Phosphoenolpyruvate Carboxykinase 1 Gene (Pck1) Displays Parallel Evolution between Old World and New World Fruit Bats

PubMed Central

Irwin, David M.; Zhang, Shuyi

2015-01-01

Bats are an ideal mammalian group for exploring adaptations to fasting due to their large variety of diets and because fasting is a regular part of their life cycle. Mammals fed on a carbohydrate-rich diet experience a rapid decrease in blood glucose levels during a fast, thus, the development of mechanisms to resist the consequences of regular fasts, experienced on a daily basis, must have been crucial in the evolution of frugivorous bats. Phosphoenolpyruvate carboxykinase 1 (PEPCK1, encoded by the Pck1 gene) is the rate-limiting enzyme in gluconeogenesis and is largely responsible for the maintenance of glucose homeostasis during fasting in fruit-eating bats. To test whether Pck1 has experienced adaptive evolution in frugivorous bats, we obtained Pck1 coding sequence from 20 species of bats, including five Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our molecular evolutionary analyses of these sequences revealed that Pck1 was under purifying selection in both Old World and New World fruit bats with no evidence of positive selection detected in either ancestral branch leading to fruit bats. Interestingly, however, six specific amino acid substitutions were detected on the ancestral lineage of OWFBs. In addition, we found considerable evidence for parallel evolution, at the amino acid level, between the PEPCK1 sequences of Old World fruit bats and New World fruit bats. Test for parallel evolution showed that four parallel substitutions (Q276R, R503H, I558V and Q593R) were driven by natural selection. Our study provides evidence that Pck1 underwent parallel evolution between Old World and New World fruit bats, two lineages of mammals that feed on a carbohydrate-rich diet and experience regular periods of fasting as part of their life cycle. PMID:25807515

The glycogen synthase 2 gene (Gys2) displays parallel evolution between Old World and New World fruit bats.

PubMed

Qian, Yamin; Fang, Tao; Shen, Bin; Zhang, Shuyi

2014-01-01

Frugivorous and nectarivorous bats rely largely on hepatic glycogenesis and glycogenolysis for postprandial blood glucose disposal and maintenance of glucose homeostasis during short time starvation, respectively. The glycogen synthase 2 encoded by the Gys2 gene plays a critical role in liver glycogen synthesis. To test whether the Gys2 gene has undergone adaptive evolution in bats with carbohydrate-rich diets in relation to their insect-eating sister taxa, we sequenced the coding region of the Gys2 gene in a number of bat species, including three Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our results showed that the Gys2 coding sequences are highly conserved across all bat species we examined, and no evidence of positive selection was detected in the ancestral branches leading to OWFBs and NWFBs. Our explicit convergence test showed that posterior probabilities of convergence between several branches of OWFBs, and the NWFBs were markedly higher than that of divergence. Three parallel amino acid substitutions (Q72H, K371Q, and E666D) were detected among branches of OWFBs and NWFBs. Tests for parallel evolution showed that two parallel substitutions (Q72H and E666D) were driven by natural selection, while the K371Q was more likely to be fixed randomly. Thus, our results suggested that the Gys2 gene has undergone parallel evolution on amino acid level between OWFBs and NWFBs in relation to their carbohydrate metabolism.

Fast hydrological model calibration based on the heterogeneous parallel computing accelerated shuffled complex evolution method

NASA Astrophysics Data System (ADS)

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Hong, Yang; Zuo, Depeng; Ren, Minglei; Lei, Tianjie; Liang, Ke

2018-01-01

Hydrological model calibration has been a hot issue for decades. The shuffled complex evolution method developed at the University of Arizona (SCE-UA) has been proved to be an effective and robust optimization approach. However, its computational efficiency deteriorates significantly when the amount of hydrometeorological data increases. In recent years, the rise of heterogeneous parallel computing has brought hope for the acceleration of hydrological model calibration. This study proposed a parallel SCE-UA method and applied it to the calibration of a watershed rainfall-runoff model, the Xinanjiang model. The parallel method was implemented on heterogeneous computing systems using OpenMP and CUDA. Performance testing and sensitivity analysis were carried out to verify its correctness and efficiency. Comparison results indicated that heterogeneous parallel computing-accelerated SCE-UA converged much more quickly than the original serial version and possessed satisfactory accuracy and stability for the task of fast hydrological model calibration.

Global analysis of genes involved in freshwater adaptation in threespine sticklebacks (Gasterosteus aculeatus).

PubMed

DeFaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Goto, Akira; Merilä, Juha

2011-06-01

Examples of parallel evolution of phenotypic traits have been repeatedly demonstrated in threespine sticklebacks (Gasterosteus aculeatus) across their global distribution. Using these as a model, we performed a targeted genome scan--focusing on physiologically important genes potentially related to freshwater adaptation--to identify genetic signatures of parallel physiological evolution on a global scale. To this end, 50 microsatellite loci, including 26 loci within or close to (<6 kb) physiologically important genes, were screened in paired marine and freshwater populations from six locations across the Northern Hemisphere. Signatures of directional selection were detected in 24 loci, including 17 physiologically important genes, in at least one location. Although no loci showed consistent signatures of selection in all divergent population pairs, several outliers were common in multiple locations. In particular, seven physiologically important genes, as well as reference ectodysplasin gene (EDA), showed signatures of selection in three or more locations. Hence, although these results give some evidence for consistent parallel molecular evolution in response to freshwater colonization, they suggest that different evolutionary pathways may underlie physiological adaptation to freshwater habitats within the global distribution of the threespine stickleback. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution: (Nei Lecture, SMBE 2014, Puerto Rico).

PubMed

Gaut, Brandon S

2015-07-01

In this commentary, I make inferences about the level of repeatability and constraint in the evolutionary process, based on two sets of replicated experiments. The first experiment is crop domestication, which has been replicated across many different species. I focus on results of whole-genome scans for genes selected during domestication and ask whether genes are, in fact, selected in parallel across different domestication events. If genes are selected in parallel, it implies that the number of genetic solutions to the challenge of domestication is constrained. However, I find no evidence for parallel selection events either between species (maize vs. rice) or within species (two domestication events within beans). These results suggest that there are few constraints on genetic adaptation, but conclusions must be tempered by several complicating factors, particularly the lack of explicit design standards for selection screens. The second experiment involves the evolution of Escherichia coli to thermal stress. Unlike domestication, this highly replicated experiment detected a limited set of genes that appear prone to modification during adaptation to thermal stress. However, the number of potentially beneficial mutations within these genes is large, such that adaptation is constrained at the genic level but much less so at the nucleotide level. Based on these two experiments, I make the general conclusion that evolution is remarkably flexible, despite the presence of epistatic interactions that constrain evolutionary trajectories. I also posit that evolution is so rapid that we should establish a Speciation Prize, to be awarded to the first researcher who demonstrates speciation with a sexual organism in the laboratory. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites.

