed spicule exhibits the upflow/downfall of plasma during its total lifetime of around 3–4 minutes, and it follows the typical characteristics of a classical spicule, which is modeled by magnetohydrodynamics. The simulated spicule consists of a dense and cold core that is dominated by neutrals. The general dynamics of ion and neutral spicules are very similar to each other. Minor differences in those dynamics result in different widths of both spicules with increasing rarefaction of the ion spicule in time.« less
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Brain enlargement and dental reduction were not linked in hominin evolution
Smaers, Jeroen B.; Holloway, Ralph L.
2017-01-01
The large brain and small postcanine teeth of modern humans are among our most distinctive features, and trends in their evolution are well studied within the hominin clade. Classic accounts hypothesize that larger brains and smaller teeth coevolved because behavioral changes associated with increased brain size allowed a subsequent dental reduction. However, recent studies have found mismatches between trends in brain enlargement and posterior tooth size reduction in some hominin species. We use a multiple-variance Brownian motion approach in association with evolutionary simulations to measure the tempo and mode of the evolution of endocranial and dental size and shape within the hominin clade. We show that hominin postcanine teeth have evolved at a relatively consistent neutral rate, whereas brain size evolved at comparatively more heterogeneous rates that cannot be explained by a neutral model, with rapid pulses in the branches leading to later Homo species. Brain reorganization shows evidence of elevated rates only much later in hominin evolution, suggesting that fast-evolving traits such as the acquisition of a globular shape may be the result of direct or indirect selection for functional or structural traits typical of modern humans. PMID:28049819
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NASA Astrophysics Data System (ADS)
Orsini, S.; Npa-Serena Team
The Neutral Particle Analyser SERENA, proposed on board the BepiColombo Mer- cury Planetary Orbiter (MPO), has the purpose of investigating the Hermean exo- spheric and energetic neutral populations. Local and detailed analysis of the exo- spheric composition will be performed by a ram-pointing sensor (MAIA), while en- ergetic neutrals produced through sputtering and charge-exchange processes will be collected by two nadir-pointing sensors (L-ENA, MH-ENA). A central problem in the understanding of the evolution of solar system bodies is the role played by the so- lar wind, solar radiation and micro-meteorite bombardment in controlling mass losses. The direct in situ detection of the Hermean exosphere, the gas evolving from the planet as a product of the different physical processes acting onto the surface, is of crucial importance to understand the past and present evolution of the crust. Current knowl- edge of the origin and evolution of the solar system is based on detailed measurement of chemical, elemental, and isotopic composition of matter. The proposed instrument suite is unique in its capability to perform quantitative analysis and resolve exospheric gas composition under all these three aspects. The value of neutral particles mea- surements for getting a comprehensive picture of the solar wind-planets interaction has been appreciated since the late eighties. Comparison of the measurements in the Mercury environment with those achieved by neutral particle imagers already flying around Earth (IMAGE), Mars (Mars Express), Jupiter and Saturn (Cassini) will allow comparative investigations of evolution and dynamics of planetary magnetospheres.
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Laroche, Fabien; Jarne, Philippe; Perrot, Thomas; Massol, Francois
2016-04-27
Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities. © 2016 The Author(s).
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Mineral induced phosphorylation of glycolate ion--a metaphor in chemical evolution
NASA Technical Reports Server (NTRS)
Kolb, V.; Zhang, S.; Xu, Y.; Arrhenius, G.
1997-01-01
Bilateral surface-active minerals with excess positive charge concentrate glycolate and trimetaphosphate ion from l0(-3) m aqueous solution to half-saturation of the internal surface sites, and induce phosphorylation of glycolate ion in the mineral with trimetaphosphate, sorbed from l0(-2) m solution. By utilizing reactants from dilute solution at near-neutral pH, and eliminating the need for participating organic nitrogen compounds, the reaction comprises several elements considered necessary for geochemical realism in models for molecular evolution.
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Dust cloud evolution in sub-stellar atmospheres via plasma deposition and plasma sputtering
NASA Astrophysics Data System (ADS)
Stark, C. R.; Diver, D. A.
2018-04-01
Context. In contemporary sub-stellar model atmospheres, dust growth occurs through neutral gas-phase surface chemistry. Recently, there has been a growing body of theoretical and observational evidence suggesting that ionisation processes can also occur. As a result, atmospheres are populated by regions composed of plasma, gas and dust, and the consequent influence of plasma processes on dust evolution is enhanced. Aim. This paper aims to introduce a new model of dust growth and destruction in sub-stellar atmospheres via plasma deposition and plasma sputtering. Methods: Using example sub-stellar atmospheres from DRIFT-PHOENIX, we have compared plasma deposition and sputtering timescales to those from neutral gas-phase surface chemistry to ascertain their regimes of influence. We calculated the plasma sputtering yield and discuss the circumstances where plasma sputtering dominates over deposition. Results: Within the highest dust density cloud regions, plasma deposition and sputtering dominates over neutral gas-phase surface chemistry if the degree of ionisation is ≳10-4. Loosely bound grains with surface binding energies of the order of 0.1-1 eV are susceptible to destruction through plasma sputtering for feasible degrees of ionisation and electron temperatures; whereas, strong crystalline grains with binding energies of the order 10 eV are resistant to sputtering. Conclusions: The mathematical framework outlined sets the foundation for the inclusion of plasma deposition and plasma sputtering in global dust cloud formation models of sub-stellar atmospheres.
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Modeling the Extended Neutral Atmosphere and Plasma Environment near Saturn
NASA Technical Reports Server (NTRS)
Richardson, John D.
2003-01-01
In the three years of this study we have published five papers in refereed journals. We have first examined satellite sources and their contribution to the observed neutral cloud. Based on the total calculated satellite sources and the spatial distribution of sputtered H20, we concluded that they cannot produce observed OH cloud. The E-ring contribution has been also studied in detail.In order to produce observed OH cloud we suggested that the E-ring might be the dominant source in inner Saturnian magnetosphere. We proposed a possible resupply mechanism which is needed to keep both E-ring and OH cloud in the present state: collisions between E-ring grains and remains of a disrupted satellite near Enceladus Lagrangian points. In this scenario a large amount of material, ranging from a few micrometers to hundred of meters, which is optically invisible at present, is likely to exist there. The fourth paper compares the magnetosheaths of the outer planets. A surprising result is that the hot proton component comprises about 40% of the total density, much larger than predicted by shock theory. Gas dynamic models of the boundaries show that the magnetospheres of Jupiter and Saturn are flattened at the poles. The last paper was published in GRL and is the first based of the model of neutrals developed as a main goal of this grant and which is now operational.This Monte Carlo collision code self- consistently determines the neutral distribution. from the rings and satellites until they are lost by ionization, by collisions with rings, moons, or Saturn, or by escape from Saturn. Our model is unique in that it includes the effects of plasma chemistry and both plasma-neutral and neutral neutral collisions to determine the dynamical evolution of the water group neutrals in Saturn's magnetosphere. The lifetimes of the neutrals against loss to photoionization, charge exchange, electron dissociation and electron impact dissociation are based on the model given by (Richardson et al. 1998) and vary with position in the magnetosphere. The dominant neutral dissociation channels H20->OH+H, H20-> O+H2, and OH->O+H2 are considered.
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Studies of the pedestal structure and inter-ELM pedestal evolution in JET with the ITER-like wall
NASA Astrophysics Data System (ADS)
Maggi, C. F.; Frassinetti, L.; Horvath, L.; Lunniss, A.; Saarelma, S.; Wilson, H.; Flanagan, J.; Leyland, M.; Lupelli, I.; Pamela, S.; Urano, H.; Garzotti, L.; Lerche, E.; Nunes, I.; Rimini, F.; Contributors, JET
2017-11-01
The pedestal structure of type I ELMy H-modes has been analysed for JET with the ITER-like Wall (JET-ILW). The electron pressure pedestal width is independent of ρ * and increases proportionally to √β pol,PED. Additional broadening of the width is observed, at constant β pol, PED, with increasing ν * and/or neutral gas injection and the contribution of atomic physics effects in setting the pedestal width cannot as yet be ruled out. Neutral penetration alone does not determine the shape of the edge density profile in JET-ILW. The ratio of electron density to electron temperature scale lengths in the edge transport barrier region, η e, is of order 2-3 within experimental uncertainties. Existing understanding, represented in the stationary linear peeling-ballooning mode stability and the EPED pedestal structure models, is extended to the dynamic evolution between ELM crashes in JET-ILW, in order to test the assumptions underlying these two models. The inter-ELM temporal evolution of the pedestal structure in JET-ILW is not unique, but depends on discharge conditions, such as heating power and gas injection levels. The strong reduction in p e,PED with increasing D 2 gas injection at high power is primarily due to clamping of \
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Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.
Uchi, Ryutaro; Takahashi, Yusuke; Niida, Atsushi; Shimamura, Teppei; Hirata, Hidenari; Sugimachi, Keishi; Sawada, Genta; Iwaya, Takeshi; Kurashige, Junji; Shinden, Yoshiaki; Iguchi, Tomohiro; Eguchi, Hidetoshi; Chiba, Kenichi; Shiraishi, Yuichi; Nagae, Genta; Yoshida, Kenichi; Nagata, Yasunobu; Haeno, Hiroshi; Yamamoto, Hirofumi; Ishii, Hideshi; Doki, Yuichiro; Iinuma, Hisae; Sasaki, Shin; Nagayama, Satoshi; Yamada, Kazutaka; Yachida, Shinichi; Kato, Mamoru; Shibata, Tatsuhiro; Oki, Eiji; Saeki, Hiroshi; Shirabe, Ken; Oda, Yoshinao; Maehara, Yoshihiko; Komune, Shizuo; Mori, Masaki; Suzuki, Yutaka; Yamamoto, Ken; Aburatani, Hiroyuki; Ogawa, Seishi; Miyano, Satoru; Mimori, Koshi
2016-02-01
Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients' ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.
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Neutral aggregation in finite-length genotype space
NASA Astrophysics Data System (ADS)
Houchmandzadeh, Bahram
2017-01-01
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual-based model of Wright and Fisher, we compute the amplitude of neutral aggregation in the genome space, i.e., the probability of finding two individuals at genetic (Hamming) distance k as a function of the genome size L , population size N , and mutation probability per base ν . In well-mixed populations, we show that for N ν <1 /L , neutral aggregation is the dominant force and most individuals are found at short genetic distances from each other. For N ν >1 , on the contrary, individuals are randomly dispersed in genome space. The results are extended to a geographically dispersed population, where the controlling parameter is shown to be a combination of mutation and migration probability. The theory we develop can be used to test the neutrality hypothesis in various ecological and evolutionary systems.
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A case study of the thermospheric neutral wind response to geomagnetic storm
NASA Astrophysics Data System (ADS)
Jiang, Guoying; Zhang, Shunrong; Wang, Wenbin; Yuan, Wei; Wu, Qian; Xu, Jiyao
A minor geomagnetic storm (Kp=5) occurred on March 27-28, 2012. The response of the thermospheric neutral wind at ~ 250 km to this storm was investigated by the 630.0 nm nightglow measurements of Fabry-Perot interferometers (FPIs) over Xinglong (geographic location: 40.2N, 117.4E; geomagnetic location: 29.8N, 193.2E) and Millstone Hill (geographic location: 42.6N, 71.5W; geomagnetic location: 53.1N, 65.1W). Our results show that the minor storm on March 27-28, 2012 obviously effected on the thermospheric neutral winds over Xinglong and Millstone Hill, especially Millstone Hill had larger response because of its higher geomagnetic latitude. Another interesting result is that a small variation in geomagnetic activity (Kp=2.7) could enough introduce a clear disturbance in the nighttime thermospheric neutral wind over Millstone hill. NCAR-TIME-GCM (National Center for Atmospheric Research-Thermosphere Ionosphere Mesosphere Electrodynamics-General Circulation Model) was employed to study the evolution and mechanism of the thermospheric neutral wind response.
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Allowing for Slow Evolution of Background Plasma in the 3D FDTD Plasma, Sheath, and Antenna Model
NASA Astrophysics Data System (ADS)
Smithe, David; Jenkins, Thomas; King, Jake
2015-11-01
We are working to include a slow-time evolution capability for what has previously been the static background plasma parameters, in the 3D finite-difference time-domain (FDTD) plasma and sheath model used to model ICRF antennas in fusion plasmas. A key aspect of this is SOL-density time-evolution driven by ponderomotive rarefaction from the strong fields in the vicinity of the antenna. We demonstrate and benchmark a Scalar Ponderomotive Potential method, based on local field amplitudes, which is included in the 3D simulation. And present a more advanced Tensor Ponderomotive Potential approach, which we hope to employ in the future, which should improve the physical fidelity in the highly anisotropic environment of the SOL. Finally, we demonstrate and benchmark slow time (non-linear) evolution of the RF sheath, and include realistic collisional effects from the neutral gas. Support from US DOE Grants DE-FC02-08ER54953, DE-FG02-09ER55006.
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Spatial vs. individual variability with inheritance in a stochastic Lotka-Volterra system
NASA Astrophysics Data System (ADS)
Dobramysl, Ulrich; Tauber, Uwe C.
2012-02-01
We investigate a stochastic spatial Lotka-Volterra predator-prey model with randomized interaction rates that are either affixed to the lattice sites and quenched, and / or specific to individuals in either population. In the latter situation, we include rate inheritance with mutations from the particles' progenitors. Thus we arrive at a simple model for competitive evolution with environmental variability and selection pressure. We employ Monte Carlo simulations in zero and two dimensions to study the time evolution of both species' densities and their interaction rate distributions. The predator and prey concentrations in the ensuing steady states depend crucially on the environmental variability, whereas the temporal evolution of the individualized rate distributions leads to largely neutral optimization. Contrary to, e.g., linear gene expression models, this system does not experience fixation at extreme values. An approximate description of the resulting data is achieved by means of an effective master equation approach for the interaction rate distribution.
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Multiple rings around Wolf-Rayet evolution
NASA Technical Reports Server (NTRS)
Marston, A. P.
1995-01-01
We present optical narrow-band imaging of multiple rings existing around galactic Wolf-Rayet (WR) stars. The existence of multiple rings of material around Wolf-Rayet stars clearly illustrates the various phases of evolution that massive stars go through. The objects presented here show evidence of a three stage evolution. O stars produce an outer ring with the cavity being partially filled by ejecta from a red supergiant of luminous blue variable phase. A wind from the Wolf-Rayet star then passes into the ejecta materials. A simple model is presented for this three stage evolution. Using observations of the size and dynamics of the rings allows estimates of time scales for each stage of the massive star evolution. These are consistent with recent theoretical evolutionary models. Mass estimates for the ejecta, from the model presented, are consistent with previous ring nebula mass estimates from IRAS data, showing a number of ring nebulae to have large masses, most of which must in be in the form of neutral material. Finally, we illustrate how further observations will allow the determination of many of the parameters of the evolution of massive stars such as total mass loss, average mass loss rates, stellar abundances, and total time spent in each evolutionary phase.
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Cultural selection drives the evolution of human communication systems
Tamariz, Monica; Ellison, T. Mark; Barr, Dale J.; Fay, Nicolas
2014-01-01
Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems. PMID:24966310
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Cultural selection drives the evolution of human communication systems.
Tamariz, Monica; Ellison, T Mark; Barr, Dale J; Fay, Nicolas
2014-08-07
Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.
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Evolution of disease response genes in loblolly pine: insights from candidate genes.
Ersoz, Elhan S; Wright, Mark H; González-Martínez, Santiago C; Langley, Charles H; Neale, David B
2010-12-06
Host-pathogen interactions that may lead to a competitive co-evolution of virulence and resistance mechanisms present an attractive system to study molecular evolution because strong, recent (or even current) selective pressure is expected at many genomic loci. However, it is unclear whether these selective forces would act to preserve existing diversity, promote novel diversity, or reduce linked neutral diversity during rapid fixation of advantageous alleles. In plants, the lack of adaptive immunity places a larger burden on genetic diversity to ensure survival of plant populations. This burden is even greater if the generation time of the plant is much longer than the generation time of the pathogen. Here, we present nucleotide polymorphism and substitution data for 41 candidate genes from the long-lived forest tree loblolly pine, selected primarily for their prospective influences on host-pathogen interactions. This dataset is analyzed together with 15 drought-tolerance and 13 wood-quality genes from previous studies. A wide range of neutrality tests were performed and tested against expectations from realistic demographic models. Collectively, our analyses found that axr (auxin response factor), caf1 (chromatin assembly factor) and gatabp1 (gata binding protein 1) candidate genes carry patterns consistent with directional selection and erd3 (early response to drought 3) displays patterns suggestive of a selective sweep, both of which are consistent with the arm-race model of disease response evolution. Furthermore, we have identified patterns consistent with diversifying selection at erf1-like (ethylene responsive factor 1), ccoaoemt (caffeoyl-CoA-O-methyltransferase), cyp450-like (cytochrome p450-like) and pr4.3 (pathogen response 4.3), expected under the trench-warfare evolution model. Finally, a drought-tolerance candidate related to the plant cell wall, lp5, displayed patterns consistent with balancing selection. In conclusion, both arms-race and trench-warfare models seem compatible with patterns of polymorphism found in different disease-response candidate genes, indicating a mixed strategy of disease tolerance evolution for loblolly pine, a major tree crop in southeastern United States.
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Kishimoto, Toshihiko; Iijima, Leo; Tatsumi, Makoto; Ono, Naoaki; Oyake, Ayana; Hashimoto, Tomomi; Matsuo, Moe; Okubo, Masato; Suzuki, Shingo; Mori, Kotaro; Kashiwagi, Akiko; Furusawa, Chikara; Ying, Bei-Wen; Yomo, Tetsuya
2010-10-21
It remains to be determined experimentally whether increasing fitness is related to positive selection, while stationary fitness is related to neutral evolution. Long-term laboratory evolution in Escherichia coli was performed under conditions of thermal stress under defined laboratory conditions. The complete cell growth data showed common continuous fitness recovery to every 2°C or 4°C stepwise temperature upshift, finally resulting in an evolved E. coli strain with an improved upper temperature limit as high as 45.9°C after 523 days of serial transfer, equivalent to 7,560 generations, in minimal medium. Two-phase fitness dynamics, a rapid growth recovery phase followed by a gradual increasing growth phase, was clearly observed at diverse temperatures throughout the entire evolutionary process. Whole-genome sequence analysis revealed the transition from positive to neutral in mutation fixation, accompanied with a considerable escalation of spontaneous substitution rate in the late fitness recovery phase. It suggested that continually increasing fitness not always resulted in the reduction of genetic diversity due to the sequential takeovers by fit mutants, but caused the accumulation of a considerable number of mutations that facilitated the neutral evolution.
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Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography.
Albert, James S; Schoolmaster, Donald R; Tagliacollo, Victor; Duke-Sylvester, Scott M
2017-03-01
Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust mechanistic framework to connect these seemingly disparate patterns. Here we present SEAMLESS (Spatially Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g., Lagrange, GeoSSE, BayArea, and BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here toward the formulation of a general theory of continental biogeography. [Diversification, extinction, geodispersal, macroevolution, river capture, vicariance.]. Published by Oxford University Press on behalf of Society of Systematic Biologists 2016. This work is written by a US Government employee and is in the public domain in the US.
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Llopart, Ana
2018-05-01
The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genomewide test of this hypothesis is still missing. Here, I use whole genome sequence data in Drosophila yakuba and D. santomea to evaluate this hypothesis and report positive correlations between sequence divergence at 5' noncoding sequences and gene expression divergence. I also examine polymorphism and divergence in 9,279 noncoding sequences located at the 5' end of annotated genes and detected multiple signals of positive selection. Notably, I used the traditional synonymous sites as neutral reference to test for adaptive evolution, but I also used bases 8-30 of introns <65 bp, which have been proposed to be a better neutral choice. X-linked genes with high degree of male-biased expression show the most extreme adaptive pattern at 5' noncoding regions, in agreement with faster-X evolution for gene expression divergence and a higher incidence of positively selected recessive mutations. © 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.
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The impact of exospheric neutral dynamics on ring current decay
NASA Astrophysics Data System (ADS)
Ilie, R.; Liemohn, M. W.; Skoug, R. M.; Funsten, H. O.; Gruntman, M.; Bailey, J. J.; Toth, G.
2015-12-01
The geocorona plays an important role in the energy budget of the Earth's inner magnetosphere since charge exchange of energetic ions with exospheric neutrals makes the exosphere act as an energy sink for ring current particles. Long-term ring current decay following a magnetic storm is mainly due to these electron transfer reactions, leading to the formation energetic neutral atoms (ENAs) that leave the ring current system on ballistic trajectories. The number of ENAs emitted from a given region of space depends on several factors, such as the energy and species of the energetic ion population in that region and the density of the neutral gas with which the ions undergo charge exchange. However, the density and structure of the exosphere are strongly dependent on changes in atmospheric temperature and density as well as charge exchange with the ions of plasmaspheric origin, which depletes the geocorona (by having a neutral removed from the system). Moreover, the radiation pressure exerted by solar far-ultraviolet photons pushes the geocoronal hydrogen away from the Earth in an anti-sunward direction to form a tail of neutral hydrogen. TWINS ENA images provide a direct measurement of these ENA losses and therefore insight into the dynamics of the ring current decay through interactions with the geocorona. We assess the influence of geocoronal neutrals on ring current formation and decay by analysis of the predicted ENA emissions using 6 different geocoronal models and simulations from the HEIDI ring current model during storm time. Comparison with TWINS ENA images shows that the location of the peak ENA enhancements is highly dependent on the distribution of geocoronal hydrogen density. We show that the neutral dynamics has a strong influence on the time evolution of the ring current populations as well as on the formation of energetic neutral atoms.
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NASA Astrophysics Data System (ADS)
Carrillo-Sánchez, J. D.; Plane, J. M. C.; Withers, P.; Fallows, K.; Nesvorny, D.; Pokorný, P.
2016-12-01
Sporadic metal layers have been detected in the Martian atmosphere by radio occultation measurements using the Mars Express Orbiter and Mars Global Surveyor spacecraft. More recently, metallic ion layers produced by the meteor storm event following the close encounter between Comet Siding Spring (C/2013 A1) and Mars were identified by the Imaging UltraViolet Spectrograph (IUVS) and the Neutral Gas and Ion Mass Spectrometer (NGIMS) on the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft. Work is now in progress to detect the background metal layers produced by the influx of sporadic meteors. In this study we predict the likely appearance of these layers. The Zodiacal Dust Cloud (ZDC) model for particle populations released by asteroids (AST), and dust grains from Jupiter Family Comets (JFCs) and Halley-Type Comets (HTCs) has been combined with a Monte Carlo sampling method and the Chemical ABlation MODel (CABMOD) to predict the ablation rates of Na, K, Fe, Si, Mg, Ca and Al above 40 km altitude in the Martian atmosphere. CABMOD considers the standard treatment of meteor physics, including the balance of frictional heating by radiative losses and the absorption of heat energy through temperature increases, melting phase transitions and vaporization, as well as sputtering by inelastic collisions with the air molecules. The vertical injection profiles are input into the Leeds 1-D Mars atmospheric model which includes photo-ionization, and gas-phase ion-molecule and neutral chemistry, in order to explore the evolution of the resulting metallic ions and atoms. We conclude that the dominant contributor in the Martian's atmosphere is the JFCs over other sources. Finally, we explore the changes of the neutral and ionized Na, Mg and Fe layers over a diurnal cycle.
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Austerlitz, Frédéric; Heyer, Evelyne
2018-06-01
Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.
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Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi
2016-10-24
Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.
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Rosenzweig instability in a thin layer of a magnetic fluid
NASA Astrophysics Data System (ADS)
Korovin, V. M.
2013-12-01
A simple mathematical model of the initial stage of nonlinear evolution of the Rosenzweig instability in a thin layer of a nonlinearly magnetized viscous ferrofluid coating a horizontal nonmagnetizable plate is constructed on the basis of the system of equations and boundary conditions of ferrofluid dynamics. A dispersion relation is derived and analyzed using the linearized equations of this model. The critical magnetization of the initial layer with a flat free surface, the threshold wavenumber, and the characteristic time of evolution of the most rapidly growing mode are determined. The equation for the neutral stability curve, which is applicable for any physically admissible law of magnetization of a ferrofluid, is derived analytically.
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Competition, coinfection and strain replacement in models of Bordetella pertussis.
Nicoli, Emily J; Ayabina, Diepreye; Trotter, Caroline L; Turner, Katherine M E; Colijn, Caroline
2015-08-01
Pertussis, or whooping cough, is an important respiratory infection causing considerable infant mortality worldwide. Recently, incidence has risen in countries with strong vaccine programmes and there are concerns about antigenic shift resulting in vaccine evasion. Interactions between pertussis and non-vaccine-preventable strains will play an important role in the evolution and population dynamics of pertussis. In particular, if we are to understand the role strain replacement plays in vaccinated settings, it will be essential to understand how strains or variants of pertussis interact. Here we explore under what conditions we would expect strain replacement to be of concern in pertussis. We develop a dynamic transmission model that allows for coinfection between Bordetella pertussis (the main causative agent of pertussis) and a strain or variant unaffected by the vaccine. We incorporate both neutrality (in the sense of ecological/population genetic neutrality) and immunity into the model, leaving the specificity of the immune response flexible. We find that strain replacement may be considerable when immunity is non-specific. This is in contrast to previous findings where neutrality was not considered. We conclude that the extent to which models reflect ecological neutrality can have a large impact on conclusions regarding strain replacement. This will likely have onward consequences for estimates of vaccine efficacy and cost-effectiveness. Copyright © 2015 Elsevier Inc. All rights reserved.
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Models of microbiome evolution incorporating host and microbial selection.
Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen
2017-09-25
Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.
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Simulated GOLD Observations of Atmospheric Waves
NASA Astrophysics Data System (ADS)
Correira, J.; Evans, J. S.; Lumpe, J. D.; Rusch, D. W.; Chandran, A.; Eastes, R.; Codrescu, M.
2016-12-01
The Global-scale Observations of the Limb and Disk (GOLD) mission will measure structures in the Earth's airglow layer due to dynamical forcing by vertically and horizontally propagating waves. These measurements focus on global-scale structures, including compositional and temperature responses resulting from dynamical forcing. Daytime observations of far-UV emissions by GOLD will be used to generate two-dimensional maps of the ratio of atomic oxygen and molecular nitrogen column densities (ΣO/N2 ) as well as neutral temperature that provide signatures of large-scale spatial structure. In this presentation, we use simulations to demonstrate GOLD's capability to deduce periodicities and spatial dimensions of large-scale waves from the spatial and temporal evolution observed in composition and temperature maps. Our simulations include sophisticated forward modeling of the upper atmospheric airglow that properly accounts for anisotropy in neutral and ion composition, temperature, and solar illumination. Neutral densities and temperatures used in the simulations are obtained from global circulation and climatology models that have been perturbed by propagating waves with a range of amplitudes, periods, and sources of excitation. Modeling of airglow emission and predictions of ΣO/N2 and neutral temperatures are performed with the Atmospheric Ultraviolet Radiance Integrated Code (AURIC) and associated derived product algorithms. Predicted structure in ΣO/N2 and neutral temperature due to dynamical forcing by propagating waves is compared to existing observations. Realistic GOLD Level 2 data products are generated from simulated airglow emission using algorithm code that will be implemented operationally at the GOLD Science Data Center.
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Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution
Niida, Atsushi; Shimamura, Teppei; Hirata, Hidenari; Sugimachi, Keishi; Sawada, Genta; Iwaya, Takeshi; Kurashige, Junji; Shinden, Yoshiaki; Iguchi, Tomohiro; Eguchi, Hidetoshi; Chiba, Kenichi; Shiraishi, Yuichi; Nagae, Genta; Yoshida, Kenichi; Nagata, Yasunobu; Haeno, Hiroshi; Yamamoto, Hirofumi; Ishii, Hideshi; Doki, Yuichiro; Iinuma, Hisae; Sasaki, Shin; Nagayama, Satoshi; Yamada, Kazutaka; Yachida, Shinichi; Kato, Mamoru; Shibata, Tatsuhiro; Oki, Eiji; Saeki, Hiroshi; Shirabe, Ken; Oda, Yoshinao; Maehara, Yoshihiko; Komune, Shizuo; Mori, Masaki; Suzuki, Yutaka; Yamamoto, Ken; Aburatani, Hiroyuki; Ogawa, Seishi; Miyano, Satoru; Mimori, Koshi
2016-01-01
Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients’ ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease. PMID:26890883
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Early time evolution of a chemically produced electron depletion
NASA Technical Reports Server (NTRS)
Scales, W. A.; Bernhardt, P. A.; Ganguli, G.
1995-01-01
The early time evolution of an ionospheric electron depletion produced by a radially expanding electron attachment chemical release is studied with a two-dimensional simulation model. The model includes electron attachment chemistry, incorporates fluid electrons, particle ions and neutrals, and considers the evolution in a plane perpendicular to the geomagnetic field for a low beta plasma. Timescales considered are of the order of or less than the cyclotron period of the negative ions that result as a by-product of the electron attacment reaction. This corresponds to time periods of tenths of seconds during recent experiemts. Simulation results show that a highly sheared azimuthal electron flow velocity develops in the radially expanding depletion boundary. This sheared electron flow velocity and the steep density gradients in the boundary give rise to small-scale irregulatities in the form of electron density cavities and spikes. The nonlinear evolution of these irregularities results in trapping and ultimately turbulent heating of the negative ions.
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Neutron measurements from beam-target reactions at the ELISE neutral beam test facility
DOE Office of Scientific and Technical Information (OSTI.GOV)
Xufei, X., E-mail: xiexufei@pku.edu.cn; Fan, T.; Nocente, M.
2014-11-15
Measurements of 2.5 MeV neutron emission from beam-target reactions performed at the ELISE neutral beam test facility are presented in this paper. The measurements are used to study the penetration of a deuterium beam in a copper dump, based on the observation of the time evolution of the neutron counting rate from beam-target reactions with a liquid scintillation detector. A calculation based on a local mixing model of deuterium deposition in the target up to a concentration of 20% at saturation is used to evaluate the expected neutron yield for comparison with data. The results are of relevance to understandmore » neutron emission associated to beam penetration in a solid target, with applications to diagnostic systems for the SPIDER and MITICA Neutral Beam Injection prototypes.« less
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NASA Astrophysics Data System (ADS)
McCormack, J. P.; Sassi, F.; Hoppel, K.; Ma, J.; Eckermann, S. D.
2015-12-01
We investigate the evolution of neutral atmospheric dynamics in the 10-100 km altitude range before, during, and after recent stratospheric sudden warmings (SSWs) using a prototype high-altitude version of the Navy Global Environmental Model (NAVGEM), which combines a 4-dimensional variational (4DVAR) data assimilation system with a 3-time-level semi-Lagrangian semi-implicit global forecast model. In addition to assimilating conventional meteorological observations, NAVGEM also assimilates middle atmospheric temperature and constituent observations from both operational and research satellite platforms to provide global synoptic meteorological analyses of winds, temperatures, ozone, and water vapor from the surface to ~90 km. In this study, NAVGEM analyses are used to diagnose the spatial and temporal evolution of the main dynamical drivers in the mesosphere and lower thermosphere (MLT) before, during, and after specific SSW events during the 2009-2013 period when large disturbances were observed in the thermosphere/ionosphere (TI) region. Preliminary findings show strong modulation of the semidiurnal tide in the MLT during the onset of an SSW. To assess the impact of the neutral atmosphere dynamical variability on the TI system, NAVGEM analyses are used to constrain simulations of select SSW events using the specified dynamics (SD) configuration of the extended Whole Atmosphere Community Climate Model (WACCM-X).
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Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.
Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi
2016-06-01
A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Human genomic disease variants: a neutral evolutionary explanation.
Dudley, Joel T; Kim, Yuseob; Liu, Li; Markov, Glenn J; Gerold, Kristyn; Chen, Rong; Butte, Atul J; Kumar, Sudhir
2012-08-01
Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.
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Human genomic disease variants: A neutral evolutionary explanation
Dudley, Joel T.; Kim, Yuseob; Liu, Li; Markov, Glenn J.; Gerold, Kristyn; Chen, Rong; Butte, Atul J.; Kumar, Sudhir
2012-01-01
Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease. PMID:22665443
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The effect of recombination and attachment on meteor radar diffusion coefficient profiles
NASA Astrophysics Data System (ADS)
Lee, C. S.; Younger, J. P.; Reid, I. M.; Kim, Y. H.; Kim, J.-H.
2013-04-01
Estimates of the ambipolar diffusion coefficient producedusing meteor radar echo decay times display an increasing trend below 80-85 km, which is inconsistent with a diffusion-only theory of the evolution of meteor trails. Data from the 33 MHz meteor radar at King Sejong Station, Antarctica, have been compared with observations from the Aura Earth Observing System Microwave Limb Sounder satellite instrument. It has been found that the height at which the diffusion coefficient gradient reverses follows the height of a constant neutral atmospheric density surface. Numerical simulations of meteor trail diffusion including dissociative recombination with atmospheric ions and three-body attachment of free electrons to neutral molecules indicate that three-body attachment is responsible for the distortion of meteor radar diffusion coefficient profiles at heights below 90 km, including the gradient reversal below 80-85 km. Further investigation has revealed that meteor trails with low initial electron line density produce decay times more consistent with a diffusion-only model of meteor trail evolution.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less
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NASA Astrophysics Data System (ADS)
Szejka, Agnes; Drossel, Barbara
2010-02-01
We study the evolution of Boolean networks as model systems for gene regulation. Inspired by biological networks, we select simultaneously for robust attractors and for the ability to respond to external inputs by changing the attractor. Mutations change the connections between the nodes and the update functions. In order to investigate the influence of the type of update functions, we perform our simulations with canalizing as well as with threshold functions. We compare the properties of the fitness landscapes that result for different versions of the selection criterion and the update functions. We find that for all studied cases the fitness landscape has a plateau with maximum fitness resulting in the fact that structurally very different networks are able to fulfill the same task and are connected by neutral paths in network (“genotype”) space. We find furthermore a connection between the attractor length and the mutational robustness, and an extremely long memory of the initial evolutionary stage.
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Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.; ...
2018-02-14
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less
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2018-01-01
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed. PMID:29442996
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Selective sweeps of mitochondrial DNA can drive the evolution of uniparental inheritance.
Christie, Joshua R; Beekman, Madeleine
2017-08-01
Although the uniparental (or maternal) inheritance of mitochondrial DNA (mtDNA) is widespread, the reasons for its evolution remain unclear. Two main hypotheses have been proposed: selection against individuals containing different mtDNAs (heteroplasmy) and selection against "selfish" mtDNA mutations. Recently, uniparental inheritance was shown to promote adaptive evolution in mtDNA, potentially providing a third hypothesis for its evolution. Here, we explore this hypothesis theoretically and ask if the accumulation of beneficial mutations provides a sufficient fitness advantage for uniparental inheritance to invade a population in which mtDNA is inherited biparentally. In a deterministic model, uniparental inheritance increases in frequency but cannot replace biparental inheritance if only a single beneficial mtDNA mutation sweeps through the population. When we allow successive selective sweeps of mtDNA, however, uniparental inheritance can replace biparental inheritance. Using a stochastic model, we show that a combination of selection and drift facilitates the fixation of uniparental inheritance (compared to a neutral trait) when there is only a single selective mtDNA sweep. When we consider multiple mtDNA sweeps in a stochastic model, uniparental inheritance becomes even more likely to replace biparental inheritance. Our findings thus suggest that selective sweeps of beneficial mtDNA haplotypes can drive the evolution of uniparental inheritance. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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The role of ecology, neutral processes and antagonistic coevolution in an apparent sexual arms race.
Perry, Jennifer C; Garroway, Colin J; Rowe, Locke
2017-09-01
Some of the strongest examples of a sexual 'arms race' come from observations of correlated evolution in sexually antagonistic traits among populations. However, it remains unclear whether these cases truly represent sexually antagonistic coevolution; alternatively, ecological or neutral processes might also drive correlated evolution. To investigate these alternatives, we evaluated the contributions of intersex genetic correlations, ecological context, neutral genetic divergence and sexual coevolution in the correlated evolution of antagonistic traits among populations of Gerris incognitus water striders. We could not detect intersex genetic correlations for these sexually antagonistic traits. Ecological variation was related to population variation in the key female antagonistic trait (spine length, a defence against males), as well as body size. Nevertheless, population covariation between sexually antagonistic traits remained substantial and significant even after accounting for all of these processes. Our results therefore provide strong evidence for a contemporary sexual arms race. © 2017 John Wiley & Sons Ltd/CNRS.
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Present Day Biology seen in the Looking Glass of Physics of Complexity
NASA Astrophysics Data System (ADS)
Schuster, P.
Darwin's theory of variation and selection in its simplest form is directly applicable to RNA evolution in vitro as well as to virus evolution, and it allows for quantitative predictions. Understanding evolution at the molecular level is ultimately related to the central paradigm of structural biology: sequence⇒ structure ⇒ function. We elaborate on the state of the art in modeling and understanding evolution of RNA driven by reproduction and mutation. The focus will be laid on the landscape concept—originally introduced by Sewall Wright—and its application to problems in biology. The relation between genotypes and phenotypes is the result of two consecutive mappings from a space of genotypes called sequence space onto a space of phenotypes or structures, and fitness is the result of a mapping from phenotype space into non-negative real numbers. Realistic landscapes as derived from folding of RNA sequences into structures are characterized by two properties: (i) they are rugged in the sense that sequences lying nearby in sequence space may have very different fitness values and (ii) they are characterized by an appreciable degree of neutrality implying that a certain fraction of genotypes and/or phenotypes cannot be distinguished in the selection process. Evolutionary dynamics on realistic landscapes will be studied as a function of the mutation rate, and the role of neutrality in the selection process will be discussed.
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Evolutionary advantage via common action of recombination and neutrality
NASA Astrophysics Data System (ADS)
Saakian, David B.; Hu, Chin-Kun
2013-11-01
We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.
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Genetics and the making of Homo sapiens.
Carroll, Sean B
2003-04-24
Understanding the genetic basis of the physical and behavioural traits that distinguish humans from other primates presents one of the great new challenges in biology. Of the millions of base-pair differences between humans and chimpanzees, which particular changes contributed to the evolution of human features after the separation of the Pan and Homo lineages 5-7 million years ago? How can we identify the 'smoking guns' of human genetic evolution from neutral ticks of the molecular evolutionary clock? The magnitude and rate of morphological evolution in hominids suggests that many independent and incremental developmental changes have occurred that, on the basis of recent findings in model animals, are expected to be polygenic and regulatory in nature. Comparative genomics, population genetics, gene-expression analyses and medical genetics have begun to make complementary inroads into the complex genetic architecture of human evolution.
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Big Bang Tumor Growth and Clonal Evolution.
Sun, Ruping; Hu, Zheng; Curtis, Christina
2018-05-01
The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.
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Martin, Guillaume; Chapuis, Elodie; Goudet, Jérôme
2008-01-01
Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Qst–Fst) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2Fst/(1 − Fst)G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2Fst/(1 − Fst)] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Qst–Fst comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions. PMID:18245845
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Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.
Goldman, N
1994-09-01
The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)
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A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function
Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.
2012-01-01
Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983
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Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A
2012-09-21
Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.
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De Boer, Rob J.; Perelson, Alan S.
2017-09-06
Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than othermore » lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing. Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. In conclusion, we suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
De Boer, Rob J.; Perelson, Alan S.
Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than othermore » lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing. Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. In conclusion, we suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.« less
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Aguirre, Jacobo; Buldú, Javier M; Manrubia, Susanna C
2009-12-01
Networks of selectively neutral genotypes underlie the evolution of populations of replicators in constant environments. Previous theoretical analysis predicted that such populations will evolve toward highly connected regions of the genome space. We first study the evolution of populations of replicators on simple networks and quantify how the transient time to equilibrium depends on the initial distribution of sequences on the neutral network, on the topological properties of the latter, and on the mutation rate. Second, network neutrality is broken through the introduction of an energy for each sequence. This allows to study the competition between two features (neutrality and energetic stability) relevant for survival and subjected to different selective pressures. In cases where the two features are negatively correlated, the population experiences sudden migrations in the genome space for values of the relevant parameters that we calculate. The numerical study of larger networks indicates that the qualitative behavior to be expected in more realistic cases is already seen in representative examples of small networks.
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NASA Astrophysics Data System (ADS)
Aguirre, Jacobo; Buldú, Javier M.; Manrubia, Susanna C.
2009-12-01
Networks of selectively neutral genotypes underlie the evolution of populations of replicators in constant environments. Previous theoretical analysis predicted that such populations will evolve toward highly connected regions of the genome space. We first study the evolution of populations of replicators on simple networks and quantify how the transient time to equilibrium depends on the initial distribution of sequences on the neutral network, on the topological properties of the latter, and on the mutation rate. Second, network neutrality is broken through the introduction of an energy for each sequence. This allows to study the competition between two features (neutrality and energetic stability) relevant for survival and subjected to different selective pressures. In cases where the two features are negatively correlated, the population experiences sudden migrations in the genome space for values of the relevant parameters that we calculate. The numerical study of larger networks indicates that the qualitative behavior to be expected in more realistic cases is already seen in representative examples of small networks.
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Three species one-dimensional kinetic model for weakly ionized plasmas
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gonzalez, J., E-mail: jorge.gonzalez@upm.es; Donoso, J. M.; Tierno, S. P.
2016-06-15
A three species one-dimensional kinetic model is presented for a spatially homogeneous weakly ionized plasma subjected to the action of a time varying electric field. Planar geometry is assumed, which means that the plasma evolves in the privileged direction of the field. The energy transmitted to the electric charges is channelized to the neutrals thanks to collisions, a mechanism that influences the plasma dynamics. Charge-charge interactions have been designed as a one-dimensional collision term equivalent to the Landau operator used for fully ionized plasmas. Charge-neutral collisions are modelled by a conservative drift-diffusion operator in the Dougherty's form. The resulting setmore » of coupled integro-differential equations is solved with the stable and robust propagator integral method. This semi–analytical method feasibility accounts for non–linear effects without appealing to linearisation or simplifications, providing conservative physically meaningful solutions even for initial or emerging sharp velocity distribution function profiles. It is found that charge-neutral collisions exert a significant effect since a quite different plasma evolution arises if compared to the collisionless limit. In addition, substantial differences in the system motion are found for constant and temperature dependent collision frequencies cases.« less
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Walthour, C. S.; Schaeffer, S. W.
1994-01-01
The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Comparisons of the tra coding region among Drosophila species have revealed an unusually high degree of divergence in synonymous and nonsynonymous sites. In this study, we tested the hypothesis that the tra gene will be polymorphic in synonymous and nonsynonymous sites within species by investigating nucleotide sequence variation in eleven tra alleles within D. melanogaster. Of the 1063 nucleotides examined, two synonymous sites were polymorphic and no amino acid variation was detected. Three statistical tests were used to detect departures from an equilibrium neutral model. Two tests failed to reject a neutral model of molecular evolution because of low statisitical power associated with low levels of genetic variation (Tajima/Fu and Li). The Hudson, Kreitman, and Aguade test rejected a neutral model when the tra region was compared to the 5'-flanking region of alcohol dehydrogenase (Adh). The lack of variability in the tra gene is consistent with a recent selective sweep of a beneficial allele in or near the tra locus. PMID:8013913
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Ion energy balance in enhanced-confinement reversed-field pinch plasmas
NASA Astrophysics Data System (ADS)
Xing, Z. A.; Nornberg, M. D.; Boguski, J.; Craig, D.; den Hartog, D. J.; McCollam, K.
2017-10-01
Testing the applicability of collisional ion transport theory using tearing suppressed RFP plasma in MST achieved through Pulsed Poloidal Current Drive (PPCD), we find that the ion temperature dynamics in the core to be well-predicted by classical and collisional terms. Prior work demonstrated that impurity ion particle transport in PPCD plasmas is classical. Neoclassical effects on ions in the RFP are small and the stochastic transport is greatly suppressed during PPCD. Recent neutral modelling with DEGAS2 suggests higher core neutral temperatures than expected due to the preferential penetration of higher temperature neutrals generated by charge exchange. Further, investigations through equilibrium reconstruction point to the existence of an inward pinch flow associated with ExB drift. The heat balance model pulls together a wide range of diagnostic data to forward model Ti evolution in PPCD, which is then compared to charge exchange spectroscopy measurements of Ti. Ion power balance is mostly driven by classical effects including compressional heating, electron collisional heating, and charge exchange transport. This understanding provides a good baseline for investigations of anomalous heating in plasmas with tearing mode activity. This work is supported by US DOE.
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The Puzzle of HIV Neutral and Selective Evolution.
Leitner, Thomas
2018-06-01
HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell types and using the same replication machinery year after year. Hence, one would think that most mutations that HIV accumulates are neutral. But the picture is more complicated than that. HIV evolution is also a clear example of strong positive selection, that is, mutants have a survival advantage. How do these facts come together?
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Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition
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
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Spatial constraints govern competition of mutant clones in human epidermis.
Lynch, M D; Lynch, C N S; Craythorne, E; Liakath-Ali, K; Mallipeddi, R; Barker, J N; Watt, F M
2017-10-24
Deep sequencing can detect somatic DNA mutations in tissues permitting inference of clonal relationships. This has been applied to human epidermis, where sun exposure leads to the accumulation of mutations and an increased risk of skin cancer. However, previous studies have yielded conflicting conclusions about the relative importance of positive selection and neutral drift in clonal evolution. Here, we sequenced larger areas of skin than previously, focusing on cancer-prone skin spanning five decades of life. The mutant clones identified were too large to be accounted for solely by neutral drift. Rather, using mathematical modelling and computational lattice-based simulations, we show that observed clone size distributions can be explained by a combination of neutral drift and stochastic nucleation of mutations at the boundary of expanding mutant clones that have a competitive advantage. These findings demonstrate that spatial context and cell competition cooperate to determine the fate of a mutant stem cell.
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The importance of selection in the evolution of blindness in cavefish.
Cartwright, Reed A; Schwartz, Rachel S; Merry, Alexandra L; Howell, Megan M
2017-02-07
Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus. Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.
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Etch Profile Simulation Using Level Set Methods
NASA Technical Reports Server (NTRS)
Hwang, Helen H.; Meyyappan, Meyya; Arnold, James O. (Technical Monitor)
1997-01-01
Etching and deposition of materials are critical steps in semiconductor processing for device manufacturing. Both etching and deposition may have isotropic and anisotropic components, due to directional sputtering and redeposition of materials, for example. Previous attempts at modeling profile evolution have used so-called "string theory" to simulate the moving solid-gas interface between the semiconductor and the plasma. One complication of this method is that extensive de-looping schemes are required at the profile corners. We will present a 2D profile evolution simulation using level set theory to model the surface. (1) By embedding the location of the interface in a field variable, the need for de-looping schemes is eliminated and profile corners are more accurately modeled. This level set profile evolution model will calculate both isotropic and anisotropic etch and deposition rates of a substrate in low pressure (10s mTorr) plasmas, considering the incident ion energy angular distribution functions and neutral fluxes. We will present etching profiles of Si substrates in Ar/Cl2 discharges for various incident ion energies and trench geometries.
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Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
Covert, Arthur W.; Lenski, Richard E.; Wilke, Claus O.; Ofria, Charles
2013-01-01
Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions. PMID:23918358
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Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.
Covert, Arthur W; Lenski, Richard E; Wilke, Claus O; Ofria, Charles
2013-08-20
Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions.
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Dynamics of ion beam charge neutralization by ferroelectric plasma sources
Stepanov, Anton D.; Gilson, Erik P.; Grisham, Larry R.; ...
2016-04-27
Ferroelectric Plasma Sources (FEPSs) can generate plasma that provides effective space-charge neutralization of intense high-perveance ion beams, as has been demonstrated on the Neutralized Drift Compression Experiment NDCX-I and NDCX-II. This article presents experimental results on charge neutralization of a high-perveance 38 keV Ar + beam by a plasma produced in a FEPS discharge. By comparing the measured beam radius with the envelope model for space-charge expansion, it is shown that a charge neutralization fraction of 98% is attainable with sufficiently dense FEPS plasma. The transverse electrostatic potential of the ion beam is reduced from 15V before neutralization to 0.3more » V, implying that the energy of the neutralizing electrons is below 0.3 eV. Measurements of the time-evolution of beam radius show that near-complete charge neutralization is established similar to –5 μs after the driving pulse is applied to the FEPS and can last for 35 μs. It is argued that the duration of neutralization is much longer than a reasonable lifetime of the plasma produced in the sub-mu s surface discharge. Measurements of current flow in the driving circuit of the FEPS show the existence of electron emission into vacuum, which lasts for tens of mu s after the high voltage pulse is applied. Lastly, it is argued that the beam is neutralized by the plasma produced by this process and not by a surface discharge plasma that is produced at the instant the high-voltage pulse is applied.« less
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Nonneutral mitochondrial DNA variation in humans and chimpanzees
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nachman, M.W.; Aquadro, C.F.; Brown, W.M.
1996-03-01
We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions.more » We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases. 59 refs., 2 figs., 8 tabs.« less
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In-silico studies of neutral drift for functional protein interaction networks
NASA Astrophysics Data System (ADS)
Ali, Md Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan
We have developed a minimal physically-motivated model of protein-protein interaction networks. Our system consists of two classes of enzymes, activators (e.g. kinases) and deactivators (e.g. phosphatases), and the enzyme-mediated activation/deactivation rates are determined by sequence-dependent binding strengths between enzymes and their targets. The network is evolved by introducing random point mutations in the binding sequences where we assume that each new mutation is either fixed or entirely lost. We apply this model to studies of neutral drift in networks that yield oscillatory dynamics, where we start, for example, with a relatively simple network and allow it to evolve by adding nodes and connections while requiring that dynamics be conserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. Surprisingly, in addition to this redistribution time we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains.
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Star formation in a hierarchical model for Cloud Complexes
NASA Astrophysics Data System (ADS)
Sanchez, N.; Parravano, A.
The effects of the external and initial conditions on the star formation processes in Molecular Cloud Complexes are examined in the context of a schematic model. The model considers a hierarchical system with five predefined phases: warm gas, neutral gas, low density molecular gas, high density molecular gas and protostars. The model follows the mass evolution of each substructure by computing its mass exchange with their parent and children. The parent-child mass exchange depends on the radiation density at the interphase, which is produced by the radiation coming from the stars that form at the end of the hierarchical structure, and by the external radiation field. The system is chaotic in the sense that its temporal evolution is very sensitive to small changes in the initial or external conditions. However, global features such as the star formation efficience and the Initial Mass Function are less affected by those variations.
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Understanding intratumor heterogeneity by combining genome analysis and mathematical modeling.
Niida, Atsushi; Nagayama, Satoshi; Miyano, Satoru; Mimori, Koshi
2018-04-01
Cancer is composed of multiple cell populations with different genomes. This phenomenon called intratumor heterogeneity (ITH) is supposed to be a fundamental cause of therapeutic failure. Therefore, its principle-level understanding is a clinically important issue. To achieve this goal, an interdisciplinary approach combining genome analysis and mathematical modeling is essential. For example, we have recently performed multiregion sequencing to unveil extensive ITH in colorectal cancer. Moreover, by employing mathematical modeling of cancer evolution, we demonstrated that it is possible that this ITH is generated by neutral evolution. In this review, we introduce recent advances in a research field related to ITH and also discuss strategies for exploiting novel findings on ITH in a clinical setting. © 2018 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.
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Extinction in neutrally stable stochastic Lotka-Volterra models
NASA Astrophysics Data System (ADS)
Dobrinevski, Alexander; Frey, Erwin
2012-05-01
Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. Here, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: It destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations.
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Extinction in neutrally stable stochastic Lotka-Volterra models.
Dobrinevski, Alexander; Frey, Erwin
2012-05-01
Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. Here, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: It destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations.
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NASA Astrophysics Data System (ADS)
K. Karmakar, P.; Borah, B.
2014-05-01
This paper adopts an inertia-centric evolutionary model to study the excitation mechanism of new gravito-electrostatic eigenmode structures in a one-dimensional (1-D) planar self-gravitating dust molecular cloud (DMC) on the Jeans scale. A quasi-neutral multi-fluid consisting of warm electrons, warm ions, neutral gas and identical inertial cold dust grains with partial ionization is considered. The grain-charge is assumed not to vary at the fluctuation evolution time scale. The neutral gas particles form the background, which is weakly coupled with the collapsing grainy plasma mass. The gravitational decoupling of the background neutral particles is justifiable for a higher inertial mass of the grains with higher neutral population density so that the Jeans mode frequency becomes reasonably large. Its physical basis is the Jeans assumption of a self-gravitating uniform medium adopted for fiducially analytical simplification by neglecting the zero-order field. So, the equilibrium is justifiably treated initially as “homogeneous”. The efficacious inertial role of the thermal species amidst weak collisions of the neutral-charged grains is taken into account. A standard multiscale technique over the gravito-electrostatic equilibrium yields a unique pair of Korteweg-de Vries (KdV) equations. It is integrated numerically by the fourth-order Runge-Kutta method with multi-parameter variation for exact shape analyses. Interestingly, the model is conducive for the propagation of new conservative solitary spectral patterns. Their basic physics, parametric features and unique characteristics are discussed. The results go qualitatively in good correspondence with the earlier observations made by others. Tentative applications relevant to space and astrophysical environments are concisely highlighted.
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Unraveling Selection in the Mitochondrial Genome of Drosophila
Ballard, JWO.; Kreitman, M.
1994-01-01
We examine mitochondrial DNA variation at the cytochrome b locus within and between three species of Drosophila to determine whether patterns of variation conform to the predictions of neutral molecular evolution. The entire 1137-bp cytochrome b locus was sequenced in 16 lines of Drosophila melanogaster, 18 lines of Drosophila simulans and 13 lines of Drosophila yakuba. Patterns of variation depart from neutrality by several test criteria. Analysis of the evolutionary clock hypothesis shows unequal rates of change along D. simulans lineages. A comparison within and between species of the ratio of amino acid replacement change to synonymous change reveals a relative excess of amino acid replacement polymorphism compared to the neutral prediction, suggestive of slightly deleterious or diversifying selection. There is evidence for excess homozygosity in our world wide sample of D. melanogaster and D. simulans alleles, as well as a reduction in the number of segregating sites in D. simulans, indicative of selective sweeps. Furthermore, a test of neutrality for codon usage shows the direction of mutations at third positions differs among different topological regions of the gene tree. The analyses indicate that molecular variation and evolution of mtDNA are governed by many of the same selective forces that have been shown to govern nuclear genome evolution and suggest caution be taken in the use of mtDNA as a ``neutral'' molecular marker. PMID:7851772
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Spoken language achieves robustness and evolvability by exploiting degeneracy and neutrality.
Winter, Bodo
2014-10-01
As with biological systems, spoken languages are strikingly robust against perturbations. This paper shows that languages achieve robustness in a way that is highly similar to many biological systems. For example, speech sounds are encoded via multiple acoustically diverse, temporally distributed and functionally redundant cues, characteristics that bear similarities to what biologists call "degeneracy". Speech is furthermore adequately characterized by neutrality, with many different tongue configurations leading to similar acoustic outputs, and different acoustic variants understood as the same by recipients. This highlights the presence of a large neutral network of acoustic neighbors for every speech sound. Such neutrality ensures that a steady backdrop of variation can be maintained without impeding communication, assuring that there is "fodder" for subsequent evolution. Thus, studying linguistic robustness is not only important for understanding how linguistic systems maintain their functioning upon the background of noise, but also for understanding the preconditions for language evolution. © 2014 WILEY Periodicals, Inc.
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Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wu, Xueling; Zhou, Tongqing; Zhu, Jiang
2013-03-04
Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution ofmore » antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.« less
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Dissipative instability in a partially ionised prominence plasma slab
NASA Astrophysics Data System (ADS)
Ballai, I.; Pintér, B.; Oliver, R.; Alexandrou, M.
2017-07-01
Aims: We aim to investigate the nature of dissipative instability appearing in a prominence planar thread filled with partially ionised plasma in the incompressible limit. The importance of partial ionisation is investigated in terms of the ionisation factor and the wavelength of sausage and kink waves propagating in the slab. Methods: In order to highlight the role of partial ionisation, we have constructed models describing various situations we can meet in solar prominence fine structure. Matching the solutions for the transversal component of the velocity and total pressure at the interfaces between the prominence slab and surrounding plasmas, we derived a dispersion relation whose imaginary part describes the evolution of the instability. Results were obtained in the limit of weak dissipation. We have investigated the appearance of instabilities in prominence dark plumes using single and two-fluid approximations. Results: Using simple analytical methods, we show that dissipative instabilities appear for flow speeds that are less than the Kelvin-Helmholtz instability threshold. The onset of instability is determined by the equilibrium flow strength, the ionisation factor of the plasma, the wavelength of waves and the ion-neutral collisional rate. For a given wavelength and for ionisation degrees closer to a neutral gas, the propagating waves become unstable for a narrow band of flow speeds, meaning that neutrals have a stabilising effect. Our results show that the partially ionised plasma describing prominence dark plumes becomes unstable only in a two-fluid (charged particles-neutrals) model, that is for periods that are smaller than the ion-neutral collision time. Conclusions: The present study improves our understanding of the complexity of dynamical processes and stability of solar prominences and the role partial ionisation in destabilising the plasma. We showed the necessity of two-fluid approximation when discussing the nature of instabilities: waves in a single fluid approximation show a great deal of stability. Our results clearly show that the problem of partial ionisation introduces new aspects of plasma stability with consequences on the evolution of partially ionised plasmas and solar prominences, in particular.
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Tracking the evolution of a hydrothermal event plume with a RAFOS neutrally buoyant drifter
Lupton; Baker; Garfield; Massoth; Feely; Cowen; Greene; Rago
1998-05-15
The migration and evolution of a deep ocean hydrothermal event plume were tracked with a neutrally buoyant RAFOS float. The float remained entrained in the plume for 60 days, and the plume vorticity was calculated directly from the anticyclonic motion of the float. Concentrations of suspended particles, particulate iron, and dissolved manganese in the plume did not decay significantly during the 60 days, which indicates that event plumes would be easily detectable a year after formation.
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Neutral mutation as the source of genetic variation in life history traits.
Brcić-Kostić, Krunoslav
2005-08-01
The mechanism underlying the maintenance of adaptive genetic variation is a long-standing question in evolutionary genetics. There are two concepts (mutation-selection balance and balancing selection) which are based on the phenotypic differences between alleles. Mutation - selection balance and balancing selection cannot properly explain the process of gene substitution, i.e. the molecular evolution of quantitative trait loci affecting fitness. I assume that such loci have non-essential functions (small effects on fitness), and that they have the potential to evolve into new functions and acquire new adaptations. Here I show that a high amount of neutral polymorphism at these loci can exist in real populations. Consistent with this, I propose a hypothesis for the maintenance of genetic variation in life history traits which can be efficient for the fixation of alleles with very small selective advantage. The hypothesis is based on neutral polymorphism at quantitative trait loci and both neutral and adaptive gene substitutions. The model of neutral - adaptive conversion (NAC) assumes that neutral alleles are not neutral indefinitely, and that in specific and very rare situations phenotypic (relative fitness) differences between them can appear. In this paper I focus on NAC due to phenotypic plasticity of neutral alleles. The important evolutionary consequence of NAC could be the increased adaptive potential of a population. Loci responsible for adaptation should be fast evolving genes with minimally discernible phenotypic effects, and the recent discovery of genes with such characteristics implicates them as suitable candidates for loci involved in adaptation.
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Transient Plume Model Testing Using LADEE Spacecraft Attitude Control System Operations
NASA Technical Reports Server (NTRS)
Woronowicz, Michael
2011-01-01
We have learned it is conceivable that the Neutral Mass Spectrometer on board the Lunarr Atmosphere Dust Environment Explorer (LADEE) could measure gases from surface-reflected Attitude Control System (ACS) thruster plume. At minimum altitude, the measurement would be maximized, and gravitational influence minimized ("short" time-of-flight (TOF) situation) Could use to verify aspects of thruster plume modeling Model the transient disturbance to NMS measurements due to ACS gases reflected from lunar surface Observe evolution of various model characteristics as measured by NMS Species magnitudes, TOF measurements, angular distribution, species separation effects
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Physical Model for the Evolution of the Genetic Code
NASA Astrophysics Data System (ADS)
Yamashita, Tatsuro; Narikiyo, Osamu
2011-12-01
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.
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Cobey, Sarah; Wilson, Patrick; Matsen, Frederick A.
2015-01-01
The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics. PMID:26194749
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NASA Astrophysics Data System (ADS)
Lu, Sheng-Jie
2018-05-01
We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.
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Estimating Collisionally-Induced Escape Rates of Light Neutrals from Early Mars
NASA Astrophysics Data System (ADS)
Gacesa, M.; Zahnle, K. J.
2016-12-01
Collisions of atmospheric gases with hot oxygen atoms constitute an important non-thermal mechanism of escape of light atomic and molecular species at Mars. In this study, we present revised theoretical estimates of non-thermal escape rates of neutral O, H, He, and H2 based on recent atmospheric density profiles obtained from the NASA Mars Atmosphere and Volatile Evolution (MAVEN) mission and related theoretical models. As primary sources of hot oxygen, we consider dissociative recombination of O2+ and CO2+ molecular ions. We also consider hot oxygen atoms energized in primary and secondary collisions with energetic neutral atoms (ENAs) produced in charge-exchange of solar wind H+ and He+ ions with atmospheric gases1,2. Scattering of hot oxygen and atmospheric species of interest is modeled using fully-quantum reactive scattering formalism3. This approach allows us to construct distributions of vibrationally and rotationally excited states and predict the products' emission spectra. In addition, we estimate formation rates of excited, translationally hot hydroxyl molecules in the upper atmosphere of Mars. The escape rates are calculated from the kinetic energy distributions of the reaction products using an enhanced 1D model of the atmosphere for a range of orbital and solar parameters. Finally, by considering different scenarios, we estimate the influence of these escape mechanisms on the evolution of Mars's atmosphere throughout previous epochs and their impact on the atmospheric D/H ratio. M.G.'s research was supported by an appointment to the NASA Postdoctoral Program at the NASA Ames Research Center, administered by Universities Space Research Association under contract with NASA. 1N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere", Astroph. J., 790, 98 (2014) 2M. Gacesa, N. Lewkow, and V. Kharchenko, "Non-thermal production and escape of OH from the upper atmosphere of Mars", arXiv:1607.03602 (2016) 3M. Gacesa and V. Kharchenko, "Non-thermal escape of molecular hydrogen from Mars", Geophys. Res. Lett., 39, L10203 (2012).
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Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A
2011-01-01
The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.
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The Growth of the Disk Galaxy UGC8802
NASA Astrophysics Data System (ADS)
Chang, R. X.; Shen, S. Y.; Hou, J. L.
2012-07-01
The disk galaxy UGC8802 has high neutral gas content and a flat profile of star formation rate compared to other disk galaxies with similar stellar mass. It also shows a steep metallicity gradient. We construct a chemical evolution model to explore its growth history by assuming its disk grows gradually from continuous gas infall, which is shaped by a free parameter—the infall-peak time. By adopting the recently observed molecular surface density related star formation law, we show that a late infall-peak time can naturally explain the observed high neutral gas content, while an inside-out disk formation scenario can fairly reproduce the steep oxygen abundance gradient. Our results show that most of the observed features of UGC8802 can be well reproduced by simply "turning the knob" on gas inflow with one single parameter, which implies that the observed properties of gas-rich galaxies could also be modeled in a similar way.
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Hydrodynamic-to-ballistic crossover in Dirac materials
NASA Astrophysics Data System (ADS)
Svintsov, D.
2018-03-01
We develop an analytically solvable classical kinetic model of spatially dispersive transport in Dirac materials accounting for strong electron-electron (e-e) and electron-hole (e-h) collisions. We use this model to track the evolution of graphene conductivity and properties of its collective excitations across the hydrodynamic-to-ballistic crossover. We find the relaxation rate of electric current by e-e collisions that is possible due to the lack of Galilean invariance and introduce a universal numerical measure of this noninvariance. We find the two branches of collective excitations in the Dirac fluid: plasmons and electron-hole sound. The sound waves persist at frequencies exceeding the e-e collision frequency, have a small viscous damping at the neutrality point, but acquire large damping due to e-h friction even at slight doping. On the contrary, plasmons acquire strong frictional damping at the neutrality point and become well defined in doped samples.
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Vines, L; Bhoodoo, C; von Wenckstern, H; Grundmann, M
2017-12-13
The evolution of sheet resistance of n-type In 2 O 3 and Ga 2 O 3 exposed to bombardment with MeV 12 C and 28 Si ions at 35 K is studied in situ. While the sheet resistance of Ga 2 O 3 increased by more than eight orders of magnitude as a result of ion irradiation, In 2 O 3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga 2 O 3 remained highly resistive, while In 2 O 3 showed a lower resistance than as deposited samples. Thermal admittance spectroscopy and deep level transient spectroscopy did not reveal new defect levels for irradiation up to [Formula: see text] cm -2 . A model where larger defect complexes preferentially produce donor like defects in In 2 O 3 is proposed, and may reveal a microscopic view of a charge neutrality level within the conduction band, as previously proposed.
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NASA Astrophysics Data System (ADS)
Vines, L.; Bhoodoo, C.; von Wenckstern, H.; Grundmann, M.
2018-01-01
The evolution of sheet resistance of n-type In2O3 and Ga2O3 exposed to bombardment with MeV 12C and 28Si ions at 35 K is studied in situ. While the sheet resistance of Ga2O3 increased by more than eight orders of magnitude as a result of ion irradiation, In2O3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga2O3 remained highly resistive, while In2O3 showed a lower resistance than as deposited samples. Thermal admittance spectroscopy and deep level transient spectroscopy did not reveal new defect levels for irradiation up to 2 × 1012 cm-2. A model where larger defect complexes preferentially produce donor like defects in In2O3 is proposed, and may reveal a microscopic view of a charge neutrality level within the conduction band, as previously proposed.
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Miklós, István
2003-10-01
As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. The source code in C is available on request from the author.
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Stochastic processes constrain the within and between host evolution of influenza virus.
McCrone, John T; Woods, Robert J; Martin, Emily T; Malosh, Ryan E; Monto, Arnold S; Lauring, Adam S
2018-05-03
The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1-2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses. © 2018, McCrone et al.
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Nuclear Modification of Neutral Pion Production at Low x in √s=200 GeV d+Au and p+p Collisions
NASA Astrophysics Data System (ADS)
Sedgwick, Kenneth Blair
Nuclear modification factors quantify suppression in particle production due to nuclear effects. They are defined as a ratio of invariant yields, with a numerator derived from a given species of nuclear collision and a denominator derived from a hypothetically equivalent ensemble of independent proton-proton collisions. At large momentum transfer Q 2 and low momentum fraction x, the neutral pion nuclear modification factor Rd+Au for d+Au collisions is useful for investigating initial state gluon saturation. The large initial state gluon multiplicity of the Au nucleus causes saturation effects to occur at lower energies in d+Au collisions, as compared to p+p collisions, resulting in a relative suppression. Measuring the relative suppression R d+Au can therefore test the validity of competing models describing saturation, including the framework of a color glass condensate (CGC). Measurements at low x are of particular interest because in this region linear pQCD evolution equations begin to break down. The Froissart theorem places a robust theoretical upper limit on the behavior of hadronic cross sections: a cross section can increase at most like ln2 E. Equivalently, an hadronic structure function can increase at most like ln2(1/x). Adherence to this theorem is necessary to preserve S-matrix unitarity; no physical system should exhibit behavior to the contrary. However linear evolution equations, which dictate structure function behavior, predict an unchecked growth of low-x gluons, in violation of the theorem. For this reason, it is expected that gluon saturation, via non-linear evolution, will take place at low x to steer the gluon distribution function back within the limitations of the Froissart bound. Greater suppression is expected at lower Q2; however, at low x, regions of high Q 2 are more difficult to access experimentally. Pushing out to higher Q2 is important for discriminating between competing theoretical models. In practice, regions of low x and high Q 2 translate to measurements at, respectively, high rapidity eta and high transverse momentum p⊥. The high rapidity 3.1 < eta < 3.9 Muon Piston Calorimeter (MPC) detector at PHENIX is ideally suited for measurements of neutral pion R d+Au probing regions of low x. At √s = 200 GeV, a combinatoric analysis of neutral pion decay products in the MPC can obtain measurements of Rd+Au up to a transverse momentum of p⊥ = 2 GeV/c. However, at p ⊥ greater than 2 GeV/c, photons from neutral pion decay have insufficient spatial separation to be independently resolved in the detector. In this analysis the transverse momentum range of the detector, measuring R d+Au at √s = 200 GeV, is extended to p⊥ = 3.5 GeV/c by studying photon pairs from neutral pions that resolve in the MPC as a single cluster. Increased suppression is reproduced at low p⊥, in agreement with previous data. For p⊥ > 2 GeV/c Cronin enhancement is not observed, as anticipated by the CGC framework. However, the data can not rule out the possibility that the observed suppression is the result of extreme nuclear shadowing. Also presented are invariant neutral pion yields for p+p and d+Au collisions and the invariant neutral pion cross section for p+p collisions at √s = 200 GeV.
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Community assembly rules affect the diversity of expanding communities.
Peng, Zechen; Zhou, Shurong
2014-11-01
Despite centuries of interest in species range limits, few studies have taken a whole community into consideration. Actually, multiple species may simultaneously respond to environmental changes, for example, global warming, leading a series of dynamical communities toward the advancing front. We investigated multiple species range expansions through the analysis of a two-species dispersion model and simulations of multiple species assemblages regulated by neutral and fecundity-survival trade-offs (FSTs), respectively, and found that species assemblages regulated by different mechanisms would initiate different expanding patterns in geographic ranges in response to environmental changes. The neutral model generally predicts a higher biodiversity near the core of an expanding range, and a lower community similarity compared with a FST model. Without considering the evolution of life history traits, an assortment of the reproduction ability happens at the advancing front under FSTs at the expense of a higher death rate or lower competitive ability. These results emphasize the importance of community assembly rules to the biodiversity maintenance of range expanding communities.
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Adiabatic quantum computation with neutral atoms via the Rydberg blockade
NASA Astrophysics Data System (ADS)
Goyal, Krittika; Deutsch, Ivan
2011-05-01
We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We acknowledge funding from the AQUARIUS project, Sandia National Laboratories
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Molecular clock on a neutral network.
Raval, Alpan
2007-09-28
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating aspects of neutral network topology from empirical measurements of the substitution process.
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Molecular Clock on a Neutral Network
NASA Astrophysics Data System (ADS)
Raval, Alpan
2007-09-01
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating aspects of neutral network topology from empirical measurements of the substitution process.
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Driven waves in a two-fluid plasma
NASA Astrophysics Data System (ADS)
Roberge, W. G.; Ciolek, Glenn E.
2007-12-01
We study the physics of wave propagation in a weakly ionized plasma, as it applies to the formation of multifluid, magnetohydrodynamics (MHD) shock waves. We model the plasma as separate charged and neutral fluids which are coupled by ion-neutral friction. At times much less than the ion-neutral drag time, the fluids are decoupled and so evolve independently. At later times, the evolution is determined by the large inertial mismatch between the charged and neutral particles. The neutral flow continues to evolve independently; the charged flow is driven by and slaved to the neutral flow by friction. We calculate this driven flow analytically by considering the special but realistic case where the charged fluid obeys linearized equations of motion. We carry out an extensive analysis of linear, driven, MHD waves. The physics of driven MHD waves is embodied in certain Green functions which describe wave propagation on short time-scales, ambipolar diffusion on long time-scales and transitional behaviour at intermediate times. By way of illustration, we give an approximate solution for the formation of a multifluid shock during the collision of two identical interstellar clouds. The collision produces forward and reverse J shocks in the neutral fluid and a transient in the charged fluid. The latter rapidly evolves into a pair of magnetic precursors on the J shocks, wherein the ions undergo force-free motion and the magnetic field grows monotonically with time. The flow appears to be self-similar at the time when linear analysis ceases to be valid.
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NASA Astrophysics Data System (ADS)
Ferdousi, B.; Nishimura, Y.; Maruyama, N.; Lyons, L. R.
2017-12-01
Subauroral Polarization Streams (SAPS), which can be identified as intense northward electric field driving sunward plasma convection, are mostly observed at the dusk-premidnight subauroral region. Their existence is associated with the closure of region 2 field-aligned current (R2 FAC) through the low conductivity region equatorward of the electron equatorward boundary. Observations suggest that SAPS flow speed increases with geomagnetic activity. So far, most studies have focused on the magnetosphere-ionosphere (M-I) coupling process of SAPS. However, recent observation of subauroral neutral wind suggest that there is a strong interaction between SAPS and the thermosphere (T). In this study, we focus on the effect of thermospheric wind on the ionosphere plasma drift associated with SAPS during the March 17, 2013 "St. Patrick's day" geomagnetic storm. We use both observations and the self-consistent magnetosphere-ionosphere-thermosphere (M-I-T) numerical "RCM-CTIPe" model to study such a relation. Observation results from DMSP-18 and GOCE satellites show that as the storm progresses, sunward ion flows intensify and move equatorward, and are accompanied by strengthening of subauroral neutral winds with a 2-hour delay. Our model successfully reproduces time evolution of the sunward ion drift and neutral wind. However, the simulated ion drift spreads considerably wider in latitude than the observations. To seek for better agreement between the observation and simulation results, we adopt a conductance distribution more consistent with input from the magnetosphere based on RCM aurora precipitation. We also perform a force term analysis to investigate the rate of momentum transfer from the neutral wind to ion flow. We then compare simulation runs with and without thermosphere coupling to study the effect of the feedback from neutral winds to SAPS.
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On the improbability of intelligent extraterrestrials
NASA Astrophysics Data System (ADS)
Bond, A.
1982-05-01
Discussions relating to the prevalence of extraterrestrial life generally remain ambiguous due to the lack of a suitable model for the development of biology. In this paper a simple model is proposed based on neutral evolution theory which leads to quantitative values for the genome growth rate within a biosphere. It is hypothesised that the genome size is a measure of organism complexity and hence an indicator of the likelihood of intelligence. The calculations suggest that organisms with the complexity of human beings may be rare and only occur with a probability below once per galaxy.
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Aris-Brosou, Stéphane; Bielawski, Joseph P
2006-08-15
A popular approach to examine the roles of mutation and selection in the evolution of genomes has been to consider the relationship between codon bias and synonymous rates of molecular evolution. A significant relationship between these two quantities is taken to indicate the action of weak selection on substitutions among synonymous codons. The neutral theory predicts that the rate of evolution is inversely related to the level of functional constraint. Therefore, selection against the use of non-preferred codons among those coding for the same amino acid should result in lower rates of synonymous substitution as compared with sites not subject to such selection pressures. However, reliably measuring the extent of such a relationship is problematic, as estimates of synonymous rates are sensitive to our assumptions about the process of molecular evolution. Previous studies showed the importance of accounting for unequal codon frequencies, in particular when synonymous codon usage is highly biased. Yet, unequal codon frequencies can be modeled in different ways, making different assumptions about the mutation process. Here we conduct a simulation study to evaluate two different ways of modeling uneven codon frequencies and show that both model parameterizations can have a dramatic impact on rate estimates and affect biological conclusions about genome evolution. We reanalyze three large data sets to demonstrate the relevance of our results to empirical data analysis.
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SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage
Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent
2016-01-01
Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences. PMID:27401173
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kojima, M.; Kakinuma, T.
1987-07-01
The solar cycle evolution of solar wind speed structure was studied for the years from 1973 to 1985 on a basis of interplanetary scintillation observations using a new method for mapping solar wind speed to the source surface. The major minimum-speed regions are distributed along a neutral line through the whole period of a solar cycle: when solar activity is low, they are distributed on the wavy neutral line along the solar equator; in the active phase they also tend to be distributed along the neutral line, which has a large latitudinal amplitude. The minimum-speed regions tend to be distributedmore » not only along the neutral line but also at low magnetic intensity regions and/or coronal bright regions which do not correspond to the neutral line. As the polar high-speed regions extend equatorward around the minimum phase, the latitudinal gradient of speed increases at the boundaries of the low-speed region, and the width of the low-speed region decreases. One or two years before the minimum of solar activity, two localized minimum-speed regions appear on the neutral line, and their locations are longitudinally separated by 180. copyright American Geophysical Union 1987« less
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Collisional Evolution of the Enceladus Neutral Cloud
NASA Technical Reports Server (NTRS)
Cassidy, T. A.; Johnson, R. E.; Hendrix, A. R.
2011-01-01
Water vapor ejected from Saturn's small moon Enceladus easily escapes its meager gravity to form a Saturn-encircling cloud with a low collision rate. Observations show that the cloud is quite broad in the radial direction, and we show here that collisions, though quite rare, may be largely responsible for this radial spreading. We modeled this cloud using the Direct Simulation Monte Carlo method, as fluid methods would be inappropriate for such a tenuous gas.
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Moran model as a dynamical process on networks and its implications for neutral speciation.
de Aguiar, Marcus A M; Bar-Yam, Yaneer
2011-09-01
In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.
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Moran model as a dynamical process on networks and its implications for neutral speciation
NASA Astrophysics Data System (ADS)
de Aguiar, Marcus A. M.; Bar-Yam, Yaneer
2011-03-01
In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.
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Improvements to the ICRH antenna time-domain 3D plasma simulation model
NASA Astrophysics Data System (ADS)
Smithe, David N.; Jenkins, Thomas G.; King, J. R.
2015-12-01
We present a summary of ongoing improvements to the 3D time-domain plasma modeling software that has been used to look at ICRH antennas on Alcator C-Mod, NSTX, and ITER [1]. Our past investigations have shown that in low density cases where the slow wave is propagating, strong amplitude lower hybrid resonant fields can occur. Such a scenario could result in significant parasitic power loss in the SOL. The primary resonance broadening in this case is likely collisions with neutral gas, and thus we are upgrading the model to include realistic neutral gas in the SOL, in order to provide a better understanding of energy balance in these situations. Related to this, we are adding a temporal variation capability to the local plasma density in front of the antenna in order to investigate whether the near fields of the antenna could modify the local density sufficiently to initiate a low density situation. We will start with a simple scalar ponderomotive potential density expulsion model [2] for the density evolution, but are also looking to eventually couple to a more complex fluid treatment that would include tensor pressures and convective physics and sources of neutrals and ionization. We also review continued benchmarking efforts, and ongoing and planned improvements to the computational algorithms, resulting from experience gained during our recent supercomputing runs on the Titan supercomputer, including GPU operations.
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Evolution of canalizing Boolean networks
NASA Astrophysics Data System (ADS)
Szejka, A.; Drossel, B.
2007-04-01
Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive walk, which allows us to explore the fitness landscape. Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations. We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness. Furthermore, in spite of having such a high degree of robustness, the evolved networks still share many features with “chaotic” networks.
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Rainford, James L; Hofreiter, Michael; Mayhew, Peter J
2016-01-08
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.
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Ripamonti, Chiara; Leitner, Thomas; Laurén, Anna; Karlsson, Ingrid; Pastore, Angela; Cavarelli, Mariangela; Antonsson, Liselotte; Plebani, Anna; Fenyö, Eva Maria; Scarlatti, Gabriella
2007-12-01
To investigate the immunological and virological factors that may lead to different patterns of disease progression characteristic of HIV-1-infected children, two HIV-1-infected siblings, a slow and a fast progressor, were followed prospectively before the onset of highly active antiretroviral therapy. Viral coreceptor usage, including the use of CCR5/CXCR4 chimeric receptors, macrophage tropism, and sensitivity to the CC-chemokine RANTES, has been studied. An autologous and heterologous neutralizing antibody response has been documented using peripheral blood mononuclear cells- and GHOST(3) cell line-based assays. Viral evolution was investigated by env C2-V3 region sequence analysis. Although both siblings were infected with HIV-1 of the R5 phenotype, their viruses showed important biological differences. In the fast progressor there was a higher RANTES sensitivity of the early virus, an increased trend to change the mode of CCR5 receptor use, and a larger genetic evolution. Both children developed an autologous neutralizing antibody response starting from the second year with evidence of the continuous emergence of resistant variants. A marked viral genetic and phenotypic evolution was documented in the fast progressor sibling, which is accompanied by a high viral RANTES sensitivity and persistent neutralizing antibodies.
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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.
HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less
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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A; Joyce, M Gordon; Kwon, Young Do; Zhou, Tongqing; Sheng, Zizhang; Zhang, Baoshan; O'Dell, Sijy; McKee, Krisha; Georgiev, Ivelin S; Chuang, Gwo-Yu; Longo, Nancy S; Lynch, Rebecca M; Saunders, Kevin O; Soto, Cinque; Srivatsan, Sanjay; Yang, Yongping; Bailer, Robert T; Louder, Mark K; Mullikin, James C; Connors, Mark; Kwong, Peter D; Mascola, John R; Shapiro, Lawrence
2015-04-23
HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of ∼2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization. Copyright © 2015 Elsevier Inc. All rights reserved.
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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection
Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.; ...
2015-04-09
HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less
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Greenbaum, Gili
2015-09-07
Evaluation of the time scale of the fixation of neutral mutations is crucial to the theoretical understanding of the role of neutral mutations in evolution. Diffusion approximations of the Wright-Fisher model are most often used to derive analytic formulations of genetic drift, as well as for the time scales of the fixation of neutral mutations. These approximations require a set of assumptions, most notably that genetic drift is a stochastic process in a continuous allele-frequency space, an assumption appropriate for large populations. Here equivalent approximations are derived using a coalescent theory approach which relies on a different set of assumptions than the diffusion approach, and adopts a discrete allele-frequency space. Solutions for the mean and variance of the time to fixation of a neutral mutation derived from the two approaches converge for large populations but slightly differ for small populations. A Markov chain analysis of the Wright-Fisher model for small populations is used to evaluate the solutions obtained, showing that both the mean and the variance are better approximated by the coalescent approach. The coalescence approximation represents a tighter upper-bound for the mean time to fixation than the diffusion approximation, while the diffusion approximation and coalescence approximation form an upper and lower bound, respectively, for the variance. The converging solutions and the small deviations of the two approaches strongly validate the use of diffusion approximations, but suggest that coalescent theory can provide more accurate approximations for small populations. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Selfish evolution of cytonuclear hybrid incompatibility in Mimulus
Finseth, Findley R.; Barr, Camille M.; Fishman, Lila
2016-01-01
Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus. In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. PMID:27629037
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Selfish evolution of cytonuclear hybrid incompatibility in Mimulus.
Case, Andrea L; Finseth, Findley R; Barr, Camille M; Fishman, Lila
2016-09-14
Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. © 2016 The Author(s).
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2 years with comet 67P/Churyumov-Gerasimenko: H2O, CO2, CO as seen by ROSINA RTOF
NASA Astrophysics Data System (ADS)
Hoang, M.; Garnier, P.; Lasue, J.; Reme, H.; Altwegg, K.; Balsiger, H. R.; Bieler, A. M.; Calmonte, U.; Capria, M. T.; Combi, M. R.; De Keyser, J. M.; Fiethe, B.; Fougere, N.; Fuselier, S. A.; Galli, A.; Gasc, S.; Gombosi, T. I.; Hansen, K. C.; Jäckel, A.; Korth, A.; Mall, U.; Migliorini, A.; Rubin, M.; Sémon, T.; Tzou, C. Y.; Waite, J. H., Jr.; Wurz, P.
2017-12-01
The Rosetta space mission investigated comet 67P/Churyumov-Gerasimenko (67P) over two years from August 2014 to September 2016. Onboard the spacecraft, the ROSINA experiment included two mass spectrometers to derive the composition of neutrals and ions, and a COmet Pressure Sensor (COPS) to monitor the density and velocity of the neutrals in the coma. We will here analyse and discuss data from the Reflectron-type Time-Of-Flight instrument during the comet escort phase. The RTOF mass spectrometer possessed a wide mass range and a high temporal resolution (Balsiger et al., 2007). The analysis of 67P/C-G's coma major molecules over the mission showed strong variability of the comet coma's main volatiles concentrations (H2O, CO2, CO) and their relative abundances. The 2 years long Rosetta mission allowed us to observe the seasonal evolution in the atmosphere of 67P, in particular the change occurring during the equinoxes and at perihelion. In this work, we analyze the asymmetry in the outgassing rate before and after the perihelion (13/08/2015), the evolution of abundance ratios through the whole mission, and in particular the behavior of the very volatile CO molecules. Density maps projected on the surface of 67P demonstrate the evolution of the three main coma species after the outbound equinox. We will present first results of our comet nucleus thermal modelling used to simulate the internal structure and temperature evolution of 67P at characteristic surface areas. These results will be compared with the coma composition measurements obtained by ROSINA.
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Host Switching in Lyssavirus History from the Chiroptera to the Carnivora Orders
Badrane, Hassan; Tordo, Noël
2001-01-01
Lyssaviruses are unsegmented RNA viruses causing rabies. Their vectors belong to the Carnivora and Chiroptera orders. We studied 36 carnivoran and 17 chiropteran lyssaviruses representing the main genotypes and variants. We compared their genes encoding the surface glycoprotein, which is responsible for receptor recognition and membrane fusion. The glycoprotein is the main protecting antigen and bears virulence determinants. Point mutation is the main force in lyssavirus evolution, as Sawyer's test and phylogenetic analysis showed no evidence of recombination. Tests of neutrality indicated a neutral model of evolution, also supported by globally high ratios of synonymous substitutions (dS) to nonsynonymous substitutions (dN) (>7). Relative-rate tests suggested similar rates of evolution for all lyssavirus lineages. Therefore, the absence of recombination and similar evolutionary rates make phylogeny-based conclusions reliable. Phylogenetic reconstruction strongly supported the hypothesis that host switching occurred in the history of lyssaviruses. Indeed, lyssaviruses evolved in chiropters long before the emergence of carnivoran rabies, very likely following spillovers from bats. Using dated isolates, the average rate of evolution was estimated to be roughly 4.3 × 10−4 dS/site/year. Consequently, the emergence of carnivoran rabies from chiropteran lyssaviruses was determined to have occurred 888 to 1,459 years ago. Glycoprotein segments accumulating more dN than dS were distinctly detected in carnivoran and chiropteran lyssaviruses. They may have contributed to the adaptation of the virus to the two distinct mammal orders. In carnivoran lyssaviruses they overlapped the main antigenic sites, II and III, whereas in chiropteran lyssaviruses they were located in regions of unknown functions. PMID:11483755
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Gavrilin, Gene V.; Cherkasova, Elena A.; Lipskaya, Galina Y.; Kew, Olen M.; Agol, Vadim I.
2000-01-01
We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis. PMID:10906191
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Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun
2012-01-01
Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272
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Both adaptive and neutral trait evolution can contribute to divergence, but the relative contributions of the two remain unclear. Oviposition preference, a trait that has been demonstrated to contribute to divergence among populations, is often presumed to be an adaptive trait. F...
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Detuning dependence of Rabi oscillations in an InAs self-assembled quantum dot ensemble
NASA Astrophysics Data System (ADS)
Suzuki, Takeshi; Singh, Rohan; Bayer, Manfred; Ludzwig, Arne; Wieck, Andreas D.; Cundiff, Steven T.