PubMed

Leinweber, Matthias; Fober, Thomas; Freisleben, Bernd

2018-01-01

In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations. Binary classification tests based on the ATP, NADH, and FAD protein subsets of CavBase, a database containing putative binding sites, show average classification rate improvements from about 92 percent (CPU) to 96 percent (GPU). Further experiments indicate that the proposed GPU-based labeled point cloud superpositioning approach can be superior to traditional protein comparison approaches based on sequence alignments.

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

PubMed Central

Pankey, M. Sabrina; Minin, Vladimir N.; Imholte, Greg C.; Suchard, Marc A.; Oakley, Todd H.

2014-01-01

Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species’ photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them. PMID:25336755

Experimental evolution reveals hidden diversity in evolutionary pathways.

PubMed

Lind, Peter A; Farr, Andrew D; Rainey, Paul B

2015-03-25

Replicate populations of natural and experimental organisms often show evidence of parallel genetic evolution, but the causes are unclear. The wrinkly spreader morph of Pseudomonas fluorescens arises repeatedly during experimental evolution. The mutational causes reside exclusively within three pathways. By eliminating these, 13 new mutational pathways were discovered with the newly arising WS types having fitnesses similar to those arising from the commonly passaged routes. Our findings show that parallel genetic evolution is strongly biased by constraints and we reveal the genetic bases. From such knowledge, and in instances where new phenotypes arise via gene activation, we suggest a set of principles: evolution proceeds firstly via pathways subject to negative regulation, then via promoter mutations and gene fusions, and finally via activation by intragenic gain-of-function mutations. These principles inform evolutionary forecasting and have relevance to interpreting the diverse array of mutations associated with clinically identical instances of disease in humans.

Parallel Electrochemical Treatment System and Application for Identifying Acid-Stable Oxygen Evolution Electrocatalysts

DOE PAGES

Jones, Ryan J. R.; Shinde, Aniketa; Guevarra, Dan; ...

2015-01-05

There are many energy technologies require electrochemical stability or preactivation of functional materials. Due to the long experiment duration required for either electrochemical preactivation or evaluation of operational stability, parallel screening is required to enable high throughput experimentation. We found that imposing operational electrochemical conditions to a library of materials in parallel creates several opportunities for experimental artifacts. We discuss the electrochemical engineering principles and operational parameters that mitigate artifacts int he parallel electrochemical treatment system. We also demonstrate the effects of resistive losses within the planar working electrode through a combination of finite element modeling and illustrative experiments. Operationmore » of the parallel-plate, membrane-separated electrochemical treatment system is demonstrated by exposing a composition library of mixed metal oxides to oxygen evolution conditions in 1M sulfuric acid for 2h. This application is particularly important because the electrolysis and photoelectrolysis of water are promising future energy technologies inhibited by the lack of highly active, acid-stable catalysts containing only earth abundant elements.« less

Genomics of parallel adaptation at two timescales in Drosophila

PubMed Central

Begun, David J.

2017-01-01

Two interesting unanswered questions are the extent to which both the broad patterns and genetic details of adaptive divergence are repeatable across species, and the timescales over which parallel adaptation may be observed. Drosophila melanogaster is a key model system for population and evolutionary genomics. Findings from genetics and genomics suggest that recent adaptation to latitudinal environmental variation (on the timescale of hundreds or thousands of years) associated with Out-of-Africa colonization plays an important role in maintaining biological variation in the species. Additionally, studies of interspecific differences between D. melanogaster and its sister species D. simulans have revealed that a substantial proportion of proteins and amino acid residues exhibit adaptive divergence on a roughly few million years long timescale. Here we use population genomic approaches to attack the problem of parallelism between D. melanogaster and a highly diverged conger, D. hydei, on two timescales. D. hydei, a member of the repleta group of Drosophila, is similar to D. melanogaster, in that it too appears to be a recently cosmopolitan species and recent colonizer of high latitude environments. We observed parallelism both for genes exhibiting latitudinal allele frequency differentiation within species and for genes exhibiting recurrent adaptive protein divergence between species. Greater parallelism was observed for long-term adaptive protein evolution and this parallelism includes not only the specific genes/proteins that exhibit adaptive evolution, but extends even to the magnitudes of the selective effects on interspecific protein differences. Thus, despite the roughly 50 million years of time separating D. melanogaster and D. hydei, and despite their considerably divergent biology, they exhibit substantial parallelism, suggesting the existence of a fundamental predictability of adaptive evolution in the genus. PMID:28968391

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice.

PubMed

Vigueira, C C; Li, W; Olsen, K M

2013-08-01

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution.

PubMed

Reno, Philip L

2014-01-01

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.(1-4) However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan-Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo-devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution. © 2014 Wiley Periodicals, Inc.

Cancer heterogeneity: converting a limitation into a source of biologic information.

PubMed

Rübben, Albert; Araujo, Arturo

2017-09-08

Analysis of spatial and temporal genetic heterogeneity in human cancers has revealed that somatic cancer evolution in most cancers is not a simple linear process composed of a few sequential steps of mutation acquisitions and clonal expansions. Parallel evolution has been observed in many early human cancers resulting in genetic heterogeneity as well as multilineage progression. Moreover, aneuploidy as well as structural chromosomal aberrations seems to be acquired in a non-linear, punctuated mode where most aberrations occur at early stages of somatic cancer evolution. At later stages, the cancer genomes seem to get stabilized and acquire only few additional rearrangements. While parallel evolution suggests positive selection of driver mutations at early stages of somatic cancer evolution, stabilization of structural aberrations at later stages suggests that negative selection takes effect when cancer cells progressively lose their tolerance towards additional mutation acquisition. Mixing of genetically heterogeneous subclones in cancer samples reduces sensitivity of mutation detection. Moreover, driver mutations present only in a fraction of cancer cells are more likely to be mistaken for passenger mutations. Therefore, genetic heterogeneity may be considered a limitation negatively affecting detection sensitivity of driver mutations. On the other hand, identification of subclones and subclone lineages in human cancers may lead to a more profound understanding of the selective forces which shape somatic cancer evolution in human cancers. Identification of parallel evolution by analyzing spatial heterogeneity may hint to driver mutations which might represent additional therapeutic targets besides driver mutations present in a monoclonal state. Likewise, stabilization of cancer genomes which can be identified by analyzing temporal genetic heterogeneity might hint to genes and pathways which have become essential for survival of cancer cell lineages at later stages of cancer evolution. These genes and pathways might also constitute patient specific therapeutic targets.

Genetic adaptations of the plateau zokor in high-elevation burrows.

PubMed

Shao, Yong; Li, Jin-Xiu; Ge, Ri-Li; Zhong, Li; Irwin, David M; Murphy, Robert W; Zhang, Ya-Ping

2015-11-25

The plateau zokor (Myospalax baileyi) spends its entire life underground in sealed burrows. Confronting limited oxygen and high carbon dioxide concentrations, and complete darkness, they epitomize a successful physiological adaptation. Here, we employ transcriptome sequencing to explore the genetic underpinnings of their adaptations to this unique habitat. Compared to Rattus norvegicus, genes belonging to GO categories related to energy metabolism (e.g. mitochondrion and fatty acid beta-oxidation) underwent accelerated evolution in the plateau zokor. Furthermore, the numbers of positively selected genes were significantly enriched in the gene categories involved in ATPase activity, blood vessel development and respiratory gaseous exchange, functional categories that are relevant to adaptation to high altitudes. Among the 787 genes with evidence of parallel evolution, and thus identified as candidate genes, several GO categories (e.g. response to hypoxia, oxygen homeostasis and erythrocyte homeostasis) are significantly enriched, are two genes, EPAS1 and AJUBA, involved in the response to hypoxia, where the parallel evolved sites are at positions that are highly conserved in sequence alignments from multiple species. Thus, accelerated evolution of GO categories, positive selection and parallel evolution at the molecular level provide evidences to parse the genetic adaptations of the plateau zokor for living in high-elevation burrows.

Linguistics: evolution and language change.

PubMed

Bowern, Claire

2015-01-05

Linguists have long identified sound changes that occur in parallel. Now novel research shows how Bayesian modeling can capture complex concerted changes, revealing how evolution of sounds proceeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Convergent, Parallel and Correlated Evolution of Trophic Morphologies in the Subfamily Schizothoracinae from the Qinghai-Tibetan Plateau

PubMed Central

Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

2012-01-01

Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP. PMID:22470515

Experimental evolution reveals hidden diversity in evolutionary pathways

PubMed Central

Lind, Peter A; Farr, Andrew D; Rainey, Paul B

2015-01-01

Replicate populations of natural and experimental organisms often show evidence of parallel genetic evolution, but the causes are unclear. The wrinkly spreader morph of Pseudomonas fluorescens arises repeatedly during experimental evolution. The mutational causes reside exclusively within three pathways. By eliminating these, 13 new mutational pathways were discovered with the newly arising WS types having fitnesses similar to those arising from the commonly passaged routes. Our findings show that parallel genetic evolution is strongly biased by constraints and we reveal the genetic bases. From such knowledge, and in instances where new phenotypes arise via gene activation, we suggest a set of principles: evolution proceeds firstly via pathways subject to negative regulation, then via promoter mutations and gene fusions, and finally via activation by intragenic gain-of-function mutations. These principles inform evolutionary forecasting and have relevance to interpreting the diverse array of mutations associated with clinically identical instances of disease in humans. DOI: http://dx.doi.org/10.7554/eLife.07074.001 PMID:25806684

In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases.

PubMed

Li, Mingai; Xu, Jia; Algarra Alarcon, Alberto; Carlin, Silvia; Barbaro, Enrico; Cappellin, Luca; Velikova, Violeta; Vrhovsek, Urska; Loreto, Francesco; Varotto, Claudio

2017-10-01

Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals.

PubMed

Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Ren, Hai-Qing; Shi, Peng

2014-09-01

Echolocation is a sensory system whereby certain mammals navigate and forage using sound waves, usually in environments where visibility is limited. Curiously, echolocation has evolved independently in bats and whales, which occupy entirely different environments. Based on this phenotypic convergence, recent studies identified several echolocation-related genes with parallel sites at the protein sequence level among different echolocating mammals, and among these, prestin seems the most promising. Although previous studies analyzed the evolutionary mechanism of prestin, the functional roles of the parallel sites in the evolution of mammalian echolocation are not clear. By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency (CF) bat, the Stoliczka's trident bat (Aselliscus stoliczkanus). The parallel site of I384T between toothed whales and CF bats was responsible for this functional convergence. Furthermore, the two parameters (1/α and V1/2) were correlated with mammalian high-frequency hearing, suggesting that the convergent changes of the prestin function in echolocating mammals may play important roles in mammalian echolocation. To our knowledge, these findings present the functional patterns of echolocation-related genes in echolocating mammals for the first time and rigorously demonstrate adaptive parallel evolution at the protein sequence level, paving the way to insights into the molecular mechanism underlying mammalian echolocation. © 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.

Parallel Evolution of Sperm Hyper-Activation Ca2+ Channels.

PubMed

Cooper, Jacob C; Phadnis, Nitin

2017-07-01

Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence. Here, we use a comprehensive phylogenomic approach to investigate the selective pressures on these sperm hyper-activation channels. First, we find that the entire CatSper complex evolves rapidly under recurrent positive selection in primates. Second, we find that pkd2 has parallel patterns of adaptive evolution in Drosophila. Third, we show that this adaptive evolution of pkd2 is driven by its role in sperm hyper-activation. These patterns of selection suggest that the evolution of the sperm hyper-activation machinery is driven by sexual conflict with antagonistic ligands that modulate channel activity. Together, our results add sperm hyper-activation channels to the class of fast evolving reproductive proteins and provide insights into the mechanisms used by the sexes to manipulate sperm behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases

PubMed Central

Li, Mingai; Xu, Jia; Algarra Alarcon, Alberto; Carlin, Silvia; Barbaro, Enrico; Cappellin, Luca; Velikova, Violeta; Vrhovsek, Urska; Loreto, Francesco; Varotto, Claudio

2017-01-01

Abstract Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance. PMID:28637270

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; Beers, Andrew; Woodrow, Thomas S. (Technical Monitor)

1996-01-01

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

Proton core-beam system in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Hellinger, Petr; Trávníček, Pavel M.