2018-04-01
We study the coherent evolution of an InAs self-assembled quantum dot (QD) ensemble in the ultrafast regime. The evolution of the entire frequency distribution is revealed by performing prepulse two-dimensional (2D) coherent spectroscopy. Charged and neutral QDs display distinct nonlinear responses arising from two-level trion and four-level exciton-biexciton systems, respectively, and each signal is clearly separated in 2D spectra. Whereas the signals for charged QDs are symmetric with respect to the detuning, those for neutral QDs are asymmetric due to the asymmetric four-level energy structure. Experimental results for charged and neutral QDs are well reproduced by solving the optical Bloch equations, including detuning and excitation-induced dephasing (EID) effects. The temperature dependence suggests that wetting-layer carriers play an important role in EID.
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Numberical simulation of the effects of radially injected barium plasma in the ionosphere
NASA Technical Reports Server (NTRS)
Swift, D. W.
1985-01-01
The morphology of the ion cloud in the radial shaped charge barium injection was studied. The shape of the ion cloud that remains after the explosive products and neutral barium clears away was examined. The ion cloud which has the configuration of a rimless wagon wheel is shown. The major features are the 2.5 km radius black hole in the center of the cloud, the surrounding ring of barium ion and the spokes of barium ionization radiating away from the center. The cloud shows no evolution after it emerges from the neutral debris and it is concluded that it is formed within 5 seconds of the event. A numerical model is used to calculate the motion of ions and electrons subject to the electrostatic and lorenz forces.
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Coevolution of cooperation and network structure under natural selection
NASA Astrophysics Data System (ADS)
Yang, D.-P.; Lin, H.; Shuai, J. W.
2011-02-01
A coevolution model by coupling mortality and fertility selection is introduced to investigate the evolution of cooperation and network structure in the prisoner's dilemma game. The cooperation level goes through a continuous phase transition vs. defection temptation b for low mortality selection intensity β and through a discontinuous one for infinite β. The cooperation level is enhanced most at β≈1 for any b. The local and global properties of the network structure, such as cluster and cooperating k-core, are investigated for the understanding of cooperation evolution. Cooperation is promoted by forming a tight cooperating k-core at moderate β, but too large β will destroy the cooperating k-core rapidly resulting in a rapid drop of the cooperation level. Importantly, the infinite β changes the normalized sucker's payoff S from 0 to 1-b and its dynamics of the cooperation level undergoes a very slow power-law decay, which leads the evolution into the regime of neutral evolution.
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Model-based Optimization and Feedback Control of the Current Density Profile Evolution in NSTX-U
NASA Astrophysics Data System (ADS)
Ilhan, Zeki Okan
Nuclear fusion research is a highly challenging, multidisciplinary field seeking contributions from both plasma physics and multiple engineering areas. As an application of plasma control engineering, this dissertation mainly explores methods to control the current density profile evolution within the National Spherical Torus eXperiment-Upgrade (NSTX-U), which is a substantial upgrade based on the NSTX device, which is located in Princeton Plasma Physics Laboratory (PPPL), Princeton, NJ. Active control of the toroidal current density profile is among those plasma control milestones that the NSTX-U program must achieve to realize its next-step operational goals, which are characterized by high-performance, long-pulse, MHD-stable plasma operation with neutral beam heating. Therefore, the aim of this work is to develop model-based, feedforward and feedback controllers that can enable time regulation of the current density profile in NSTX-U by actuating the total plasma current, electron density, and the powers of the individual neutral beam injectors. Motivated by the coupled, nonlinear, multivariable, distributed-parameter plasma dynamics, the first step towards control design is the development of a physics-based, control-oriented model for the current profile evolution in NSTX-U in response to non-inductive current drives and heating systems. Numerical simulations of the proposed control-oriented model show qualitative agreement with the high-fidelity physics code TRANSP. The next step is to utilize the proposed control-oriented model to design an open-loop actuator trajectory optimizer. Given a desired operating state, the optimizer produces the actuator trajectories that can steer the plasma to such state. The objective of the feedforward control design is to provide a more systematic approach to advanced scenario planning in NSTX-U since the development of such scenarios is conventionally carried out experimentally by modifying the tokamak's actuator trajectories and analyzing the resulting plasma evolution. Finally, the proposed control-oriented model is embedded in feedback control schemes based on optimal control and Model Predictive Control (MPC) approaches. Integrators are added to the standard Linear Quadratic Gaussian (LQG) and MPC formulations to provide robustness against various modeling uncertainties and external disturbances. The effectiveness of the proposed feedback controllers in regulating the current density profile in NSTX-U is demonstrated in closed-loop nonlinear simulations. Moreover, the optimal feedback control algorithm has been implemented successfully in closed-loop control simulations within TRANSP through the recently developed Expert routine. (Abstract shortened by ProQuest.).
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The Redshift Evolution of Rest-UV Spectroscopic Properties in Lyman-break Galaxies at z ∼ 2–4
NASA Astrophysics Data System (ADS)
Du, Xinnan; Shapley, Alice E.; Reddy, Naveen A.; Jones, Tucker; Stark, Daniel P.; Steidel, Charles C.; Strom, Allison L.; Rudie, Gwen C.; Erb, Dawn K.; Ellis, Richard S.; Pettini, Max
2018-06-01
We present the first comprehensive evolutionary analysis of the rest-frame UV spectroscopic properties of star-forming galaxies at z ∼ 2–4. We match samples at different redshifts in UV luminosity and stellar mass, and perform systematic measurements of spectral features and stellar population modeling. By creating composite spectra grouped according to Lyα equivalent width (EW) and various galaxy properties, we study the evolutionary trends among Lyα, low- and high-ionization interstellar (LIS and HIS) absorption features, and integrated galaxy properties. We also examine the redshift evolution of Lyα and LIS absorption kinematics, and fine-structure emission EWs. The connections among the strengths of Lyα, LIS lines, and dust extinction are redshift independent, as is the decoupling of the Lyα and HIS line strengths, and the bulk outflow kinematics as traced by the LIS lines. Stronger Lyα emission is observed at higher redshift at fixed UV luminosity, stellar mass, SFR, and age. Much of this variation in the average Lyα strength with redshift, and the variation in Lyα strength at fixed redshift, can be explained in terms of variations in the neutral gas covering fraction and/or dust content in the ISM and CGM. However, based on the connection between Lyα and C III] emission strengths, we additionally find evidence for variations in the intrinsic production rate of Lyα photons at the highest Lyα EWs. The challenge now is to understand the observed evolution of the neutral gas covering fraction and dust extinction within a coherent model for galaxy formation, and make robust predictions for the escape of ionizing radiation at z > 6.
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Between-Region Genetic Divergence Reflects the Mode and Tempo of Tumor Evolution
Sun, Ruping; Hu, Zheng; Sottoriva, Andrea; Graham, Trevor A.; Harpak, Arbel; Ma, Zhicheng; Fischer, Jared M.; Shibata, Darryl; Curtis, Christina
2017-01-01
Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural selection within established human tumors are lacking. By simulating spatial tumor growth under different evolutionary modes and examining patterns of between-region subclonal genetic divergence from multi-region sequencing (MRS) data, we demonstrate that it is feasible to distinguish tumors driven by strong positive subclonal selection from those evolving neutrally or under weak selection, as the latter fail to dramatically alter subclonal composition. We developed a classifier based on measures of between-region subclonal genetic divergence and projected patient data into model space, revealing different modes of evolution both within and between solid tumor types. Our findings have broad implications for how human tumors progress, accumulate intra-tumor heterogeneity, and ultimately how they may be more effectively treated. PMID:28581503
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Mate-choice copying: A fitness-enhancing behavior that evolves by indirect selection.
Santos, Mauro; Sapage, Manuel; Matos, Margarida; Varela, Susana A M
2017-06-01
A spatially explicit, individual-based simulation model is used to study the spread of an allele for mate-choice copying (MCC) through horizontal cultural transmission when female innate preferences do or do not coevolve with a male viability-increasing trait. Evolution of MCC is unlikely when innate female preferences coevolve with the trait, as copier females cannot express a higher preference than noncopier females for high-fitness males. However, if a genetic polymorphism for innate preference persists in the population, MCC can evolve by indirect selection through hitchhiking: the copying allele hitchhikes on the male trait. MCC can be an adaptive behavior-that is, a behavior that increases a population's average fitness relative to populations without MCC-even though the copying allele itself may be neutral or mildly deleterious. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes.
Figuet, Emeric; Nabholz, Benoît; Bonneau, Manon; Mas Carrio, Eduard; Nadachowska-Brzyska, Krystyna; Ellegren, Hans; Galtier, Nicolas
2016-06-01
The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of nonsynonymous (dN) versus synonymous (dS) substitution rates in birds versus mammals, however, has provided contradictory results, questioning the generality of the nearly neutral theory. Here we analyzed the impact of life history traits, taken as proxies of the effective population size, on molecular evolutionary and population genetic processes in amniotes, including the so far neglected reptiles. We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations-and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, short-lived species of birds. We show that this unexpected pattern is not due to a more narrow range of life history traits, a lack of correlation between traits and Ne, or a peculiar distribution of fitness effects of mutations in birds. Our analysis therefore highlights the bird dN/dS ratio as a molecular evolutionary paradox and a challenge for future research. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Nabholz, Benoit; Lartillot, Nicolas
2013-01-01
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment. PMID:23711670
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Zurovcová, Martina; Ayala, Francisco J
2002-01-01
A new developmental gene family, recently identified in D. melanogaster, has been called imaginal disc growth factors (IDGF) because the proteins promote growth of cell lineages derived from imaginal discs. These are the first genes reported that encode polypeptide factors with mitotic activity in invertebrates. Characteristics such as similar arrangement of introns and exons, small size, and different cytological localization make this family an excellent candidate for evolutionary studies. We focus on the loci Idgf1 and Idgf3, two genes that possess the most distinctive features. We examine the pattern of intra- and interspecific nucleotide variation in the sequences from 20 isogenic lines of D. melanogaster and sequences from D. simulans and D. yakuba. While MK, HKA, and Tajima's tests of neutrality fail to reject a neutral model of molecular evolution, Fu and Li's test with outgroup and McDonald's test suggest that balancing selection is modulating the evolution of the Idgf1 locus. The rate of recombination between the two loci is high enough to uncouple any linkage disequilibrium arising between Idgf1 and Idgf3, despite their close physical proximity. PMID:12242232
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Evolution of plant growth and defense in a continental introduction.
Agrawal, Anurag A; Hastings, Amy P; Bradburd, Gideon S; Woods, Ellen C; Züst, Tobias; Harvey, Jeffrey A; Bukovinszky, Tibor
2015-07-01
Substantial research has addressed adaptation of nonnative biota to novel environments, yet surprisingly little work has integrated population genetic structure and the mechanisms underlying phenotypic differentiation in ecologically important traits. We report on studies of the common milkweed Asclepias syriaca, which was introduced from North America to Europe over the past 400 years and which lacks most of its specialized herbivores in the introduced range. Using 10 populations from each continent grown in a common environment, we identified several growth and defense traits that have diverged, despite low neutral genetic differentiation between continents. We next developed a Bayesian modeling approach to account for relationships between molecular and phenotypic differences, confirming that continental trait differentiation was greater than expected from neutral genetic differentiation. We found evidence that growth-related traits adaptively diverged within and between continents. Inducible defenses triggered by monarch butterfly herbivory were substantially reduced in European populations, and this reduction in inducibility was concordant with altered phytohormonal dynamics, reduced plant growth, and a trade-off with constitutive investment. Freedom from the community of native and specialized herbivores may have favored constitutive over induced defense. Our replicated analysis of plant growth and defense, including phenotypically plastic traits, suggests adaptive evolution following a continental introduction.
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Measurements of Discrete Symmetries in the Neutral Kaon System with the CPLEAR (PS195) Experiment
NASA Astrophysics Data System (ADS)
Ruf, Thomas
2015-07-01
The antiproton storage ring LEAR offered unique opportunities to study the symmetries which exist between matter and antimatter. At variance with other approaches at this facility, CPLEAR was an experiment devoted to the study of T, \\{CPT} and \\{CP} symmetries in the neutral kaon system. It measured with high precision the time evolution of initially strangeness-tagged K0 and overline K ^0 states to determine the size of violations with respect to these symmetries in the context of a systematic study. In parallel, limits concerning quantum-mechanical predictions (EPR paradox, coherence of the wave function) or the equivalence principle of general relativity have been obtained. This article will first discuss briefly the unique low energy antiproton storage ring LEAR followed by a description of the CPLEAR experiment, including the basic formalism necessary to understand the time evolution of a neutral kaon state and the main results related to measurements of discrete symmetries in the neutral kaon system. An excellent and exhaustive review of the CPLEAR experiment and all its measurements is given in Ref. 1.
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Looking for the optimal rate of recombination for evolutionary dynamics
NASA Astrophysics Data System (ADS)
Saakian, David B.
2018-01-01
We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.
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NASA Technical Reports Server (NTRS)
Hess, P. C.; Parmentier, E. M.
1993-01-01
We explore a model for the chemical evolution of the lunar interior that explains the origin and evolution of lunar magmatism and possibly the existence of a lunar core. A magma ocean formed during accretion differentiates into the anorthositic crust and chemically stratified cumulate mantle. The cumulative mantle is gravitationally unstable with dense ilmenite cumulate layers overlying olivine-orthopyroxene cumulates with Fe/Mg that decreases with depth. The dense ilmenite layer sinks to the center of the moon forming the core. The remainder of the gravitationally unstable cumulate pile also overturns. Any remaining primitive lunar mantle rises to its level of neutral buoyancy in the cumulate pile. Perhaps melting of primitive lunar mantle due to this decompression results in early lunar Mg-rich magmatism. Because of its high concentration of incompatible heat producing elements, the ilmenite core heats the overlying orthopyroxene-bearing cumulates. As a conductively thickening thermal boundary layer becomes unstable, the resulting mantle plumes rise, decompress, and partially melt to generate the mare basalts. This model explains both the timing and chemical characteristics of lunar magmatism.
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Evolution of HI from Z=5 to the present
NASA Technical Reports Server (NTRS)
Storrie-Lombardi, L. J.
2002-01-01
Studies of damped Lya systems provide us with a good measure of the evolution of the HI column density distribution function and the contribution to the comoving mass density in neutral gas out to redshifts of z = 5 . The column density distribution function at high redshift steepens for the highest column density HI absorbers, though the contribution to the comoving mass density of neutral gas remains fiat from 2 < z < 5 . Results from studies at z < 2 are finding substantial numbers of damped absorbers identified from MgII absorption, compared to previous blind surveys. These results indicate that the contribution to the comoving mass density in neutral gas may be constant from z 0 to z 5. Details of recent work in the redshift range z < 2 work is covered elsewhere in this volume (see D. Nestor). We review here recent results for the redshift range 2 < z < 5.
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Studies of Ion Beam Charge Neutralization by Ferroelectric Plasma Sources
NASA Astrophysics Data System (ADS)
Stepanov, A.; Gilson, E. P.; Grisham, L.; Davidson, R. C.
2013-10-01
Space-charge forces limit the possible transverse compression of high perveance ion beams that are used in ion-beam-driven high energy density physics applications; the minimum radius to which a beam can be focused is an increasing function of perveance. The limit can be overcome if a plasma is introduced in the beam path between the focusing element and the target in order to neutralize the space charge of the beam. This concept has been implemented on the Neutralized Drift Compression eXperiment (NDCX) at LBNL using Ferroelectric Plasma Sources (FEPS). In our experiment at PPPL, we propagate a perveance-dominated ion beam through a FEPS to study the effect of the neutralizing plasma on the beam envelope and its evolution in time. A 30-60 keV space-charge-dominated Argon beam is focused with an Einzel lens into a FEPS located at the beam waist. The beam is intercepted downstream from the FEPS by a movable Faraday cup that provides time-resolved 2D current density profiles of the beam spot on target. We report results on: (a) dependence of charge neutralization on FEPS plasma density; (b) effects on beam emittance, and (c) time evolution of the beam envelope after the FEPS pulse. Research supported by the U.S. Department of Energy.
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Some Physical Principles Governing Spatial and Temporal Organization in Living Systems
NASA Astrophysics Data System (ADS)
Ali, Md Zulfikar
Spatial and temporal organization in living organisms are crucial for a variety of biological functions and arise from the interplay of large number of interacting molecules. One of the central questions in systems biology is to understand how such an intricate organization emerges from the molecular biochemistry of the cell. In this dissertation we explore two projects. The first project relates to pattern formation in a cell membrane as an example of spatial organization, and the second project relates to the evolution of oscillatory networks as a simple example of temporal organization. For the first project, we introduce a model for pattern formation in a two-component lipid bilayer and study the interplay between membrane composition and membrane geometry, demonstrating the existence of a rich phase diagram. Pattern formation is governed by the interplay between phase separation driven by lipid-lipid interactions and tendency of lipid domains with high intrinsic curvature to deform the membrane away from its preferred position. Depending on membrane parameters, we find the formation of compact lipid micro-clusters or of striped domains. We calculate the stripe width analytically and find good agreement with stripe widths obtained from the simulations. For the second project, we introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm and apply it to study the following problems. Using the model, we study robustness and designabilty of a 2-component network that generate oscillations. We completely enumerate the sequence space and the phenotypic space, and discuss the relationship between designabilty, robustness and evolvability. We further apply the model to studies of neutral drift in networks that yield oscillatory dynamics, e.g. starting with a relatively simple network and allowing it to evolve by adding nodes and connections while requiring that oscillatory dynamics be preserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. In addition we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains. Finally, we use the model to study the evolution of an oscillator from a non-oscillatory network under the influence of external periodic forcing as a model for evolution of circadian rhythm in living systems. We use a greedy algorithm based on optimizing biologically motivated fitness functions and find that the algorithm successfully produces oscillators. However, the distribution of free-period of evolved oscillators depends on the choice of fitness functions and the nature of forcing.
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Renzette, Nicholas; Kowalik, Timothy F; Jensen, Jeffrey D
2016-01-01
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms. © 2015 John Wiley & Sons Ltd.
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Rand, D M; Kann, L M
1996-07-01
Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.
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Altitude-dependent Drift of a Chemical Release Cloud at Middle Latitudes
NASA Astrophysics Data System (ADS)
Pedersen, T.; Holmes, J. M.; Sutton, E. K.
2017-12-01
A chemical release experiment conducted at the White Sands Missile Range in February 2015 consisted of firing of three identical canisters at different altitudes along a near-vertical trajectory, creating a large structured cloud after diffusion and expansion of the three initial dispersals. Dedicated optical observations from near the launch site and a remote site allow determination of the position and motion of the extended optical cloud as a function of time, while photographs captured and posted by members of the general public provide additional look angles to constrain the cloud shape in more detail. We compare the observed drift and evolution of the cloud with empirical and theoretical models of the neutral winds to examine the altitudinal shear in the neutral winds and their effects on the motion and shape of the extended optical cloud.
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Neutral dynamics and cell renewal of colonic crypts in homeostatic regime
NASA Astrophysics Data System (ADS)
Fendrik, A. J.; Romanelli, L.; Rotondo, E.
2018-05-01
The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: (a) we distinguish different classes of cells: stem cells, six generations of transit amplifying cells and the differentiated cells; (b) in order to take into account the monoclonal character of crypts in homeostatic regimes we include symmetric divisions of the stem cells. We first consider the dynamic differential equations that describe the evolution of the mean values of the populations, but the small observed value of the total number of cells involved plus the huge dispersion of experimental data found in the literature leads us to study the stochastic discrete process. This analysis allows us to study fluctuations, the neutral drift that leads to monoclonality, and the effects of the fixation of mutant clones.
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Dugas, Diana V; Hernandez, David; Koenen, Erik J M; Schwarz, Erika; Straub, Shannon; Hughes, Colin E; Jansen, Robert K; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T; Hajrah, Nahid H; Alharbi, Njud S; Al-Malki, Abdulrahman L; Sabir, Jamal S M; Bailey, C Donovan
2015-11-23
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.
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Shirani, Sahar; Hellweger, Ferdi L
2017-08-01
Molecular observations reveal substantial biogeographic patterns of cyanobacteria within systems of connected lakes. An important question is the relative role of environmental selection and neutral processes in the biogeography of these systems. Here, we quantify the effect of genetic drift and dispersal limitation by simulating individual cyanobacteria cells using an agent-based model (ABM). In the model, cells grow (divide), die, and migrate between lakes. Each cell has a full genome that is subject to neutral mutation (i.e., the growth rate is independent of the genome). The model is verified by simulating simplified lake systems, for which theoretical solutions are available. Then, it is used to simulate the biogeography of the cyanobacterium Microcystis aeruginosa in a number of real systems, including the Great Lakes, Klamath River, Yahara River, and Chattahoochee River. Model output is analyzed using standard bioinformatics tools (BLAST, MAFFT). The emergent patterns of nucleotide divergence between lakes are dynamic, including gradual increases due to accumulation of mutations and abrupt changes due to population takeovers by migrant cells (coalescence events). The model predicted nucleotide divergence is heterogeneous within systems, and for weakly connected lakes, it can be substantial. For example, Lakes Superior and Michigan are predicted to have an average genomic nucleotide divergence of 8200 bp or 0.14%. The divergence between more strongly connected lakes is much lower. Our results provide a quantitative baseline for future biogeography studies. They show that dispersal limitation can be an important factor in microbe biogeography, which is contrary to the common belief, and could affect how a system responds to environmental change.
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Population dynamics in the presence of quasispecies effects and changing environments
NASA Astrophysics Data System (ADS)
Forster, Robert Burke
2006-12-01
This thesis explores how natural selection acts on organisms such as viruses that have either highly error-prone reproduction or face variable environmental conditions or both. By modeling population dynamics under these conditions, we gain a better understanding of the selective forces at work, both in our simulations and hopefully also in real organisms. With an understanding of the important factors in natural selection we can forecast not only the immediate fate of an existing population but also in what directions such a population might evolve in the future. We demonstrate that the concept of a quasispecies is relevant to evolution in a neutral fitness landscape. Motivated by RNA viruses such as HIV, we use RNA secondary structure as our model system and find that quasispecies effects arise both rapidly and in realistically small populations. We discover that the evolutionary effects of neutral drift, punctuated equilibrium and the selection for mutational robustness extend to the concept of a quasispecies. In our study of periodic environments, we consider the tradeoffs faced by quasispecies in adapting to environmental change. We develop an analytical model to predict whether evolution favors short-term or long-term adaptation and validate our model through simulation. Our results bear directly on the population dynamics of viruses such as West Nile that alternate between two host species. More generally, we discover that a selective pressure exists under these conditions to fuse or split genes with complementary environmental functions. Lastly, we study the general effects of frequency-dependent selection on two strains competing in a periodic environment. Under very general assumptions, we prove that stable coexistence rather than extinction is the likely outcome. The population dynamics of this system may be as simple as stable equilibrium or as complex as deterministic chaos.
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Shaffer, J Scott; Moore, Penny L; Kardar, Mehran; Chakraborty, Arup K
2016-10-24
Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs.
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Pickup ion processes associated with spacecraft thrusters: Implications for solar probe plus
DOE Office of Scientific and Technical Information (OSTI.GOV)
Clemens, Adam, E-mail: a.j.clemens@qmul.ac.uk; Burgess, David
2016-03-15
Chemical thrusters are widely used in spacecraft for attitude control and orbital manoeuvres. They create an exhaust plume of neutral gas which produces ions via photoionization and charge exchange. Measurements of local plasma properties will be affected by perturbations caused by the coupling between the newborn ions and the plasma. A model of neutral expansion has been used in conjunction with a fully three-dimensional hybrid code to study the evolution and ionization over time of the neutral cloud produced by the firing of a mono-propellant hydrazine thruster as well as the interactions of the resulting ion cloud with the ambientmore » solar wind. Results are presented which show that the plasma in the region near to the spacecraft will be perturbed for an extended period of time with the formation of an interaction region around the spacecraft, a moderate amplitude density bow wave bounding the interaction region and evidence of an instability at the forefront of the interaction region which causes clumps of ions to be ejected from the main ion cloud quasi-periodically.« less
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Shaffer, J. Scott; Moore, Penny L.; Kardar, Mehran; Chakraborty, Arup K.
2016-01-01
Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs. PMID:27791170
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Comparing High-latitude Ionospheric and Thermospheric Lagrangian Coherent Structures
NASA Astrophysics Data System (ADS)
Wang, N.; Ramirez, U.; Flores, F.; Okic, D.; Datta-Barua, S.
2015-12-01
Lagrangian Coherent Structures (LCSs) are invisible boundaries in time varying flow fields that may be subject to mixing and turbulence. The LCS is defined by the local maxima of the finite time Lyapunov exponent (FTLE), a scalar field quantifying the degree of stretching of fluid elements over the flow domain. Although the thermosphere is dominated by neutral wind processes and the ionosphere is governed by plasma electrodynamics, we can compare the LCS in the two modeled flow fields to yield insight into transport and interaction processes in the high-latitude IT system. For obtaining thermospheric LCS, we use the Horizontal Wind Model 2014 (HWM14) [1] at a single altitude to generate the two-dimensional velocity field. The FTLE computation is applied to study the flow field of the neutral wind, and to visualize the forward-time Lagrangian Coherent Structures in the flow domain. The time-varying structures indicate a possible thermospheric LCS ridge in the auroral oval area. The results of a two-day run during a geomagnetically quiet period show that the structures are diurnally quasi-periodic, thus that solar radiation influences the neutral wind flow field. To find the LCS in the high-latitude ionospheric drifts, the Weimer 2001 [2] polar electric potential model and the International Geomagnetic Reference Field 11 [3] are used to compute the ExB drift flow field in ionosphere. As with the neutral winds, the Lagrangian Coherent Structures are obtained by applying the FTLE computation. The relationship between the thermospheric and ionospheric LCS is analyzed by comparing overlapping FTLE maps. Both a publicly available FTLE solver [4] and a custom-built FTLE computation are used and compared for validation [5]. Comparing the modeled IT LCSs on a quiet day with the modeled IT LCSs on a storm day indicates important factors on the structure and time evolution of the LCS.
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Zhou, Y. L.; Wang, Z. H.; Xu, X. Q.; ...
2015-01-09
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Furthermore, two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density,more » heat and momentum transport equations along with neutral density, and momentum transport equations. In transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. Moreover, it is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhou, Y. L.; Wang, Z. H.; Xu, X. Q.
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Furthermore, two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density,more » heat and momentum transport equations along with neutral density, and momentum transport equations. In transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. Moreover, it is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhou, Y. L.; Southwestern Institute of Physics, Chengdu 610041; Wang, Z. H., E-mail: zhwang@swip.ac.cn
Plasma fueling with high efficiency and deep injection is very important to enable fusion power performance requirements. It is a powerful and efficient way to study neutral transport dynamics and find methods of improving the fueling performance by doing large scale simulations. Two basic fueling methods, gas puffing (GP) and supersonic molecular beam injection (SMBI), are simulated and compared in realistic divertor geometry of the HL-2A tokamak with a newly developed module, named trans-neut, within the framework of BOUT++ boundary plasma turbulence code [Z. H. Wang et al., Nucl. Fusion 54, 043019 (2014)]. The physical model includes plasma density, heatmore » and momentum transport equations along with neutral density, and momentum transport equations. Transport dynamics and profile evolutions of both plasma and neutrals are simulated and compared between GP and SMBI in both poloidal and radial directions, which are quite different from one and the other. It finds that the neutrals can penetrate about four centimeters inside the last closed (magnetic) flux surface during SMBI, while they are all deposited outside of the LCF during GP. It is the radial convection and larger inflowing flux which lead to the deeper penetration depth of SMBI and higher fueling efficiency compared to GP.« less
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A model of directional selection applied to the evolution of drug resistance in HIV-1.
Seoighe, Cathal; Ketwaroo, Farahnaz; Pillay, Visva; Scheffler, Konrad; Wood, Natasha; Duffet, Rodger; Zvelebil, Marketa; Martinson, Neil; McIntyre, James; Morris, Lynn; Hide, Winston
2007-04-01
Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the neutral rate. Rapid evolution at sites that confer resistance to drugs can be used to help elucidate the mechanisms of evolution of drug resistance and to discover or corroborate novel resistance mutations. We have implemented standard maximum likelihood methods that are used to detect diversifying selection and adapted them for use with serially sampled reverse transcriptase (RT) coding sequences isolated from a group of 300 HIV-1 subtype C-infected women before and after single-dose nevirapine (sdNVP) to prevent mother-to-child transmission. We have also extended the standard models of codon evolution for application to the detection of directional selection. Through simulation, we show that the directional selection model can provide a substantial improvement in sensitivity over models of diversifying selection. Five of the sites within the RT gene that are known to harbor mutations that confer resistance to nevirapine (NVP) strongly supported the directional selection model. There was no evidence that other mutations that are known to confer NVP resistance were selected in this cohort. The directional selection model, applied to serially sampled sequences, also had more power than the diversifying selection model to detect selection resulting from factors other than drug resistance. Because inference of selection from serial samples is unlikely to be adversely affected by recombination, the methods we describe may have general applicability to the analysis of positive selection affecting recombining coding sequences when serially sampled data are available.
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Fast-ion D(alpha) measurements and simulations in DIII-D
NASA Astrophysics Data System (ADS)
Luo, Yadong
The fast-ion Dalpha diagnostic measures the Doppler-shifted Dalpha light emitted by neutralized fast ions. For a favorable viewing geometry, the bright interferences from beam neutrals, halo neutrals, and edge neutrals span over a small wavelength range around the Dalpha rest wavelength and are blocked by a vertical bar at the exit focal plane of the spectrometer. Background subtraction and fitting techniques eliminate various contaminants in the spectrum. Fast-ion data are acquired with a time evolution of ˜1 ms, spatial resolution of ˜5 cm, and energy resolution of ˜10 keV. A weighted Monte Carlo simulation code models the fast-ion Dalpha spectra based on the fast-ion distribution function from other sources. In quiet plasmas, the spectral shape is in excellent agreement and absolute magnitude also has reasonable agreement. The fast-ion D alpha signal has the expected dependencies on plasma and neutral beam parameters. The neutral particle diagnostic and neutron diagnostic corroborate the fast-ion Dalpha measurements. The relative spatial profile is in agreement with the simulated profile based on the fast-ion distribution function from the TRANSP analysis code. During ion cyclotron heating, fast ions with high perpendicular energy are accelerated, while those with low perpendicular energy are barely affected. The spatial profile is compared with the simulated profiles based on the fast-ion distribution functions from the CQL Fokker-Planck code. In discharges with Alfven instabilities, both the spatial profile and spectral shape suggests that fast ions are redistributed. The flattened fast-ion Dalpha profile is in agreement with the fast-ion pressure profile.
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ERIC Educational Resources Information Center
Skoog, Gerald
2005-01-01
Efforts to eliminate or neutralize the coverage of evolution in high school biology textbooks in the United States have persisted with varying degrees of intensity and success since the 1920s. In particular, the coverage of human evolution has been impacted by these efforts. Evidence of the success of these efforts can be chronicled by the…
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NASA Astrophysics Data System (ADS)
Wang, Shenshen; Burton, Dennis; Kardar, Mehran; Chakraborty, Arup
2014-03-01
The immune system comprises an intricate and evolving collection of cells and molecules that enables a defense against pathogenic agents. Its workings present a rich source of physical problems that impact human health. One intriguing example is the process of affinity maturation (AM) through which an antibody (Ab)--a component of the host immune system--evolves to more efficiently bind an antigen (Ag)--a unique part of a foreign pathogen such as a virus. Sufficiently strong binding to the Ag enables recognition and neutralization. A major challenge is to contain a diversifying mixture of Ag variants, that arise in natural infection, from evading Ab neutralization. This entails a thorough understanding of AM against multiple Ag species and mutating Ag. During AM, Ab-encoding cells undergo cycles of mutation and selection, a process reminiscent of Darwinian evolution yet occurring in real time. We first cast affinity-dependent selection into an extreme value problem and show how the binding characteristics scale with Ag diversity. We then develop an agent-based residue-resolved computational model of AM which allows us to track the evolutionary trajectories of individual cells. This dynamic model not only reveals significant stochastic effects associated with the relatively small and highly dynamic population size, it also uncovers the markedly distinct maturation outcomes if designed Ag variants are presented in different temporal procedures. Insights thus obtained would guide rational design of vaccination protocols.
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Modeling the unidentified infrared emission with combinations of polycyclic aromatic hydrocarbons
NASA Technical Reports Server (NTRS)
Allamandola, L. J.; Hudgins, D. M.; Sandford, S. A.
1999-01-01
The infrared emission band spectrum associated with many different interstellar objects can be modeled successfully by using combined laboratory spectra of neutral and positively charged polycyclic aromatic hydrocarbons (PAHs). These model spectra, shown here for the first time, alleviate the principal spectroscopic criticisms previously leveled at the PAH hypothesis and demonstrate that mixtures of free molecular PAHs can indeed account for the overall appearance of the widespread interstellar infrared emission spectrum. Furthermore, these models give us insight into the structures, stabilities, abundances, and ionization balance of the interstellar PAH population. These, in turn, reflect conditions in the emission zones and shed light on the microscopic processes involved in the carbon nucleation, growth, and evolution in circumstellar shells and the interstellar medium.
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From sparse to dense and from assortative to disassortative in online social networks
Li, Menghui; Guan, Shuguang; Wu, Chensheng; Gong, Xiaofeng; Li, Kun; Wu, Jinshan; Di, Zengru; Lai, Choy-Heng
2014-01-01
Inspired by the analysis of several empirical online social networks, we propose a simple reaction-diffusion-like coevolving model, in which individuals are activated to create links based on their states, influenced by local dynamics and their own intention. It is shown that the model can reproduce the remarkable properties observed in empirical online social networks; in particular, the assortative coefficients are neutral or negative, and the power law exponents γ are smaller than 2. Moreover, we demonstrate that, under appropriate conditions, the model network naturally makes transition(s) from assortative to disassortative, and from sparse to dense in their characteristics. The model is useful in understanding the formation and evolution of online social networks. PMID:24798703
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From sparse to dense and from assortative to disassortative in online social networks.
Li, Menghui; Guan, Shuguang; Wu, Chensheng; Gong, Xiaofeng; Li, Kun; Wu, Jinshan; Di, Zengru; Lai, Choy-Heng
2014-05-06
Inspired by the analysis of several empirical online social networks, we propose a simple reaction-diffusion-like coevolving model, in which individuals are activated to create links based on their states, influenced by local dynamics and their own intention. It is shown that the model can reproduce the remarkable properties observed in empirical online social networks; in particular, the assortative coefficients are neutral or negative, and the power law exponents γ are smaller than 2. Moreover, we demonstrate that, under appropriate conditions, the model network naturally makes transition(s) from assortative to disassortative, and from sparse to dense in their characteristics. The model is useful in understanding the formation and evolution of online social networks.
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Propagation of large amplitude Alfven waves in the solar wind neutral sheet
NASA Technical Reports Server (NTRS)
Malara, F.; Primavera, L.; Veltri, P.
1995-01-01
Analysis of solar wind fluctuation data show that the correlation between velocity and magnetic field fluctuations decreases when going farther away from the Sun. This decorrelation can be attributed either to the time evolution of the fluctuations, carried away by the solar wind, or to the interaction between the solar wind neutral sheet and Alfven waves. To check this second hypothesis we have numerically studied the propagation of Alfven waves in the solar wind neutral sheet. The initial conditions have been set up in order to guarantee B(exp 2) = const, so that the following numerical evolution is only due to the inhomogeneity in the background magnetic field. The analysis of the results shows that compressive structures are formed, mainly in the neutral sheet where they have been identified as pressure balanced structures, i.e., tangential discontinuities. Fast perturbations, which are also produced, have a tendency to leave the simulation domain, propagating also perpendicularly to the mean magnetic field. For this reason the level of fast perturbations is always smaller with respect to the previously cited plasma balanced structures, which are slow mode perturbations. A comparison between the numerical results and some particular observational issues is also presented.
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Working group report on beam plasmas, electronic propulsion, and active experiments using beams
NASA Technical Reports Server (NTRS)
Dawson, J. M.; Eastman, T.; Gabriel, S.; Hawkins, J.; Matossian, J.; Raitt, J.; Reeves, G.; Sasaki, S.; Szuszczewicz, E.; Winkler, J. R.
1986-01-01
The JPL Workshop addressed a number of plasma issues that bear on advanced spaceborne technology for the years 2000 and beyond. Primary interest was on the permanently manned space station with a focus on identifying environmentally related issues requiring early clarification by spaceborne plasma experimentation. The Beams Working Group focused on environmentally related threats that platform operations could have on the conduct and integrity of spaceborne beam experiments and vice versa. Considerations were to include particle beams and plumes. For purposes of definition it was agreed that the term particle beams described a directed flow of charged or neutral particles allowing single-particle trajectories to represent the characteristics of the beam and its propagation. On the other hand, the word plume was adopted to describe a multidimensional flow (or expansion) of a plasma or neutral gas cloud. Within the framework of these definitions, experiment categories included: (1) Neutral- and charged-particle beam propagation, with considerations extending to high powers and currents. (2) Evolution and dynamics of naturally occurring and man-made plasma and neutral gas clouds. In both categories, scientific interest focused on interactions with the ambient geoplasma and the evolution of particle densities, energy distribution functions, waves, and fields.
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Molecular hyperdiversity and evolution in very large populations.
Cutter, Asher D; Jovelin, Richard; Dey, Alivia
2013-04-01
The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements. © 2013 Blackwell Publishing Ltd.
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Self-similar space-time evolution of an initial density discontinuity
NASA Astrophysics Data System (ADS)
Rekaa, V. L.; Pécseli, H. L.; Trulsen, J. K.
2013-07-01
The space-time evolution of an initial step-like plasma density variation is studied. We give particular attention to formulate the problem in a way that opens for the possibility of realizing the conditions experimentally. After a short transient time interval of the order of the electron plasma period, the solution is self-similar as illustrated by a video where the space-time evolution is reduced to be a function of the ratio x/t. Solutions of this form are usually found for problems without characteristic length and time scales, in our case the quasi-neutral limit. By introducing ion collisions with neutrals into the numerical analysis, we introduce a length scale, the collisional mean free path. We study the breakdown of the self-similarity of the solution as the mean free path is made shorter than the system length. Analytical results are presented for charge exchange collisions, demonstrating a short time collisionless evolution with an ensuing long time diffusive relaxation of the initial perturbation. For large times, we find a diffusion equation as the limiting analytical form for a charge-exchange collisional plasma, with a diffusion coefficient defined as the square of the ion sound speed divided by the (constant) ion collision frequency. The ion-neutral collision frequency acts as a parameter that allows a collisionless result to be obtained in one limit, while the solution of a diffusion equation is recovered in the opposite limit of large collision frequencies.
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Is there a role for amplifiers in sexual selection?
Gualla, Filippo; Cermelli, Paolo; Castellano, Sergio
2008-05-21
The amplifier hypothesis states that selection could favour the evolution of traits in signallers that improve the ability of receivers to extract honest information from other signals or cues. We provide a formal definition of amplifiers based on the receiver's mechanisms of signal perception and we present a game-theoretical model in which males advertise their quality and females use sequential-sampling tactics to choose among prospective mates. The main effect of an amplifier on the female mating strategy is to increase her mating threshold, making the female more selective as the effectiveness of the amplifier increases. The effects of the amplifier on male advertising strategy depends both on the context and on the types of the amplifier involved. We consider two different contexts for the evolution of amplifiers (when the effect of amplifiers is on signals and when it is on cues) and two types of amplifiers (the 'neutral amplifier', when it improves quality assessment without altering male attractiveness, and the 'attractive amplifier', when it improves both quality assessment and male attractiveness). The game-theoretical model provides two main results. First, neutral and attractive amplifiers represent, respectively, a conditional and an unconditional signalling strategy. In fact, at the equilibrium, neutral amplifiers are displayed only by males whose advertising level lays above the female acceptance threshold, whereas attractive amplifiers are displayed by all signalling males, independent of their quality. Second, amplifiers of signals increase the differences in advertising levels between amplifying and not-amplifying males, but they decrease the differences within each group, so that the system converges towards an 'all-or-nothing' signalling strategy. By applying concepts from information theory, we show that the increase in information transfer at the perception level due to the amplifier of signals is contrasted by a decrease in information transfer at the emitter level due to the increased stereotypy of male advertising strategy.
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Orr, H A
1998-01-01
Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed. PMID:9691061
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Costales, Aurora; Blanco, M A; Francisco, E; Pendas, A Martín; Pandey, Ravindra
2006-03-09
We report the results of a theoretical study of AlnNn (n=7-16) clusters that is based on density functional theory. We will focus on the evolution of structural and electronic properties with the cluster size in the stoichiometric AlN clusters considered. The results reveal that the structural and electronic properties tend to evolve toward their respective bulk limits. The rate of evolution is, however, slow due to the hollow globular shape exhibited by the clusters, which introduces large surface effects that dominate the properties studied. We will also discuss the changes induced upon addition of an extra electron to the respective neutral clusters.
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On the Rayleigh-Taylor Instability in Presence of a Background Shear
NASA Astrophysics Data System (ADS)
Shvydkoy, Roman
2018-01-01
In this note we revisit the classical subject of the Rayleigh-Taylor instability in presence of an incompressible background shear flow. We derive a formula for the essential spectral radius of the evolution group generated by the linearization near the steady state and reveal that the velocity variations neutralize shortwave instabilities. The formula is a direct generalization of the result of Hwang and Guo (Arch Ration Mech Anal 167(3):235-253, (2003). Furthermore, we construct a class of steady states which posses unstable discrete spectrum with neutral essential spectrum. The technique involves the WKB analysis of the evolution equation and contains novel compactness criterion for pseudo-differential operators on unbounded domains.
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Structural drift: the population dynamics of sequential learning.
Crutchfield, James P; Whalen, Sean
2012-01-01
We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.
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Moody, M. Anthony; Gao, Feng; Gurley, Thaddeus C.; ...
2015-09-09
The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Moody, M. Anthony; Gao, Feng; Gurley, Thaddeus C.
The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less
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Labonne, Jacques; Hendry, Andrew P
2010-07-01
The standard predictions of ecological speciation might be nuanced by the interaction between natural and sexual selection. We investigated this hypothesis with an individual-based model tailored to the biology of guppies (Poecilia reticulata). We specifically modeled the situation where a high-predation population below a waterfall colonizes a low-predation population above a waterfall. Focusing on the evolution of male color, we confirm that divergent selection causes the appreciable evolution of male color within 20 generations. The rate and magnitude of this divergence were reduced when dispersal rates were high and when female choice did not differ between environments. Adaptive divergence was always coupled to the evolution of two reproductive barriers: viability selection against immigrants and hybrids. Different types of sexual selection, however, led to contrasting results for another potential reproductive barrier: mating success of immigrants. In some cases, the effects of natural and sexual selection offset each other, leading to no overall reproductive isolation despite strong adaptive divergence. Sexual selection acting through female choice can thus strongly modify the effects of divergent natural selection and thereby alter the standard predictions of ecological speciation. We also found that under no circumstances did divergent selection cause appreciable divergence in neutral genetic markers.
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Erramuzpe, Asier; Cortés, Jesús M; López, José I
2018-02-01
Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.
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Morphological rates of angiosperm seed size evolution.
Sims, Hallie J
2013-05-01
The evolution of seed size among angiosperms reflects their ecological diversification in a complex fitness landscape of life-history strategies. The lineages that have evolved seeds beyond the upper and lower boundaries that defined nonflowering seed plants since the Paleozoic are more dispersed across the angiosperm phylogeny than would be expected under a neutral model of phenotypic evolution. Morphological rates of seed size evolution estimated for 40 clades based on 17,375 species ranged from 0.001 (Garryales) to 0.207 (Malvales). Comparative phylogenetic analysis indicated that morphological rates are not associated with the clade's seed size but are negatively correlated with the clade's position in the overall distribution of angiosperm seed sizes; clades with seed sizes closer to the angiosperm mean had significantly higher morphological rates than clades with extremely small or extremely large seeds. Likewise, per-clade taxonomic diversification rates are not associated with the seed size of the clade but with where the clade falls within the angiosperm seed size distribution. These results suggest that evolutionary rates (morphological and taxonomic) are elevated in densely occupied regions of the seed morphospace relative to lineages whose ecophenotypic innovations have moved them toward the edges. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.