2011-11-01

Results of a two-dimensional hybrid expanding box simulation of a proton beam-core system in the solar wind are presented. The expansion with a strictly radial magnetic field leads to a decrease of the ratio between the proton perpendicular and parallel temperatures as well as to an increase of the ratio between the beam-core differential velocity and the local Alfvén velocity creating a free energy for many different instabilities. The system is indeed most of the time marginally stable with respect to the parallel magnetosonic, oblique Alfvén, proton cyclotron and parallel fire hose instabilities which determine the system evolution counteracting some effects of the expansion and interacting with each other. Nonlinear evolution of these instabilities leads to large modifications of the proton velocity distribution function. The beam and core protons are slowed with respect to each other and heated, and at later stages of the evolution the two populations are not clearly distinguishable. On the macroscopic level the instabilities cause large departures from the double adiabatic prediction leading to an efficient isotropization of effective proton temperatures in agreement with Helios observations.

Parallel Evolution of Sperm Hyper-Activation Ca2+ Channels

PubMed Central

Phadnis, Nitin

2017-01-01

Abstract Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence. Here, we use a comprehensive phylogenomic approach to investigate the selective pressures on these sperm hyper-activation channels. First, we find that the entire CatSper complex evolves rapidly under recurrent positive selection in primates. Second, we find that pkd2 has parallel patterns of adaptive evolution in Drosophila. Third, we show that this adaptive evolution of pkd2 is driven by its role in sperm hyper-activation. These patterns of selection suggest that the evolution of the sperm hyper-activation machinery is driven by sexual conflict with antagonistic ligands that modulate channel activity. Together, our results add sperm hyper-activation channels to the class of fast evolving reproductive proteins and provide insights into the mechanisms used by the sexes to manipulate sperm behavior. PMID:28810709

Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form.

PubMed Central

Morrison, C L; Harvey, A W; Lavery, S; Tieu, K; Huang, Y; Cunningham, C W

2002-01-01

The repeated appearance of strikingly similar crab-like forms in independent decapod crustacean lineages represents a remarkable case of parallel evolution. Uncertainty surrounding the phylogenetic relationships among crab-like lineages has hampered evolutionary studies. As is often the case, aligned DNA sequences by themselves were unable to fully resolve these relationships. Four nested mitochondrial gene rearrangements--including one of the few reported movements of an arthropod protein-coding gene--are congruent with the DNA phylogeny and help to resolve a crucial node. A phylogenetic analysis of DNA sequences, and gene rearrangements, supported five independent origins of the crab-like form, and suggests that the evolution of the crab-like form may be irreversible. This result supports the utility of mitochondrial gene rearrangements in phylogenetic reconstruction. PMID:11886621

Waterfalls drive parallel evolution in a freshwater goby

PubMed Central

Kano, Yuichi; Nishida, Shin; Nakajima, Jun

2012-01-01

Waterfalls may affect fish distribution and genetic structure within drainage networks even to the extent of leading evolutionary events. Here, parallel evolution was studied by focusing on waterfall and the landlocked freshwater goby Rhinogobius sp. YB (YB), which evolved from amphidromous R. brunneus (BR). The fish fauna was surveyed at 30 sites in 11 rivers on Iriomote Island, Japan, the geography of which was characterized by terraces/tablelands with many waterfalls. We found that all YB individuals were distributed only above waterfalls (height 6.8–58.7 m), whereas BR, and other fishes, were mostly distributed below waterfalls. Mitochondrial DNA analysis showed that every YB local population above the waterfall was independently evolved from BR. In contrast, cluster analysis of nine morphological characters, such as fin color and body pattern, showed that the morphology of YB individuals held a similarity beyond the genetic divergence, suggesting parallel evolution has occurred relating to their morphology. Genetic distance between each YB local population and BR was significantly correlated with waterfall height (r2 = 0.94), suggesting that the waterfalls have been heightened due to the constant geological erosion and that their height represents the isolation period of YB local populations from BR (ca. 11,000–88,000 years). Each local population of BR was once landlocked in upstream by waterfall formation, consequently evolving to YB in each site. Although the morphology of YB had a high degree of similarity among local populations, finer scale analysis showed that the morphology of YB was significantly correlated with the genetic distance from BR. Consequently, there could be simultaneous multiple phases of allopatric/parallel evolution of the goby due to variations in waterfall height on this small island. PMID:22957183

A Balanced Mixture of Antagonistic Pressures Promotes the Evolution of Parallel Movement

NASA Astrophysics Data System (ADS)

Demšar, Jure; Štrumbelj, Erik; Lebar Bajec, Iztok

2016-12-01

A common hypothesis about the origins of collective behaviour suggests that animals might live and move in groups to increase their chances of surviving predator attacks. This hypothesis is supported by several studies that use computational models to simulate natural evolution. These studies, however, either tune an ad-hoc model to ‘reproduce’ collective behaviour, or concentrate on a single type of predation pressure, or infer the emergence of collective behaviour from an increase in prey density. In nature, prey are often targeted by multiple predator species simultaneously and this might have played a pivotal role in the evolution of collective behaviour. We expand on previous research by using an evolutionary rule-based system to simulate the evolution of prey behaviour when prey are subject to multiple simultaneous predation pressures. We analyse the evolved behaviour via prey density, polarization, and angular momentum. Our results suggest that a mixture of antagonistic external pressures that simultaneously steer prey towards grouping and dispersing might be required for prey individuals to evolve dynamic parallel movement.

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

NASA Astrophysics Data System (ADS)

Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

2017-02-01

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

Teaching and Learning: Highlighting the Parallels between Education and Participatory Evaluation.

ERIC Educational Resources Information Center

Vanden Berk, Eric J.; Cassata, Jennifer Coyne; Moye, Melinda J.; Yarbrough, Donald B.; Siddens, Stephanie K.

As an evaluation team trained in educational psychology and committed to participatory evaluation and its evolution, the researchers have found the parallel between evaluator-stakeholder roles in the participatory evaluation process and educator-student roles in educational psychology theory to be important. One advantage then is that the theories…

New Parallel Algorithms for Landscape Evolution Model

NASA Astrophysics Data System (ADS)

Jin, Y.; Zhang, H.; Shi, Y.

2017-12-01

Most landscape evolution models (LEM) developed in the last two decades solve the diffusion equation to simulate the transportation of surface sediments. This numerical approach is difficult to parallelize due to the computation of drainage area for each node, which needs huge amount of communication if run in parallel. In order to overcome this difficulty, we developed two parallel algorithms for LEM with a stream net. One algorithm handles the partition of grid with traditional methods and applies an efficient global reduction algorithm to do the computation of drainage areas and transport rates for the stream net; the other algorithm is based on a new partition algorithm, which partitions the nodes in catchments between processes first, and then partitions the cells according to the partition of nodes. Both methods focus on decreasing communication between processes and take the advantage of massive computing techniques, and numerical experiments show that they are both adequate to handle large scale problems with millions of cells. We implemented the two algorithms in our program based on the widely used finite element library deal.II, so that it can be easily coupled with ASPECT.

Parallel genetic origins of pelvic reduction in vertebrates

PubMed Central

Shapiro, Michael D.; Bell, Michael A.; Kingsley, David M.

2006-01-01

Despite longstanding interest in parallel evolution, little is known about the genes that control similar traits in different lineages of vertebrates. Pelvic reduction in stickleback fish (family Gasterosteidae) provides a striking example of parallel evolution in a genetically tractable system. Previous studies suggest that cis-acting regulatory changes at the Pitx1 locus control pelvic reduction in a population of threespine sticklebacks (Gasterosteus aculeatus). In this study, progeny from intergeneric crosses between pelvic-reduced threespine and ninespine (Pungitius pungitius) sticklebacks also showed severe pelvic reduction, implicating a similar genetic origin for this trait in both genera. Comparative sequencing studies in complete and pelvic-reduced Pungitius revealed no differences in the Pitx1 coding sequences, but Pitx1 expression was absent from the prospective pelvic region of larvae from pelvic-reduced parents. A much more phylogenetically distant example of pelvic reduction, loss of hindlimbs in manatees, shows a similar left–right size bias that is a morphological signature of Pitx1-mediated pelvic reduction in both sticklebacks and mice. These multiple lines of evidence suggest that changes in Pitx1 may represent a key mechanism of morphological evolution in multiple populations, species, and genera of sticklebacks, as well as in distantly related vertebrate lineages. PMID:16945911

Protons and alpha particles in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Hellinger, Petr; Trávníček, Pavel M.

2013-09-01

We present results of a two‒dimensional hybrid expanding box simulation of a plasma system with three ion populations, beam and core protons, and alpha particles (and fluid electrons), drifting with respect to each other. The expansion with a strictly radial magnetic field leads to a decrease of the ion perpendicular to parallel temperature ratios as well as to an increase of the ratio between the ion relative velocities and the local Alfvén velocity creating a free energy for many different instabilities. The system is most of the time marginally stable with respect to kinetic instabilities mainly due to the ion relative velocities; these instabilities determine the system evolution counteracting some effects of the expansion. Nonlinear evolution of these instabilities leads to large modifications of the ion velocity distribution functions. The beam protons and alpha particles are decelerated with respect to the core protons and all the populations are cooled in the parallel direction and heated in the perpendicular one. On the macroscopic level, the kinetic instabilities cause large departures of the system evolution from the double adiabatic prediction and lead to perpendicular heating and parallel cooling rates which are comparable to the heating rates estimated from the Helios observations.

Candidate genes and adaptive radiation: insights from transcriptional adaptation to the limnetic niche among coregonine fishes (Coregonus spp., Salmonidae).

PubMed

Jeukens, Julie; Bittner, David; Knudsen, Rune; Bernatchez, Louis

2009-01-01

In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In the lake whitefish species complex (Coregonus clupeaformis), previous microarray experiments have led to the identification of candidate genes potentially implicated in the parallel evolution of the limnetic dwarf lake whitefish, which is highly distinct from the benthic normal lake whitefish in life history, morphology, metabolism, and behavior, and yet diverged from it only approximately 15,000 years before present. The aim of the present study was to address transcriptional divergence for six candidate genes among lake whitefish and European whitefish (Coregonus lavaretus) species pairs, as well as lake cisco (Coregonus artedi) and vendace (Coregonus albula). The main goal was to test the hypothesis that parallel phenotypic adaptation toward the use of the limnetic niche in coregonine fishes is accompanied by parallelism in candidate gene transcription as measured by quantitative real-time polymerase chain reaction. Results obtained for three candidate genes, whereby parallelism in expression was observed across all whitefish species pairs, provide strong support for the hypothesis that divergent natural selection plays an important role in the adaptive radiation of whitefish species. However, this parallelism in expression did not extend to cisco and vendace, thereby infirming transcriptional convergence between limnetic whitefish species and their limnetic congeners for these genes. As recently proposed (Lynch 2007a. The evolution of genetic networks by non-adaptive processes. Nat Rev Genet. 8:803-813), these results may suggest that convergent phenotypic evolution can result from nonadaptive shaping of genome architecture in independently evolved coregonine lineages.

Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change.

PubMed

Thorpe, Roger S; Barlow, Axel; Malhotra, Anita; Surget-Groba, Yann

2015-03-01

Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot. © 2015 John Wiley & Sons Ltd.

Parallel evolution of mound-building and grass-feeding in Australian nasute termites.

PubMed

Arab, Daej A; Namyatova, Anna; Evans, Theodore A; Cameron, Stephen L; Yeates, David K; Ho, Simon Y W; Lo, Nathan

2017-02-01

Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes. © 2017 The Author(s).

The genomics of selection in dogs and the parallel evolution between dogs and humans.

PubMed

Wang, Guo-dong; Zhai, Weiwei; Yang, He-chuan; Fan, Ruo-xi; Cao, Xue; Zhong, Li; Wang, Lu; Liu, Fei; Wu, Hong; Cheng, Lu-guang; Poyarkov, Andrei D; Poyarkov, Nikolai A; Tang, Shu-sheng; Zhao, Wen-ming; Gao, Yun; Lv, Xue-mei; Irwin, David M; Savolainen, Peter; Wu, Chung-I; Zhang, Ya-ping

2013-01-01

The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

Phylogeny of the TRAF/MATH domain.