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A Study of Neutral B Meson Time Evolution Using Exclusively Reconstructed Semileptonic Decays
DOE Office of Scientific and Technical Information (OSTI.GOV)
Meyer, T
2003-11-05
The Standard Model of particle physics describes the fundamental building blocks of the Universe and their basic interactions. The model naturally describes the time evolution of the basic particles, of which lifetime and mixing are two examples. The neutral B meson, consisting of a bottom quark and an oppositely charged down quark, enjoys a lifetime of about 1.5 ps and the special property of mixing with its antiparticle partner, the {bar B}{sup 0}. That is, due to second order weak interactions, the B{sup 0} meson can change into a {bar B}{sup 0} meson and back again as it evolves throughmore » time. The details of this behavior offer an opportunity to closely examine the Standard Model. In this dissertation, I report on a measurement of the lifetime and mixing frequency of the neutral B meson. Using the semileptonic decay channel B{sup 0} {yields} D*{sup -}{ell}{sup +}{bar {nu}}{sub {ell}}, we select more than 68,000 signal and background candidates from about 23 million B{bar B} pairs collected in 1999-2000 with the BABAR detector located at the Stanford Linear Accelerator Center. The other B in the event is reconstructed inclusively. By constructing a master probability density function that describes the distribution of decay time differences in the sample, we use a maximum likelihood technique to simultaneously extract the B{sup 0} lifetime and mixing parameters with precision comparable to the year 2000 world average. The results are {tau}{sub B{sup 0}} = (1.523{sub -0.023}{sup +0.024} {+-} 0.022) ps and {Delta}m{sub d} = (0.492 {+-} 0.018 {+-} 0.013) ps{sup -1}. The statistical correlation coefficient between {tau}{sub B{sup 0}} and {Delta}m{sub d} is -0.22. I describe in detail several cutting-edge strategies this analysis uses to study these phenomena, laying important groundwork for the future. I also discuss several extensions of this work to include possible measurements of higher order parameters such as {Delta}{Lambda}{sub d}.« less
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Ferns, R Bridget; Tarr, Alexander W; Hue, Stephane; Urbanowicz, Richard A; McClure, C Patrick; Gilson, Richard; Ball, Jonathan K; Nastouli, Eleni; Garson, Jeremy A; Pillay, Deenan
2016-05-01
HIV-1 infected patients who acquire HCV infection have higher rates of chronicity and liver disease progression than patients with HCV mono-infection. Understanding early events in this pathogenic process is important. We applied single genome sequencing of the E1 to NS3 regions and viral pseudotype neutralization assays to explore the consequences of viral quasispecies evolution from pre-seroconversion to chronicity in four co-infected individuals (mean follow up 566 days). We observed that one to three founder viruses were transmitted. Relatively low viral sequence diversity, possibly related to an impaired immune response, due to HIV infection was observed in three patients. However, the fourth patient, after an early purifying selection displayed increasing E2 sequence evolution, possibly related to being on suppressive antiretroviral therapy. Viral pseudotypes generated from HCV variants showed relative resistance to neutralization by autologous plasma but not to plasma collected from later time points, confirming ongoing virus escape from antibody neutralization. Copyright © 2016 Elsevier Inc. All rights reserved.
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Learning about evolution from sequence data
NASA Astrophysics Data System (ADS)
Dayarian, Adel; Shraiman, Boris
2012-02-01
Recent advances in sequencing and in laboratory evolution experiments have made possible to obtain quantitative data on genetic diversity of populations and on the dynamics of evolution. This dynamics is shaped by the interplay between selection acting on beneficial and deleterious mutations and recombination which reshuffles genotypes. Mounting evidence suggests that natural populations harbor extensive fitness diversity, yet most of the currently available tools for analyzing polymorphism data are based on the neutral theory. Our aim is to develop methods to analyze genomic data for populations in the presence of the above-mentioned factors. We consider different evolutionary regimes - Muller's ratchet, mutation-recombination-selection balance and positive adaption rate - and revisit a number of observables considered in the nearly-neutral theory of evolution. In particular, we examine the coalescent structure in the presence of recombination and calculate quantities such as the distribution of the coalescent times along the genome, the distribution of haplotype block sizes and the correlation between ancestors of different loci along the genome. In addition, we characterize the probability and time of fixation of mutations as a function of their fitness effect.
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Observation of Signatures of Meteoroidal Water in the Lunar Exosphere by the LADEE NMS Instrument
NASA Astrophysics Data System (ADS)
Benna, M.; Elphic, R. C.; Hurley, D.; Stubbs, T. J.; Mahaffy, P. R.
2017-12-01
During its seven months in orbit, the Neutral Mass Spectrometer (NMS) of the Lunar Atmosphere and Dust Environment Explorer (LADEE) Mission measured the composition and variability of the tenuous lunar atmosphere. These measurements led to the detection of signatures of water group neutrals (H2O and/or OH) in the exosphere of the Moon. The signature of water has been measured as sporadic, short-lived signal increases above instrument background levels. The NMS data show that the occurrence rate of the high signal water "spikes" is correlated with periods of major annual meteoroid streams. Moreover, the daily water detection rate is in agreement with the expected evolution of the incoming meteoroidal impact flux at the Moon. Monte Carlo modeling of the evolution of vaporized water indicates that the signatures detected by the NMS instrument are commensurate in size and distribution of the energetic fraction of the vapors released by impacts that occurred near the location of the spacecraft. These measurements provide the first direct constraints on the contribution of meteoroid-delivered water to the sequestered ice in the permanently shadow regions of the lunar poles. They also provide a new technique for real-time observations of meteoroid impacts on airless bodies of the solar system through the detection of their associated volatile signatures.
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Vines, Lasse; Bhoodoo, Chidanand; von Wenckstern, Holger; Grundmann, Marius
2017-11-29
The evolution of sheet resistance of n-type In2O3 and Ga2O3 exposed to bombardment with MeV 12C and 28Si ions at 35 K is studied in situ. While the sheet resistance of Ga2O3 increased by more than 8 orders of magnitude as a result of ion irradiation, In2O3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga2O3 remained highly resistive, while In2O3 showed a lower resistance than as deposited samples. Thermal admittance spectroscopy and deep level transient spectroscopy did not reveal new defect levels for irradiation up to 2 1012 cm2. A model where larger defect complexes preferentially produce donor like defects in In2O3 is proposed, and may reveal a microscopic view of a charge neutrality level within the conduction band, as previously proposed. © 2017 IOP Publishing Ltd.
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Kinetic Simulation and Energetic Neutral Atom Imaging of the Magnetosphere
NASA Technical Reports Server (NTRS)
Fok, Mei-Ching H.
2011-01-01
Advanced simulation tools and measurement techniques have been developed to study the dynamic magnetosphere and its response to drivers in the solar wind. The Comprehensive Ring Current Model (CRCM) is a kinetic code that solves the 3D distribution in space, energy and pitch-angle information of energetic ions and electrons. Energetic Neutral Atom (ENA) imagers have been carried in past and current satellite missions. Global morphology of energetic ions were revealed by the observed ENA images. We have combined simulation and ENA analysis techniques to study the development of ring current ions during magnetic storms and substorms. We identify the timing and location of particle injection and loss. We examine the evolution of ion energy and pitch-angle distribution during different phases of a storm. In this talk we will discuss the findings from our ring current studies and how our simulation and ENA analysis tools can be applied to the upcoming TRIO-CINAMA mission.
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Torres, Marina W; Corrêa, Régis L; Schrago, Carlos G
2005-12-30
The coat protein (CP) of the family Luteoviridae is directly associated with the success of infection. It participates in various steps of the virus life cycle, such as virion assembly, stability, systemic infection, and transmission. Despite its importance, extensive studies on the molecular evolution of this protein are lacking. In the present study, we investigate the action of differential selective forces on the CP coding region using maximum likelihood methods. We found that the protein is subjected to heterogeneous selective pressures and some sites may be evolving near neutrality. Based on the proposed 3-D model of the CP S-domain, we showed that nearly neutral sites are predominantly located in the region of the protein that faces the interior of the capsid, in close contact with the viral RNA, while highly conserved sites are mainly part of beta-strands, in the protein's major framework.
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Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.
Kostadinov, Rumen; Maley, Carlo C; Kuhner, Mary K
2016-04-01
When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.
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Composition and evolution of the atmosphere of Venus
NASA Technical Reports Server (NTRS)
Donahue, Thomas (Principal Investigator)
1996-01-01
The contract year started by analyzing Jovian atmospheric data acquired by the Galileo Probe Mass Spectrometer (GPMS). Two Venus hydrogen projects got underway as well. The first study strives to understand how to reconcile the standard treatment of the evolution of the H2O and HDO resevoirs on Venus over 4.5 Gyr in the presence of H and D escape and injection by comets. The second study is calculating the charge exchange contribution to hydrogen loss rates, using realistic models for exospheric H, H(+), D, D(+), and ion temperature from PV data. This report includes the following papers as attachments and supporting data: 'The Galileo Probe Mass Spectrometer: Composition of Jupiter's Atmosphere'; 'Chemical Composition Measurements of the Atmosphere of Jupiter with the Galileo Probe Mass Spectrometer'; 'Ion/Neutral Escape of Hydrogen and Deuterium: Evolution of Water'; 'Hydrogen and Deuterium in the Thermosphere of Venus: Solar Cycle Variations and Escape'; and 'Solar Cycle Variations in H(+) and D(+) Densities in the Venus Ionosphere: Implications for Escape'.
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Island Rule, quantitative genetics and brain–body size evolution in Homo floresiensis
2017-01-01
Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis, a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60–90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus, which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa. PMID:28637851
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A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes
McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J
2011-01-01
Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792
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Island Rule, quantitative genetics and brain-body size evolution in Homo floresiensis.
Diniz-Filho, José Alexandre Felizola; Raia, Pasquale
2017-06-28
Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis , a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60-90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus , which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa. © 2017 The Author(s).
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Dynamic modification of optical nonlinearities related to femtosecond laser filamentation in gases
NASA Astrophysics Data System (ADS)
Romanov (1, 3), Dmitri; Tarazkar (2, 3), Maryam; Levis (2, 3), Robert
2017-04-01
During and immediately after the passing of a filamenting laser pulse through a gas-phase medium, the nonlinear optical characteristics of the emerging filament-wake channel undergo substantial transient modification, which stems from ionization and electronic excitation of constituent atoms/molecules. We calculate the related hyperpolarizability coefficients of individual ions, and we develop a theoretical model of filament channel evolution applicable to atmospheric-pressure and high-pressure gases. The evolution is mediated by energetic free-electron gas that results from the strong-field ionization and gains considerable energy via inverse Bremsstrahlung process. The ensuing impact ionization and excitation of the residual neutral atoms/molecules proceeds inhomogeneously both inside the channel and on its surface, being strongly influenced by the thermal conduction of the electron gas. The model shows critical importance of channel-surface effects, especially as regards the effective electron temperature. The calculated spatial-temporal evolution patterns ultimately determine the transient modifications of linear and nonlinear optical properties of filament wake channels. Medium-specific estimates are made for atmospheric- and high-pressure argon, as well as for molecular nitrogen gas. Support of Defense Threat Reduction Agency (Grant No. HDTRA1-12-1-0014) is gratefully acknowledged.
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The Limits to Parapatric Speciation: Dobzhansky–Muller Incompatibilities in a Continent–Island Model
Bank, Claudia; Bürger, Reinhard; Hermisson, Joachim
2012-01-01
How much gene flow is needed to inhibit speciation by the accumulation of Dobzhansky–Muller incompatibilities (DMIs) in a structured population? Here, we derive these limits in a classical migration–selection model with two haploid or diploid loci and unidirectional gene flow from a continent to an island. We discuss the dependence of the maximum gene-flow rate on ecological factors (exogeneous selection), genetic factors (epistasis, recombination), and the evolutionary history. Extensive analytical and numerical results show the following: (1) The maximum rate of gene flow is limited by exogeneous selection. In particular, maintenance of neutral DMIs is impossible with gene flow. (2) There are two distinct mechanisms that drive DMI evolution in parapatry, selection against immigrants in a heterogeneous environment and selection against hybrids due to the incompatibility. (3) Depending on the mechanism, opposite predictions result concerning the genetic architecture that maximizes the rate of gene flow a DMI can sustain. Selection against immigrants favors evolution of tightly linked DMIs of arbitrary strength, whereas selection against hybrids promotes the evolution of strong unlinked DMIs. In diploids, the fitness of the double heterozygotes is the decisive factor to predict the pattern of DMI stability. PMID:22542972
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Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric
2016-01-01
Background and Aims Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple–yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Key Results Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Conclusions Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. PMID:27084922
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Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric
2016-05-01
Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple-yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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The accuracy of seminumerical reionization models in comparison with radiative transfer simulations
NASA Astrophysics Data System (ADS)
Hutter, Anne
2018-06-01
We have developed a modular seminumerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I), and single-ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different seminumerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the seminumerical approaches produce similar H II and He II morphologies and power spectra of the H I 21 cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double-ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our seminumerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20 per cent ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggest that constraining ionizing emissivity-sensitive parameters from seminumerical galaxy formation-reionization models are subject to photon nonconservation.
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Chemical evolution of the gas in C-type shocks in dark clouds
NASA Astrophysics Data System (ADS)
Nesterenok, A. V.
2018-07-01
A magnetohydrodynamic model of a steady, transverse C-type shock in a dense molecular cloud is presented. A complete gas-grain chemical network is taken into account: the gas-phase chemistry, the adsorption of gas species on dust grains, various desorption mechanisms, the grain surface chemistry, the ion neutralization on dust grains, the sputtering of grain mantles. The population densities of energy levels of ions CI, CII and OI and molecules H2, CO, H2O are computed in parallel with the dynamical and chemical rate equations. The large velocity gradient approximation is used in the line radiative transfer calculations. The simulations consist of two steps: (i) modelling of the chemical and thermal evolution of a static molecular cloud and (ii) shock simulations. A comparison is made with the results of publicly available models of similar physical systems. The focus of the paper is on the chemical processing of gas material and ice mantles of dust grains by the shock. Sputtering of ice mantles takes place in the shock region close to the temperature peak of the neutral gas. At high shock speeds, molecules ejected from ice mantles are effectively destroyed in hot gas, and their survival time is low—of the order of dozens of years. After a passage of high-speed C-type shock, a zone of high abundance of atomic hydrogen appears in the cooling postshock gas that triggers formation of complex organic species such as methanol. It is shown that abundances of some complex organic molecules (COMs) in the postshock region can be much higher than in the preshock gas. These results are important for interpretation of observations of COMs in protostellar outflows.
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The accuracy of semi-numerical reionization models in comparison with radiative transfer simulations
NASA Astrophysics Data System (ADS)
Hutter, Anne
2018-03-01
We have developed a modular semi-numerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I) and singly ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different semi-numerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the semi-numerical approaches produce similar H II and He II morphologies and power spectra of the H I 21cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our semi-numerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20% ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggests that constraining ionizing emissivity sensitive parameters from semi-numerical galaxy formation-reionization models are subject to photon nonconservation.
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A Suzaku, NuSTAR and XMMNewton} view on variable absorption and relativistic reflection in NGC 4151
NASA Astrophysics Data System (ADS)
Beuchert, T.; Markowitz, A.; Dauser, T.; Garcia, J.; Keck, M.; Wilms, J.; Kadler, M.; Brenneman, L.; Zdziarski, A.
2017-10-01
We disentangle X-ray disk reflection from complex line-of-sight absorption in NGC 4151 using Suzaku, NuSTAR, and XMMNewton}. Extending upon Keck et al. (2015), we develop a physically-motivated baseline model using the latest lamp-post reflection code relxillCp_lp, which includes a Comptonization continuum. We identify two components at heights of 1.2 and 15.0 gravitational radii using a long-look simultaneous Suzaku/NuSTAR observation but argue for a vertically extended corona as opposed to distinct primary sources. We also find two neutral absorbers (one full-covering and one partial-covering), an ionized absorber (log ξ=2.8), and a highly-ionized ultra-fast outflow, all reported previously. All analyzed spectra are well described by this baseline model. The bulk of the spectral variability on time-scales from days to years can be attributed to changes of both neutral absorbers, which are inversely correlated with the hard X-ray continuum flux. The observed evolution is either consistent with changes in the absorber structure (clumpy absorber in the outer BLR or a dusty radiatively driven wind) or a geometrically stable neutral absorber that becomes increasingly ionized at a rising flux level. The soft X-rays below 1 keV are dominated by photoionized emission from extended gas, which may act as a warm mirror for the nuclear radiation.
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Crossing fitness canyons by a finite population
NASA Astrophysics Data System (ADS)
Saakian, David B.; Bratus, Alexander S.; Hu, Chin-Kun
2017-06-01
We consider the Wright-Fisher model of the finite population evolution on a fitness landscape defined in the sequence space by a path of nearly neutral mutations. We study a specific structure of the fitness landscape: One of the intermediate mutations on the mutation path results in either a large fitness value (climbing up a fitness hill) or a low fitness value (crossing a fitness canyon), the rest of the mutations besides the last one are neutral, and the last sequence has much higher fitness than any intermediate sequence. We derive analytical formulas for the first arrival time of the mutant with two point mutations. For the first arrival problem for the further mutants in the case of canyon crossing, we analytically deduce how the mean first arrival time scales with the population size and fitness difference. The location of the canyon on the path of sequences has a crucial role. If the canyon is at the beginning of the path, then it significantly prolongs the first arrival time; otherwise it just slightly changes it. Furthermore, the fitness hill at the beginning of the path strongly prolongs the arrival time period; however, the hill located near the end of the path shortens it. We optimize the first arrival time by applying a nonzero selection to the intermediate sequences. We extend our results and provide a scaling for the valley crossing time via the depth of the canyon and population size in the case of a fitness canyon at the first position. Our approach is useful for understanding some complex evolution systems, e.g., the evolution of cancer.
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Theoretical constraints on masses of heavy particles in Left-Right symmetric models
NASA Astrophysics Data System (ADS)
Chakrabortty, J.; Gluza, J.; Jeliński, T.; Srivastava, T.
2016-08-01
Left-Right symmetric models with general gL ≠gR gauge couplings which include bidoublet and triplet scalar multiplets are studied. Possible scalar mass spectra are outlined by imposing Tree-Unitarity, and Vacuum Stability criteria and also using the bounds on neutral scalar masses MHFCNC which assure the absence of Flavour Changing Neutral Currents (FCNC). We are focusing on mass spectra relevant for the LHC analysis, i.e., the scalar masses are around TeV scale. As all non-standard heavy particle masses are related to the vacuum expectation value (VEV) of the right-handed triplet (vR), the combined effects of relevant Higgs potential parameters and MHFCNC regulate the lower limits of heavy gauge boson masses. The complete set of Renormalization Group Evolutions for all couplings are provided at the 1-loop level, including the mixing effects in the Yukawa sector. Most of the scalar couplings suffer from the Landau poles at the intermediate scale Q ∼106.5 GeV, which in general coincides with violation of the Tree-Unitarity bounds.
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Divertor, scrape-off layer and pedestal particle dynamics in the ELM cycle on ASDEX Upgrade
NASA Astrophysics Data System (ADS)
Laggner, F. M.; Keerl, S.; Gnilsen, J.; Wolfrum, E.; Bernert, M.; Carralero, D.; Guimarais, L.; Nikolaeva, V.; Potzel, S.; Cavedon, M.; Mink, F.; Dunne, M. G.; Birkenmeier, G.; Fischer, R.; Viezzer, E.; Willensdorfer, M.; Wischmeier, M.; Aumayr, F.; the EUROfusion MST1 Team; the ASDEX Upgrade Team
2018-02-01
In addition to the relaxation of the pedestal, edge localised modes (ELMs) introduce changes to the divertor and scrape-off layer (SOL) conditions. Their impact on the inter-ELM pedestal recovery is investigated, with emphasis on the electron density (n e) evolution. The typical ELM cycle occurring in an exemplary ASDEX Upgrade discharge interval at moderate applied gas puff and heating power is characterised, utilising several divertor, SOL and pedestal diagnostics. In the studied discharge interval the inner divertor target is detached before the ELM crash, while the outer target is attached. The particles and power expelled by the ELM crash lead to a re-attachment of the inner target plasma. After the ELM crash, the outer divertor target moves into a high recycling regime with large n e in front of the plate, which is accompanied by high main chamber neutral fluxes. On similar timescales, the inner target fully detaches and the high field side high density region (HFSHD) is formed reaching up to the high field side midplane. This state evolves again to the pre-ELM state, when the main chamber neutral fluxes are reduced later in the ELM cycle. Neither the timescale of the appearance of the HFSHD nor the increase of the main chamber neutral fluxes fit the timescale of the n e pedestal, which is faster. It is found that during the n e pedestal recovery, the magnetic activity at the low field side midplane is strongly reduced indicating a lower level of fluctuations. A rough estimation of the particle flux across the pedestal suggests that the particle flux is reduced in this period. In conclusion, the evolution of the n e pedestal is determined by a combination of neutral fluxes, HFSHD and reduced particle flux across the pedestal. A reduced particle flux explains the fast, experimentally observed re-establishment of the n e pedestal best, whereas neutrals and HFSHD impact on the evolution of the SOL and separatrix conditions.
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Structure and composition of the neutral upper atmosphere of Mars from the MAVEN NGIMS investigation
Benna, M.; Elrod, M.; Yelle, R. V.; Bougher, S. W.; Stone, S. W.; Jakosky, B. M.
2015-01-01
Abstract The Mars Atmosphere and Volatile EvolutioN (MAVEN) Neutral Gas and Ion Mass Spectrometer (NGIMS) provides sensitive detections of neutral gas and ambient ion composition. NGIMS measurements of nine atomic and molecular neutral species, and their variation with altitude, latitude, and solar zenith angle are reported over several months of operation of the MAVEN mission. Sampling NGIMS signals from multiple neutral species every several seconds reveals persistent and unexpectedly large amplitude density structures. The scale height temperatures are mapped over the course of the first few months of the mission from high down to midlatitudes. NGIMS measurements near the homopause of 40Ar/N2 ratios agree with those reported by the Sample Analysis at Mars investigation and allow the altitude of the homopause for the most abundant gases to be established. PMID:27667873
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Mr. Red in the American South: A Response to Lisa Borgerding
ERIC Educational Resources Information Center
Meadows, Lee
2017-01-01
This review essay affirms the work Mr. Red does with his students to support their learning about evolution and how his approach agrees with the realities of teaching evolution in the American South. It then shows how focusing on understanding, but not necessarily belief, adds to Mr. Red's apparent neutrality a complimentary pedagogical approach…
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Reasons Given by UK Churchgoers for Their Stance on Evolution
ERIC Educational Resources Information Center
Village, Andrew; Baker, Sylvia
2013-01-01
A sample of 661 churchgoers from a range of Christian denominations in the United Kingdom was asked about Darwinian evolution (defined as the common origin of all species, including humans). Respondents were categorised as those who accepted the idea, those who rejected it, and those who were unsure or neutral. People in each category were given a…
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Ion neutral mass spectrometer results from the first flyby of Titan.
Waite, J Hunter; Niemann, Hasso; Yelle, Roger V; Kasprzak, Wayne T; Cravens, Thomas E; Luhmann, Janet G; McNutt, Ralph L; Ip, Wing-Huen; Gell, David; De La Haye, Virginie; Müller-Wordag, Ingo; Magee, Brian; Borggren, Nathan; Ledvina, Steve; Fletcher, Greg; Walter, Erin; Miller, Ryan; Scherer, Stefan; Thorpe, Rob; Xu, Jing; Block, Bruce; Arnett, Ken
2005-05-13
The Cassini Ion Neutral Mass Spectrometer (INMS) has obtained the first in situ composition measurements of the neutral densities of molecular nitrogen, methane, molecular hydrogen, argon, and a host of stable carbon-nitrile compounds in Titan's upper atmosphere. INMS in situ mass spectrometry has also provided evidence for atmospheric waves in the upper atmosphere and the first direct measurements of isotopes of nitrogen, carbon, and argon, which reveal interesting clues about the evolution of the atmosphere. The bulk composition and thermal structure of the moon's upper atmosphere do not appear to have changed considerably since the Voyager 1 flyby.
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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.
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Moody, M Anthony; Gao, Feng; Gurley, Thaddeus C; Amos, Joshua D; Kumar, Amit; Hora, Bhavna; Marshall, Dawn J; Whitesides, John F; Xia, Shi-Mao; Parks, Robert; Lloyd, Krissey E; Hwang, Kwan-Ki; Lu, Xiaozhi; Bonsignori, Mattia; Finzi, Andrés; Vandergrift, Nathan A; Alam, S Munir; Ferrari, Guido; Shen, Xiaoying; Tomaras, Georgia D; Kamanga, Gift; Cohen, Myron S; Sam, Noel E; Kapiga, Saidi; Gray, Elin S; Tumba, Nancy L; Morris, Lynn; Zolla-Pazner, Susan; Gorny, Miroslaw K; Mascola, John R; Hahn, Beatrice H; Shaw, George M; Sodroski, Joseph G; Liao, Hua-Xin; Montefiori, David C; Hraber, Peter T; Korber, Bette T; Haynes, Barton F
2015-09-09
The third variable (V3) loop and the CD4 binding site (CD4bs) of the HIV-1 envelope are frequently targeted by neutralizing antibodies (nAbs) in infected individuals. In chronic infection, HIV-1 escape mutants repopulate the plasma, and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3 and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses. Copyright © 2015 Elsevier Inc. All rights reserved.
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A forecast for extinction debt in the presence of speciation.
Sgardeli, Vasiliki; Iwasa, Yoh; Varvoglis, Harry; Halley, John M
2017-02-21
Predicting biodiversity relaxation following a disturbance is of great importance to conservation biology. Recently-developed models of stochastic community assembly allow us to predict the evolution of communities on the basis of mechanistic processes at the level of individuals. The neutral model of biodiversity, in particular, has provided closed-form solutions for the relaxation of biodiversity in isolated communities (no immigration or speciation). Here, we extend these results by deriving a relaxation curve for a neutral community in which new species are introduced through the mechanism of random fission speciation (RFS). The solution provides simple closed-form expressions for the equilibrium species richness, the relaxation time and the species-individual curve, which are good approximation to the more complicated formulas existing for the same model. The derivation of the relaxation curve is based on the assumption of a broken-stick species-abundance distribution (SAD) as an initial community configuration; yet for commonly observed SADs, the maximum deviation from the curve does not exceed 10%. Importantly, the solution confirms theoretical results and observations showing that the relaxation time increases with community size and thus habitat area. Such simple and analytically tractable models can help crystallize our ideas on the leading factors affecting biodiversity loss. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Universality in a Neutral Evolution Model
NASA Astrophysics Data System (ADS)
King, Dawn; Scott, Adam; Maric, Nevena; Bahar, Sonya
2013-03-01
Agent-based models are ideal for investigating the complex problems of biodiversity and speciation because they allow for complex interactions between individuals and between individuals and the environment. Presented here is a ``null'' model that investigates three mating types - assortative, bacterial, and random - in phenotype space, as a function of the percentage of random death δ. Previous work has shown phase transition behavior in an assortative mating model with variable fitness landscapes as the maximum mutation size (μ) was varied (Dees and Bahar, 2010). Similarly, this behavior was recently presented in the work of Scott et al. (submitted), on a completely neutral landscape, for bacterial-like fission as well as for assortative mating. Here, in order to achieve an appropriate ``null'' hypothesis, the random death process was changed so each individual, in each generation, has the same probability of death. Results show a continuous nonequilibrium phase transition for the order parameters of the population size and the number of clusters (analogue of species) as δ is varied for three different mutation sizes of the system. The system shows increasing robustness as μ increases. Universality classes and percolation properties of this system are also explored. This research was supported by funding from: University of Missouri Research Board and James S. McDonnell Foundation
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Model for macroevolutionary dynamics.
Maruvka, Yosef E; Shnerb, Nadav M; Kessler, David A; Ricklefs, Robert E
2013-07-02
The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21-87], which neglects extinction, or a simple birth-death (speciation-extinction) process. Here, we extend the more recent development of a generic, neutral speciation-extinction (of species)-origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom-sized taxonomic groups. The model's predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.
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Adiabatic Quantum Computing with Neutral Atoms
NASA Astrophysics Data System (ADS)
Hankin, Aaron; Biedermann, Grant; Burns, George; Jau, Yuan-Yu; Johnson, Cort; Kemme, Shanalyn; Landahl, Andrew; Mangan, Michael; Parazzoli, L. Paul; Schwindt, Peter; Armstrong, Darrell
2012-06-01
We are developing, both theoretically and experimentally, a neutral atom qubit approach to adiabatic quantum computation. Using our microfabricated diffractive optical elements, we plan to implement an array of optical traps for cesium atoms and use Rydberg-dressed ground states to provide a controlled atom-atom interaction. We will develop this experimental capability to generate a two-qubit adiabatic evolution aimed specifically toward demonstrating the two-qubit quadratic unconstrained binary optimization (QUBO) routine.
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Electron cyclotron plasma startup in the GDT experiment
NASA Astrophysics Data System (ADS)
Yakovlev, D. V.; Shalashov, A. G.; Gospodchikov, E. D.; Solomakhin, A. L.; Savkin, V. Ya.; Bagryansky, P. A.
2017-01-01
We report on a new plasma startup scenario in the gas dynamic trap (GDT) magnetic mirror device. The primary 5 MW neutral beam injection (NBI) plasma heating system fires into a sufficiently dense plasma target (‘seed plasma’), which is commonly supplied by an arc plasma generator. In the reported experiments, a different approach to seed plasma generation is explored. One of the channels of the electron cyclotron resonance (ECR) heating system is used to ionize the neutral gas and build up the density of plasma to a level suitable for NBI capture. After a short transition of approximately 1 ms the discharge becomes essentially similar to a standard one initiated by the plasma gun. This paper presents the discharge scenario and experimental data on the seed plasma evolution during ECRH, along with the dependencies on incident microwave power, magnetic configuration and pressure of a neutral gas. The characteristics of the consequent high-power NBI discharge are studied and differences from the conventional scenario are discussed. A theoretical model describing the ECR breakdown and the seed plasma accumulation in a large-scale mirror trap is developed on the basis of the GDT experiment.
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Neutral theory, microbial practice: challenges in bacterial population genetics.
Rocha, Eduardo P C
2018-04-19
Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.
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Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G
2012-10-01
Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.
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Analyzing the Signatures of High Red-shift Hydrogen: The Lyman Alpha and 21cm Emission Lines
NASA Astrophysics Data System (ADS)
Hansen, Matthew
Hydrogen line emission is an important window on galaxy formation due to the large abundance of neutral hydrogen in the early Universe. This dissertation comprises two theoretical/computational studies of two types of hydrogen line emission: Lyman alpha emission and escape from young stellar populations, and 21cm radiation from neutral hydrogen clouds at the time of the first luminous objects. The Lyman alpha research concerns the radiative transfer of resonant line radiation from a central source escaping from a multi-phase medium appropriate to young star forming regions. To analyze the properties of this novel radiative transfer problem I develop new theoretical formulations of the problem, substantiated by physically accurate monte carlo simulations of photon scattering and absorption through multi-phase gas geometries. I find that the escape fraction of resonant line photons from young star forming regions--ionized gas filled with neutral hydrogen clouds with low dust content--can exceed the continuum photon escape fraction by up to an order of magnitude. Additionally, I study the effect of gas outflow on the line profile of escaping resonant photons. In light of these results, I discuss why a young normal stellar populations surrounded by a clumpy multi-phase gas outflow can explain the Lyman alpha spectra seen from high red-shift Lyman Alpha Emitters (LAEs). The 21cm research concerns the ionization evolution of the Intergalactic Medium (IGM) during the era of the first luminous objects in the Universe. Large radio-array observatories are currently being built to specifically detect the red-shifted 21cm radiation from neutral hydrogen at red-shifts z ˜ 12 - - 6; the output will be three dimensional maps of ionized regions across the plane of the sky at various red-shift depths. The signal in the resulting ionization maps will be limited by observational noise, mainly from foreground galactic emission in radio frequencies. The research presented here is a unique approach to data mining the planned observational ionization map data. I develop the one-point statistics of the observed 21cm intensity appropriate for the IGM at high red-shifts using a mixture model technique. I show that physically interesting parameters of such mixture models, such as the total ionized gas fraction at a given red-shift slice, can be estimated by applying Maximum Likelihood Expectation to the mixture model of the observed 21cm intensity distribution. The confidence intervals on the expected model parameters are rigorously calculated, and applied to expected detection capabilities of the planned radio-array observatories. I find that at least one of the observatories, the Low Frequency Array (LOFAR), will be able to statistically detect the evolution of the total ionized gas fraction with good precision.
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Valenzuela, Carlos Y
2010-01-01
Analysis for the homogeneity of the distribution of the second base of dinucleotides in relation to the first, whose bases are separated by 0, 1, 2,... 21 nucleotide sites, was performed with the VIH-1 genome (cDNA), the Drosophila mtDNA, the Drosophila Torso gene and the human p-globin gene. These four DNA segments showed highly significant heterogeneities of base distributions that cannot be accounted for by neutral or nearly neutral evolution or by the "neighbor influence" of nucleotides on mutation rates. High correlations are found in the bases of dinucleotides separated by 0, 1 and more number of sites. A periodicity of three consecutive significance values (measured by the x²9) was found only in Drosophila mtDNA. This periodicity may be due to an unknown structure or organization of mtDNA. This non-random distribution of the two bases of dinucleotides widespread throughout these DNA segments is rather compatible with panselective evolution and generalized internucleotide co-adaptation.
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Rapid evolution of cis-regulatory sequences via local point mutations
NASA Technical Reports Server (NTRS)
Stone, J. R.; Wray, G. A.
2001-01-01
Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.
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Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination.
Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael
2014-05-02
The Axelrod model of cultural diffusion is an apparently simple model that is capable of complex behaviour. A recent work used a real-world dataset of opinions as initial conditions, demonstrating the effects of the ultrametric distribution of empirical opinion vectors in promoting cultural diversity in the model. Here we quantify the degree of ultrametricity of the initial culture vectors and investigate the effect of varying degrees of ultrametricity on the absorbing state of both a simple and extended model. Unlike the simple model, ultrametricity alone is not sufficient to sustain long-term diversity in the extended Axelrod model; rather, the initial conditions must also have sufficiently large variance in intervector distances. Further, we find that a scheme for evolving synthetic opinion vectors from cultural "prototypes" shows the same behaviour as real opinion data in maintaining cultural diversity in the extended model; whereas neutral evolution of cultural vectors does not.
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Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination
NASA Astrophysics Data System (ADS)
Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael
2014-05-01
The Axelrod model of cultural diffusion is an apparently simple model that is capable of complex behaviour. A recent work used a real-world dataset of opinions as initial conditions, demonstrating the effects of the ultrametric distribution of empirical opinion vectors in promoting cultural diversity in the model. Here we quantify the degree of ultrametricity of the initial culture vectors and investigate the effect of varying degrees of ultrametricity on the absorbing state of both a simple and extended model. Unlike the simple model, ultrametricity alone is not sufficient to sustain long-term diversity in the extended Axelrod model; rather, the initial conditions must also have sufficiently large variance in intervector distances. Further, we find that a scheme for evolving synthetic opinion vectors from cultural ``prototypes'' shows the same behaviour as real opinion data in maintaining cultural diversity in the extended model; whereas neutral evolution of cultural vectors does not.
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Modeling Neutral Densities Downstream of a Gridded Ion Thruster
NASA Technical Reports Server (NTRS)
Soulas, George C.
2010-01-01
The details of a model for determining the neutral density downstream of a gridded ion thruster are presented. An investigation of the possible sources of neutrals emanating from and surrounding a NEXT ion thruster determined that the most significant contributors to the downstream neutral density include discharge chamber neutrals escaping through the perforated grids, neutrals escaping from the neutralizer, and vacuum facility background neutrals. For the neutral flux through the grids, near- and far-field equations are presented for rigorously determining the neutral density downstream of a cylindrical aperture. These equations are integrated into a spherically-domed convex grid geometry with a hexagonal array of apertures for determining neutral densities downstream of the ion thruster grids. The neutrals escaping from an off-center neutralizer are also modeled assuming diffuse neutral emission from the neutralizer keeper orifice. Finally, the effect of the surrounding vacuum facility neutrals is included and assumed to be constant. The model is used to predict the neutral density downstream of a NEXT ion thruster with and without neutralizer flow and a vacuum facility background pressure. The impacts of past simplifying assumptions for predicting downstream neutral densities are also examined for a NEXT ion thruster.
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Models of Solar Wind Structures and Their Interaction with the Earth's Space Environment
NASA Astrophysics Data System (ADS)
Watermann, J.; Wintoft, P.; Sanahuja, B.; Saiz, E.; Poedts, S.; Palmroth, M.; Milillo, A.; Metallinou, F.-A.; Jacobs, C.; Ganushkina, N. Y.; Daglis, I. A.; Cid, C.; Cerrato, Y.; Balasis, G.; Aylward, A. D.; Aran, A.
2009-11-01
The discipline of “Space Weather” is built on the scientific foundation of solar-terrestrial physics but with a strong orientation toward applied research. Models describing the solar-terrestrial environment are therefore at the heart of this discipline, for both physical understanding of the processes involved and establishing predictive capabilities of the consequences of these processes. Depending on the requirements, purely physical models, semi-empirical or empirical models are considered to be the most appropriate. This review focuses on the interaction of solar wind disturbances with geospace. We cover interplanetary space, the Earth’s magnetosphere (with the exception of radiation belt physics), the ionosphere (with the exception of radio science), the neutral atmosphere and the ground (via electromagnetic induction fields). Space weather relevant state-of-the-art physical and semi-empirical models of the various regions are reviewed. They include models for interplanetary space, its quiet state and the evolution of recurrent and transient solar perturbations (corotating interaction regions, coronal mass ejections, their interplanetary remnants, and solar energetic particle fluxes). Models of coupled large-scale solar wind-magnetosphere-ionosphere processes (global magnetohydrodynamic descriptions) and of inner magnetosphere processes (ring current dynamics) are discussed. Achievements in modeling the coupling between magnetospheric processes and the neutral and ionized upper and middle atmospheres are described. Finally we mention efforts to compile comprehensive and flexible models from selections of existing modules applicable to particular regions and conditions in interplanetary space and geospace.
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Yang, Jian-Rong; Maclean, Calum J; Park, Chungoo; Zhao, Huabin; Zhang, Jianzhi
2017-09-01
It is commonly, although not universally, accepted that most intra and interspecific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra and interspecific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Mr. Red in the American South: a response to Lisa Borgerding
NASA Astrophysics Data System (ADS)
Meadows, Lee
2017-03-01
This review essay affirms the work Mr. Red does with his students to support their learning about evolution and how his approach agrees with the realities of teaching evolution in the American South. It then shows how focusing on understanding, but not necessarily belief, adds to Mr. Red's apparent neutrality a complimentary pedagogical approach that legitimizes more strongly accepted science while at the same time attending to the deep conflict many rural students feel when they are asked to learn evolution.
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Superposed epoch analysis of ion temperatures during CME- and CIR/HSS-driven storms
NASA Astrophysics Data System (ADS)
Keesee, A. M.; Scime, E. E.
2012-12-01
The NASA Two Wide-angle Imaging Neutral atom Spectrometers (TWINS) Mission provides a global view of the magnetosphere with near-continuous coverage. Utilizing a novel technique to calculate ion temperatures from the TWINS energetic neutral atom (ENA) measurements, we generate ion temperature maps of the magnetosphere. These maps can be used to study ion temperature evolution during geomagnetic storms. A superposed epoch analysis of the ion temperature evolution during 48 storms will be presented. Zaniewski et al. [2006] performed a superposed epoch analysis of ion temperatures by storm interval using data from the MENA instrument on the IMAGE mission, demonstrating significant dayside ion heating during the main phase. The TWINS measurements provide more continuous coverage and improved spatial and temporal resolution. Denton and Borovsky [2008] noted differences in ion temperature evolution at geosynchronous orbit between coronal mass ejection (CME)- and corotating interaction region (CIR)/high speed stream (HSS)- driven storms. Using our global ion temperature maps, we have found consistent results for select individual storms [Keesee et al., 2012]. We will present superposed epoch analyses for the subgroups of CME- and CIR/HSS-driven storms to compare global ion temperature evolution during the two types of storms.
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Determining the Effect of Natural Selection on Linked Neutral Divergence across Species
Phung, Tanya N.; Lohmueller, Kirk E.
2016-01-01
A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation. PMID:27508305
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Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.
Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E
2016-08-01
A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation.
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Landais, Elise; Murrell, Ben; Briney, Bryan; Murrell, Sasha; Rantalainen, Kimmo; Berndsen, Zachary T; Ramos, Alejandra; Wickramasinghe, Lalinda; Smith, Melissa Laird; Eren, Kemal; de Val, Natalia; Wu, Mengyu; Cappelletti, Audrey; Umotoy, Jeffrey; Lie, Yolanda; Wrin, Terri; Algate, Paul; Chan-Hui, Po-Ying; Karita, Etienne; Ward, Andrew B; Wilson, Ian A; Burton, Dennis R; Smith, Davey; Pond, Sergei L Kosakovsky; Poignard, Pascal
2017-11-21
Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes.
Soghigian, John; Andreadis, Theodore G; Livdahl, Todd P
2017-12-19
Invasive mosquito species are responsible for millions of vector-borne disease cases annually. The global invasive success of Aedes mosquitoes such as Aedes aegypti and Aedes albopictus has relied on the human transport of immature stages in container habitats. However, despite the importance of these mosquitoes and this ecological specialization to their widespread dispersal, evolution of habitat specialization in this group has remained largely unstudied. We use comparative methods to evaluate the evolution of habitat specialization and its potential influence on larval morphology, and evaluate whether container dwelling and invasiveness are monophyletic in Aedes. We show that habitat specialization has evolved repeatedly from ancestral ground pool usage to specialization in container habitats. Furthermore, we find that larval morphological scores are significantly associated with larval habitat when accounting for evolutionary relationships. We find that Ornstein-Uhleinbeck models with unique optima for each larval habitat type are preferred over several other models based predominantly on neutral processes, and that OU models can reliably simulate real morphological data. Our results demonstrate that multiple lineages of Aedes have convergently evolved a key trait associated with invasive success: the use of container habitats for immature stages. Moreover, our results demonstrate convergence in morphological characteristics as well, and suggest a role of adaptation to habitat specialization in driving phenotypic diversity in this mosquito lineage. Finally, our results highlight that the genus Aedes is not monophyletic.
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The Quiet Revolution: A New Synthesis of Biological Knowledge
ERIC Educational Resources Information Center
Dyer, K. F.
1971-01-01
Reviews evidence from molecular genetics and biochemistry, which supports the idea of some evolution, due to chance and selectively neutral mutations, occurring independently of natural selection. (AL)
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gemain, F.; Robin, I. C.; Feuillet, G.
2013-12-07
HgCdTe films grown by liquid phase epitaxy with different Cd compositions were post-annealed to control the Hg vacancy concentration. Then temperature-dependent Hall measurements and photoluminescence measurements allowed us to study the evolution of the Hg vacancy acceptor levels with the cadmium composition. For Cd compositions below 33% the Hg vacancies in HgCdTe present a negative-U property with the ionized state V{sup −} stabilized compared to the neutral state V{sup 0}. For Cd compositions higher than 45%, the Hg vacancies in HgCdTe present a more standard level ordering with the ionized state V{sup −} at higher energy than the neutral statemore » V{sup 0}.« less
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A new technique for in situ measurement of the composition of neutral gas in interplanetary space
NASA Technical Reports Server (NTRS)
Gruntman, Michael A.
1993-01-01
Neutral atoms in interplanetary space play an important role in many processes relevant to the formation and evolution of the Solar System. An experimental approach is proposed for in situ atom detection based on the conversion of neutral atoms to negative ions at a specially prepared sensitive surface. Negative ions are subsequently analyzed and detected in an essentially noise-free mode. The use of the technique for in situ study of the composition of neutral interstellar atoms is considered. It is shown that interstellar H, D, and O atoms and possibly H2 molecules can be measured by the proposed technique. The experiment can be performed from a high-apogee Earth-orbiting satellite or from a deep space probe. Possible applications of the technique are discussed.
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Spectroscopic observation of Lyα emitters at z ∼ 7.7 and implications on re-ionization
DOE Office of Scientific and Technical Information (OSTI.GOV)
Faisst, A. L.; Carollo, C. M.; Capak, P.
2014-06-10
We present spectroscopic follow-up observations on two bright Lyα emitter (LAE) candidates originally found by Krug et al. at a redshift of z ∼ 7.7 using the Multi-Object Spectrometer for Infra-Red Exploration at Keck. We rule out any line emission at the >5σ level for both objects, putting on solid ground a previous null result for one of the objects. The limits inferred from the non-detections rule out the previous claim of no or even reversed evolution between 5.7 < z < 7.7 in the Lyα luminosity function (LF) and suggest a drop in the Lyα LF consistent with thatmore » seen in Lyman break galaxy (LBG) samples. We model the redshift evolution of the LAE LF using the LBG UV-continuum LF and the observed rest-frame equivalent width distribution. From the comparison of our empirical model with the observed LAE distribution, we estimate lower limits of the neutral hydrogen fraction to be 50%-70% at z ∼ 7.7. Together with this, we find a strong evolution in the Lyα optical depth characterized by (1 + z){sup 2.2} {sup ±} {sup 0.5} beyond z = 6, indicative of a strong evolution of the intergalactic medium. Finally, we extrapolate the LAE LF to z ∼ 9 using our model and show that it is unlikely that large area surveys, like UltraVISTA or Euclid, pick up LAEs at this redshift assuming the current depths and area.« less
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Effects of stream topology on ecological community results from neutral models
While neutral theory and models have stimulated considerable literature, less well investigated is the effect of topology on neutral metacommunity model simulations. We implemented a neutral metacommunity model using two different stream network topologies, a widely branched netw...
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Universal features in the genome-level evolution of protein domains.
Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno
2009-01-01
Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.
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A test for selection employing quantitative trait locus and mutation accumulation data.
Rice, Daniel P; Townsend, Jeffrey P
2012-04-01
Evolutionary biologists attribute much of the phenotypic diversity observed in nature to the action of natural selection. However, for many phenotypic traits, especially quantitative phenotypic traits, it has been challenging to test for the historical action of selection. An important challenge for biologists studying quantitative traits, therefore, is to distinguish between traits that have evolved under the influence of strong selection and those that have evolved neutrally. Most existing tests for selection employ molecular data, but selection also leaves a mark on the genetic architecture underlying a trait. In particular, the distribution of quantitative trait locus (QTL) effect sizes and the distribution of mutational effects together provide information regarding the history of selection. Despite the increasing availability of QTL and mutation accumulation data, such data have not yet been effectively exploited for this purpose. We present a model of the evolution of QTL and employ it to formulate a test for historical selection. To provide a baseline for neutral evolution of the trait, we estimate the distribution of mutational effects from mutation accumulation experiments. We then apply a maximum-likelihood-based method of inference to estimate the range of selection strengths under which such a distribution of mutations could generate the observed QTL. Our test thus represents the first integration of population genetic theory and QTL data to measure the historical influence of selection.
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Exploring Connectivity in Sequence Space of Functional RNA
NASA Technical Reports Server (NTRS)
Wei, Chenyu; Pohorille, Andrzej; Popovic, Milena; Ditzler, Mark
2017-01-01
Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.
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Diversifying mechanisms in the on-farm evolution of crop mixtures.
Thomas, Mathieu; Thépot, Stéphanie; Galic, Nathalie; Jouanne-Pin, Sophie; Remoué, Carine; Goldringer, Isabelle
2015-06-01
While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio-genetic model is an original experimental evolution design referred to as on-farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environments. We studied a French farmer-led initiative where a mixture of four wheat landraces called 'Mélange de Touselles' (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty-one space-time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a 'common-garden' experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within-variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes. © 2015 John Wiley & Sons Ltd.
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Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution.
Peabody, George; Winkler, James; Fountain, Weston; Castro, David A; Leiva-Aravena, Enzo; Kao, Katy C
2016-11-15
Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution
Peabody, George; Winkler, James; Fountain, Weston; Castro, David A.; Leiva-Aravena, Enzo
2016-01-01
ABSTRACT Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. PMID:27613685
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Radio Astronomy at the Centre for High Performance Computing in South Africa
NASA Astrophysics Data System (ADS)
Catherine Cress; UWC Simulation Team
2014-04-01
I will present results on galaxy evolution and cosmology which we obtained using the supercomputing facilities at the CHPC. These include cosmological-scale N-body simulations modelling neutral hydrogen as well as the study of the clustering of radio galaxies to probe the relationship between dark and luminous matter in the universe. I will also discuss the various roles that the CHPC is playing in Astronomy in SA, including the provision of HPC for a variety of Astronomical applications, the provision of storage for radio data, our educational programs and our participation in planning for the SKA.
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SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY
WILLIAMS, PAUL D.; POLLOCK, DAVID D.
2010-01-01
Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population. PMID:25473139
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Selective Advantage of Recombination in Evolving Protein Populations:. a Lattice Model Study
NASA Astrophysics Data System (ADS)
Williams, Paul D.; Pollock, David D.; Goldstein, Richard A.
Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.
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Comparison of model predictions for the composition of the ionosphere of Mars to MAVEN NGIMS data
NASA Astrophysics Data System (ADS)
Withers, Paul; Vogt, Marissa; Mayyasi, Majd; Mahaffy, Paul; Benna, Mehdi; Elrod, Meredith; Bougher, Stephen; Dong, Chuanfei; Chaufray, Jean-Yves; Ma, Yingjuan; Jakosky, Bruce
2015-11-01
Prior to the arrival of the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft at Mars, the only available measurements of the composition of the planet's ionosphere were those acquired by the two Viking Landers during their atmospheric entries. Many numerical models of the composition of the ionosphere of Mars have been developed, but these have only been validated for species, altitudes, and conditions for which Viking data exist. Here we compare the ionospheric composition and structure predicted by 10 ionospheric models at solar zenith angles of 45-60° against ion density measurements acquired by the MAVEN Neutral Gas and Ion Mass Spectrometer (NGIMS). The most successful models included three-dimensional plasma transport driven by interactions with the surrounding space environment but had relatively simple ionospheric chemistry.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Martínez-Sykora, Juan; Pontieu, Bart De; Hansteen, Viggo H.
2017-09-20
We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion–neutral interaction effects using the generalized Ohm’s law, i.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolarmore » diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.« less
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NASA Astrophysics Data System (ADS)
Martínez-Sykora, Juan; De Pontieu, Bart; Carlsson, Mats; Hansteen, Viggo H.; Nóbrega-Siverio, Daniel; Gudiksen, Boris V.
2017-09-01
We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion-neutral interaction effects using the generalized Ohm’s law, I.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolar diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.
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What Is the "One Thing" You Should Know before Teaching about Evolution?
ERIC Educational Resources Information Center
Billingsley, Berry
2014-01-01
In practice, in the classroom, teachers are still faced with the issue of what to say to children if they believe that evolution conflicts with their own or other people's religious faith. When asked how they plan to respond, most teacher trainees and teachers respond that they will be a neutral chair and try to give children a balanced view.…
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Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.
Lv, Jie; Havlak, Paul; Putnam, Nicholas H
2011-10-05
Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c. A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
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Evolution of vector magnetic fields and the August 27 1990 X-3 flare
NASA Technical Reports Server (NTRS)
Wang, Haimin
1992-01-01
Vector magnetic fields in an active region of the sun are studied by means of continuous observations of magnetic-field evolution emphasizing magnetic shear build-up. The vector magnetograms are shown to measure magnetic fields correctly based on concurrent observations and a comparison of the transverse field with the H alpha fibril structure. The morphology and velocity pattern are examined, and these data and the shear build-up suggest that the active region's two major footprints are separated by a region with flows, new flux emergence, and several neutral lines. The magnetic shear appears to be caused by the collision and shear motion of two poles of opposite polarities. The transverse field is shown to turn from potential to sheared during the process of flux cancellation, and this effect can be incorporated into existing models of magnetic flux cancellation.
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Antigenic Drift Defines a New D4 Subgenotype of Measles Virus.
Muñoz-Alía, Miguel Ángel; Muller, Claude P; Russell, Stephen J
2017-06-01
The measles virus hemagglutinin (MeV-H) protein is the main target of protective neutralizing antibodies. Using a panel of monoclonal antibodies (MAbs) that recognize known major antigenic sites in MeV-H, we identified a D4 genotype variant that escapes neutralization by MAbs targeting the neutralizing epitope (NE) antigenic site. By site-directed mutagenesis, L249P was identified as the critical mutation disrupting the NE in this genotype D4 variant. Forty-two available D4 genotype gene sequences were subsequently analyzed and divided into 2 groups according to the presence or absence of the L249P MeV-H mutation. Further analysis of the MeV-N gene sequences of these 2 groups confirmed that they represent clearly definable, sequence-divergent D4 subgenotypes, which we named subgenotypes D4.1 and D4.2. The subgenotype D4.1 MeVs were isolated predominantly in Kenya and Ethiopia, whereas the MAb-resistant subgenotype D4.2 MeVs were isolated predominantly in France and Great Britain, countries with higher vaccine coverage rates. Interestingly, D4.2 subgenotype viruses showed a trend toward diminished susceptibility to neutralization by human sera pooled from approximately 60 to 80 North American donors. Escape from MAb neutralization may be a powerful epidemiological surveillance tool to monitor the evolution of new MeV subgenotypes. IMPORTANCE Measles virus is a paradigmatic RNA virus, as the antigenic composition of the vaccination has not needed to be updated since its discovery. The vaccine confers protection by inducing neutralizing antibodies that interfere with the function of the hemagglutinin protein. Viral strains are indistinguishable serologically, although characteristic nucleotide sequences differentiate 24 genotypes. In this work, we describe a distant evolutionary branch within genotype D4. Designated subgenotype D4.2, this virus is distinguishable by neutralization with vaccine-induced monoclonal antibodies that target the neutralizing epitope (NE). The subgenotype D4.2 viruses have a higher predominance in countries with intermediary levels of vaccine coverage. Our studies demonstrate that subgenotype D4.2 lacks epitopes associated with half of the known antigenic sites, which significantly impacts our understanding of measles virus evolution. Copyright © 2017 American Society for Microbiology.
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Antigenic Drift Defines a New D4 Subgenotype of Measles Virus
Muller, Claude P.
2017-01-01
ABSTRACT The measles virus hemagglutinin (MeV-H) protein is the main target of protective neutralizing antibodies. Using a panel of monoclonal antibodies (MAbs) that recognize known major antigenic sites in MeV-H, we identified a D4 genotype variant that escapes neutralization by MAbs targeting the neutralizing epitope (NE) antigenic site. By site-directed mutagenesis, L249P was identified as the critical mutation disrupting the NE in this genotype D4 variant. Forty-two available D4 genotype gene sequences were subsequently analyzed and divided into 2 groups according to the presence or absence of the L249P MeV-H mutation. Further analysis of the MeV-N gene sequences of these 2 groups confirmed that they represent clearly definable, sequence-divergent D4 subgenotypes, which we named subgenotypes D4.1 and D4.2. The subgenotype D4.1 MeVs were isolated predominantly in Kenya and Ethiopia, whereas the MAb-resistant subgenotype D4.2 MeVs were isolated predominantly in France and Great Britain, countries with higher vaccine coverage rates. Interestingly, D4.2 subgenotype viruses showed a trend toward diminished susceptibility to neutralization by human sera pooled from approximately 60 to 80 North American donors. Escape from MAb neutralization may be a powerful epidemiological surveillance tool to monitor the evolution of new MeV subgenotypes. IMPORTANCE Measles virus is a paradigmatic RNA virus, as the antigenic composition of the vaccination has not needed to be updated since its discovery. The vaccine confers protection by inducing neutralizing antibodies that interfere with the function of the hemagglutinin protein. Viral strains are indistinguishable serologically, although characteristic nucleotide sequences differentiate 24 genotypes. In this work, we describe a distant evolutionary branch within genotype D4. Designated subgenotype D4.2, this virus is distinguishable by neutralization with vaccine-induced monoclonal antibodies that target the neutralizing epitope (NE). The subgenotype D4.2 viruses have a higher predominance in countries with intermediary levels of vaccine coverage. Our studies demonstrate that subgenotype D4.2 lacks epitopes associated with half of the known antigenic sites, which significantly impacts our understanding of measles virus evolution. PMID:28356529
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Effects of MHD instabilities on neutral beam current drive
NASA Astrophysics Data System (ADS)
Podestà, M.; Gorelenkova, M.; Darrow, D. S.; Fredrickson, E. D.; Gerhardt, S. P.; White, R. B.
2015-05-01
Neutral beam injection (NBI) is one of the primary tools foreseen for heating, current drive (CD) and q-profile control in future fusion reactors such as ITER and a Fusion Nuclear Science Facility. However, fast ions from NBI may also provide the drive for energetic particle-driven instabilities (e.g. Alfvénic modes (AEs)), which in turn redistribute fast ions in both space and energy, thus hampering the control capabilities and overall efficiency of NB-driven current. Based on experiments on the NSTX tokamak (M. Ono et al 2000 Nucl. Fusion 40 557), the effects of AEs and other low-frequency magneto-hydrodynamic instabilities on NB-CD efficiency are investigated. A new fast ion transport model, which accounts for particle transport in phase space as required for resonant AE perturbations, is utilized to obtain consistent simulations of NB-CD through the tokamak transport code TRANSP. It is found that instabilities do indeed reduce the NB-driven current density over most of the plasma radius by up to ∼50%. Moreover, the details of the current profile evolution are sensitive to the specific model used to mimic the interaction between NB ions and instabilities. Implications for fast ion transport modeling in integrated tokamak simulations are briefly discussed.
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NASA Astrophysics Data System (ADS)
Clark, G.; Paranicas, C.; Santos-Costa, D.; Livi, S.; Krupp, N.; Mitchell, D. G.; Roussos, E.; Tseng, W.-L.
2014-12-01
We provide a global view of ~20 to 800 keV electron pitch angle distributions (PADs) close to Saturn's current sheet using observations from the Cassini MIMI/LEMMS instrument. Previous work indicated that the nature of pitch angle distributions in Saturn's inner to middle magnetosphere changes near the radial distance of 10RS. This work confirms the existence of a PAD transition region. Here we go further and develop a new technique to statistically quantify the spatial profile of butterfly PADs as well as present new spatial trends on the isotropic PAD. Additionally, we perform a case study analysis and show the PADs exhibit strong energy dependent features throughout this transition region. We also present a diffusion theory model based on adiabatic transport, Coulomb interactions with Saturn's neutral gas torus, and an energy dependent radial diffusion coefficient. A data-model comparison reveals that adiabatic transport is the dominant transport mechanism between ~8 to 12RS, however interactions with Saturn's neutral gas torus become dominant inside ~7RS and govern the flux level of ~20 to 800 keV electrons. We have also found that field-aligned fluxes were not well reproduced by our modeling approach. We suggest that wave-particle interactions and/or a polar source of the energetic particles needs further investigation.
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Effects of MHD instabilities on neutral beam current drive
Podestà, M.; Gorelenkova, M.; Darrow, D. S.; ...
2015-04-17
One of the primary tools foreseen for heating, current drive (CD) and q-profile control in future fusion reactors such as ITER and a Fusion Nuclear Science Facility is the neutral beam injection (NBI). However, fast ions from NBI may also provide the drive for energetic particle-driven instabilities (e.g. Alfvénic modes (AEs)), which in turn redistribute fast ions in both space and energy, thus hampering the control capabilities and overall efficiency of NB-driven current. Based on experiments on the NSTX tokamak (M. Ono et al 2000 Nucl. Fusion 40 557), the effects of AEs and other low-frequency magneto-hydrodynamic instabilities on NB-CDmore » efficiency are investigated. When looking at the new fast ion transport model, which accounts for particle transport in phase space as required for resonant AE perturbations, is utilized to obtain consistent simulations of NB-CD through the tokamak transport code TRANSP. It is found that instabilities do indeed reduce the NB-driven current density over most of the plasma radius by up to ~50%. Moreover, the details of the current profile evolution are sensitive to the specific model used to mimic the interaction between NB ions and instabilities. Finally, implications for fast ion transport modeling in integrated tokamak simulations are briefly discussed.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Horsten, N., E-mail: niels.horsten@kuleuven.be; Baelmans, M.; Dekeyser, W.
2016-01-15
We derive fluid neutral approximations for a simplified 1D edge plasma model, suitable to study the neutral behavior close to the target of a nuclear fusion divertor, and compare its solutions to the solution of the corresponding kinetic Boltzmann equation. The plasma is considered as a fixed background extracted from a detached 2D simulation. We show that the Maxwellian equilibrium distribution is already obtained very close to the target, justifying the use of a fluid approximation. We compare three fluid neutral models: (i) a diffusion model; (ii) a pressure-diffusion model (i.e., a combination of a continuity and momentum equation) assumingmore » equal neutral and ion temperatures; and (iii) the pressure-diffusion model coupled to a neutral energy equation taking into account temperature differences between neutrals and ions. Partial reflection of neutrals reaching the boundaries is included in both the kinetic and fluid models. We propose two methods to obtain an incident neutral flux boundary condition for the fluid models: one based on a diffusion approximation and the other assuming a truncated Chapman-Enskog distribution. The pressure-diffusion model predicts the plasma sources very well. The diffusion boundary condition gives slightly better results overall. Although including an energy equation still improves the results, the assumption of equal ion and neutral temperature already gives a very good approximation.« less
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Evolution of the central safety factor during stabilized sawtooth instabilities at KSTAR
NASA Astrophysics Data System (ADS)
Messmer, M. C. C.; Ko, J.; Chung, J.; Woo, M. H.; Lee, K.-D.; Jaspers, R. J. E.
2018-01-01
A motional Stark effect (MSE) diagnostic has recently been installed in the KSTAR tokamak. A difficulty faced at KSTAR and common to other MSE diagnostics is calibration of the system for absolute measurements. In this report we present our novel calibration routine and discuss first results, evaluating the evolution of the the central safety factor during sawtooth instabilities. The calibration scheme ensures that the bandpass filters typically used in MSE systems are aligned correctly and identifies and removes systematic offsets present in the measurement. This is verified by comparing the reconstructed safety factor profile against various discharges where the locations of rational q surfaces have been obtained from MHD markers. The calibration is applied to analyse the evolution of q 0 in a shot where the sawteeth are stabilized by neutral beam injection. Within the analysed sawtooth periods q 0 drops below unity during the quiescent phase and relaxes close to or slightly above unity at the sawtooth crash. This finding is in line with the classical Kadomtsev model of full magnetic reconnection and earlier findings at JET.
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Implementation of a plasma-neutral model in NIMROD
NASA Astrophysics Data System (ADS)
Taheri, S.; Shumlak, U.; King, J. R.
2016-10-01
Interaction between plasma fluid and neutral species is of great importance in the edge region of magnetically confined fusion plasmas. The presence of neutrals can have beneficial effects such as fueling burning plasmas and quenching the disruptions in tokamaks, as well as deleterious effects like depositing high energy particles on the vessel wall. The behavior of edge plasmas in magnetically confined systems has been investigated using computational approaches that utilize the fluid description for the plasma and Monte Carlo transport for neutrals. In this research a reacting plasma-neutral model is implemented in NIMROD to study the interaction between plasma and neutral fluids. This model, developed by E. T. Meier and U. Shumlak, combines a single-fluid magnetohydrodynamic (MHD) plasma model with a gas dynamic neutral fluid model which accounts for electron-impact ionization, radiative recombination, and resonant charge exchange. Incorporating this model into NIMROD allows the study of the interaction between neutrals and plasma in a variety of plasma science problems. An accelerated plasma moving through a neutral gas background in a coaxial electrode configuration is modeled, and the results are compared with previous calculations from the HiFi code.
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Qiu, Chao; Huang, Yang; Wang, Qian; Tian, Di; Zhang, Wanju; Hu, Yunwen; Yuan, Zhenghong; Zhang, Xiaoyan; Xu, Jianqing
2012-01-01
A mass vaccination has been implemented to prevent the spread of 2009 pandemic influenza virus in China. Highly limited information is available on whether this vaccine induces cross-reactive neutralization antibodies against other subtypes of influenza viruses. We employed pseudovirus-based assays to analyze heterosubtypic neutralization responses in serum samples of 23 recipients of 2009 pandemic influenza vaccine. One dose of pandemic vaccine not only stimulated good neutralization antibodies against cognate influenza virus 2009 influenza A (H1N1), but also raised broad cross-reactive neutralization activities against seasonal H3N2 and highly pathogenic avian influenza virus H5N1 and lesser to H2N2. The cross-reactive neutralization activities were completely abolished after the removal of immunoglobin G (IgG). In contrast, H1N1 vaccination alone in influenza-naive mice elicited only vigorous homologous neutralizing activities but not cross-reactive neutralization activities. Our data suggest that the cross-reactive neutralization epitopes do exist in this vaccine and could elicit significant cross-reactive neutralizing IgG antibodies in the presence of preexisting responses. The exposure to H1N1 vaccine is likely to modify the hierarchical order of preexisting immune responses to influenza viruses. These findings provide insights into the evolution of human immunity to influenza viruses after experiencing multiple influenza virus infections and vaccinations.
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Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R
2014-01-01
Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950
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Surname distribution in population genetics and in statistical physics.
Rossi, Paolo
2013-12-01
Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents. Copyright © 2013 Elsevier B.V. All rights reserved.
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Nuclear Neutrino Spectra in Late Stellar Evolution
NASA Astrophysics Data System (ADS)
Misch, G. Wendell; Sun, Yang; Fuller, George
2018-05-01
Neutrinos are the principle carriers of energy in massive stars, beginning from core carbon burning and continuing through core collapse and after the core bounce. In fact, it may be possible to detect neutrinos from nearby pre-supernova stars. Therefore, it is of great interest to understand the neutrino energy spectra from these stars. Leading up to core collapse, beginning around core silicon burning, nuclei become dominant producers of neutrinos, particularly at high neutrino energy, so a systematic study of nuclear neutrino spectra is desirable. We have done such a study, and we present our sd-shell model calculations of nuclear neutrino energy spectra for nuclei in the mass number range A = 21 - 35. Our study includes neutrinos produced by charged lepton capture, charged lepton emission, and neutral current nuclear deexcitation. Previous authors have tabulated the rates of charged current nuclear weak interactions in astrophysical conditions, but the present work expands on this not only by providing neutrino energy spectra, but also by including the heretofore untabulated neutral current de-excitation neutrino pairs.
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Surname distribution in population genetics and in statistical physics
NASA Astrophysics Data System (ADS)
Rossi, Paolo
2013-12-01
Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents.
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Visco-instability of shear viscoelastic collisional dusty plasma systems
NASA Astrophysics Data System (ADS)
Mahdavi-Gharavi, M.; Hajisharifi, K.; Mehidan, H.
2018-04-01
In this paper, the stability of Newtonian and non-Newtonian viscoelastic collisional shear-velocity dusty plasmas is studied, using the framework of a generalized hydrodynamic (GH) model. Motivated by Banerjee et al.'s work (Banerjee et al., New J. Phys., vol. 12 (12), 2010, p. 123031), employing linear perturbation theory as well as the local approximation method in the inhomogeneous direction, the dispersion relations of the Fourier modes are obtained for Newtonian and non-Newtonian dusty plasma systems in the presence of a dust-neutral friction term. The analysis of the obtained dispersion relation in the non-Newtonian case shows that the inhomogeneous viscosity force depending on the velocity shear profile can be the genesis of a free energy source which leads the shear system to be unstable. Study of the dust-neutral friction effect on the instability of the considered systems using numerical analysis of the dispersion relation in the Newtonian case demonstrates that the maximum growth rate decreases considerably by increasing the collision frequency in the hydrodynamic regime, while this reduction can be neglected in the kinetic regime. Results show a more significant stabilization role of the dust-neutral friction term in the non-Newtonian cases, through decreasing the maximum growth rate at any fixed wavenumber and construction of the instable wavenumber region. The results of the present investigation will greatly contribute to study of the time evolution of viscoelastic laboratory environments with externally applied shear; where in these experiments the dust-neutral friction process can play a considerable role.
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Lyman-α emitters gone missing: the different evolution of the bright and faint populations
NASA Astrophysics Data System (ADS)
Weinberger, Lewis H.; Kulkarni, Girish; Haehnelt, Martin G.; Choudhury, Tirthankar Roy
2018-06-01
We model the transmission of the Lyman-α line through the circum- and intergalactic media around dark matter haloes expected to host Lyman-alpha emitters (LAEs) at z ≥ 5.7, using the high-dynamic-range Sherwood simulations. We find very different CGM environments around more massive haloes (˜1011M⊙) compared to less massive haloes (˜109M⊙) at these redshifts, which can contribute to a different evolution of the Lyα transmission from LAEs within these haloes. Additionally we confirm that part of the differential evolution could result from bright LAEs being more likely to reside in larger ionized regions. We conclude that a combination of the CGM environment and the IGM ionization structure is likely to be responsible for the differential evolution of the bright and faint ends of the LAE luminosity function at z ≥ 6. More generally, we confirm the suggestion that the self-shielded neutral gas in the outskirts of the host halo can strongly attenuate the Lyα emission from high redshift galaxies. We find that this has a stronger effect on the more massive haloes hosting brighter LAEs. The faint-end of the LAE luminosity function is thus a more reliable probe of the average ionization state of the IGM. Comparing our model for LAEs with a range of observational data we find that the favoured reionization histories are our previously advocated `Late' and `Very Late' reionization histories, in which reionization finishes rather rapidly at around z ≃ 6.
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Investigating the Martian Ionospheric Conductivity Using MAVEN Key Parameter Data
NASA Astrophysics Data System (ADS)
Aleryani, O.; Raftery, C. L.; Fillingim, M. O.; Fogle, A. L.; Dunn, P.; McFadden, J. P.; Connerney, J. E. P.; Mahaffy, P. R.; Ergun, R. E.; Andersson, L.
2015-12-01
Since the Viking orbiters and landers in 1976, the Martian atmospheric composition has scarcely been investigated. New data from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, launched in 2013, allows for a thorough study of the electrically conductive nature of the Martian ionosphere. Determinations of the electrical conductivity will be made using in-situ atmospheric and ionospheric measurements, rather than scientific models for the first time. The objective of this project is to calculate the conductivity of the Martian atmosphere, whenever possible, throughout the trajectory of the MAVEN spacecraft. MAVEN instrumentation used includes the Neutral Gas and Ion Mass Spectrometer (NGIMS) for neutral species density, the Suprathermal and Thermal Ion Compositions (STATIC) for ion composition, temperature and density, the Magnetometer (MAG) for the magnetic field strength and the Langmuir Probe and Waves (LPW) for electron temperature and density. MAVEN key parameter data are used for these calculations. We compare our results with previous, model-based estimates of the conductivity. These results will allow us to quantify the flow of atmospheric electric currents which can be analyzed further for a deeper understanding of the Martian ionospheric electrodynamics, bringing us closer to understanding the mystery of the loss of the Martian atmosphere.
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Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.
Kronholm, Ilkka; Picó, F Xavier; Alonso-Blanco, Carlos; Goudet, Jérôme; de Meaux, Juliette
2012-07-01
Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation. © 2012 The Author(s).
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A Particle-In-Cell Gun Code for Surface-Converter H- Ion Source Modeling
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chacon-Golcher, Edwin; Bowers, Kevin J.
2007-08-10
We present the current status of a particle-in-cell with Monte Carlo collisions (PIC-MCC) gun code under development at Los Alamos for the study of surface-converter H- ion sources. The program preserves a first-principles approach to a significant extent and simulates the production processes without ad hoc models within the plasma region. Some of its features include: solution of arbitrary electrostatic and magnetostatic fields in an axisymmetric (r,z) geometry to describe the self-consistent time evolution of a plasma; simulation of a multi-species (e-,H+,H{sub 2}{sup +},H{sub 3}{sup +},H-) plasma discharge from a neutral hydrogen gas and filament-originated seed electrons; full 2-dimensional (r,z)more » 3-velocity (vr,vz,v{phi}) dynamics for all species with exact conservation of the canonical angular momentum p{phi}; detailed collision physics between charged particles and neutrals and the ability to represent multiple smooth (not stair-stepped) electrodes of arbitrary shape and voltage whose surfaces may be secondary-particle emitters (H- and e-). The status of this development is discussed in terms of its physics content and current implementation details.« less
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m=1 diocotron mode damping in the Electron Diffusion Gauge (EDG) experiment
NASA Astrophysics Data System (ADS)
Paul, Stephen F.; Morrison, Kyle A.; Davidson, Ronald C.; Jenkins, Thomas G.
2002-01-01
The evolution of the amplitude of the m=1 diocotron mode is used to measure the background neutral pressure in the Electron Diffusion Gauge (EDG), a Malmberg-Penning trap. Below 5×10-8 Torr, the dependence on pressure scales as P1/4, and is sensitive to pressure changes as small as ΔP=5×10-11 Torr. Previous studies on the EDG showed that the diocotron mode is more strongly damped at higher neutral pressures. Both the diocotron mode damping rate and the plasma expansion rate depend similarly on experimental parameters, i.e., conditions which favor expansion also favor suppression of the diocotron mode. The sensitivity of the mode evolution is examined as a function of the resistive growth driving conditions, which are controlled by the amount of wall resistance connected to the trap.
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Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus
2014-11-01
The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
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Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus
2014-01-01
The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. PMID:25244680
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Probing the Martian Exosphere and Neutral Escape Using Pickup Ions Measured by MAVEN
NASA Astrophysics Data System (ADS)
Rahmati, A.; Larson, D. E.; Cravens, T.; Halekas, J. S.; Lillis, R. J.; McFadden, J. P.; Mitchell, D. L.; Thiemann, E.; Connerney, J. E. P.; Dunn, P.; DiBraccio, G. A.; Espley, J. R.; Eparvier, F. G.; Jakosky, B. M.
2016-12-01
Soon after the MAVEN (Mars Atmosphere and Volatile EvolutioN) spacecraft started orbiting Mars in September 2014, the SEP (Solar Energetic Particle), SWIA (Solar Wind Ion Analyzer), and STATIC (Supra-Thermal and Thermal Ion Composition) instruments onboard the spacecraft started detecting planetary pickup ions. SEP can measure energetic (>50 keV) oxygen pickup ions, the source of which is the extended hot oxygen exosphere of Mars. Model results show that these pickup ions originate from tens of Martian radii upstream of Mars and are energized by the solar wind motional electric field as they gyrate back towards Mars. SEP is blind to pickup hydrogen, as the low energy threshold for detection of hydrogen in SEP is 20 keV; well above the maximum pickup hydrogen energy, which is four times the solar wind proton energy. SWIA and STATIC, on the other hand, can detect both pickup oxygen and pickup hydrogen with energies below 30 keV and created closer to Mars. During the times when MAVEN is outside the Martian bow shock and in the upstream undisturbed solar wind, the solar wind velocity measured by SWIA and the solar wind (or interplanetary) magnetic field measured by the MAG (magnetometer) instrument can be used to model pickup oxygen and hydrogen fluxes near Mars. Solar wind flux measurements of the SWIA instrument are used in calculating charge-exchange frequencies, and data from the EUVM (Extreme Ultraviolet Monitor) and SWEA (Solar Wind Electron Analyzer) instruments are also used in calculating photo-ionization and electron impact frequencies of neutral species in the Martian exosphere. By comparing SEP, SWIA, and STATIC measured pickup ion fluxes with model results, the Martian thermal hydrogen and hot oxygen neutral densities can be probed outside the bow shock, which would place constraints on estimates of oxygen and hydrogen neutral escape rates. We will present model-data comparisons of pickup ions measured outside the Martian bow shock. Our analysis reveals an order of magnitude density change with Mars season in the hydrogen exosphere, whereas the hot oxygen exosphere densities vary less than a factor of 2.
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A Model of Titan-like Chemistry to Connect Experiments and Cassini Observations
NASA Astrophysics Data System (ADS)
Raymond, Alexander W.; Sciamma-O’Brien, Ella; Salama, Farid; Mazur, Eric
2018-02-01
A numerical model is presented for interpreting the chemical pathways that lead to the experimental mass spectra acquired in the Titan Haze Simulation (THS) laboratory experiments and for comparing the electron density and temperature of the THS plasma to observations made at Titan by the Cassini spacecraft. The THS plasma is a pulsed glow-discharge experiment designed to simulate the reaction of N2/CH4-dominated gas in Titan's upper atmosphere. The transient, one-dimensional model of THS chemistry tracks the evolution of more than 120 species in the direction of the plasma flow. As the minor species C2H2 and C2H4 are added to the N2/CH4-based mixture, the model correctly predicts the emergence of reaction products with up to five carbon atoms in relative abundances that agree well with measured mass spectra. Chemical growth in Titan's upper atmosphere transpires through ion–neutral and neutral–neutral chemistry, and the main reactions involving a series of known atmospheric species are retrieved from the calculation. The model indicates that the electron density and chemistry are steady during more than 99% of the 300 μs long discharge pulse. The model also suggests that the THS ionization fraction and electron temperature are comparable to those measured in Titan's upper atmosphere. These findings reaffirm that the THS plasma is a controlled analog environment for studying the first and intermediate steps of chemistry in Titan's upper atmosphere.
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Self-consistent discharge growing model of helicon plasma
NASA Astrophysics Data System (ADS)
Isayama, Shogo; Hada, Tohru; Shinohara, Shunjiro; Tanikawa, Takao
2015-11-01
Helicon plasma is a high-density and low-temperature plasma generated by the electromagnetic (Helicon) wave excited in the plasma. It is thought to be useful for various applications including electric thrusters. Physics of helicon plasma production involves such fundamental processes as the wave propagation (dispersion relation), collisional and non-collisional wave damping, plasma heating, ionization/recombination of neutral particles, and modification of the dispersion relation by newly ionized plasma. There remain a number of unsolved physical issues such as, how the Helicon and the TG modes influence the plasma density, electron temperature and their spatial profiles. While the Helicon mode is absorbed in the bulk plasma, the TG mode is mostly absorbed near the edge of the plasma. The local power deposition in the helicon plasma is mostly balanced by collisional loss. This local power balance can give rise to the inhomogeneous electron temperature profile that leads to time evolution of density profile and dispersion relation. In our study, we construct a self-consistent model of the discharge evolution that includes the wave excitation, electron heat transfer, and diffusion of charged particles.
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Klaus, Sebastian; Mendoza, José C E; Liew, Jia Huan; Plath, Martin; Meier, Rudolf; Yeo, Darren C J
2013-04-23
This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations of Sundathelphusa freshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722-271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits-just like constructive traits-is most likely driven by strong directional selection.
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Space weathering on near-Earth objects investigated by neutral-particle detection
NASA Astrophysics Data System (ADS)
Plainaki, C.; Milillo, A.; Orsini, S.; Mura, A.; De Angelis, E.; Di Lellis, A. M.; Dotto, E.; Livi, S.; Mangano, V.; Massetti, S.; Palumbo, M. E.
2009-03-01
The ion-sputtering (IS) process is active in many planetary environments in the solar system where plasma precipitates directly on the surface (for instance, Mercury, Moon and Europa). In particular, solar wind sputtering is one of the most important agents for the surface erosion of a near-Earth object (NEO), acting together with other surface release processes, such as photon stimulated desorption (PSD), thermal desorption (TD) and micrometeoroid impact vaporization (MIV). The energy distribution of the IS-released neutrals peaks at a few eVs and extends up to hundreds of eVs. Since all other release processes produce particles of lower energies, the presence of neutral atoms in the energy range above 10 eV and below a few keVs (sputtered high-energy atoms (SHEA)) identifies the IS process. SHEA easily escape from the NEO, due to NEO's extremely weak gravity. Detection and analysis of SHEA will give important information on surface-loss processes as well as on surface elemental composition. The investigation of the active release processes, as a function of the external conditions and the NEO surface properties, is crucial for obtaining a clear view of the body's present loss rate as well as for getting clues on its evolution, which depends significantly on space weather. In this work, an attempt to analyze processes that take place on the surface of these small airless bodies, as a result of their exposure to the space environment, has been realized. For this reason, a new space weathering model (space weathering on NEO-SPAWN) is presented. Moreover, an instrument concept of a neutral-particle analyzer specifically designed for the measurement of neutral density and the detection of SHEA from a NEO is proposed.
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Space weathering on near-Earth objects investigated by neutral-particle detection
NASA Astrophysics Data System (ADS)
Plainaki, C.; Milillo, A.; Orsini, S.; Mura, A.; de Angelis, E.; di Lellis, A. M.; Dotto, E.; Livi, S.; Mangano, V.; Palumbo, M. E.
2009-04-01
The ion-sputtering (IS) process is active in many planetary environments in the solar system where plasma precipitates directly on the surface (for instance, Mercury, Moon and Europa). In particular, solar wind sputtering is one of the most important agents for the surface erosion of a near-Earth object (NEO), acting together with other surface release processes, such as photon stimulated desorption (PSD), thermal desorption (TD) and micrometeoroid impact vaporization (MIV). The energy distribution of the IS-released neutrals peaks at a few eVs and extends up to hundreds of eVs. Since all other release processes produce particles of lower energies, the presence of neutral atoms in the energy range above 10 eV and below a few keVs (sputtered high-energy atoms (SHEA)) identifies the IS process. SHEA easily escape from the NEO, due to NEO's extremely weak gravity. Detection and analysis of SHEA will give important information on surface-loss processes as well as on surface elemental composition. The investigation of the active release processes, as a function of the external conditions and the NEO surface properties, is crucial for obtaining a clear view of the body's present loss rate as well as for getting clues on its evolution, which depends significantly on space weather. In this work, an attempt to analyze processes that take place on the surface of these small airless bodies, as a result of their exposure to the space environment, has been realized. For this reason, a new space weathering model (space weathering on NEO-SPAWN) is presented. Moreover, an instrument concept of a neutral-particle analyzer specifically designed for the measurement of neutral density and the detection of SHEA from a NEO is proposed.
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A numerical study of neutral-plasma interaction in magnetically confined plasmas
NASA Astrophysics Data System (ADS)
Taheri, S.; Shumlak, U.; King, J. R.
2017-10-01
Interactions between plasma and neutral species can have a large effect on the dynamic behavior of magnetically confined plasma devices, such as the edge region of tokamaks and the plasma formation of Z-pinches. The presence of neutrals can affect the stability of the pinch and change the dynamics of the pinch collapse, and they can lead to deposition of high energy particles on the first wall. However, plasma-neutral interactions can also have beneficial effects such as quenching the disruptions in tokamaks. In this research a reacting plasma-neutral model, which combines a magnetohydrodynamic (MHD) plasma model with a gas dynamic neutral fluid model, is used to study the interaction between plasma and neutral gas. Incorporating this model into NIMROD allows the study of electron-impact ionization, radiative recombination, and resonant charge-exchange in plasma-neutral systems. An accelerated plasma moving through a neutral gas background is modeled in both a parallel plate and a coaxial electrode configuration to explore the effect of neutral gas in pinch-like devices. This work is supported by a Grant from US DOE.
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NASA Technical Reports Server (NTRS)
Chakrabarti, A. C.; Deamer, D. W.; Miller, S. L. (Principal Investigator)
1994-01-01
The flux of amino acids and other nutrient solutes such as phosphate across lipid bilayers (liposomes) is 10(5) slower than facilitated inward transport across biological membranes. This suggest that primitive cells lacking highly evolved transport systems would have difficulty transporting sufficient nutrients for cell growth to occur. There are two possible ways by which early life may have overcome this difficulty: (1) The membranes of the earliest cellular life-forms may have been intrinsically more permeable to solutes; or (2) some transport mechanism may have been available to facilitate transbilayer movement of solutes essential for cell survival and growth prior to the evolution of membrane transport proteins. Translocation of neutral species represents one such mechanism. The neutral forms of amino acids modified by methylation (creating protonated weak bases) permeate membranes up to 10(10) times faster than charged forms. This increased permeability when coupled to a transmembrane pH gradient can result in significantly increased rates of net unidirectional transport. Such pH gradients can be generated in vesicles used to model protocells that preceded and were presumably ancestral to early forms of life. This transport mechanism may still play a role in some protein translocation processes (e.g. for certain signal sequences, toxins and thylakoid proteins) in vivo.
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2010-08-31
genital fluids HIV -1 infected cells are present in more substantial numbers than free virus, and the former may account for the majority of...Severe acquired immunodeficiency in male homosexuals, manifested by chronic perianal ulcerative herpes simplex lesions. N Engl J Med 1981 , 305:1439...1994,179:463-472. 59. Miller CJ: Localization of Simian immunodeficiency virus-infected cells in the genital tract of male and female Rhesus macaques. J
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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.
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Modeling the genealogy of a cultural trait.
Aguilar, Elliot; Ghirlanda, Stefano
2015-05-01
The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of individuals, a cultural common ancestor does not necessarily exist. We then introduce a related concept: the most recent unique ancestor (MRUA), i.e., the most recent single individual who is the earliest cultural ancestor of the sample. We show that, under neutral evolution, the time to the MRUA can be staggeringly larger than the time to MRCA in a single ancestor model, except when the average number of learning opportunities per individuals is small. Our results point out that the properties of cultural genealogies may be very different from those of genetic genealogies, with potential implications for reconstructing the histories of cultural traits. Copyright © 2014 Elsevier Inc. All rights reserved.
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Neutral Evolution of Multiple Quantitative Characters: A Genealogical Approach
Griswold, Cortland K.; Logsdon, Benjamin; Gomulkiewicz, Richard
2007-01-01
The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonuniformity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation. PMID:17339224
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NASA Technical Reports Server (NTRS)
Head, James W.; Wilson, Lionel
1992-01-01
The production of magma reservoirs and neutral buoyancy zones (NBZs) on Venus and the implications of their development for the formation and evolution of volcanic landforms are examined. The high atmospheric pressure on Venus reduces volatile exsolution and generally serves to inhibit the formation of NBZs and shallow magma reservoirs. For a range of common terrestrial magma-volatile contents, magma ascending and erupting near or below mean planetary radius (MPR) should not stall at shallow magma reservoirs; such eruptions are characterized by relatively high total volumes and effusion rates. For the same range of volatile contents at 2 km above MPR, about half of the cases result in the direct ascent of magma to the surface and half in the production of neutral buoyancy zones. NBZs and shallow magma reservoirs begin to appear as gas content increases and are nominally shallower on Venus than on earth. For a fixed volatile content, NBZs become deeper with increasing elevation: over the range of elevations treated in this study (-1 km to +4.4 km) depths differ by a factor of 2-4. Factors that may account for the low height of volcanoes on Venus are discussed.