PubMed

Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

2007-01-01

The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

The modern temperature-accelerated dynamics approach

DOE PAGES

Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny; ...

2016-06-01

Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, thesemore » enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. Here, we review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD.« less

Pursuing Darwin’s curious parallel: Prospects for a science of cultural evolution

PubMed Central

2017-01-01

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities. PMID:28739929

Pursuing Darwin's curious parallel: Prospects for a science of cultural evolution.

PubMed

Mesoudi, Alex

2017-07-24

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities.

Creationism as a Misconception: Socio-Cognitive Conflict in the Teaching of Evolution

ERIC Educational Resources Information Center

Foster, Colin

2012-01-01

This position paper argues that students' understanding and acceptance of evolution may be supported, rather than hindered, by classroom discussion of creationism. Parallels are drawn between creationism and other scientific misconceptions, both of the scientific community in the past and of students in the present. Science teachers frequently…

A low-altitude mechanism for mesoscale dynamics, structure, and current filamentation in the discrete aurora

NASA Technical Reports Server (NTRS)

Keskinen, M. J.; Chaturvedi, P. K.; Ossakow, S. L.

1992-01-01

The 2D nonlinear evolution of the ionization-driven adiabatic auroral arc instability is studied. We find: (1) the adiabatic auroral arc instability can fully develop on time scales of tens to hundreds of seconds and on spatial scales of tens to hundreds of kilometers; (2) the evolution of this instability leads to nonlinear 'hook-shaped' conductivity structures: (3) this instability can lead to parallel current filamentation over a wide range of scale sizes; and (4) the k-spectra of the density, electric field, and parallel current develop into inverse power laws in agreement with satellite observations. Comparison with mesoscale auroral phenomenology and current filamentation structures is made.

Generation and evolution of anisotropic turbulence and related energy transfer in a multi-species solar wind

NASA Astrophysics Data System (ADS)

Maneva, Yana; Poedts, Stefaan

2017-04-01

The electromagnetic fluctuations in the solar wind represent a zoo of plasma waves with different properties, whose wavelengths range from largest fluid scales to the smallest dissipation scales. By nature the power spectrum of the magnetic fluctuations is anisotropic with different spectral slopes in parallel and perpendicular directions with respect to the background magnetic field. Furthermore, the magnetic field power spectra steepen as one moves from the inertial to the dissipation range and we observe multiple spectral breaks with different slopes in parallel and perpendicular direction at the ion scales and beyond. The turbulent dissipation of magnetic field fluctuations at the sub-ion scales is believed to go into local ion heating and acceleration, so that the spectral breaks are typically associated with particle energization. The gained energy can be in the form of anisotropic heating, formation of non-thermal features in the particle velocity distributions functions, and redistribution of the differential acceleration between the different ion populations. To study the relation between the evolution of the anisotropic turbulent spectra and the particle heating at the ion and sub-ion scales we perform a series of 2.5D hybrid simulations in a collisionless drifting proton-alpha plasma. We neglect the fast electron dynamics and treat the electrons as an isothermal fluid electrons, whereas the protons and a minor population of alpha particles are evolved in a fully kinetic manner. We start with a given wave spectrum and study the evolution of the magnetic field spectral slopes as a function of the parallel and perpendicular wave¬numbers. Simultaneously, we track the particle response and the energy exchange between the parallel and perpendicular scales. We observe anisotropic behavior of the turbulent power spectra with steeper slopes along the dominant energy-containing direction. This means that for parallel and quasi-parallel waves we have steeper spectral slope in parallel direction, whereas for highly oblique waves the dissipation occurs predominantly in perpendicular direction and the spectral slopes are steeper across the background magnetic field. The value of the spectral slopes depends on the angle of propagation, the spectral range, as well as the plasma properties. In general the dissipation is stronger at small scales and the corresponding spectral slopes there are steeper. For parallel and quasi-parallel propagation the prevailing energy cascade remains along the magnetic field, whereas for initially isotropic oblique turbulence the cascade develops mainly in perpendicular direction.

A Parallel Genetic Algorithm for Automated Electronic Circuit Design

NASA Technical Reports Server (NTRS)

Lohn, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris; Norvig, Peter (Technical Monitor)

2000-01-01

We describe a parallel genetic algorithm (GA) that automatically generates circuit designs using evolutionary search. A circuit-construction programming language is introduced and we show how evolution can generate practical analog circuit designs. Our system allows circuit size (number of devices), circuit topology, and device values to be evolved. We present experimental results as applied to analog filter and amplifier design tasks.

Genetic Parallel Programming: design and implementation.

PubMed

Cheang, Sin Man; Leung, Kwong Sak; Lee, Kin Hong

2006-01-01

This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.

Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations.

PubMed

Tobler, Ray; Hermisson, Joachim; Schlötterer, Christian

2015-07-01

Thermal stress is a pervasive selective agent in natural populations that impacts organismal growth, survival, and reproduction. Drosophila melanogaster exhibits a variety of putatively adaptive phenotypic responses to thermal stress in natural and experimental settings; however, accompanying assessments of fitness are typically lacking. Here, we quantify changes in fitness and known thermal tolerance traits in replicated experimental D. melanogaster populations following more than 40 generations of evolution to either cyclic cold or hot temperatures. By evaluating fitness for both evolved populations alongside a reconstituted starting population, we show that the evolved populations were the best adapted within their respective thermal environments. More strikingly, the evolved populations exhibited increased fitness in both environments and improved resistance to both acute heat and cold stress. This unexpected parallel response appeared to be an adaptation to the rapid temperature changes that drove the cycling thermal regimes, as parallel fitness changes were not observed when tested in a constant thermal environment. Our results add to a small, but growing group of studies that demonstrate the importance of fluctuating temperature changes for thermal adaptation and highlight the need for additional work in this area. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

PubMed

Schrider, Daniel R; Hahn, Matthew W; Begun, David J

2016-05-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. © 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.

Parallel dynamics between non-Hermitian and Hermitian systems

NASA Astrophysics Data System (ADS)

Wang, P.; Lin, S.; Jin, L.; Song, Z.

2018-06-01

We reveals a connection between non-Hermitian and Hermitian systems by studying the connection between a family of non-Hermitian and Hermitian Hamiltonians based on exact solutions. In general, for a dynamic process in a non-Hermitian system H , there always exists a parallel dynamic process governed by the corresponding Hermitian conjugate system H†. We show that a linear superposition of the two parallel dynamics is exactly equivalent to the time evolution of a state under a Hermitian Hamiltonian H , and we present the relations between {H ,H ,H†} .