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Evolution of Functional Diversification within Quasispecies
Colizzi, Enrico Sandro; Hogeweg, Paulien
2014-01-01
According to quasispecies theory, high mutation rates limit the amount of information genomes can store (Eigen’s Paradox), whereas genomes with higher degrees of neutrality may be selected even at the expenses of higher replication rates (the “survival of the flattest” effect). Introducing a complex genotype to phenotype map, such as RNA folding, epitomizes such effect because of the existence of neutral networks and their exploitation by evolution, affecting both population structure and genome composition. We reexamine these classical results in the light of an RNA-based system that can evolve its own ecology. Contrary to expectations, we find that quasispecies evolving at high mutation rates are steep and characterized by one master sequence. Importantly, the analysis of the system and the characterization of the evolved quasispecies reveal the emergence of functionalities as phenotypes of nonreplicating genotypes, whose presence is crucial for the overall viability and stability of the system. In other words, the master sequence codes for the information of the entire ecosystem, whereas the decoding happens, stochastically, through mutations. We show that this solution quickly outcompetes strategies based on genomes with a high degree of neutrality. In conclusion, individually coded but ecosystem-based diversity evolves and persists indefinitely close to the Information Threshold. PMID:25056399
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NASA Astrophysics Data System (ADS)
Liu, D.; Medley, S. S.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.
2014-10-01
A cloud of halo neutrals is created in the vicinity of beam footprint during the neutral beam injection and the halo neutral density can be comparable with beam neutral density. Proper modeling of halo neutrals is critical to correctly interpret neutral particle analyzers (NPA) and fast ion D-alpha (FIDA) signals since these signals strongly depend on local beam and halo neutral density. A 3D halo neutral model has been recently developed and implemented inside TRANSP code. The 3D halo neutral code uses a ``beam-in-a-box'' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce thermal halo neutrals that are tracked through successive halo neutral generations until an ionization event occurs or a descendant halo exits the box. A benchmark between 3D halo neural model in TRANSP and in FIDA/NPA synthetic diagnostic code FIDASIM is carried out. Detailed comparison of halo neutral density profiles from two codes will be shown. The NPA and FIDA simulations with and without 3D halos are applied to projections of plasma performance for the National Spherical Tours eXperiment-Upgrade (NSTX-U) and the effects of halo neutral density on NPA and FIDA signal amplitude and profile will be presented. Work supported by US DOE.
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Rodrigue, Nicolas; Lartillot, Nicolas
2017-01-01
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and non-synonymous substitutions. Another modeling approach, known as the mutation-selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some approaches allowing for heterogeneity in these patterns across codon sites. Under such a model, substitutions at a given position occur at the neutral or nearly neutral rate when they are synonymous, or when they correspond to replacements between amino acids of similar fitness; substitutions from high to low (low to high) fitness amino acids have comparatively low (high) rates. Here, we study the use of such a mutation-selection framework as a null model for the detection of adaptation. Following previous works in this direction, we include a deviation parameter that has the effect of capturing the surplus, or deficit, in non-synonymous rates, relative to what would be expected under a mutation-selection modeling framework that includes a Dirichlet process approach to account for across-codon-site variation in amino acid fitness profiles. We use simulations, along with a few real data sets, to study the behavior of the approach, and find it to have good power with a low false-positive rate. Altogether, we emphasize the potential of recent mutation-selection models in the detection of adaptation, calling for further model refinements as well as large-scale applications. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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3D Modeling of Antenna Driven Slow Waves Excited by Antennas Near the Plasma Edge
NASA Astrophysics Data System (ADS)
Smithe, David; Jenkins, Thomas
2016-10-01
Prior work with the 3D finite-difference time-domain (FDTD) plasma and sheath model used to model ICRF antennas in fusion plasmas has highlighted the possibility of slow wave excitation at the very low end of the SOL density range, and thus the prudent need for a slow-time evolution model to treat SOL density modifications due to the RF itself. At higher frequency, the DIII-D helicon antenna has much easier access to a parasitic slow wave excitation, and in this case the Faraday screen provides the dominant means of controlling the content of the launched mode, with antenna end-effects remaining a concern. In both cases, the danger is the same, with the slow-wave propagating into a lower-hybrid resonance layer a short distance ( cm) away from the antenna, which would parasitically absorb power, transferring energy to the SOL edge plasma, primarily through electron-neutral collisions. We will present 3D modeling of antennas at both ICRF and helicon frequencies. We've added a slow-time evolution capability for the SOL plasma density to include ponderomotive force driven rarefaction from the strong fields in the vicinity of the antenna, and show initial application to NSTX antenna geometry and plasma configurations. The model is based on a Scalar Ponderomotive Potential method, using self-consistently computed local field amplitudes from the 3D simulation.
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Evolution dynamics of a model for gene duplication under adaptive conflict
NASA Astrophysics Data System (ADS)
Ancliff, Mark; Park, Jeong-Man
2014-06-01
We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.
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Large Eddy Simulation of a Turbulent Jet
NASA Technical Reports Server (NTRS)
Webb, A. T.; Mansour, Nagi N.
2001-01-01
Here we present the results of a Large Eddy Simulation of a non-buoyant jet issuing from a circular orifice in a wall, and developing in neutral surroundings. The effects of the subgrid scales on the large eddies have been modeled with the dynamic large eddy simulation model applied to the fully 3D domain in spherical coordinates. The simulation captures the unsteady motions of the large-scales within the jet as well as the laminar motions in the entrainment region surrounding the jet. The computed time-averaged statistics (mean velocity, concentration, and turbulence parameters) compare well with laboratory data without invoking an empirical entrainment coefficient as employed by line integral models. The use of the large eddy simulation technique allows examination of unsteady and inhomogeneous features such as the evolution of eddies and the details of the entrainment process.
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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.
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An extended macro model accounting for acceleration changes with memory and numerical tests
NASA Astrophysics Data System (ADS)
Cheng, Rongjun; Ge, Hongxia; Sun, Fengxin; Wang, Jufeng
2018-09-01
Considering effect of acceleration changes with memory, an improved continuum model of traffic flow is proposed in this paper. By applying the linear stability theory, we derived the new model's linear stability condition. Through nonlinear analysis, the KdV-Burgers equation is derived to describe the propagating behavior of traffic density wave near the neutral stability line. Numerical simulation is carried out to study the extended traffic flow model, which explores how acceleration changes with memory affected each car's velocity, density and fuel consumption and exhaust emissions. Numerical results demonstrate that acceleration changes with memory have significant negative effect on dynamic characteristic of traffic flow. Furthermore, research results verify that the effect of acceleration changes with memory will deteriorate the stability of traffic flow and increase cars' total fuel consumptions and emissions during the whole evolution of small perturbation.
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Reyes-Velasco, Jacobo; Card, Daren C; Andrew, Audra L; Shaney, Kyle J; Adams, Richard H; Schield, Drew R; Casewell, Nicholas R; Mackessy, Stephen P; Castoe, Todd A
2015-01-01
Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, including information from tissue-specific patterns of gene expression. We identified the orthologs of snake venom genes in the python genome, and conducted detailed analysis of gene expression of these venom homologs to identify patterns that differ between snake venom gene families and all other genes. We found that venom gene homologs in the python are expressed in many different tissues outside of oral glands, which illustrates the pitfalls of using transcriptomic data alone to define "venom toxins." We hypothesize that the python may represent an ancestral state prior to major venom development, which is supported by our finding that the expansion of venom gene families is largely restricted to highly venomous caenophidian snakes. Therefore, the python provides insight into biases in which genes were recruited for snake venom systems. Python venom homologs are generally expressed at lower levels, have higher variance among tissues, and are expressed in fewer organs compared with all other python genes. We propose a model for the evolution of snake venoms in which venom genes are recruited preferentially from genes with particular expression profile characteristics, which facilitate a nearly neutral transition toward specialized venom system expression. © The Author 2014. 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.
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Yang, Zujun; Zhang, Tao; Bolshoy, Alexander; Beharav, Alexander; Nevo, Eviatar
2009-05-01
'Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum, the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the 'African' dry slope (AS) and the 'European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene (Dhn1) between the opposite slopes. We analysed 47 plants (genotypes), 4-10 individuals in each of seven stations (populations) in an area of 7000 m(2), for Dhn1 sequence diversity located in the 5' upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at 'Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force.
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Iron and Silicate Dust Growth in the Galactic Interstellar Medium: Clues from Element Depletions
NASA Astrophysics Data System (ADS)
Zhukovska, Svitlana; Henning, Thomas; Dobbs, Clare
2018-04-01
The interstellar abundances of refractory elements indicate a substantial depletion from the gas phase, which increases with gas density. Our recent model of dust evolution, based on hydrodynamic simulations of the life cycle of giant molecular clouds (GMCs), proves that the observed trend for [Sigas/H] is driven by a combination of dust growth by accretion in the cold diffuse interstellar medium (ISM) and efficient destruction by supernova (SN) shocks. With an analytic model of dust evolution, we demonstrate that even with optimistic assumptions for the dust input from stars and without destruction of grains by SNe it is impossible to match the observed [Sigas/H]–n H relation without growth in the ISM. We extend the framework developed in our previous work for silicates to include the evolution of iron grains and address a long-standing conundrum: “Where is the interstellar iron?” Much higher depletion of Fe in the warm neutral medium compared to Si is reproduced by the models, in which a large fraction of interstellar iron (70%) is locked as inclusions in silicate grains, where it is protected from efficient sputtering by SN shocks. The slope of the observed [Fegas/H]–n H relation is reproduced if the remaining depleted iron resides in a population of metallic iron nanoparticles with sizes in the range of 1–10 nm. Enhanced collision rates due to the Coulomb focusing are important for both silicate and iron dust models to match the slopes of the observed depletion–density relations and the magnitudes of depletion at high gas density.
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Effect of ion-neutral collisions on the evolution of kinetic Alfvén waves in plasmas
NASA Astrophysics Data System (ADS)
Goyal, R.; Sharma, R. P.
2018-03-01
This paper studies the effect of ion-neutral collisions on the propagation of kinetic Alfvén waves (KAWs) in inhomogeneous magnetized plasma. The inhomogeneity in the plasma imposed by background density in a direction transverse as well as parallel to the ambient magnetic field plays a vital role in the localization process. The mass loading of ions takes place due to their collisions with neutral fluid leading to the damping of the KAWs. Numerical analysis of linear KAWs in inhomogeneous magnetized plasma is done for a fixed finite frequency taking into consideration the ion-neutral collisions. There is a prominent effect of collisional damping on the wave localization, wave magnetic field, and frequency spectrum. A semi-analytical technique has been employed to study the magnetic field amplitude decay process and the effect of wave frequency in the range of ion cyclotron frequency on the propagation of waves leading to damping.
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Efficient simulation and likelihood methods for non-neutral multi-allele models.
Joyce, Paul; Genz, Alan; Buzbas, Erkan Ozge
2012-06-01
Throughout the 1980s, Simon Tavaré made numerous significant contributions to population genetics theory. As genetic data, in particular DNA sequence, became more readily available, a need to connect population-genetic models to data became the central issue. The seminal work of Griffiths and Tavaré (1994a , 1994b , 1994c) was among the first to develop a likelihood method to estimate the population-genetic parameters using full DNA sequences. Now, we are in the genomics era where methods need to scale-up to handle massive data sets, and Tavaré has led the way to new approaches. However, performing statistical inference under non-neutral models has proved elusive. In tribute to Simon Tavaré, we present an article in spirit of his work that provides a computationally tractable method for simulating and analyzing data under a class of non-neutral population-genetic models. Computational methods for approximating likelihood functions and generating samples under a class of allele-frequency based non-neutral parent-independent mutation models were proposed by Donnelly, Nordborg, and Joyce (DNJ) (Donnelly et al., 2001). DNJ (2001) simulated samples of allele frequencies from non-neutral models using neutral models as auxiliary distribution in a rejection algorithm. However, patterns of allele frequencies produced by neutral models are dissimilar to patterns of allele frequencies produced by non-neutral models, making the rejection method inefficient. For example, in some cases the methods in DNJ (2001) require 10(9) rejections before a sample from the non-neutral model is accepted. Our method simulates samples directly from the distribution of non-neutral models, making simulation methods a practical tool to study the behavior of the likelihood and to perform inference on the strength of selection.
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Dong, Xinran; Wang, Xiao; Zhang, Feng; Tian, Weidong
2016-01-01
Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes. PMID:27401230
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Magnetohydrodynamic Modeling of Coronal Evolution and Disruption
NASA Technical Reports Server (NTRS)
Linker, Jon
2002-01-01
Flux cancellation, defined observationally as the mutual disappearance of magnetic fields of opposite polarity at the neutral line separating them, has been found to occur frequently at the site of filaments (called prominences when observed on the limb of the Sun). During the second year of this project, we have studied theoretically the role that flux cancellation may play in prominence formation, prominence eruption, and the initiation of coronal mass ejections. This work has been in published in two papers: "Magnetic Field Topology in Prominences" by Lionello, Mikic, Linker, and Amari and "Flux Cancellation and Coronal Mass Ejections" by Linker, Mikic, Riley, Lionello, Amari, and Odstrcil.
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Demixing of polymers under nanoimprinting process
NASA Astrophysics Data System (ADS)
Wang, Zhen
Polymer blend has been an important area in polymer science for decades. The knowledge of polymer blend in bulk is well established and technologies based on it have created products ubiquitous in our daily life. More intriguing problem arises when the phase separation of a polymer blend occurs under physical confinement. In this thesis, we investigated the effect of interfacial interactions between constituent polymers and confinement environment on phase evolution. Specifically, morphologies of thin films of binary polymer blends were examined on chemically homogenous substrates (preferential surface, neutral surface), on chemical pattern, between two parallel rigid substrates, and under thermal embossing/step-and-flash nanoimprint lithography conditions. We found that preferential wetting of selective component dominates the phase evolution, which can be suppressed by the use of neutral surfaces or external pressure. By manipulating these factors, a wide range of unique non-equilibrium micro or nanostructures can thus be achieved.
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Ren, Xiang; Wang, Weiyi; Ge, Ruixiang; Hao, Shuai; Qu, Fengli; Du, Gu; Asiri, Abdullah M; Wei, Qin; Chen, Liang; Sun, Xuping
2017-08-08
It is highly attractive to develop efficient hydrogen-evolving electrocatalysts under neutral conditions. In this communication, we report an amorphous FeMoS 4 nanorod array on carbon cloth (FeMoS 4 NRA/CC) prepared by hydrothermal treatment of an FeOOH nanorod array on carbon cloth (FeOOH NRA/CC) in (NH 4 ) 2 MoS 4 solution. As a 3D electrode for hydrogen evolution electrocatalysis, this FeMoS 4 NRA/CC demonstrates superior catalytic activity and strong long-term electrochemical durability in 1.0 M phosphate buffered saline (pH: 7). It needs an overpotential of 204 mV to drive a geometrical current density of 10 mA cm -2 , which is 450 mV less than that for FeOOH NRA/CC. Density functional theory calculations suggest that FeMoS 4 has a more favourable hydrogen adsorption free energy than FeOOH.
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Blagoev, Krastan B.; Wilkerson, Julia; Burotto, Mauricio; Kim, Chul; Espinal-Domínguez, Edward; García-Alfonso, Pilar; Alimchandani, Meghna; Miettinen, Markku; Blanco-Codesido, Montserrat
2017-01-01
Emergence of tumor resistance to an anti-cancer therapy directed against a putative target raises several questions including: (1) do mutations in the target/pathway confer resistance? (2) Are these mutations pre-existing? (3) What is the relative fitness of cells with/without the mutation? We addressed these questions in patients with metastatic colorectal cancer (mCRC). We conducted an exhaustive review of published data to establish a median doubling time for CRCs and stained a cohort of CRCs to document mitotic indices. We analyzed published data and our own data to calculate rates of growth (g) and regression (d, decay) of tumors in patients with CRC correlating these results with the detection of circulating MT-KRAS DNA. Additionally we estimated mathematically the caloric burden of such tumors using data on mitotic and apoptotic indices. We conclude outgrowth of cells harboring intrinsic or acquired MT-KRAS cannot explain resistance to anti-EGFR (epidermal growth factor receptor) antibodies. Rates of tumor growth with panitumumab are unaffected by presence/absence of MT-KRAS. While MT-KRAS cells may be resistant to anti-EGFR antibodies, WT-KRAS cells also rapidly bypass this blockade suggesting inherent resistance mechanisms are responsible and a neutral evolution model is most appropriate. Using the above clinical data on tumor doubling times and mitotic and apoptotic indices we estimated the caloric intake required to support tumor growth and suggest it may explain in part cancer-associated cachexia. PMID:28981524
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Blagoev, Krastan B; Wilkerson, Julia; Burotto, Mauricio; Kim, Chul; Espinal-Domínguez, Edward; García-Alfonso, Pilar; Alimchandani, Meghna; Miettinen, Markku; Blanco-Codesido, Montserrat; Fojo, Tito
2017-01-01
Emergence of tumor resistance to an anti-cancer therapy directed against a putative target raises several questions including: (1) do mutations in the target/pathway confer resistance? (2) Are these mutations pre-existing? (3) What is the relative fitness of cells with/without the mutation? We addressed these questions in patients with metastatic colorectal cancer (mCRC). We conducted an exhaustive review of published data to establish a median doubling time for CRCs and stained a cohort of CRCs to document mitotic indices. We analyzed published data and our own data to calculate rates of growth (g) and regression (d, decay) of tumors in patients with CRC correlating these results with the detection of circulating MT-KRAS DNA. Additionally we estimated mathematically the caloric burden of such tumors using data on mitotic and apoptotic indices. We conclude outgrowth of cells harboring intrinsic or acquired MT-KRAS cannot explain resistance to anti-EGFR (epidermal growth factor receptor) antibodies. Rates of tumor growth with panitumumab are unaffected by presence/absence of MT-KRAS. While MT-KRAS cells may be resistant to anti-EGFR antibodies, WT-KRAS cells also rapidly bypass this blockade suggesting inherent resistance mechanisms are responsible and a neutral evolution model is most appropriate. Using the above clinical data on tumor doubling times and mitotic and apoptotic indices we estimated the caloric intake required to support tumor growth and suggest it may explain in part cancer-associated cachexia.
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Complex and changing patterns of natural selection explain the evolution of the human hip.
Grabowski, Mark; Roseman, Charles C
2015-08-01
Causal explanations for the dramatic changes that occurred during the evolution of the human hip focus largely on selection for bipedal function and locomotor efficiency. These hypotheses rest on two critical assumptions. The first-that these anatomical changes served functional roles in bipedalism-has been supported in numerous analyses showing how postcranial changes likely affected locomotion. The second-that morphological changes that did play functional roles in bipedalism were the result of selection for that behavior-has not been previously explored and represents a major gap in our understanding of hominin hip evolution. Here we use evolutionary quantitative genetic models to test the hypothesis that strong directional selection on many individual aspects of morphology was responsible for the large differences observed across a sample of fossil hominin hips spanning the Plio-Pleistocene. Our approach uses covariance among traits and the differences between relatively complete fossils to estimate the net selection pressures that drove the major transitions in hominin hip evolution. Our findings show a complex and changing pattern of natural selection drove hominin hip evolution, and that many, but not all, traits hypothesized to play functional roles in bipedalism evolved as a direct result of natural selection. While the rate of evolutionary change for all transitions explored here does not exceed the amount expected if evolution was occurring solely through neutral processes, it was far above rates of evolution for morphological traits in other mammalian groups. Given that stasis is the norm in the mammalian fossil record, our results suggest that large shifts in the adaptive landscape drove hominin evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Unveiling the Diffuse, Neutral Interstellar Medium: Absorption Spectroscopy of Galactic Hydrogen
NASA Astrophysics Data System (ADS)
Murray, Claire Elizabeth
The formation of stars and evolution of galaxies depends on the cycle of interstellar matter between supernova-expelled plasma and molecule-rich gas. At the center of this cycle is multiphase neutral hydrogen (HI), whose physical conditions provide key ingredients to theoretical models. However, constraints for HI properties require measurements of gas emission and absorption which have been severely limited by previous observational capabilities. In this thesis, I present the largest survey of Galactic HI absorption ever undertaken with the Karl G. Jansky Very Large Array (VLA). The survey, 21 cm Spectral Line Observations of Neutral Gas with the VLA (21-SPONGE), is a statistical study of HI in all phases using direct absorption measurements. Leveraging novel calibration techniques, I demonstrate the capability of the VLA to detect a significant sample of 21 cm absorption lines from warm, diffuse HI. To maximize observational sensitivity, I stack the 21-SPONGE spectra and detect a pervasive signature of the warm neutral medium in absorption. The inferred excitation (or spin) temperature is consistent with existing estimates, yet higher than predictions from theoretical models of collisional HI excitation. This suggests that radiative feedback via resonant scattering of Lyalpha photons, known as the Wouthuysen-Field effect, is influential with important implications for cosmological 21 cm observations. Next, I compare 21-SPONGE with synthetic HI spectra from 3D numerical simulations using a new, objective decomposition and radiative transfer tool. I quantify the recovery of HI structures and their properties by Gaussian-fitted 21 cm spectral lines for the first time. I find that 21 cm absorption line shapes are sensitive to simulated physics, and demonstrate that my analysis method is a powerful tool for diagnosing neutral ISM conditions. Finally, I compare properties inferred from synthetic spectra with "true" simulation results to construct a bias correction function for estimating HI properties. I apply this correction to the mass distribution of HI as a function of temperature from 21-SPONGE, and find a significant fraction of thermally unstable gas. This confirms that non-steady radiative and dynamical processes, such as turbulence and supernovae, have a strong influence on the thermodynamic state of the ISM.
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Neurovirulent Vaccine-Derived Polioviruses in Sewage from Highly Immune Populations
Shulman, Lester M.; Manor, Yossi; Sofer, Danit; Handsher, Rachel; Swartz, Tiberio; Delpeyroux, Francis; Mendelson, Ella
2006-01-01
Background Vaccine-derived polioviruses (VDPVs) have caused poliomyelitis outbreaks in communities with sub-optimal vaccination. Israeli environmental surveillance of sewage from populations with high (>95%) documented vaccine coverage of confirmed efficacy identified two separate evolutionary clusters of VDPVs: Group 1 (1998–2005, one system, population 1.6×106) and Group 2 (2006, 2 systems, populations 0.7×106 and 5×104). Principal Findings Molecular analyses support evolution of nine Group 1 VDPVs along five different lineages, starting from a common ancestral type 2 vaccine-derived Sabin-2/Sabin-1 recombinant strain, and independent evolution of three Group 2 VDPVs along one lineage starting from a different recombinant strain. The primary evidence for two independent origins was based on comparison of unique recombination fingerprints, the number and distribution of identical substitutions, and evolutionary rates. Geometric mean titers of neutralizing antibodies against Group 1 VDPVs were significantly lower than against vaccine strains in all age-group cohorts tested. All individuals had neutralizing titers >1∶8 against these VDPVs except 7% of the 20–50 year cohort. Group 1 VDPVs were highly neurovirulent in a transgenic mouse model. Intermediate levels of protective immunity against Group 2 VDPVs correlated with fewer (5.0+1.0) amino acid substitutions in neutralizing antigenic sites than in Group 1 VDPV's (12.1±1.5). Significance VDPVs that revert from live oral attenuated vaccines and reacquire characteristics of wild-type polioviruses not only threaten populations with poor immune coverage, but are also a potential source for re-introduction of poliomyelitis into highly immune populations through older individuals with waning immunity. The presence of two independently evolved groups of VDPVs in Israel and the growing number of reports of environmental VDPV elsewhere make it imperative to determine the global frequency of environmental VDPV. Our study underscores the importance of the environmental surveillance and the need to reconsider the global strategies for polio eradication and the proposed cessation of vaccination. PMID:17183700
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Cryptic genetic variation, evolution's hidden substrate
Paaby, Annalise B.; Rockman, Matthew V.
2016-01-01
Cryptic genetic variation is invisible under normal conditions but fuel for evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles in need of constant suppression. CGV emerges from both neutral and selective processes and it may inform how human populations respond to change. In experimental settings, CGV facilitates adaptation, but does it play an important role in the real world? We review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution. PMID:24614309
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NASA Astrophysics Data System (ADS)
Yamamoto, T.; Shibata, T.; Ohta, M.; Yasumoto, M.; Nishida, K.; Hatayama, A.; Mattei, S.; Lettry, J.; Sawada, K.; Fantz, U.
2014-02-01
To control the H0 atom production profile in the H- ion sources is one of the important issues for the efficient and uniform surface H- production. The purpose of this study is to construct a collisional radiative (CR) model to calculate the effective production rate of H0 atoms from H2 molecules in the model geometry of the radio-frequency (RF) H- ion source for Linac4 accelerator. In order to validate the CR model by comparison with the experimental results from the optical emission spectroscopy, it is also necessary for the model to calculate Balmer photon emission rate in the source. As a basic test of the model, the time evolutions of H0 production and the Balmer Hα photon emission rate are calculated for given electron energy distribution functions in the Linac4 RF H- ion source. Reasonable test results are obtained and basis for the detailed comparisons with experimental results have been established.
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Matthews, Thomas J; Whittaker, Robert J
2014-01-01
Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research. PMID:25360266
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Matthews, Thomas J; Whittaker, Robert J
2014-06-01
Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.
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Durable rechargeable zinc-air batteries with neutral electrolyte and manganese oxide catalyst
NASA Astrophysics Data System (ADS)
Sumboja, Afriyanti; Ge, Xiaoming; Zheng, Guangyuan; Goh, F. W. Thomas; Hor, T. S. Andy; Zong, Yun; Liu, Zhaolin
2016-11-01
Neutral chloride-based electrolyte and directly grown manganese oxide on carbon paper are used as the electrolyte and air cathode respectively for rechargeable Zn-air batteries. Oxygen reduction and oxygen evolution reactions on manganese oxide show dependence of activities on the pH of the electrolyte. Zn-air batteries with chloride-based electrolyte and manganese oxide catalyst exhibit satisfactory voltage profile (discharge and charge voltage of 1 and 2 V at 1 mA cm-2) and excellent cycling stability (≈90 days of continuous cycle test), which is attributed to the reduced carbon corrosion on the air cathode and decreased carbonation in neutral electrolyte. This work describes a robust electrolyte system that improves the cycle life of rechargeable Zn-air batteries.
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Spontaneously Broken Neutral Symmetry in an Ecological System
NASA Astrophysics Data System (ADS)
Borile, C.; Muñoz, M. A.; Azaele, S.; Banavar, Jayanth R.; Maritan, A.
2012-07-01
Spontaneous symmetry breaking plays a fundamental role in many areas of condensed matter and particle physics. A fundamental problem in ecology is the elucidation of the mechanisms responsible for biodiversity and stability. Neutral theory, which makes the simplifying assumption that all individuals (such as trees in a tropical forest)—regardless of the species they belong to—have the same prospect of reproduction, death, etc., yields gross patterns that are in accord with empirical data. We explore the possibility of birth and death rates that depend on the population density of species, treating the dynamics in a species-symmetric manner. We demonstrate that dynamical evolution can lead to a stationary state characterized simultaneously by both biodiversity and spontaneously broken neutral symmetry.
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Chapter A6. Section 6.6. Alkalinity and Acid Neutralizing Capacity
Rounds, Stewart A.; Wilde, Franceska D.
2002-01-01
Alkalinity (determined on a filtered sample) and Acid Neutralizing Capacity (ANC) (determined on a whole-water sample) are measures of the ability of a water sample to neutralize strong acid. Alkalinity and ANC provide information on the suitability of water for uses such as irrigation, determining the efficiency of wastewater processes, determining the presence of contamination by anthropogenic wastes, and maintaining ecosystem health. In addition, alkalinity is used to gain insights on the chemical evolution of an aqueous system. This section of the National Field Manual (NFM) describes the USGS field protocols for alkalinity/ANC determination using either the inflection-point or Gran function plot methods, including calculation of carbonate species, and provides guidance on equipment selection.
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Vincent, Bourret; Dionne, Mélanie; Kent, Matthew P; Lien, Sigbjørn; Bernatchez, Louis
2013-12-01
A growing number of studies are examining the factors driving historical and contemporary evolution in wild populations. By combining surveys of genomic variation with a comprehensive assessment of environmental parameters, such studies can increase our understanding of the genomic and geographical extent of local adaptation in wild populations. We used a large-scale landscape genomics approach to examine adaptive and neutral differentiation across 54 North American populations of Atlantic salmon representing seven previously defined genetically distinct regional groups. Over 5500 genome-wide single nucleotide polymorphisms were genotyped in 641 individuals and 28 bulk assays of 25 pooled individuals each. Genome scans, linkage map, and 49 environmental variables were combined to conduct an innovative landscape genomic analysis. Our results provide valuable insight into the links between environmental variation and both neutral and potentially adaptive genetic divergence. In particular, we identified markers potentially under divergent selection, as well as associated selective environmental factors and biological functions with the observed adaptive divergence. Multivariate landscape genetic analysis revealed strong associations of both genetic and environmental structures. We found an enrichment of growth-related functions among outlier markers. Climate (temperature-precipitation) and geological characteristics were significantly associated with both potentially adaptive and neutral genetic divergence and should be considered as candidate loci involved in adaptation at the regional scale in Atlantic salmon. Hence, this study significantly contributes to the improvement of tools used in modern conservation and management schemes of Atlantic salmon wild populations. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.
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NASA Astrophysics Data System (ADS)
Sutherland, D. A.; Hansen, C. J.; Jarboe, T. R.
2017-10-01
A self-consistent, two-fluid (plasma-neutral) dynamic neutral model has been implemented into the 3-D, Extended-MHD code PSI-Tet. A monatomic, hydrogenic neutral fluid reacts with a plasma fluid through elastic scattering collisions and three inelastic collision reactions: electron-impact ionization, radiative recombination, and resonant charge-exchange. Density, momentum, and energy are evolved for both the plasma and neutral species. The implemented plasma-neutral model in PSI-Tet is being used to simulate decaying spheromak configurations in the HIT-SI experimental geometry, which is being compare to two-photon absorption laser induced fluorescence measurements (TALIF) made on the HIT-SI3 experiment. TALIF is used to measure the absolute density and temperature of monatomic deuterium atoms. Neutral densities on the order of 1015 m-3 and neutral temperatures between 0.6-1.7 eV were measured towards the end of decay of spheromak configurations with initial toroidal currents between 10-12 kA. Validation results between TALIF measurements and PSI-Tet simulations with the implemented dynamic neutral model will be presented. Additionally, preliminary dynamic neutral simulations of the HIT-SI/HIT-SI3 spheromak plasmas sustained with inductive helicity injection will be presented. Lastly, potential benefits of an expansion of the two-fluid model into a multi-fluid model that includes multiple neutral species and tracking of charge states will be discussed.
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Femtosecond Multidimensional Imaging - Watching Chemistry from the Molecule's Point of View
NASA Astrophysics Data System (ADS)
Geßner, O.; Lee, A. M. D.; Chrysostom, E. t.-H.; Hayden, C. C.; Stolow, Albert
Using Femtosecond Multidimensional Imaging we disentangle the complex neutral dissociation mechanism of the NO dimer. We characterize all electronic configurations from start to finish and directly observe the evolution of intramolecular vibrational energy redistribution (IVR).
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The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection
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
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Dissociative recombination in interstellar clouds
NASA Technical Reports Server (NTRS)
Black, John H.; Van Dishoeck, Ewine F.
1989-01-01
Molecular ions play a significant role in the chemistry and evolution of interstellar molecular clouds, even though these regions are overwhelmingly neutral. The dissociative recombination (DR) process governs the abundances of many of these ions and of related neutral species. The gas-phase ion-molecule chemistry of the simplest species is summarized, with emphasis on those problems which are most sensitive to uncertain rates or product branching ratios of DR processes. Examples of the kinds of information needed about DR processes are presented. The importance of the H3(+) ion and prospects for its direct observation are discussed.
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Evolutionary constraints and the neutral theory. [mutation-caused nucleotide substitutions in DNA
NASA Technical Reports Server (NTRS)
Jukes, T. H.; Kimura, M.
1984-01-01
The neutral theory of molecular evolution postulates that nucleotide substitutions inherently take place in DNA as a result of point mutations followed by random genetic drift. In the absence of selective constraints, the substitution rate reaches the maximum value set by the mutation rate. The rate in globin pseudogenes is about 5 x 10 to the -9th substitutions per site per year in mammals. Rates slower than this indicate the presence of constraints imposed by negative (natural) selection, which rejects and discards deleterious mutations.
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Neutral changes during divergent evolution of hemoglobins
NASA Technical Reports Server (NTRS)
Jukes, T. H.
1978-01-01
A comparison of the mRNAs for rabbit and human beta-hemoglobins shows that synonymous changes in codons have accumulated three times as rapidly as nucleotide replacements that produced changes in amino acids. This agrees with predictions based on the so-called neutral theory. In addition, seven codon changes that appear to be single-base changes (according to maximum parsimony) are actually two-base changes. This indicates that the construction of primordial sequences is of limited significance when based on inferences that assume minimum base changes for amino acid replacements.
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A Test of the Interstellar Boundary EXplorer Ribbon Formation in the Outer Heliosheath
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gamayunov, Konstantin V.; Rassoul, Hamid; Heerikhuisen, Jacob, E-mail: kgamayunov@fit.edu
NASA’s Interstellar Boundary EXplorer ( IBEX ) mission is imaging energetic neutral atoms (ENAs) propagating to Earth from the outer heliosphere and local interstellar medium (LISM). A dominant feature in all ENA maps is a ribbon of enhanced fluxes that was not predicted before IBEX . While more than a dozen models of the ribbon formation have been proposed, consensus has gathered around the so-called secondary ENA model. Two classes of secondary ENA models have been proposed; the first class assumes weak scattering of the energetic pickup protons in the LISM, and the second class assumes strong but spatially localizedmore » scattering. Here we present a numerical test of the “weak scattering” version of the secondary ENA model using our gyro-averaged kinetic model for the evolution of the phase-space distribution of protons in the outer heliosheath. As input for our test, we use distributions of the primary ENAs from our MHD-plasma/kinetic-neutral model of the heliosphere-LISM interaction. The magnetic field spectrum for the large-scale interstellar turbulence and an upper limit for the amplitude of small-scale local turbulence (SSLT) generated by protons are taken from observations by Voyager 1 in the LISM. The hybrid simulations of energetic protons are also used to set the bounding wavenumbers for the spectrum of SSLT. Our test supports the “weak scattering” version. This makes an additional solid step on the way to understanding the origin and formation of the IBEX ribbon and thus to improving our understanding of the interaction between the heliosphere and the LISM.« less
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Weaver, Timothy D; Gunz, Philipp
2018-04-01
Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.
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NASA Astrophysics Data System (ADS)
Kunz, Matthew W.; Mouschovias, Telemachos Ch.
2009-03-01
We formulate the problem of the formation and subsequent evolution of fragments (or cores) in magnetically supported, self-gravitating molecular clouds in two spatial dimensions. The six-fluid (neutrals, electrons, molecular and atomic ions, positively charged, negatively charged, and neutral grains) physical system is governed by the radiation, nonideal magnetohydrodynamic equations. The magnetic flux is not assumed to be frozen in any of the charged species. Its evolution is determined by a newly derived generalized Ohm's law, which accounts for the contributions of both elastic and inelastic collisions to ambipolar diffusion and Ohmic dissipation. The species abundances are calculated using an extensive chemical-equilibrium network. Both MRN and uniform grain size distributions are considered. The thermal evolution of the protostellar core and its effect on the dynamics are followed by employing the gray flux-limited diffusion approximation. Realistic temperature-dependent grain opacities are used that account for a variety of grain compositions. We have augmented the publicly available Zeus-MP code to take into consideration all these effects and have modified several of its algorithms to improve convergence, accuracy, and efficiency. Results of magnetic star formation simulations that accurately track the evolution of a protostellar fragment from a density sime103 cm-3 to a density sime1015 cm-3, while rigorously accounting for both nonideal MHD processes and radiative transfer, are presented in a separate paper.
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NASA Astrophysics Data System (ADS)
Yu, Qian; Fang, Debin; Zhang, Xiaoling; Jin, Chen; Ren, Qiyu
2016-06-01
Stochasticity plays an important role in the evolutionary dynamic of cyclic dominance within a finite population. To investigate the stochastic evolution process of the behaviour of bounded rational individuals, we model the Rock-Scissors-Paper (RSP) game as a finite, state dependent Quasi Birth and Death (QBD) process. We assume that bounded rational players can adjust their strategies by imitating the successful strategy according to the payoffs of the last round of the game, and then analyse the limiting distribution of the QBD process for the game stochastic evolutionary dynamic. The numerical experiments results are exhibited as pseudo colour ternary heat maps. Comparisons of these diagrams shows that the convergence property of long run equilibrium of the RSP game in populations depends on population size and the parameter of the payoff matrix and noise factor. The long run equilibrium is asymptotically stable, neutrally stable and unstable respectively according to the normalised parameters in the payoff matrix. Moreover, the results show that the distribution probability becomes more concentrated with a larger population size. This indicates that increasing the population size also increases the convergence speed of the stochastic evolution process while simultaneously reducing the influence of the noise factor.
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Yu, Qian; Fang, Debin; Zhang, Xiaoling; Jin, Chen; Ren, Qiyu
2016-06-27
Stochasticity plays an important role in the evolutionary dynamic of cyclic dominance within a finite population. To investigate the stochastic evolution process of the behaviour of bounded rational individuals, we model the Rock-Scissors-Paper (RSP) game as a finite, state dependent Quasi Birth and Death (QBD) process. We assume that bounded rational players can adjust their strategies by imitating the successful strategy according to the payoffs of the last round of the game, and then analyse the limiting distribution of the QBD process for the game stochastic evolutionary dynamic. The numerical experiments results are exhibited as pseudo colour ternary heat maps. Comparisons of these diagrams shows that the convergence property of long run equilibrium of the RSP game in populations depends on population size and the parameter of the payoff matrix and noise factor. The long run equilibrium is asymptotically stable, neutrally stable and unstable respectively according to the normalised parameters in the payoff matrix. Moreover, the results show that the distribution probability becomes more concentrated with a larger population size. This indicates that increasing the population size also increases the convergence speed of the stochastic evolution process while simultaneously reducing the influence of the noise factor.
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Observing Planets and Small Bodies in Sputtered High Energy Atom (SHEA) Fluxes
NASA Technical Reports Server (NTRS)
Milillo, A.; Orsini, S.; Hsieh, K. C.; Baragiola, R.; Fama, M.; Johnson, R.; Mura, A.; Plainaki, Ch.; Sarantos, M.; Cassidy, T. A.;
2012-01-01
The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA and suggests the need for quantitative results from laboratory simulations and molecular physic modeling in order to understand SHEA data from planetary missions. In the Appendix, referenced computer simulations using existing sputtering data are reviewed.
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Dong, Xinran; Wang, Xiao; Zhang, Feng; Tian, Weidong
2016-10-01
Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Fiscal Neutrality and Local Choice in Public Education.
ERIC Educational Resources Information Center
Weber, William L.
1991-01-01
Extends Feldstein's notion of wealth neutrality to embrace fiscal neutrality, using a representative consumer context. Employs an "ideal" demand system to model school district expenditures in a general equilibrium framework. Rejects constant price and income elasticity demand models. Supports the fiscally neutral elasticity model…
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A facility to study the particles released by ion sputtering process
NASA Astrophysics Data System (ADS)
de Angelis, E.; di Lellis, A. M.; Vannaroni, G.; Orsini, S.; Mangano, V.; Milillo, A.; Massetti, S.; Mura, A.; Vertolli, N.
2007-08-01
Research on the planetary surface erosion and planetary evolution could be enriched with the detection of the escaping material, in terms of energy and direction, caused by ions sputtering. A complete study of emitted neutral distribution from which infers the processes occurring on the impacted surface requires dedicated instrumentation, tailored on the peculiarity on the low energy profile of the sputtered signal. We propose a comprehensive facility at INAF/IFSI in Rome intended to provide the opportunity to investigate the interaction of selectable ion beam with planetary analogues through the detection of sputtered neutral atoms. The laboratory is equipped with a high volume UHV chamber, ion selectable sources in the range 0 to 10 keV, a set of 3D sample/sensor orientation motion actuation motors down to 1/100 deg resolution. The laboratory will support a set of neutral sensor heads sets derived from the Emitted for Low Energetic Neutral Atoms (ELENA) instrument under development for the ESA BepiColombo Mercury mission able to detect neutral atoms (few eV-up to 5 keV).
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Current disruptions in the near-earth neutral sheet region
NASA Technical Reports Server (NTRS)
Lui, A. T. Y.; Lopez, R. E.; Anderson, B. J.; Takahashi, K.; Zanetti, L. J.; Mcentire, R. W.; Potemra, T. A.; Klumpar, D. M.; Greene, E. M.; Strangeway, R.
1992-01-01
Current disruption events observed by the Charge Composition Explorer during 1985 and 1986 are examined. Occurrence of current disruption was accompanied by large magnetic field turbulence and frequently with reversal in the sign of the field component normal to the neutral sheet. Current disruptions in the near-earth region are found to be typically shortlived (about 1-5 min), and their onsets coincide well with the ground onsets of substorm expansion or intensification in the local time sector of the footpoint of the spacecraft. These events are found almost exclusively close to the field reversal plane of the neutral sheet (within about 0.5 RE). Prior to current disruption the field strength can be reduced to as low as one seventh of the dipole field value and can recover to nearly the dipole value after disruption. The temporal evolution of particle pressure in the near-earth neutral sheet during the onset of current disruption indicates that the current buildup during the substorm growth phase is associated with enhancement in the particle pressure at the neutral sheet.
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Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.
Kapheim, Karen M; Pan, Hailin; Li, Cai; Salzberg, Steven L; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M; Hudson, Matthew E; Venkat, Aarti; Fischman, Brielle J; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D; Kemp, William P; Bosch, Jordi; Waterhouse, Robert M; Zdobnov, Evgeny M; Stolle, Eckart; Kraus, F Bernhard; Helbing, Sophie; Moritz, Robin F A; Glastad, Karl M; Hunt, Brendan G; Goodisman, Michael A D; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D; Barribeau, Seth M; Johnson, Reed M; Massey, Jonathan H; Southey, Bruce R; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J Spencer; Hanrahan, Shawn J; Kocher, Sarah D; Wang, Jun; Robinson, Gene E; Zhang, Guojie
2015-06-05
The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. Copyright © 2015, American Association for the Advancement of Science.
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Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.
Edwards, C T T; Holmes, E C; Pybus, O G; Wilson, D J; Viscidi, R P; Abrams, E J; Phillips, R E; Drummond, A J
2006-11-01
The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic diversity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences sampled longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.
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On the soft supersymmetry-breaking parameters in gauge-mediated models
NASA Astrophysics Data System (ADS)
Wagner, C. E. M.
1998-09-01
Gauge mediation of supersymmetry breaking in the observable sector is an attractive idea, which naturally alleviates the flavor changing neutral current problem of supersymmetric theories. Quite generally, however, the number and quantum number of the messengers are not known; nor is their characteristic mass scale determined by the theory. Using the recently proposed method to extract supersymmetry-breaking parameters from wave-function renormalization, we derived general formulae for the soft supersymmetry-breaking parameters in the observable sector, valid in the small and moderate tan β regimes, for the case of split messengers. The full leading-order effects of top Yukawa and gauge couplings on the soft supersymmetry-breaking parameters are included. We give a simple interpretation of the general formulae in terms of the renormalization group evolution of the soft supersymmetry-breaking parameters. As a by-product of this analysis, the one-loop renormalization group evolution of the soft supersymmetry-breaking parameters is obtained for arbitrary boundary conditions of the scalar and gaugino mass parameters at high energies.
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DR-induced Hot Oxygen and Carbon Coronae of Early Mars
NASA Astrophysics Data System (ADS)
Zhao, J.; Chassefiere, E.; Tian, F.; Chaufray, J. Y.; Leblanc, F.
2017-12-01
The evolution of Martian atmosphere is a key aspect to understand the habitability of Mars in time. The distributions of neutral atoms above the exobase of ancient Mars (corona) is important for understanding the interactions between the corona and the solar wind, which could help improving our understanding of the evolution of Martian atmosphere. In this work, a 3-D Monte Carlo Model is built to simulate Martian corona in different period of Mars history based on thermosphere structure corresponding to 1, 3, 10, and 20 times present solar XUV conditions and dissociative recombination (DR) reaction profiles. DR reactions of O2+, CO2+, and CO+ are considered as the sources of primary O and C. Secondary O and C atoms, which are formed through collisions between primaries and background species. We will discuss the dependence of physical properties of Martian corona as functions of solar XUV flux and DR reactions. We will also discuss the potential importance of CO+ DR as a contributor to Martian corona.
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MARTINI: An event generator for relativistic heavy-ion collisions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schenke, Bjoern; Gale, Charles; Jeon, Sangyong
2009-11-15
We introduce the modular algorithm for relativistic treatment of heavy ion interactions (MARTINI), a comprehensive event generator for the hard and penetrating probes in high-energy nucleus-nucleus collisions. Its main components are a time-evolution model for the soft background, PYTHIA 8.1, and the McGill-Arnold, Moore, and Yaffe (AMY) parton-evolution scheme, including radiative as well as elastic processes. This allows us to generate full event configurations in the high p{sub T} region that take into account thermal quantum chromodynamic (QCD) and quantum electrodynamic (QED) effects as well as effects of the evolving medium. We present results for the neutral pion nuclear modificationmore » factor in Au+Au collisions at the BNL Relativistic Heavy Ion Collider as a function of p{sub T} for different centralities and also as a function of the angle with respect to the reaction plane for noncentral collisions. Furthermore, we study the production of high-transverse-momentum photons, incorporating a complete set of photon-production channels.« less
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The effect of topography on the evolution of unstable disturbances in a baroclinic atmosphere
NASA Technical Reports Server (NTRS)
Clark, J. H. E.
1985-01-01
A two layer spectral quasi-geostrophic model is used to simulate the effects of topography on the equilibria, their stability, and the long term evolution of incipient unstable waves. The flow is forced by latitudinally dependent radiative heating. Dissipation is in the form of Rayleigh friction. An analytical solution is found for the propagating finite amplitude waves which result from baroclinic instability of the zonal winds when topography is absent. The appearance of this solution for wavelengths just longer than the Rossby radius of deformation and disappearance of ultra-long wavelengths is interpreted in terms of the Hopf bifurcation theory. Simple dynamic and thermodynamic criteria for the existence of periodic Rossby solutions are presented. A Floquet stability analysis shows that the waves are neutral. The nature of the form drag instability of high index equilibria is investigated. The proximity of the equilibrium shear to a resonant value is essential for the instability, provided the equilibrium occurs at a slightly stronger shear than resonance.
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Smith, Heather F.
2011-01-01
The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world. PMID:21461369
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TWO-STAGE FRAGMENTATION FOR CLUSTER FORMATION: ANALYTICAL MODEL AND OBSERVATIONAL CONSIDERATIONS
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bailey, Nicole D.; Basu, Shantanu, E-mail: nwityk@uwo.ca, E-mail: basu@uwo.ca
2012-12-10
Linear analysis of the formation of protostellar cores in planar magnetic interstellar clouds shows that molecular clouds exhibit a preferred length scale for collapse that depends on the mass-to-flux ratio and neutral-ion collision time within the cloud. We extend this linear analysis to the context of clustered star formation. By combining the results of the linear analysis with a realistic ionization profile for the cloud, we find that a molecular cloud may evolve through two fragmentation events in the evolution toward the formation of stars. Our model suggests that the initial fragmentation into clumps occurs for a transcritical cloud onmore » parsec scales while the second fragmentation can occur for transcritical and supercritical cores on subparsec scales. Comparison of our results with several star-forming regions (Perseus, Taurus, Pipe Nebula) shows support for a two-stage fragmentation model.« less
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First-Principles-Driven Model-Based Optimal Control of the Current Profile in NSTX-U
NASA Astrophysics Data System (ADS)
Ilhan, Zeki; Barton, Justin; Wehner, William; Schuster, Eugenio; Gates, David; Gerhardt, Stefan; Kolemen, Egemen; Menard, Jonathan
2014-10-01
Regulation in time of the toroidal current profile is one of the main challenges toward the realization of the next-step operational goals for NSTX-U. A nonlinear, control-oriented, physics-based model describing the temporal evolution of the current profile is obtained by combining the magnetic diffusion equation with empirical correlations obtained at NSTX-U for the electron density, electron temperature, and non-inductive current drives. In this work, the proposed model is embedded into the control design process to synthesize a time-variant, linear-quadratic-integral, optimal controller capable of regulating the safety factor profile around a desired target profile while rejecting disturbances. Neutral beam injectors and the total plasma current are used as actuators to shape the current profile. The effectiveness of the proposed controller in regulating the safety factor profile in NSTX-U is demonstrated via closed-loop predictive simulations carried out in PTRANSP. Supported by PPPL.
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Re-Evaluating Clonal Dominance in Cancer Evolution.
Burrell, Rebecca A; Swanton, Charles
2016-05-01
Tumours are composed of genetically heterogeneous subclones which may diverge early during tumour growth. However, our strategies for treating and assessing outcome for patients are overwhelmingly based upon the classical linear paradigm for cancer evolution. Increasing numbers of studies are finding that minor subclones can determine clinical disease course, and that temporal and spatial heterogeneity needs to be considered in disease management. In this article we review evidence for cancer clonal heterogeneity, evaluating the importance of tumour subclones and their growth through both Darwinian and neutral evolution. Major shifts in current clinical practice and trial designs, aimed at understanding cancer evolution on a patient-by-patient basis, may be necessary to achieve more successful treatment of heterogeneous metastatic disease. Copyright © 2016 Elsevier Inc. All rights reserved.
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Gomez, M A; Hendry, M J; Koshinsky, J; Essilfie-Dughan, J; Paikaray, S; Chen, J
2013-07-16
The mineralogy and evolution of Al and Mg in U mill tailings are poorly understood. Elemental analyses (ICP-MS) of both solid and aqueous phases show that precipitation of large masses of secondary Al and Mg mineral phases occurs throughout the raffinate neutralization process (pH 1-11) at the Key Lake U mill, Saskatchewan, Canada. Data from a suite of analytical methods (ICP-MS, EMPA, laboratory- and synchrotron-based XRD, ATR-IR, Raman, TEM, EDX, ED) and equilibrium thermodynamic modeling showed that nanoparticle-sized, spongy, porous, Mg-Al hydrotalcite is the dominant mineralogical control on Al and Mg in the neutralized raffinate (pH ≥ 6.7). The presence of this secondary Mg-Al hydrotalcite in mineral samples of both fresh and 15-year-old tailings indicates that the Mg-Al hydrotalcite is geochemically stable, even after >16 years in the oxic tailings body. Data shows an association between the Mg-Al hydrotalcite and both As and Ni and point to this Mg-Al hydrotalcite exerting a mineralogical control on the solubility of these contaminants.
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Atomic and molecular hydrogen gas temperatures in a low-pressure helicon plasma
NASA Astrophysics Data System (ADS)
Samuell, Cameron M.; Corr, Cormac S.
2015-08-01
Neutral gas temperatures in hydrogen plasmas are important for experimental and modelling efforts in fusion technology, plasma processing, and surface modification applications. To provide values relevant to these application areas, neutral gas temperatures were measured in a low pressure (< 10 mTorr) radiofrequency helicon discharge using spectroscopic techniques. The atomic and molecular species were not found to be in thermal equilibrium with the atomic temperature being mostly larger then the molecular temperature. In low power operation (< 1 kW), the molecular hydrogen temperature was observed to be linearly proportional to the pressure while the atomic hydrogen temperature was inversely proportional. Both temperatures were observed to rise linearly with input power. For high power operation (5-20 kW), the molecular temperature was found to rise with both power and pressure up to a maximum of approximately 1200 K. Spatially resolved measurements near a graphite target demonstrated localised cooling near the sample surface. The temporal evolution of the molecular gas temperature during a high power 1.1 ms plasma pulse was also investigated and found to vary considerably as a function of pressure.
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An approximate stationary solution for multi-allele neutral diffusion with low mutation rates.
Burden, Conrad J; Tang, Yurong
2016-12-01
We address the problem of determining the stationary distribution of the multi-allelic, neutral-evolution Wright-Fisher model in the diffusion limit. A full solution to this problem for an arbitrary K×K mutation rate matrix involves solving for the stationary solution of a forward Kolmogorov equation over a (K-1)-dimensional simplex, and remains intractable. In most practical situations mutations rates are slow on the scale of the diffusion limit and the solution is heavily concentrated on the corners and edges of the simplex. In this paper we present a practical approximate solution for slow mutation rates in the form of a set of line densities along the edges of the simplex. The method of solution relies on parameterising the general non-reversible rate matrix as the sum of a reversible part and a set of (K-1)(K-2)/2 independent terms corresponding to fluxes of probability along closed paths around faces of the simplex. The solution is potentially a first step in estimating non-reversible evolutionary rate matrices from observed allele frequency spectra. Copyright © 2016 Elsevier Inc. All rights reserved.
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Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus.
Avia, Komlan; Lipinska, Agnieszka P; Mignerot, Laure; Montecinos, Alejandro E; Jamy, Mahwash; Ahmed, Sophia; Valero, Myriam; Peters, Akira F; Cock, J Mark; Roze, Denis; Coelho, Susana M
2018-06-06
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Drift-Induced Selection Between Male and Female Heterogamety.
Veller, Carl; Muralidhar, Pavitra; Constable, George W A; Nowak, Martin A
2017-10-01
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems. Copyright © 2017 by the Genetics Society of America.
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Three-dimensional modeling of the neutral gas depletion effect in a helicon discharge plasma
NASA Astrophysics Data System (ADS)
Kollasch, Jeffrey; Schmitz, Oliver; Norval, Ryan; Reiter, Detlev; Sovinec, Carl
2016-10-01
Helicon discharges provide an attractive radio-frequency driven regime for plasma, but neutral-particle dynamics present a challenge to extending performance. A neutral gas depletion effect occurs when neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. The Monte Carlo neutral particle tracking code EIRENE was setup for the MARIA helicon experiment at UW Madison to study its neutral particle dynamics. Prescribed plasma temperature and density profiles similar to those in the MARIA device are used in EIRENE to investigate the main causes of the neutral gas depletion effect. The most dominant plasma-neutral interactions are included so far, namely electron impact ionization of neutrals, charge exchange interactions of neutrals with plasma ions, and recycling at the wall. Parameter scans show how the neutral depletion effect depends on parameters such as Knudsen number, plasma density and temperature, and gas-surface interaction accommodation coefficients. Results are compared to similar analytic studies in the low Knudsen number limit. Plans to incorporate a similar Monte Carlo neutral model into a larger helicon modeling framework are discussed. This work is funded by the NSF CAREER Award PHY-1455210.
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Genome-wide signatures of convergent evolution in echolocating mammals
Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A.; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J.
2013-01-01
Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes1-3. However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures4,5. Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level6-9. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution9,10 although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised. PMID:24005325
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Molecular evolution and thermal adaptation
NASA Astrophysics Data System (ADS)
Chen, Peiqiu
2011-12-01
In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of generations. Diversity plays an important role in thermal adaptation: While monoclonal strains adapt via acquisition and rapid fixation of new early mutations, wild population adapt via standing genetic variations, and they are more robust against thermal shocks due to greater diversity within the initial population.
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A Statistical Model of the Magnetotail Neutral Sheet
NASA Astrophysics Data System (ADS)
Xiao, Sudong; Zhang, Tielong; Baumjohann, Wolfgang; Nakamura, Rumi; Ge, Yasong; Du, Aimin; Wang, Guoqiang; Lu, Quanming
2015-04-01
The neutral sheet of the magnetotail is characterized by weak magnetic field, strong cross tail current, and a reversal of the magnetic field direction across it. The dynamics of the earth's magnetosphere is greatly influenced by physical processes that occur near the neutral sheet. However, the exact position of the neutral sheet is variable in time. It is therefore essential to have a reliable estimate of the average position of the neutral sheet. Magnetic field data from ten years of Cluster, nineteen years of Geotail, four years of TC 1, and seven years of THEMIS observations have been incorporated to obtain a model of the magnetotail neutral sheet. All data in aberrated GSM (Geocentric Solar Magnetospheric) coordinate system are normalized to the same solar wind pressure condition. The shape and position of the neutral sheet, illustrated directly by the separator of positive and negative Bx on the YZ cross sections, are fitted with a displaced ellipse model. It is consistent with previous studies that the neutral sheet becomes curvier in the YZ cross section when the dipole tilt increases, yet our model shows the curviest neutral sheet compared with previous models. The new model reveals a hinging distance very close to 10 RE at a reference solar wind dynamic pressure of 2 nPa. We find that the earth dipole tilt angle not only affects the neutral sheet configuration in the YZ cross section but also in the XZ cross section. The neutral sheet becomes more tilting in the XZ cross section when the dipole tilt increases. The effect of an interplanetary magnetic field (IMF) penetration is studied, and an IMF By-related twisting of about 3° is found. Anticlockwise twisting of the neutral sheet is observed, looking along the downtail direction, for a positive IMF By, and clockwise twisting of the neutral sheet for a negative IMF By.
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Development of SSUBPIC code for modeling the neutral gas depletion effect in helicon discharges
NASA Astrophysics Data System (ADS)
Kollasch, Jeffrey; Sovenic, Carl; Schmitz, Oliver
2017-10-01
The SSUBPIC (steady-state unstructured-boundary particle-in-cell) code is being developed to model helicon plasma devices. The envisioned modeling framework incorporates (1) a kinetic neutral particle model, (2) a kinetic ion model, (3) a fluid electron model, and (4) an RF power deposition model. The models are loosely coupled and iterated until convergence to steady-state. Of the four required solvers, the kinetic ion and neutral particle simulation can now be done within the SSUBPIC code. Recent SSUBPIC modifications include implementation and testing of a Coulomb collision model (Lemons et al., JCP, 228(5), pp. 1391-1403) allowing efficient coupling of kineticly-treated ions to fluid electrons, and implementation of a neutral particle tracking mode with charge-exchange and electron impact ionization physics. These new simulation capabilities are demonstrated working independently and coupled to ``dummy'' profiles for RF power deposition to converge on steady-state plasma and neutral profiles. The geometry and conditions considered are similar to those of the MARIA experiment at UW-Madison. Initial results qualitatively show the expected neutral gas depletion effect in which neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. This work is funded by the NSF CAREER award PHY-1455210 and NSF Grant PHY-1206421.
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Elementary particles in the early Universe
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gromov, N.A., E-mail: gromov@dm.komisc.ru
The high-temperature limit of the Standard Model generated by the contractions of gauge groups is discussed. Contraction parameters of gauge group SU(2) of the Electroweak Model and gauge group SU(3) of Quantum Chromodynamics are taken identical and tending to zero when the temperature increases. Properties of the elementary particles change drastically at the infinite temperature limit: all particles lose masses, all quarks are monochromatic. Electroweak interactions become long-range and are mediated by neutral currents. Particles of different kind do not interact. It looks like some stratification with only one sort of particles in each stratum. The Standard Model passes inmore » this limit through several stages, which are distinguished by the powers of the contraction parameter. For any stage intermediate models are constructed and the exact expressions for the respective Lagrangians are presented. The developed approach describes the evolution of the Standard Model in the early Universe from the Big Bang up to the end of several nanoseconds.« less
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Nemo: an evolutionary and population genetics programming framework.
Guillaume, Frédéric; Rougemont, Jacques
2006-10-15
Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.
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NASA Astrophysics Data System (ADS)
Koechl, F.; Loarte, A.; Parail, V.; Belo, P.; Brix, M.; Corrigan, G.; Harting, D.; Koskela, T.; Kukushkin, A. S.; Polevoi, A. R.; Romanelli, M.; Saibene, G.; Sartori, R.; Eich, T.; Contributors, JET
2017-08-01
The dynamics for the transition from L-mode to a stationary high Q DT H-mode regime in ITER is expected to be qualitatively different to present experiments. Differences may be caused by a low fuelling efficiency of recycling neutrals, that influence the post transition plasma density evolution on the one hand. On the other hand, the effect of the plasma density evolution itself both on the alpha heating power and the edge power flow required to sustain the H-mode confinement itself needs to be considered. This paper presents results of modelling studies of the transition to stationary high Q DT H-mode regime in ITER with the JINTRAC suite of codes, which include optimisation of the plasma density evolution to ensure a robust achievement of high Q DT regimes in ITER on the one hand and the avoidance of tungsten accumulation in this transient phase on the other hand. As a first step, the JINTRAC integrated models have been validated in fully predictive simulations (excluding core momentum transport which is prescribed) against core, pedestal and divertor plasma measurements in JET C-wall experiments for the transition from L-mode to stationary H-mode in partially ITER relevant conditions (highest achievable current and power, H 98,y ~ 1.0, low collisionality, comparable evolution in P net/P L-H, but different ρ *, T i/T e, Mach number and plasma composition compared to ITER expectations). The selection of transport models (core: NCLASS + Bohm/gyroBohm in L-mode/GLF23 in H-mode) was determined by a trade-off between model complexity and efficiency. Good agreement between code predictions and measured plasma parameters is obtained if anomalous heat and particle transport in the edge transport barrier are assumed to be reduced at different rates with increasing edge power flow normalised to the H-mode threshold; in particular the increase in edge plasma density is dominated by this edge transport reduction as the calculated neutral influx across the separatrix remains unchanged (or even slightly decreases) following the H-mode transition. JINTRAC modelling of H-mode transitions for the ITER 15 MA / 5.3 T high Q DT scenarios with the same modelling assumptions as those being derived from JET experiments has been carried out. The modelling finds that it is possible to access high Q DT conditions robustly for additional heating power levels of P AUX ⩾ 53 MW by optimising core and edge plasma fuelling in the transition from L-mode to high Q DT H-mode. An initial period of low plasma density, in which the plasma accesses the H-mode regime and the alpha heating power increases, needs to be considered after the start of the additional heating, which is then followed by a slow density ramp. Both the duration of the low density phase and the density ramp-rate depend on boundary and operational conditions and can be optimised to minimise the resistive flux consumption in this transition phase. The modelling also shows that fuelling schemes optimised for a robust access to high Q DT H-mode in ITER are also optimum for the prevention of the contamination of the core plasma by tungsten during this phase.
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Cryptic genetic variation: evolution's hidden substrate.
Paaby, Annalise B; Rockman, Matthew V
2014-04-01
Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.
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Fera, Daniela; Schmidt, Aaron G; Haynes, Barton F; Gao, Feng; Liao, Hua-Xin; Kepler, Thomas B; Harrison, Stephen C
2014-07-15
Rapidly evolving pathogens, such as human immunodeficiency and influenza viruses, escape immune defenses provided by most vaccine-induced antibodies. Proposed strategies to elicit broadly neutralizing antibodies require a deeper understanding of antibody affinity maturation and evolution of the immune response to vaccination or infection. In HIV-infected individuals, viruses and B cells evolve together, creating a virus-antibody "arms race." Analysis of samples from an individual designated CH505 has illustrated the interplay between an antibody lineage, CH103, and autologous viruses at various time points. The CH103 antibodies, relatively broad in their neutralization spectrum, interact with the CD4 binding site of gp120, with a contact dominated by CDRH3. We show by analyzing structures of progenitor and intermediate antibodies and by correlating them with measurements of binding to various gp120s that there was a shift in the relative orientation of the light- and heavy-chain variable domains during evolution of the CH103 lineage. We further show that mutations leading to this conformational shift probably occurred in response to insertions in variable loop 5 (V5) of the HIV envelope. The shift displaced the tips of the light chain away from contact with V5, making room for the inserted residues, which had allowed escape from neutralization by the progenitor antibody. These results, which document the selective mechanism underlying this example of a virus-antibody arms race, illustrate the functional significance of affinity maturation by mutation outside the complementarity determining region surface of the antibody molecule.
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A combined spectroscopic and plasma chemical kinetic analysis of ionospheric samarium releases
NASA Astrophysics Data System (ADS)
Holmes, Jeffrey M.; Dressler, Rainer A.; Pedersen, Todd R.; Caton, Ronald G.; Miller, Daniel
2017-05-01
Two rocket-borne releases of samarium vapor in the upper atmosphere occurred in May 2013, as part of the Metal Oxide Space Clouds experiment. The releases were characterized by a combination of optical and RF diagnostic instruments located at the Roi-Namur launch site and surrounding islands and atolls. The evolution of the optical spectrum of the solar-illuminated cloud was recorded with a spectrograph covering a 400-800 nm spectral range. The spectra exhibit two distinct spectral regions centered at 496 and 636 nm within which the relative intensities change insignificantly. The ratio between the integrated intensities within these regions, however, changes with time, suggesting that they are associated with different species. With the help of an equilibrium plasma spectral model we attribute the region centered at 496 nm to neutral samarium atoms (Sm I radiance) and features peaking at 649 nm to a molecular species. No evidence for structure due to Sm+ (Sm II) is identified. The persistence of the Sm I radiance suggests a high dissociative recombination rate for the chemi-ionization product, SmO+. A one-dimensional plasma chemical kinetic model of the evolution of the density ratio NSmO/NSm(t) demonstrates that the molecular feature peaking at 649 nm can be attributed to SmO radiance. SmO+ radiance is not identified. By adjusting the Sm vapor mass of the chemical kinetic model input to match the evolution of the total electron density determined by ionosonde data, we conclude that less than 5% of the payload samarium was vaporized.
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SSIC model: A multi-layer model for intervention of online rumors spreading
NASA Astrophysics Data System (ADS)
Tian, Ru-Ya; Zhang, Xue-Fu; Liu, Yi-Jun
2015-06-01
SIR model is a classical model to simulate rumor spreading, while the supernetwork is an effective tool for modeling complex systems. Based on the Opinion SuperNetwork involving Social Sub-network, Environmental Sub-network, Psychological Sub-network, and Viewpoint Sub-network, drawing from the modeling idea of SIR model, this paper designs super SIC model (SSIC model) and its evolution rules, and also analyzes intervention effects on public opinion of four elements of supernetwork, which are opinion agent, opinion environment, agent's psychology and viewpoint. Studies show that, the SSIC model based on supernetwork has effective intervention effects on rumor spreading. It is worth noting that (i) identifying rumor spreaders in Social Sub-network and isolating them can achieve desired intervention results, (ii) improving environmental information transparency so that the public knows as much information as possible to reduce the rumors is a feasible way to intervene, (iii) persuading wavering neutrals has better intervention effects than clarifying rumors already spread everywhere, so rumors should be intervened in properly in time by psychology counseling.
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Characterization of xenon ion and neutral interactions in a well-characterized experiment
NASA Astrophysics Data System (ADS)
Patino, Marlene I.; Wirz, Richard E.
2018-06-01
Interactions between fast ions and slow neutral atoms are commonly dominated by charge-exchange and momentum-exchange collisions, which are important to understanding and simulating the performance and behavior of many plasma devices. To investigate these interactions, this work developed a simple, well-characterized experiment that accurately measures the behavior of high energy xenon ions incident on a background of xenon neutral atoms. By using well-defined operating conditions and a simple geometry, these results serve as canonical data for the development and validation of plasma models and models of neutral beam sources that need to ensure accurate treatment of angular scattering distributions of charge-exchange and momentum-exchange ions and neutrals. The energies used in this study are relevant for electric propulsion devices ˜1.5 keV and can be used to improve models of ion-neutral interactions in the plume. By comparing these results to both analytical and computational models of ion-neutral interactions, we discovered the importance of (1) accurately treating the differential cross-sections for momentum-exchange and charge-exchange collisions over a large range of neutral background pressures and (2) properly considering commonly overlooked interactions, such as ion-induced electron emission from nearby surfaces and neutral-neutral ionization collisions.
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Position of the IBEX ribbon as a key to understand its origin
NASA Astrophysics Data System (ADS)
Swaczyna, Pawel; Bzowski, Maciej; Sokół, Justyna M.; Christian, Eric R.; Funsten, Herbert O.; McComas, David J.; Schwadron, Nathan A.
2017-04-01
Observations of the energetic neutral atom (ENA) emission by the Interstellar Boundary Explorer (IBEX) allow for remote sensing of the plasma properties in heliosheath. The first IBEX results revealed an unexpected arc-like enhancement of the ENA flux in the sky, dubbed the IBEX ribbon. This discovery led to formulation of more than a dozen hypotheses on its origin. The emission source region proposed in these hypotheses span the heliospheric termination shock up to a hypothetical nearby interface between the Local Interstellar Cloud and a local bay in the Local Bubble. Among these hypotheses is the concept that the ribbon is produced by the secondary ENA mechanism, operating in the outer heliosheath. The observational strategy of IBEX allows observation of the same part of the sky from the opposite sides of the Sun every six months and thus provides parallax viewing with a baseline of 2 AU. After correcting the observations for the Compton-Getting effect and for gravitational deflection and radiation pressure, we use this parallax viewing to precisely determine the apparent position of the maximum flux associated with the ribbon. We find that the ribbon peak position differs semi-annually by an angle of 0.41±0.15 deg, which we interpret as the parallax effect. This angle corresponds to a distance of 140-38+84 AU, and thus suggests that most likely the ribbon's source is located just beyond the heliopause. Comparison of the IBEX ribbon position in five energy steps of IBEX-Hi shows a systematic shift, which changes the position of the ribbon center by ˜10 deg. We find that it can be explained using an analytic model of the secondary ENA mechanism with the neutralized supersonic solar wind as the source of the primary ENAs, which are ionized in the outer heliosheath, picked up by the ambient magnetic field, and eventually re-neutralized (as originally conceived, McComas et al. 2009). We use a realistic model of the solar wind evolution dependent on heliographic latitude, calculated the neutral solar wind flux and averaged it over the solar cycle, which was then used as the input in the analytic model of the secondary ENAs. The modeled ENA emission signal as observed at IBEX reproduces the observed features of the IBEX ribbon: the relative signal intensity along the ribbon in each energy channel and the shift of the ribbon center. The combination of the distance to the ribbon source obtained from parallax and the energy progression of the ribbon center location suggest that the secondary ENA mechanism is a plausible explanation for the ribbon origin. A better resolution of the ENA detectors expected on the IMAP mission will enable a more accurate determination of the ribbon's position and will extend observations to higher energies. In consequence, a better determination of its parallax should be possible, and time-dependent effects resulting from the evolution of the supersonic solar wind structure with time will provide additional, critical signatures of the ribbon origin.
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Continuing Development of a Hybrid Model (VSH) of the Neutral Thermosphere
NASA Technical Reports Server (NTRS)
Burns, Alan
1996-01-01
We propose to continue the development of a new operational model of neutral thermospheric density, composition, temperatures and winds to improve current engineering environment definitions of the neutral thermosphere. This model will be based on simulations made with the National Center for Atmospheric Research (NCAR) Thermosphere-Ionosphere- Electrodynamic General Circulation Model (TIEGCM) and on empirical data. It will be capable of using real-time geophysical indices or data from ground-based and satellite inputs and provides neutral variables at specified locations and times. This "hybrid" model will be based on a Vector Spherical Harmonic (VSH) analysis technique developed (over the last 8 years) at the University of Michigan that permits the incorporation of the TIGCM outputs and data into the model. The VSH model will be a more accurate version of existing models of the neutral thermospheric, and will thus improve density specification for satellites flying in low Earth orbit (LEO).
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NASA Astrophysics Data System (ADS)
Rognlien, Thomas; Rensink, Marvin
2016-10-01
Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.
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NASA Astrophysics Data System (ADS)
Leblanc, F.; Chaufray, J. Y.; Modolo, R.; Leclercq, L.; Curry, S.; Luhmann, J.; Lillis, R.; Hara, T.; McFadden, J.; Halekas, J.; Schneider, N.; Deighan, J.; Mahaffy, P. R.; Benna, M.; Johnson, R. E.; Gonzalez-Galindo, F.; Forget, F.; Lopez-Valverde, M. A.; Eparvier, F. G.; Jakosky, B.
2017-12-01
The first measurements of the emission brightness of the oxygen atomic exosphere by Mars Atmosphere and Volatile EvolutioN (MAVEN) mission have clearly shown that it is composed of a thermal component produced by the extension of the upper atmosphere and of a nonthermal component. Modeling these measurements allows us to constrain the origins of the exospheric O and, as a consequence, to estimate Mars' present oxygen escape rate. We here propose an analysis of three periods of MAVEN observations based on a set of three coupled models: a hybrid magnetospheric model (LATmos HYbrid Simulation (LatHyS)), an Exospheric General Model (EGM), and the Global Martian Circulation model of the Laboratoire de Météorologie Dynamique (LMD-GCM), which provide a description of Mars' environment from the surface up to the solar wind. The simulated magnetosphere by LatHyS is in good agreement with MAVEN Plasma and Field Package instruments data. The LMD-GCM modeled upper atmospheric profiles for the main neutral and ion species are compared to Neutral Gas and Ion Mass Spectrometer/MAVEN data showing that the LMD-GCM can provide a satisfactory global view of Mars' upper atmosphere. Finally, we were able to reconstruct the expected emission brightness intensity from the oxygen exosphere using EGM. The good agreement with the averaged measured profiles by Imaging Ultraviolet Spectrograph during these three periods suggests that Mars' exospheric nonthermal component can be fully explained by the reactions of dissociative recombination of the O2+ ion in Mars' ionosphere, limiting significantly our ability to extract information from MAVEN observations of the O exosphere on other nonthermal processes, such as sputtering.
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Quantifying evolutionary dynamics from variant-frequency time series
NASA Astrophysics Data System (ADS)
Khatri, Bhavin S.
2016-09-01
From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.
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Quantifying evolutionary dynamics from variant-frequency time series.
Khatri, Bhavin S
2016-09-12
From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.
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Du, Sean X.; Xu, Li; Zhang, Wenge; Tang, Susan; Boenig, Rebecca I.; Chen, Helen; Mariano, Ellaine B.; Zwick, Michael B.; Parren, Paul W. H. I.; Burton, Dennis R.; Wrin, Terri; Petropoulos, Christos J.; Ballantyne, John A.; Chambers, Michael; Whalen, Robert G.
2011-01-01
A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we created chimeric gp120 variants that were screened for their ability to bind neutralizing monoclonal antibodies. Hundreds of variants were identified with novel antigenic phenotypes that exhibit considerable sequence diversity. Immunization of rabbits with these gp120 variants demonstrated that the majority can induce neutralizing antibodies to HIV-1. One novel variant, called ST-008, induced significantly improved neutralizing antibody responses when assayed against a large panel of primary HIV-1 isolates. Further study of various deletion constructs of ST-008 showed that the enhanced immunogenicity results from a combination of effective DNA priming, an enhanced V3-based response, and an improved response to the constant backbone sequences. PMID:21738594
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Investigation of Relationship between QBO and Ionospheric Neutral Temperature
NASA Astrophysics Data System (ADS)
Saǧır, Selçuk; Atıcı, Ramazan; Özcan, Osman
2016-07-01
The relationship between Quasi Biennial Oscillation (QBO) measured at 10 hPa altitude and neutral temperature obtained from NRLMSIS-00 model for 90 km altitude of ionosphere is statistically investigated. For this study, multiple-regression model is used. To see effect on neutral temperature of QBO directions, Dummy variables are added to model established. In the results of performed analysis, it is observed that QBO is effected on neutral temperature of ionosphere. It is determined that 57% of variations at neutral temperature can be explainable by QBO. According to the established model, statistical explainable ratio was determined as 1% that it is the highest rate. Also, it is seen that an increase/a decrease of 1 meter per second at QBO give rise to an increase/a decrease of 0,07 K at neutral temperature.
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Lunar Neutral Exposphere Properties from Pickup Ion Analysis
NASA Technical Reports Server (NTRS)
Hartle, R. E.; Sarantos, M.; Killen, R.; Sittler, E. C. Jr.; Halekas, J.; Yokota, S.; Saito, Y.
2009-01-01
Composition and structure of neutral constituents in the lunar exosphere can be determined through measurements of phase space distributions of pickup ions borne from the exosphere [1]. An essential point made in an early study [ 1 ] and inferred by recent pickup ion measurements [2, 3] is that much lower neutral exosphere densities can be derived from ion mass spectrometer measurements of pickup ions than can be determined by conventional neutral mass spectrometers or remote sensing instruments. One approach for deriving properties of neutral exospheric source gasses is to first compare observed ion spectra with pickup ion model phase space distributions. Neutral exosphere properties are then inferred by adjusting exosphere model parameters to obtain the best fit between the resulting model pickup ion distributions and the observed ion spectra. Adopting this path, we obtain ion distributions from a new general pickup ion model, an extension of a simpler analytic description obtained from the Vlasov equation with an ion source [4]. In turn, the ion source is formed from a three-dimensional exospheric density distribution, which can range from the classical Chamberlain type distribution to one with variable exobase temperatures and nonthermal constituents as well as those empirically derived. The initial stage of this approach uses the Moon's known neutral He and Na exospheres to deriv e He+ and Na+ pickup ion exospheres, including their phase space distributions, densities and fluxes. The neutral exospheres used are those based on existing models and remote sensing studies. As mentioned, future ion measurements can be used to constrain the pickup ion model and subsequently improve the neutral exosphere descriptions. The pickup ion model is also used to estimate the exosphere sources of recently observed pickup ions on KAGUYA [3]. Future missions carrying ion spectrometers (e.g., ARTEMIS) will be able to study the lunar neutral exosphere with great sensitivity, yielding the necessary ion velocity spectra needed to further analysis of parent neutral exosphere properties.
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Greenbury, Sam F.; Schaper, Steffen; Ahnert, Sebastian E.; Louis, Ard A.
2016-01-01
Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should strongly influence evolutionary dynamics. We explore and quantify these intuitions by comparing three GP maps—a model for RNA secondary structure, the HP model for protein tertiary structure, and the Polyomino model for protein quaternary structure—to a simple random null model that maintains the number of genotypes mapping to each phenotype, but assigns genotypes randomly. The mutational neighbourhood of a genotype in these GP maps is much more likely to contain genotypes mapping to the same phenotype than in the random null model. Such neutral correlations can be quantified by the robustness to mutations, which can be many orders of magnitude larger than that of the null model, and crucially, above the critical threshold for the formation of large neutral networks of mutationally connected genotypes which enhance the capacity for the exploration of phenotypic novelty. Thus neutral correlations increase evolvability. We also study non-neutral correlations: Compared to the null model, i) If a particular (non-neutral) phenotype is found once in the 1-mutation neighbourhood of a genotype, then the chance of finding that phenotype multiple times in this neighbourhood is larger than expected; ii) If two genotypes are connected by a single neutral mutation, then their respective non-neutral 1-mutation neighbourhoods are more likely to be similar; iii) If a genotype maps to a folding or self-assembling phenotype, then its non-neutral neighbours are less likely to be a potentially deleterious non-folding or non-assembling phenotype. Non-neutral correlations of type i) and ii) reduce the rate at which new phenotypes can be found by neutral exploration, and so may diminish evolvability, while non-neutral correlations of type iii) may instead facilitate evolutionary exploration and so increase evolvability. PMID:26937652
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Pickup Ions in the Plasma Environments of Mars, Comets, and Enceladus
NASA Astrophysics Data System (ADS)
Cravens, T.; Rahmati, A.; Sakai, S.; Madanian, H.; Larson, D. E.; Lillis, R. J.; Halekas, J. S.; Goldstein, R.; Burch, J. L.; Clark, G. B.; Jakosky, B. M.
2015-12-01
Ions created within a flowing plasma by ionization of neutrals respond to the electric and magnetic fields associated with the flow becoming what are called pick-up ions (PUI). PUI play an important role in many solar system plasma environments and affect the energy and momentum balance of the plasma flow. PUI have been observed during several recent space missions and PUI data will be compared and interpreted using models. Pick-up oxygen ions were observed in the solar wind upstream of Mars by the Solar Energetic Particle (SEP) and Solar Wind Ion Analyzer (SWIA) instruments on NASA's MAVEN (Mars Atmosphere and Volatile EvolutioN) spacecraft. The pick-up oxygen ions are created when atoms in the hot corona are ionized by solar radiation and charge exchange with solar wind protons. The ion fluxes measured by SEP can constrain the oxygen escape rate from Mars. PUI were also been detected at distances of 10 - 100 km from the nucleus of comet 67P/Churyumov- Gerasimenko (67P/CG) by plasma instruments (IES and ICA) onboard the Rosetta Orbiter when the comet was at 3 AU. The newly-born cometary ions are accelerated by the solar wind motional electric field but remain un-magnetized, as suggested by pre-encounter models (Rubin et al., 2014). The inner magnetosphere of Saturn and the water plume of the icy satellite Enceladus provide a third example of PUI. H2O+ ions created by ionization of neutral water producing ions that are picked-up by the co-rotating magnetospheric plasma flow. These ions then undergo a complex interaction with the plume gas including collisions that convert most H2O+ ions to H3O+, as measured by the Ion and Neutral Mass Spectrometer (INMS) onboard the Cassini spacecraft.
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NASA Technical Reports Server (NTRS)
Rafelski, Marc; Gardner, Jonathan P.; Fumagalli, Michele; Neeleman, Marcel; Teplitz, Harry I.; Grogin, Norman; Koekemoer, Anton M.; Scarlata, Claudia
2016-01-01
Current observational evidence suggests that the star formation rate (SFR)efficiency of neutral atomic hydrogen gas measured in damped Ly(alpha) systems (DLAs) at z approx. 3 is more than 10 times lower than predicted by the Kennicutt-Schmidt (KS)relation. To understand the origin of this deficit, and to investigate possible evolution with redshift and galaxy properties, we measure the SFR efficiency of atomic gas at z approx. 1, z approx. 2, and z approx. 3 around star-forming galaxies. We use new robust photometric redshifts in the Hubble Ultra Deep Field to create galaxy stacks in these three redshift bins, and measure the SFR efficiency by combining DLA absorber statistics with the observed rest-frame UV emission in the galaxies' outskirts. We find that the SFR efficiency of H I gas at z > 1 is approx. 1%-3% of that predicted by the KS relation. Contrary to simulations and models that predict a reduced SFR efficiency with decreasing metallicity and thus with increasing redshift, we find no significant evolution in the SFR efficiency with redshift. Our analysis instead suggests that the reduced SFR efficiency is driven by the low molecular content of this atomic-dominated phase, with metallicity playing a secondary effect in regulating the conversion between atomic and molecular gas. This interpretation is supported by the similarity between the observed SFR efficiency and that observed in local atomic-dominated gas, such as in the outskirts of local spiral galaxies and local dwarf galaxies.
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Are Synonymous Sites in Primates and Rodents Functionally Constrained?
Price, Nicholas; Graur, Dan
2016-01-01
It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.
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Influence of hot and cold neutrals on scrape-off layer tokamak plasma turbulence
NASA Astrophysics Data System (ADS)
Bisai, N.; Kaw, P. K.
2018-01-01
The modification of interchange plasma turbulence in the scrape-off layer (SOL) region by the presence of hot and cold neutral gas molecules has been studied. The nonlinear equations have been solved numerically using two different simulations ("uniform-Te" and "varying-Te"), and the results obtained from both of the models have been compared. The hot neutrals, responsible for the increase in the electron density in the SOL, also account for more ionization of the cold molecules. The effect of hot and cold neutrals on the interchange turbulence is almost similar in the "uniform-Te" model, but in the "varying-Te" model, the influence of the hot neutrals is very small, specifically in the far SOL region. The neutral gas in the "varying Te" model decreases the heat load on the material walls by about 7%. A reduction in the radial velocity by about 25% and effective diffusion coefficient of the plasma particles has been found by the influence of the neutral gas.
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NASA Astrophysics Data System (ADS)
McElroy, Kenneth L., Jr.
1992-12-01
A method is presented for the determination of neutral gas densities in the ionosphere from rocket-borne measurements of UV atmospheric emissions. Computer models were used to calculate an initial guess for the neutral atmosphere. Using this neutral atmosphere, intensity profiles for the N2 (0,5) Vegard-Kaplan band, the N2 Lyman-Birge-Hopfield band system, and the OI2972 A line were calculated and compared with the March 1990 NPS MUSTANG data. The neutral atmospheric model was modified and the intensity profiles recalculated until a fit with the data was obtained. The neutral atmosphere corresponding to the intensity profile that fit the data was assumed to be the atmospheric composition prevailing at the time of the observation. The ion densities were then calculated from the neutral atmosphere using a photochemical model. The electron density profile calculated by this model was compared with the electron density profile measured by the U.S. Air Force Geophysics Laboratory at a nearby site.
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Self-consistent approach for neutral community models with speciation
NASA Astrophysics Data System (ADS)
Haegeman, Bart; Etienne, Rampal S.
2010-03-01
Hubbell’s neutral model provides a rich theoretical framework to study ecological communities. By incorporating both ecological and evolutionary time scales, it allows us to investigate how communities are shaped by speciation processes. The speciation model in the basic neutral model is particularly simple, describing speciation as a point-mutation event in a birth of a single individual. The stationary species abundance distribution of the basic model, which can be solved exactly, fits empirical data of distributions of species’ abundances surprisingly well. More realistic speciation models have been proposed such as the random-fission model in which new species appear by splitting up existing species. However, no analytical solution is available for these models, impeding quantitative comparison with data. Here, we present a self-consistent approximation method for neutral community models with various speciation modes, including random fission. We derive explicit formulas for the stationary species abundance distribution, which agree very well with simulations. We expect that our approximation method will be useful to study other speciation processes in neutral community models as well.
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The Evolution of the Third Reich.
ERIC Educational Resources Information Center
McCleary, George F., Jr.
1995-01-01
Presents a set of four maps illustrating changing German political borders. Includes the time period from 1933, when Hitler came to power, until the division of Germany in 1945. Includes a map showing the Allied Powers against Germany, nations allied with Germany, and neutral nations. (CFR)
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The diffuse interstellar bands: a tracer for organics in the diffuse interstellar medium?
NASA Technical Reports Server (NTRS)
Salama, F.
1998-01-01
The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.
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Body mass evolution and diversification within horses (family Equidae).
Shoemaker, Lauren; Clauset, Aaron
2014-02-01
Horses (family Equidae) are a classic example of adaptive radiation, exhibiting a nearly 60-fold increase in maximum body mass and a peak taxonomic diversity of nearly 100 species across four continents. Such patterns are commonly attributed to niche competition, in which increased taxonomic diversity drives increased size disparity. However, neutral processes, such as macroevolutionary 'diffusion', can produce similar increases in disparity without increased diversity. Using a comprehensive database of Equidae species size estimates and a common mathematical framework, we measure the contributions of diversity-driven and diffusion-driven mechanisms for increased disparity during the Equidae radiation. We find that more than 90% of changes in size disparity are attributable to diffusion alone. These results clarify the role of species competition in body size evolution, indicate that morphological disparity and species diversity may be only weakly coupled in general, and demonstrate that large species may evolve from neutral macroevolutionary diffusion processes alone. © 2013 John Wiley & Sons Ltd/CNRS.
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Boyer, Julie L; Kuhlman, Matthew L; Rauchfuss, Thomas B
2007-04-01
The ability of inorganic cyanometallate polymers to form interesting and useful complexes is well-known. This Account summarizes work, especially in our laboratories, aimed at replicating aspects of this inorganic chemistry in homogeneous solution using organometallic building blocks. A library of molecular organometallic cyanides and Lewis acids, with varying charges and labilities, are shown to give families of neutral and charged cages. Neutral and anionic cages, often molecular boxes, bind larger alkali metals tightly. Cubic frameworks show an unparalleled affinity for cesium cations over potassium cations. Noncubic cages are described including tetrahedranes, defect boxes, trigonal prisms, and hexagonal prisms.