MEvoLib v1.0: the first molecular evolution library for Python.

PubMed

Álvarez-Jarreta, Jorge; Ruiz-Pesini, Eduardo

2016-10-28

Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank's features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.

Constraints in cancer evolution.

PubMed

Venkatesan, Subramanian; Birkbak, Nicolai J; Swanton, Charles

2017-02-08

Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution. The presence of (1) parallel evolution, (2) convergent evolution and (3) the biological impact of acquiring mutations in specific orders suggest that cancer evolution may be exploitable. These constraints on cancer evolution may help us identify cancer evolutionary rule books, which could eventually inform both diagnostic and therapeutic approaches to improve survival outcomes. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Methodes iteratives paralleles: Applications en neutronique et en mecanique des fluides

NASA Astrophysics Data System (ADS)

Qaddouri, Abdessamad

Dans cette these, le calcul parallele est applique successivement a la neutronique et a la mecanique des fluides. Dans chacune de ces deux applications, des methodes iteratives sont utilisees pour resoudre le systeme d'equations algebriques resultant de la discretisation des equations du probleme physique. Dans le probleme de neutronique, le calcul des matrices des probabilites de collision (PC) ainsi qu'un schema iteratif multigroupe utilisant une methode inverse de puissance sont parallelises. Dans le probleme de mecanique des fluides, un code d'elements finis utilisant un algorithme iteratif du type GMRES preconditionne est parallelise. Cette these est presentee sous forme de six articles suivis d'une conclusion. Les cinq premiers articles traitent des applications en neutronique, articles qui representent l'evolution de notre travail dans ce domaine. Cette evolution passe par un calcul parallele des matrices des PC et un algorithme multigroupe parallele teste sur un probleme unidimensionnel (article 1), puis par deux algorithmes paralleles l'un mutiregion l'autre multigroupe, testes sur des problemes bidimensionnels (articles 2--3). Ces deux premieres etapes sont suivies par l'application de deux techniques d'acceleration, le rebalancement neutronique et la minimisation du residu aux deux algorithmes paralleles (article 4). Finalement, on a mis en oeuvre l'algorithme multigroupe et le calcul parallele des matrices des PC sur un code de production DRAGON ou les tests sont plus realistes et peuvent etre tridimensionnels (article 5). Le sixieme article (article 6), consacre a l'application a la mecanique des fluides, traite la parallelisation d'un code d'elements finis FES ou le partitionneur de graphe METIS et la librairie PSPARSLIB sont utilises.

Towards physical principles of biological evolution

NASA Astrophysics Data System (ADS)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.

Parallel programming with Easy Java Simulations

NASA Astrophysics Data System (ADS)

Esquembre, F.; Christian, W.; Belloni, M.

2018-01-01

Nearly all of today's processors are multicore, and ideally programming and algorithm development utilizing the entire processor should be introduced early in the computational physics curriculum. Parallel programming is often not introduced because it requires a new programming environment and uses constructs that are unfamiliar to many teachers. We describe how we decrease the barrier to parallel programming by using a java-based programming environment to treat problems in the usual undergraduate curriculum. We use the easy java simulations programming and authoring tool to create the program's graphical user interface together with objects based on those developed by Kaminsky [Building Parallel Programs (Course Technology, Boston, 2010)] to handle common parallel programming tasks. Shared-memory parallel implementations of physics problems, such as time evolution of the Schrödinger equation, are available as source code and as ready-to-run programs from the AAPT-ComPADRE digital library.

Transformation and diversification in early mammal evolution.

PubMed

Luo, Zhe-Xi

2007-12-13

Evolution of the earliest mammals shows successive episodes of diversification. Lineage-splitting in Mesozoic mammals is coupled with many independent evolutionary experiments and ecological specializations. Classic scenarios of mammalian morphological evolution tend to posit an orderly acquisition of key evolutionary innovations leading to adaptive diversification, but newly discovered fossils show that evolution of such key characters as the middle ear and the tribosphenic teeth is far more labile among Mesozoic mammals. Successive diversifications of Mesozoic mammal groups multiplied the opportunities for many dead-end lineages to iteratively evolve developmental homoplasies and convergent ecological specializations, parallel to those in modern mammal groups.

Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.

PubMed

Fox, Charles W; Wagner, James D; Cline, Sara; Thomas, Frances Ann; Messina, Frank J

2009-05-01

Independent populations subjected to similar environments often exhibit convergent evolution. An unresolved question is the frequency with which such convergence reflects parallel genetic mechanisms. We examined the convergent evolution of egg-laying behavior in the seed-feeding beetle Callosobruchus maculatus. Females avoid ovipositing on seeds bearing conspecific eggs, but the degree of host discrimination varies among geographic populations. In a previous experiment, replicate lines switched from a small host to a large one evolved reduced discrimination after 40 generations. We used line crosses to determine the genetic architecture underlying this rapid response. The most parsimonious genetic models included dominance and/or epistasis for all crosses. The genetic architecture underlying reduced discrimination in two lines was not significantly different from the architecture underlying differences between geographic populations, but the architecture underlying the divergence of a third line differed from all others. We conclude that convergence of this complex trait may in some cases involve parallel genetic mechanisms.

Parallel evolution of the glycogen synthase 1 (muscle) gene Gys1 between Old World and New World fruit bats (Order: Chiroptera).

PubMed

Fang, Lu; Shen, Bin; Irwin, David M; Zhang, Shuyi

2014-10-01

Glycogen synthase, which catalyzes the synthesis of glycogen, is especially important for Old World (Pteropodidae) and New World (Phyllostomidae) fruit bats that ingest high-carbohydrate diets. Glycogen synthase 1, encoded by the Gys1 gene, is the glycogen synthase isozyme that functions in muscles. To determine whether Gys1 has undergone adaptive evolution in bats with carbohydrate-rich diets, in comparison to insect-eating sister bat taxa, we sequenced the coding region of the Gys1 gene from 10 species of bats, including two Old World fruit bats (Pteropodidae) and a New World fruit bat (Phyllostomidae). Our results show no evidence for positive selection in the Gys1 coding sequence on the ancestral Old World and the New World Artibeus lituratus branches. Tests for convergent evolution indicated convergence of the sequences and one parallel amino acid substitution (T395A) was detected on these branches, which was likely driven by natural selection.