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Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces
Partha, Raghavendran; Raman, Karthik
2014-01-01
Robustness and evolvability are highly intertwined properties of biological systems. The relationship between these properties determines how biological systems are able to withstand mutations and show variation in response to them. Computational studies have explored the relationship between these two properties using neutral networks of RNA sequences (genotype) and their secondary structures (phenotype) as a model system. However, these studies have assumed every mutation to a sequence to be equally likely; the differences in the likelihood of the occurrence of various mutations, and the consequence of probabilistic nature of the mutations in such a system have previously been ignored. Associating probabilities to mutations essentially results in the weighting of genotype space. We here perform a comparative analysis of weighted and unweighted neutral networks of RNA sequences, and subsequently explore the relationship between robustness and evolvability. We show that assuming an equal likelihood for all mutations (as in an unweighted network), underestimates robustness and overestimates evolvability of a system. In spite of discarding this assumption, we observe that a negative correlation between sequence (genotype) robustness and sequence evolvability persists, and also that structure (phenotype) robustness promotes structure evolvability, as observed in earlier studies using unweighted networks. We also study the effects of base composition bias on robustness and evolvability. Particularly, we explore the association between robustness and evolvability in a sequence space that is AU-rich – sequences with an AU content of 80% or higher, compared to a normal (unbiased) sequence space. We find that evolvability of both sequences and structures in an AU-rich space is lesser compared to the normal space, and robustness higher. We also observe that AU-rich populations evolving on neutral networks of phenotypes, can access less phenotypic variation compared to normal populations evolving on neutral networks. PMID:25390641
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Modeling of neutral entrainment in an FRC thruster
DOE Office of Scientific and Technical Information (OSTI.GOV)
Brackbill, Jeremiah; Gimelshein, Natalia; Gimelshein, Sergey
2012-11-27
Neutral entrainment in a field reversed configuration thruster is modeled numerically with an implicit PIC code extended to include thermal and chemical interactions between plasma and neutral particles. The contribution of charge exchange and electron impact ionization reactions is analyzed, and the sensitivity of the entrainment efficiency to the plasmoid translation velocity and neutral density is evaluated.
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Accelerated and Adaptive Evolution of Yeast Sexual Adhesins
Xie, Xianfa; Qiu, Wei-Gang; Lipke, Peter N.
2011-01-01
There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337–341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by analyses using the PAML pairwise model, a modified McDonald–Kreitman test, and the PAML branch model. Moreover, using a combination of a new statistic of neutrality, an information theory–based measure of evolutionary variability, and functional characterization of amino acid changes, we found that a higher proportion of amino acid changes are fixed in the sexual adhesins than in other proteins and a greater proportion of the fixed amino acid changes either between the two species or the two subgroups of S. paradoxus are functionally dissimilar or radically different. These results suggest that the accelerated evolution of sexual adhesin genes may facilitate speciation, or incipient speciation, and promote sexual selection in general. PMID:21633112
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Genomic signatures of evolutionary transitions from solitary to group living
Kapheim, Karen M.; Pan, Hailin; Li, Cai; Salzberg, Steven L.; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M.; Hudson, Matthew E.; Venkat, Aarti; Fischman, Brielle J.; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D.; Kemp, William P.; Bosch, Jordi; Waterhouse, Robert M.; Zdobnov, Evgeny M.; Stolle, Eckart; Kraus, F. Bernhard; Helbing, Sophie; Moritz, Robin F. A.; Glastad, Karl M.; Hunt, Brendan G.; Goodisman, Michael A. D.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D.; Barribeau, Seth M.; Johnson, Reed M.; Massey, Jonathan H.; Southey, Bruce R.; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F.; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J. Spencer; Hanrahan, Shawn J.; Kocher, Sarah D.; Wang, Jun; Robinson, Gene E.; Zhang, Guojie
2017-01-01
The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. PMID:25977371
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Stochastic Spatial Models in Ecology: A Statistical Physics Approach
NASA Astrophysics Data System (ADS)
Pigolotti, Simone; Cencini, Massimo; Molina, Daniel; Muñoz, Miguel A.
2018-07-01
Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions accounting for general empirical patterns in communities of competing species. However, while neutral theory in well-mixed ecosystems is mathematically well understood, spatial models still present several open problems, limiting the quantitative understanding of spatial biodiversity. In this review, we discuss the state of the art in spatial neutral theory. We emphasize the connection between spatial ecological models and the physics of non-equilibrium phase transitions and how concepts developed in statistical physics translate in population dynamics, and vice versa. We focus on non-trivial scaling laws arising at the critical dimension D = 2 of spatial neutral models, and their relevance for biological populations inhabiting two-dimensional environments. We conclude by discussing models incorporating non-neutral effects in the form of spatial and temporal disorder, and analyze how their predictions deviate from those of purely neutral theories.
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Stochastic Spatial Models in Ecology: A Statistical Physics Approach
NASA Astrophysics Data System (ADS)
Pigolotti, Simone; Cencini, Massimo; Molina, Daniel; Muñoz, Miguel A.
2017-11-01
Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions accounting for general empirical patterns in communities of competing species. However, while neutral theory in well-mixed ecosystems is mathematically well understood, spatial models still present several open problems, limiting the quantitative understanding of spatial biodiversity. In this review, we discuss the state of the art in spatial neutral theory. We emphasize the connection between spatial ecological models and the physics of non-equilibrium phase transitions and how concepts developed in statistical physics translate in population dynamics, and vice versa. We focus on non-trivial scaling laws arising at the critical dimension D = 2 of spatial neutral models, and their relevance for biological populations inhabiting two-dimensional environments. We conclude by discussing models incorporating non-neutral effects in the form of spatial and temporal disorder, and analyze how their predictions deviate from those of purely neutral theories.
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NASA Astrophysics Data System (ADS)
Wehner, William; Schuster, Eugenio; Poli, Francesca
2016-10-01
Initial progress towards the design of non-inductive current ramp-up scenarios in the National Spherical Torus Experiment Upgrade (NSTX-U) has been made through the use of TRANSP predictive simulations. The strategy involves, first, ramping the plasma current with high harmonic fast waves (HHFW) to about 400 kA, and then further ramping to 900 kA with neutral beam injection (NBI). However, the early ramping of neutral beams and application of HHFW leads to an undesirably peaked current profile making the plasma unstable to ballooning modes. We present an optimization-based control approach to improve on the non-inductive ramp-up strategy. We combine the TRANSP code with an optimization algorithm based on sequential quadratic programming to search for time evolutions of the NBI powers, the HHFW powers, and the line averaged density that define an open-loop actuator strategy that maximizes the non-inductive current while satisfying constraints associated with the current profile evolution for MHD stable plasmas. This technique has the potential of playing a critical role in achieving robustly stable non-inductive ramp-up, which will ultimately be necessary to demonstrate applicability of the spherical torus concept to larger devices without sufficient room for a central coil. Supported by the US DOE under the SCGSR Program.
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Yu, Minda; He, Xiaosong; Liu, Jiaomei; Wang, Yuefeng; Xi, Beidou; Li, Dan; Zhang, Hui; Yang, Chao
2018-04-14
Understanding the heterogeneous evolution characteristics of dissolved organic matter fractions derived from compost is crucial to exploring the composting biodegradation process and the possible applications of compost products. Herein, two-dimensional correlation spectroscopy integrated with reversed-phase high performance liquid chromatography and size exclusion chromatography were utilized to obtain the molecular weight (MW) and polarity evolution characteristics of humic acid (HA), fulvic acid (FA), and the hydrophilic (HyI) fractions during composting. The high-MW humic substances and building blocks in the HA fraction degraded faster during composting than polymers, proteins, and organic colloids. Similarly, the low MW acid FA factions transformed faster than the low weight neutral fractions, followed by building blocks, and finally polymers, proteins, and organic colloids. The evolutions of HyI fractions during composting occurred first for building blocks, followed by low MW acids, and finally low weight neutrals. With the progress of composting, the hydrophobic properties of the HA and FA fractions were enhanced. The degradation/humification process of the hydrophilic and transphilic components was faster than that of the hydrophobic component. Compared with the FA and HyI fractions, the HA fraction exhibited a higher MW and increased hydrophobicity. Copyright © 2018 Elsevier B.V. All rights reserved.
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A nebula of gases from Io surrounding Jupiter.
Krimigis, Stamatios M; Mitchell, Donald G; Hamilton, Douglas C; Dandouras, Jannis; Armstrong, Thomas P; Bolton, Scott J; Cheng, Andrew F; Gloeckler, George; Hsieh, K C; Keath, Edwin P; Krupp, Norbert; Lagg, Andreas; Lanzerotti, Louis J; Livi, Stefano; Mauk, Barry H; McEntire, Richard W; Roelof, Edmond C; Wilken, Berend; Williams, Donald J
2002-02-28
Several planetary missions have reported the presence of substantial numbers of energetic ions and electrons surrounding Jupiter; relativistic electrons are observable up to several astronomical units (au) from the planet. A population of energetic (>30[?]keV) neutral particles also has been reported, but the instrumentation was not able to determine the mass or charge state of the particles, which were subsequently labelled energetic neutral atoms. Although images showing the presence of the trace element sodium were obtained, the source and identity of the neutral atoms---and their overall significance relative to the loss of charged particles from Jupiter's magnetosphere---were unknown. Here we report the discovery by the Cassini spacecraft of a fast (>103[?]km[?]s-1) and hot magnetospheric neutral wind extending more than 0.5[?]au from Jupiter, and the presence of energetic neutral atoms (both hot and cold) that have been accelerated by the electric field in the solar wind. We suggest that these atoms originate in volcanic gases from Io, undergo significant evolution through various electromagnetic interactions, escape Jupiter's magnetosphere and then populate the environment around the planet. Thus a 'nebula' is created that extends outwards over hundreds of jovian radii.
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Duplicate retention in signalling proteins and constraints from network dynamics.
Soyer, O S; Creevey, C J
2010-11-01
Duplications are a major driving force behind evolution. Most duplicates are believed to fix through genetic drift, but it is not clear whether this process affects all duplications equally or whether there are certain gene families that are expected to show neutral expansions under certain circumstances. Here, we analyse the neutrality of duplications in different functional classes of signalling proteins based on their effects on response dynamics. We find that duplications involving intermediary proteins in a signalling network are neutral more often than those involving receptors. Although the fraction of neutral duplications in all functional classes increase with decreasing population size and selective pressure on dynamics, this effect is most pronounced for receptors, indicating a possible expansion of receptors in species with small population size. In line with such an expectation, we found a statistically significant increase in the number of receptors as a fraction of genome size in eukaryotes compared with prokaryotes. Although not confirmative, these results indicate that neutral processes can be a significant factor in shaping signalling networks and affect proteins from different functional classes differently. © 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Reusch, J. A.; Anderson, J. K.; Eilerman, S.
2012-10-15
A new E Parallel-To B neutral particle analyzer, which has recently been installed on Madison Symmetric Torus (MST) reversed-field pinch (RFP), has now been calibrated, allowing the measurement of the fast ion density and energy distribution. This diagnostic, dubbed the advanced neutral particle analyzer (ANPA), can simultaneously produce time resolved measurements of the efflux of both hydrogen and deuterium ions from the plasma over a 35 keV energy range with an energy resolution of 2-4 keV and a time resolution of 10 {mu}s. These capabilities are needed to measure both majority ion heating that occurs during magnetic reconnection events inmore » MST and the behavior of the fast ions from the 1 MW hydrogen neutral beam injector on MST. Calibration of the ANPA was performed using a custom ion source that resides in the flight tube between the MST and the ANPA. In this work, the ANPA will be described, the calibration procedure and results will be discussed, and initial measurements of the time evolution of 25 keV neutral beam injection-born fast ions will be presented.« less
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Solar wind structure out of the ecliptic plane over solar cycles
NASA Astrophysics Data System (ADS)
Sokol, J. M.; Bzowski, M.; Tokumaru, M.
2017-12-01
Sun constantly emits a stream of plasma known as solar wind. Ground-based observations of the solar wind speed through the interplanetary scintillations (IPS) of radio flux from distant point sources and in-situ measurements by Ulysses mission revealed that the solar wind flow has different characteristics depending on the latitude. This latitudinal structure evolves with the cycle of solar activity. The knowledge on the evolution of solar wind structure is important for understanding the interaction between the interstellar medium surrounding the Sun and the solar wind, which is responsible for creation of the heliosphere. The solar wind structure must be taken into account in interpretation of most of the observations of heliospheric energetic neutral atoms, interstellar neutral atoms, pickup ions, and heliospheric backscatter glow. The information on the solar wind structure is not any longer available from direct measurements after the termination of Ulysses mission and the only source of the solar wind out of the ecliptic plane is the IPS observations. However, the solar wind structure obtained from this method contains inevitable gaps in the time- and heliolatitude coverage. Sokół et al 2015 used the solar wind speed data out of the ecliptic plane retrieved from the IPS observations performed by Institute for Space-Earth Environmental Research (Nagoya University, Japan) and developed a methodology to construct a model of evolution of solar wind speed and density from 1985 to 2013 that fills the data gaps. In this paper we will present a refined model of the solar wind speed and density structure as a function of heliographic latitude updated by the most recent data from IPS observations. And we will discuss methods of extrapolation of the solar wind structure out of the ecliptic plane for the past solar cycles, when the data were not available, as well as forecasting for few years upward.
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NASA Astrophysics Data System (ADS)
Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.
2016-02-01
A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Medley, S. S.; Liu, D.; Gorelenkova, M. V.
2016-01-12
A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less
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Probing Mechanism of Evolution of Simple Genomes
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Ditzler, Mark; Popovic, Milena; Wei, Chenyu
2016-01-01
Our overarching goal is to discover how the structure of the genotypic space of RNA polymers affects their ability to evolve. Specifically, we will address several fundamental questions that, so far, have remained largely unanswered. Was the genotypic space explored globally or only locally? Was the outcome of early evolution predictable or was it, instead, govern by chance? What was the role of neutral mutations in the evolution of increasing complex systems? As the first step, we study the problem in the example of RNA ligases. We obtain the complete, empirical fitness landscapes for short ligases and examine possible evolutionary paths for RNA molecules that are sufficiently long to preclude exhaustive search of the genotypic space.
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Parametric resonant triad interactions in a free shear layer
NASA Technical Reports Server (NTRS)
Mallier, R.; Maslowe, S. A.
1993-01-01
We investigate the weakly nonlinear evolution of a triad of nearly-neutral modes superimposed on a mixing layer with velocity profile u bar equals Um + tanh y. The perturbation consists of a plane wave and a pair of oblique waves each inclined at approximately 60 degrees to the mean flow direction. Because the evolution occurs on a relatively fast time scale, the critical layer dynamics dominate the process and the amplitude evolution of the oblique waves is governed by an integro-differential equation. The long-time solution of this equation predicts very rapid (exponential of an exponential) amplification and we discuss the pertinence of this result to vortex pairing phenomena in mixing layers.
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Collisional spreading of Enceladus’ neutral cloud
NASA Astrophysics Data System (ADS)
Cassidy, T. A.; Johnson, R. E.
2010-10-01
We describe a direct simulation Monte Carlo (DSMC) model of Enceladus' neutral cloud and compare its results to observations of OH and O orbiting Saturn. The OH and O are observed far from Enceladus (at 3.95 R S), as far out as 25 R S for O. Previous DSMC models attributed this breadth primarily to ion/neutral scattering (including charge exchange) and molecular dissociation. However, the newly reported O observations and a reinterpretation of the OH observations (Melin, H., Shemansky, D.E., Liu, X. [2009] Planet. Space Sci., 57, 1743-1753, PS&S) showed that the cloud is broader than previously thought. We conclude that the addition of neutral/neutral scattering (Farmer, A.J. [2009] Icarus, 202, 280-286), which was underestimated by previous models, brings the model results in line with the new observations. Neutral/neutral collisions primarily happen in the densest part of the cloud, near Enceladus' orbit, but contribute to the spreading by pumping up orbital eccentricity. Based on the cloud model presented here Enceladus maybe the ultimate source of oxygen for the upper atmospheres of Titan and Saturn. We also predict that large quantities of OH, O and H 2O bombard Saturn's icy satellites.
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Rational evolutionary design: the theory of in vitro protein evolution.
Voigt, C A; Kauffman, S; Wang, Z G
2000-01-01
Directed evolution uses a combination of powerful search techniques to generate proteins with improved properties. Part of the success is due to the stochastic element of random mutagenesis; improvements can be made without a detailed description of the complex interactions that constitute function or stability. However, optimization is not a conglomeration of random processes. Rather, it requires both knowledge of the system that is being optimized and a logical series of techniques that best explores the pathways of evolution (Eigen et al., 1988). The weighing of parameters associated with mutation, recombination, and screening to achieve the maximum fitness improvement is the beginning of rational evolutionary design. The optimal mutation rate is strongly influenced by the finite number of mutants that can be screened. A smooth fitness landscape implies that many mutations can be accumulated without disrupting the fitness. This has the effect of lowering the required library size to sample a higher mutation rate. As the sequence ascends the fitness landscape, the optimal mutation rate decreases as the probability of discovering improved mutations also decreases. Highly coupled regions require that many mutations be simultaneously made to generate a positive mutant. Therefore, positive mutations are discovered at uncoupled positions as the fitness of the parent increases. The benefit of recombination is twofold: it combines good mutations and searches more sequence space in a meaningful way. Recombination is most beneficial when the number of mutants that can be screened is limited and the landscape is of an intermediate ruggedness. The structure of schema in proteins leads to the conclusion that many cut points are required. The number of parents and their sequence identity are determined by the balance between exploration and exploitation. Many disparate parents can explore more space, but at the risk of losing information. The required screening effort is related to the number of uphill paths, which decreases more rapidly for rugged landscapes. Noise in the fitness measurements causes a dramatic increase in the required mutant library size, thus implying a smaller optimal mutation rate. Because of strict limitations on the number of mutants that can be screened, there is motivation to optimize the content of the mutant library. By restricting mutations to regions of the gene that are expected to show improvement, a greater return can be made with the same number of mutants. Initial studies with subtilisin E have shown that structurally tolerant positions tend to be where positive activity mutants are made during directed evolution. Mutant fitness information is produced by the screening step that has the potential to provide insight into the structure of the fitness landscape, thus aiding the setting of experimental parameters. By analyzing the mutant fitness distribution and targeting specific regions of the sequence, in vitro evolution can be accelerated. However, when expediting the search, there is a trade-off between rapid improvement and the quality of the long-term solution. The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to the less coupled region of the sequence (smooth portion of the fitness landscape), the required larger mutation rate can be tolerated. Advances in directed evolution will be achieved when the driving forces behind such proce
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The distribution of Enceladus water-group neutrals in Saturn’s Magnetosphere
NASA Astrophysics Data System (ADS)
Smith, Howard T.; Richardson, John D.
2017-10-01
Saturn’s magnetosphere is unique in that the plumes from the small icy moon, Enceladus, serve at the primary source for heavy particles in Saturn’s magnetosphere. The resulting co-orbiting neutral particles interact with ions, electrons, photons and other neutral particles to generate separate H2O, OH and O tori. Characterization of these toroidal distributions is essential for understanding Saturn magnetospheric sources, composition and dynamics. Unfortunately, limited direct observations of these features are available so modeling is required. A significant modeling challenge involves ensuring that either the plasma and neutral particle populations are not simply input conditions but can provide feedback to each population (i.e. are self-consistent). Jurac and Richardson (2005) executed such a self-consistent model however this research was performed prior to the return of Cassini data. In a similar fashion, we have coupled a 3-D neutral particle model (Smith et al. 2004, 2005, 2006, 2007, 2009, 2010) with a plasma transport model (Richardson 1998; Richardson & Jurac 2004) to develop a self-consistent model which is constrained by all available Cassini observations and current findings on Saturn’s magnetosphere and the Enceladus plume source resulting in much more accurate neutral particle distributions. Here a new self-consistent model of the distribution of the Enceladus-generated neutral tori that is validated by all available observations. We also discuss the implications for source rate and variability.
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Photochemistry of Pluto's Atmosphere
NASA Technical Reports Server (NTRS)
Krasnopolsky, Vladimir A.
1999-01-01
This work include studies of two problems: (1) Modeling thermal balance, structure. and escape processes in Pluto's upper atmosphere. This study has been completed in full. A new method, of analytic solution for the equation of hydrodynamic flow from in atmosphere been developed. It was found that the ultraviolet absorption by methane which was previously ignored is even more important in Pluto's thermal balance than the extreme ultraviolet absorption by nitrogen. Two basic models of the lower atmosphere have been suggested, with a tropopause and a planetary surface at the bottom of the stellar occultation lightcurve, respectively, Vertical profiles, of temperature, density, gas velocity, and the CH4 mixing ratio have been calculated for these two models at low, mean, and high solar activity (six models). We prove that Pluto' " s atmosphere is restricted to 3060-4500 km, which makes possible a close flyby of future spacecraft. Implication for Pluto's evolution have also been discussed. and (2) Modeling of Pluto's photochemistry. Based on the results of (1), we have made some changes in the basic continuity equation and in the boundary conditions which reflect a unique can of hydrodynamic escape and therefore have not been used in modeling of other planetary atmospheres. We model photochemistry of 44 neutral and 23 ion species. This work required solution of a set of 67 second-order nonlinear ordinary differential equations. Two models have been developed. Each model consists of the vertical profiles for 67 species, their escape and precipitation rates. These models predict the chemical structure and basic chemical processes in the current atmosphere and possible implication of these processes for evolution. This study has also been completed in full.
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Cucchi, Thomas; Barnett, Ross; Martínková, Natália; Renaud, Sabrina; Renvoisé, Elodie; Evin, Allowen; Sheridan, Alison; Mainland, Ingrid; Wickham‐Jones, Caroline; Tougard, Christelle; Quéré, Jean Pierre; Pascal, Michel; Pascal, Marine; Heckel, Gerald; O'Higgins, Paul; Searle, Jeremy B.; Dobney, Keith M.
2014-01-01
Island evolution may be expected to involve fast initial morphological divergence followed by stasis. We tested this model using the dental phenotype of modern and ancient common voles (Microtus arvalis), introduced onto the Orkney archipelago (Scotland) from continental Europe some 5000 years ago. First, we investigated phenotypic divergence of Orkney and continental European populations and assessed climatic influences. Second, phenotypic differentiation among Orkney populations was tested against geography, time, and neutral genetic patterns. Finally, we examined evolutionary change along a time series for the Orkney Mainland. Molar gigantism and anterior‐lobe hypertrophy evolved rapidly in Orkney voles following introduction, without any transitional forms detected. Founder events and adaptation appear to explain this initial rapid evolution. Idiosyncrasy in dental features among different island populations of Orkney voles is also likely the result of local founder events following Neolithic translocation around the archipelago. However, against our initial expectations, a second marked phenotypic shift occurred between the 4th and 12th centuries AD, associated with increased pastoral farming and introduction of competitors (mice and rats) and terrestrial predators (foxes and cats). These results indicate that human agency can generate a more complex pattern of morphological evolution than might be expected in island rodents. PMID:24957579
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Physical trade-offs shape the evolution of buoyancy control in sharks.
Gleiss, Adrian C; Potvin, Jean; Goldbogen, Jeremy A
2017-11-15
Buoyancy control is a fundamental aspect of aquatic life that has major implications for locomotor performance and ecological niche. Unlike terrestrial animals, the densities of aquatic animals are similar to the supporting fluid, thus even small changes in body density may have profound effects on locomotion. Here, we analysed the body composition (lipid versus lean tissue) of 32 shark species to study the evolution of buoyancy. Our comparative phylogenetic analyses indicate that although lean tissue displays minor positive allometry, liver volume exhibits pronounced positive allometry, suggesting that larger sharks evolved bulkier body compositions by adding lipid tissue to lean tissue rather than substituting lean for lipid tissue, particularly in the liver. We revealed a continuum of buoyancy control strategies that ranged from more buoyant sharks with larger livers in deeper ecosystems to relatively denser sharks with small livers in epipelagic habitats. Across this eco-morphological spectrum, our hydrodynamic modelling suggests that neutral buoyancy yields lower drag and more efficient steady swimming, whereas negative buoyancy may be more efficient during accelerated movements. The evolution of buoyancy control in sharks suggests that ecological and physiological factors mediate the selective pressures acting on these traits along two major gradients, body size and habitat depth. © 2017 The Author(s).
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Temporal change of EIA asymmetry revealed by a beacon receiver network in Southeast Asia
NASA Astrophysics Data System (ADS)
Watthanasangmechai, Kornyanat; Yamamoto, Mamoru; Saito, Akinori; Maruyama, Takashi; Yokoyama, Tatsuhiro; Nishioka, Michi; Ishii, Mamoru
2015-05-01
To reveal the temporal change of the equatorial ionization anomaly (EIA) asymmetry, a multipoint satellite-ground beacon experiment was conducted along the meridional plane of the Thailand-Indonesia sector. The observation includes one station near the magnetic equator and four stations at off-equator latitudes. This is the first EIA asymmetry study with high spatial resolution using GNU Radio Beacon Receiver (GRBR) observations in Southeast Asia. GRBR-total electron contents (TECs) from 97 polar-orbit satellite passes in March 2012 were analyzed in this study. Successive passes captured rapid evolution of EIA asymmetry, especially during geomagnetic disturbances. The penetrating electric fields that occur during geomagnetic disturbed days are not the cause of the asymmetry. Instead, high background TEC associated with an intense electric field empowers the neutral wind to produce severe asymmetry of the EIA. Such rapid evolution of EIA asymmetry was not seen during nighttime, when meridional wind mainly controlled the asymmetric structures. Additional data are necessary to identify the source of the variations, i.e., atmospheric waves. Precisely capturing the locations of the crests and the evolution of the asymmetry enhances understanding of the temporal change of EIA asymmetry at the local scale and leads to a future local modeling for TEC prediction in Southeast Asia.
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Lynch, A; Baker, A J
1993-04-01
We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, Canaries) and neighboring continental regions (Morocco, Iberia) by employing a population memetics approach. To quantify variability within populations, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The frequency distribution of memes within populations generally fit a neutral model in which there is an equilibrium between mutation, migration, and drift, which suggests that memes are functionally equivalent. The diversity of memes of single syllables is significantly greater in the Azores compared to all other regions, consistent with higher population densities of chaffinches there. On the other hand, memes of two to five syllables have greater diversity in Atlantic island and Moroccan populations compared to their Iberian counterparts. This higher diversity emanates from a looser syntax and increased recombination in songs, presumably because of relaxed selection for distinctive songs in these peripheral and depauperate avifaunas. We urge comparative population memetic studies of other species of songbirds and predict that they will lead to a formulation of a general theory for the cultural evolution of bird song analogous to population genetics theory for biological traits.
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Sikorski, Johannes; Pukall, Rüdiger; Stackebrandt, Erko
2008-10-01
The 'Evolution Canyons' I and II in Israel are model habitats to study adaptation and speciation of bacteria in the environment. These canyons represent similar ecological replicates, separated by 40 km, with a strongly sun-exposed and hot 'African' south-facing slope (SFS) vs. a cooler and mesic-lush 'European' north-facing slope (NFS). Previously, among 131 Bacillus simplex isolates, distinct genetic lineages (ecotypes), each specific for either SFS or NFS, were identified, suggesting a temperature-driven slope-specific adaptation. Here, we asked whether the ecological heterogeneity of SFS vs. NFS also affected carbon utilization abilities, as determined using the Biolog assay. Contrary to expectation, a correlation between substrate utilization patterns and the ecological origin of strains was not found. Rather, the patterns split according to the two major phylogenetic lineages each of which contain SFS and NFS ecotypes. We conclude that traits related to the general energy metabolism, as far as assessed here, are neither shaped by the major abiotic features of 'Evolution Canyon', namely solar radiation, temperature, and drought, nor by the soil characteristics. We further conclude that some traits diverge rather neutrally from each other, whereas other, more environmentally related traits are shaped by natural selection and show evolutionary convergence.
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Evolution and mass extinctions as lognormal stochastic processes
NASA Astrophysics Data System (ADS)
Maccone, Claudio
2014-10-01
In a series of recent papers and in a book, this author put forward a mathematical model capable of embracing the search for extra-terrestrial intelligence (SETI), Darwinian Evolution and Human History into a single, unified statistical picture, concisely called Evo-SETI. The relevant mathematical tools are: (1) Geometric Brownian motion (GBM), the stochastic process representing evolution as the stochastic increase of the number of species living on Earth over the last 3.5 billion years. This GBM is well known in the mathematics of finances (Black-Sholes models). Its main features are that its probability density function (pdf) is a lognormal pdf, and its mean value is either an increasing or, more rarely, decreasing exponential function of the time. (2) The probability distributions known as b-lognormals, i.e. lognormals starting at a certain positive instant b>0 rather than at the origin. These b-lognormals were then forced by us to have their peak value located on the exponential mean-value curve of the GBM (Peak-Locus theorem). In the framework of Darwinian Evolution, the resulting mathematical construction was shown to be what evolutionary biologists call Cladistics. (3) The (Shannon) entropy of such b-lognormals is then seen to represent the `degree of progress' reached by each living organism or by each big set of living organisms, like historic human civilizations. Having understood this fact, human history may then be cast into the language of b-lognormals that are more and more organized in time (i.e. having smaller and smaller entropy, or smaller and smaller `chaos'), and have their peaks on the increasing GBM exponential. This exponential is thus the `trend of progress' in human history. (4) All these results also match with SETI in that the statistical Drake equation (generalization of the ordinary Drake equation to encompass statistics) leads just to the lognormal distribution as the probability distribution for the number of extra-terrestrial civilizations existing in the Galaxy (as a consequence of the central limit theorem of statistics). (5) But the most striking new result is that the well-known `Molecular Clock of Evolution', namely the `constant rate of Evolution at the molecular level' as shown by Kimura's Neutral Theory of Molecular Evolution, identifies with growth rate of the entropy of our Evo-SETI model, because they both grew linearly in time since the origin of life. (6) Furthermore, we apply our Evo-SETI model to lognormal stochastic processes other than GBMs. For instance, we provide two models for the mass extinctions that occurred in the past: (a) one based on GBMs and (b) the other based on a parabolic mean value capable of covering both the extinction and the subsequent recovery of life forms. (7) Finally, we show that the Markov & Korotayev (2007, 2008) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the underlying lognormal stochastic process is a cubic function of the time. In conclusion: we have provided a new mathematical model capable of embracing molecular evolution, SETI and entropy into a simple set of statistical equations based upon b-lognormals and lognormal stochastic processes with arbitrary mean, of which the GBMs are the particular case of exponential growth.
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Are we witnessing the epoch of reionisation at z = 7.1 from the spectrum of J1120+0641?
NASA Astrophysics Data System (ADS)
Greig, Bradley; Mesinger, Andrei; Haiman, Zoltán; Simcoe, Robert A.
2017-04-01
We quantify the presence of Lyα damping wing absorption from a partially neutral intergalactic medium (IGM) in the spectrum of the z = 7.08 QSO, ULASJ1120+0641. Using a Bayesian framework, we simultaneously account for uncertainties in: (I) the intrinsic QSO emission spectrum; and (II) the distribution of cosmic H I patches during the epoch of reionization (EoR). For (I), we use a new intrinsic Lyα emission line reconstruction method, sampling a covariance matrix of emission line properties built from a large data base of moderate-z QSOs. For (II), we use the Evolution of 21-cm Structure (EOS; Mesinger et al.) simulations, which span a range of physically motivated EoR models. We find strong evidence for the presence of damping wing absorption redward of Lyα (where there is no contamination from the Lyα forest). Our analysis implies that the EoR is not yet complete by z = 7.1, with the volume-weighted IGM neutral fraction constrained to \\bar{x}_{H I} = 0.40^{+0.21 }_{ -0.19} at 1σ (\\bar{x}_{H I} = 0.40^{+0.41 }_{ -0.32} at 2σ). This result is insensitive to the EoR morphology. Our detection of significant neutral H I in the IGM at z = 7.1 is consistent with the latest Planck 2016 measurements of the CMB Thompson scattering optical depth.
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Modeling the Evolution of the System IV Period of the Io Torus
NASA Astrophysics Data System (ADS)
Coffin, D. A.; Delamere, P. A.
2017-12-01
The response of the Io plasma torus to superthermal electron modulation and volcanic eruptions is studied using a physical chemistry and radial/azimuthal transport model (Copper et al., 2016). The model includes radial and azimuthal transport, latitudinally-averaged physical chemistry, and prescribed System III superthermal electron modulation following Steffl et al., [2008]. Volcanic eruptions are modelled as a temporal Gaussian enhancement (e.g., 2x) of the neutral source rate and hot electron fraction (e.g., <1%). However, we adopt an alternative approach for the Steffl et al., [2008] System IV electron modulation. Radially-dependent subcorotation is prescribed, consistent with observations [Brown, 1994; Thomas et al., 2001], as well as a hot electron modulation proportional to the radial flux tube content gradient. Coupling hot electron modulation to radial transport and subcorotation, we seek to analyze magnetosphere-ionosphere coupling. We find that the model produces a radially-independent periodicity and that eruptions can alter the modeled period, consistent with multi-epoch observations of a variable System IV. This periodicity remains consistent with the prescribed subcorotation period at L = 6.3.
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Pulsational mode fluctuations and their basic conservation laws
NASA Astrophysics Data System (ADS)
Borah, B.; Karmakar, P. K.
2015-01-01
We propose a theoretical hydrodynamic model for investigating the basic features of nonlinear pulsational mode stability in a partially charged dust molecular cloud within the framework of the Jeans homogenization assumption. The inhomogeneous cloud is modeled as a quasi-neutral multifluid consisting of the warm electrons, warm ions, and identical inertial cold dust grains with partial ionization in a neutral gaseous background. The grain-charge is assumed not to vary in the fluctuation evolution time scale. The active inertial roles of the thermal species are included. We apply a standard multiple scaling technique centered on the gravito-electrostatic equilibrium to understand the fluctuations on the astrophysical scales of space and time. This is found that electrostatic and self-gravitational eigenmodes co-exist as diverse solitary spectral patterns governed by a pair of Korteweg-de Vries (KdV) equations. In addition, all the relevant classical conserved quantities associated with the KdV system under translational invariance are methodologically derived and numerically analyzed. A full numerical shape-analysis of the fluctuations, scale lengths and perturbed densities with multi-parameter variation of judicious plasma conditions is carried out. A correlation of the perturbed densities and gravito-electrostatic spectral patterns is also graphically indicated. It is demonstrated that the solitary mass, momentum and energy densities also evolve like solitary spectral patterns which remain conserved throughout the spatiotemporal scales of the fluctuation dynamics. Astrophysical and space environments significant to our results are briefly highlighted.
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Modelling the solar wind interaction with Mercury by a quasi-neutral hybrid model
NASA Astrophysics Data System (ADS)
Kallio, E.; Janhunen, P.
2003-11-01
Quasi-neutral hybrid model is a self-consistent modelling approach that includes positively charged particles and an electron fluid. The approach has received an increasing interest in space plasma physics research because it makes it possible to study several plasma physical processes that are difficult or impossible to model by self-consistent fluid models, such as the effects associated with the ions’ finite gyroradius, the velocity difference between different ion species, or the non-Maxwellian velocity distribution function. By now quasi-neutral hybrid models have been used to study the solar wind interaction with the non-magnetised Solar System bodies of Mars, Venus, Titan and comets. Localized, two-dimensional hybrid model runs have also been made to study terrestrial dayside magnetosheath. However, the Hermean plasma environment has not yet been analysed by a global quasi-neutral hybrid model.
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Fast imaging measurements and modeling of neutral and impurity density on C-2U
NASA Astrophysics Data System (ADS)
Granstedt, Erik; Deng, B.; Dettrick, S.; Gupta, D. K.; Osin, D.; Roche, T.; Zhai, K.; TAE Team
2016-10-01
The C-2U device employed neutral beam injection and end-biasing to sustain an advanced beam-driven Field-Reversed Configuration plasma for 5+ ms, beyond characteristic transport time-scales. Three high-speed, filtered cameras observed visible light emission from neutral hydrogen and impurities, as well as deuterium pellet ablation and compact-toroid injection which were used for auxiliary particle fueling. Careful vacuum practices and titanium gettering successfully reduced neutral recycling from the confinement vessel wall. As a result, a large fraction of the remaining neutrals originate from charge-exchange between the neutral beams and plasma ions. Measured H/D- α emission is used with DEGAS2 neutral particle modeling to reconstruct the strongly non-axissymmetric neutral distribution. This is then used in fast-ion modeling to more accurately estimate their charge-exchange loss rate. Oxygen emission due to electron-impact excitation and charge-exchange recombination has also been measured using fast imaging. Reconstructed emissivity of O4+ is localized on the outboard side of the core plasma near the estimated location of the separatrix inferred by external magnetic measurements. Tri Alpha Energy.
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Castello, Federico Lucco; Delzanno, Gian Luca; Borovsky, Joseph E.; ...
2018-05-29
A spacecraft-charging mitigation scheme necessary for the operation of a high-power electron beam in the low-density magnetosphere is analyzed. The scheme is based on a plasma contactor, i.e. a high-density charge-neutral plasma emitted prior to and during beam emission, and its ability to emit high ion currents without strong space-charge limitations. A simple theoretical model for the transient of the spacecraft potential and contactor expansion during beam emission is presented. The model focuses on the contactor ion dynamics and is valid in the limit when the ion contactor current is equal to the beam current. The model is found inmore » very good agreement with Particle-In-Cell simulations over a large parametric study that varies the initial expansion time of the contactor, the contactor current and the ion mass. The model highlights the physics of the spacecraft-charging mitigation scheme, indicating that the most important part of the dynamics is the evolution of the outermost ion front which is pushed away by the charge accumulated in the system by the beam. The model can be also used to estimate the long-time evolution of the spacecraft potential. For a short contactor expansion (0.3 or 0.6 ms Helium plasma or 0.8 ms Argon plasma, both with 1 mA current) it yields a peak spacecraft potential of the order of 1-3 kV. This implies that a 1-mA relativistic electron beam would be easily emitted by the spacecraft.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Castello, Federico Lucco; Delzanno, Gian Luca; Borovsky, Joseph E.
A spacecraft-charging mitigation scheme necessary for the operation of a high-power electron beam in the low-density magnetosphere is analyzed. The scheme is based on a plasma contactor, i.e. a high-density charge-neutral plasma emitted prior to and during beam emission, and its ability to emit high ion currents without strong space-charge limitations. A simple theoretical model for the transient of the spacecraft potential and contactor expansion during beam emission is presented. The model focuses on the contactor ion dynamics and is valid in the limit when the ion contactor current is equal to the beam current. The model is found inmore » very good agreement with Particle-In-Cell simulations over a large parametric study that varies the initial expansion time of the contactor, the contactor current and the ion mass. The model highlights the physics of the spacecraft-charging mitigation scheme, indicating that the most important part of the dynamics is the evolution of the outermost ion front which is pushed away by the charge accumulated in the system by the beam. The model can be also used to estimate the long-time evolution of the spacecraft potential. For a short contactor expansion (0.3 or 0.6 ms Helium plasma or 0.8 ms Argon plasma, both with 1 mA current) it yields a peak spacecraft potential of the order of 1-3 kV. This implies that a 1-mA relativistic electron beam would be easily emitted by the spacecraft.« less
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Evolution of complex adaptations in molecular systems
Pál, Csaba; Papp, Balázs
2017-01-01
A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular ’springboards’, such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. PMID:28782044
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NASA Astrophysics Data System (ADS)
Fleshman, Bobby L.
The E-ring of Saturn, located just beyond the main rings at four Saturn radii, was known to be made mostly of water and its by-products before the Cassini spacecraft arrived at Saturn in 2005. Since then, Cassini has observed water geysers on the tiny moon of Enceladus ejecting ≈ 100 kg of water per second into orbit around Saturn, which most agree is the chief contributor to neutrals in the E-ring. Following several key reactions, many of these neutrals go on to populate large, tenuous structures, known as neutral clouds, extending 10s of Saturn radii. The other side of the story are the ions, which are largely created by the ionization of same neutrals sourced from Enceladus. A key distinction between the neutrals and ions is that ions are carried along by Saturn's magnetic field, and revolve around Saturn at the rotation rate of the planet, while neutrals generally have much slower Keplerian speeds. It is the study of the chemical interaction of these separate, but related populations that is the subject of this thesis. We have developed a series of models to study how the coupling of these systems affect details of the other, such as composition. The first step (Chapter 2) was the development of a water-group physical chemistry model, which includes suprathermal electrons and the effect of radial ion transport. With this "one-box" model, we are able to reproduce observed water and hydrogen ion densities in Enceladus's orbit, but only when the hot electron density is ≈ 0.5% of the total plasma density. Radial transport is found to be slow, requiring 26 days to remove ions from the orbit of Enceladus. Moving toward the development of a radial model of ion chemistry, in Chapter 4 we present a model of Saturn's neutral clouds, which are made of material outgassing from Enceladus. The effects of dissociation and charge exchange are considered, where the details of the latter prove to be of great consequence on neutral cloud morphology. The oxygen cloud is found to the most extended, followed by H2O, and finally OH. The above efforts are combined in Chapter 5, where a neutral cloud model is used to construct a radial model of ion chemistry. It is shown that neutral H2O requires more spreading than yet modeled in order to recover observed water and hydrogen ion abundances near Enceladus. The relative abundance of water-group ion species presented will be useful for analyses of CAPS-IMS data, while loss rates derived from the model can be used to improve neutral cloud models. The case is made that ion chemistry models and neutral cloud models must be developed alongside one another in order to improve understanding of these interrelated populations at Saturn.
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When Can Species Abundance Data Reveal Non-neutrality?
Al Hammal, Omar; Alonso, David; Etienne, Rampal S.; Cornell, Stephen J.
2015-01-01
Species abundance distributions (SAD) are probably ecology’s most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889
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Spectra of Full 3-D PIC Simulations of Finite Meteor Trails
NASA Astrophysics Data System (ADS)
Tarnecki, L. K.; Oppenheim, M. M.
2016-12-01
Radars detect plasma trails created by the billions of small meteors that impact the Earth's atmosphere daily, returning data used to infer characteristics of the meteoroid population and upper atmosphere. Researchers use models to investigate the dynamic evolution of the trails. Previously, all models assumed a trail of infinite length, due to the constraints of simulation techniques. We present the first simulations of 3D meteor trails of finite length. This change more accurately captures the physics of the trails. We characterize the turbulence that develops as the trail evolves and study the effects of varying the external electric field, altitude, and initial density. The simulations show that turbulence develops in all cases, and that trails travel with the neutral wind rather than electric field. Our results will allow us to draw more detailed and accurate information from non-specular radar observations of meteors.
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PIC Modeling of Argon Plasma Flow in MNX
NASA Astrophysics Data System (ADS)
Cohen, Samuel; Sefkow, Adam
2007-11-01
A linear helicon-heated plasma device - the Magnetic Nozzle Experiment (MNX) at the Princeton Plasma Physics Laboratory - is used for studies of the formation of strong electrostatic double layers near mechanical and magnetic apertures and the acceleration of plasma ions into supersonic directed beams. In order to characterize the role of the aperture and its involvement with ion acceleration, detailed particle-in-cell simulations are employed to study the effects of the surrounding boundary geometry on the plasma dynamics near the aperture region, within which the transition from a collisional to collisionless regime occurs. The presence of a small superthermal electron population is examined, and the model includes a background neutral population which can be ionized by energetic electrons. By self-consistently evaluating the temporal evolution of the plasma in the vicinity of the aperture, the formation mechanism of the double layer is investigated.