Co-evolution of upstream waves and accelerated ions at parallel shocks

NASA Astrophysics Data System (ADS)

Fujimoto, M.; Sugiyama, T.

2016-12-01

Shock waves in space plasmas have been considered as the agents for various particle acceleration phenomena. The basic idea behind shock acceleration is that particles are accelerated as they move back-and-forth across a shock front. Detailed studies of ion acceleration at the terrestrial bow shock have been performed, however, the restricted maximum energies attained prevent a straight-forward application of obtained knowledge to more energetic astrophysical situations. Here we show by a large-scale self-consistent particle simulation that the co-evolution of magnetic turbulence and accelerated ion population is the foundation for continuous operation of shock acceleration to ever higher energies. Magnetic turbulence is created by ions reflected back upstream of a parallel shock front. The co-evolution arises because more energetic ions excite waves of longer wavelengths, and because longer wavelength modes are capable of scattering (in the upstream) and reflecting (at the shock front) more energetic ions. Via carefully designed numerical experiments, we show very clearly that this picture is true.

Triticum mosaic virus exhibits limited population variation yet shows evidence of parallel evolution after replicated serial passage in wheat.

PubMed

Bartels, Melissa; French, Roy; Graybosch, Robert A; Tatineni, Satyanarayana

2016-05-01

An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed at passages 9, 18 and 24 by single-strand conformation polymorphism, followed by nucleotide sequencing. The founding P1 region genotype was retained at high frequencies in most lineage/passage populations, while the founding CP genotype disappeared after passage 18 in two lineages. We found that rare TriMV genotypes were present only transiently and lineages followed independent evolutionary trajectories, suggesting that genetic drift dominates TriMV evolution. These results further suggest that experimental populations of TriMV exhibit lower mutant frequencies than that of Wheat streak mosaic virus (genus Tritimovirus; family Potyviridae) in wheat. Nevertheless, there was evidence for parallel evolution at a synonymous site in the TriMV CP cistron. Published by Elsevier Inc.

From planes to brains: parallels between military development of virtual reality environments and virtual neurological surgery.

PubMed

Schmitt, Paul J; Agarwal, Nitin; Prestigiacomo, Charles J

2012-01-01

Military explorations of the practical role of simulators have served as a driving force for much of the virtual reality technology that we have today. The evolution of 3-dimensional and virtual environments from the early flight simulators used during World War II to the sophisticated training simulators in the modern military followed a path that virtual surgical and neurosurgical devices have already begun to parallel. By understanding the evolution of military simulators as well as comparing and contrasting that evolution with current and future surgical simulators, it may be possible to expedite the development of appropriate devices and establish their validity as effective training tools. As such, this article presents a historical perspective examining the progression of neurosurgical simulators, the establishment of effective and appropriate curricula for using them, and the contributions that the military has made during the ongoing maturation of this exciting treatment and training modality. Copyright © 2012. Published by Elsevier Inc.

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

PubMed

Lenski, Richard E

2017-10-01

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

Nothing in the History of Spanish "Anis" Makes Sense, Except in the Light of Evolution

ERIC Educational Resources Information Center

Delgado, Juan Antonio; Palma, Ricardo Luis

2011-01-01

We describe, discuss and illustrate a metaphoric parallel between the history of the most famous Spanish liqueur, "Anis del Mono" ("Anis" of the Monkey), and the evolution of living organisms in the light of Darwinian theory and other biological hypotheses published subsequent to Charles Darwin's "Origin of Species." Also, we report the use of a…

Numerical study of the vortex tube reconnection using vortex particle method on many graphics cards

NASA Astrophysics Data System (ADS)

Kudela, Henryk; Kosior, Andrzej

2014-08-01

Vortex Particle Methods are one of the most convenient ways of tracking the vorticity evolution. In the article we presented numerical recreation of the real life experiment concerning head-on collision of two vortex rings. In the experiment the evolution and reconnection of the vortex structures is tracked with passive markers (paint particles) which in viscous fluid does not follow the evolution of vorticity field. In numerical computations we showed the difference between vorticity evolution and movement of passive markers. The agreement with the experiment was very good. Due to problems with very long time of computations on a single processor the Vortex-in-Cell method was implemented on the multicore architecture of the graphics cards (GPUs). Vortex Particle Methods are very well suited for parallel computations. As there are myriads of particles in the flow and for each of them the same equations of motion have to be solved the SIMD architecture used in GPUs seems to be perfect. The main disadvantage in this case is the small amount of the RAM memory. To overcome this problem we created a multiGPU implementation of the VIC method. Some remarks on parallel computing are given in the article.

Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants.

PubMed

Mukherjee, Krishanu; Campos, Henry; Kolaczkowski, Bryan

2013-03-01

RNA interference (RNAi) is a eukaryotic molecular system that serves two primary functions: 1) gene regulation and 2) protection against selfish elements such as viruses and transposable DNA. Although the biochemistry of RNAi has been detailed in model organisms, very little is known about the broad-scale patterns and forces that have shaped RNAi evolution. Here, we provide a comprehensive evolutionary analysis of the Dicer protein family, which carries out the initial RNA recognition and processing steps in the RNAi pathway. We show that Dicer genes duplicated and diversified independently in early animal and plant evolution, coincident with the origins of multicellularity. We identify a strong signature of long-term protein-coding adaptation that has continually reshaped the RNA-binding pocket of the plant Dicer responsible for antiviral immunity, suggesting an evolutionary arms race with viral factors. We also identify key changes in Dicer domain architecture and sequence leading to specialization in either gene-regulatory or protective functions in animal and plant paralogs. As a whole, these results reveal a dynamic picture in which the evolution of Dicer function has driven elaboration of parallel RNAi functional pathways in animals and plants.

Parallel evolution of image processing tools for multispectral imagery

NASA Astrophysics Data System (ADS)

Harvey, Neal R.; Brumby, Steven P.; Perkins, Simon J.; Porter, Reid B.; Theiler, James P.; Young, Aaron C.; Szymanski, John J.; Bloch, Jeffrey J.

2000-11-01

We describe the implementation and performance of a parallel, hybrid evolutionary-algorithm-based system, which optimizes image processing tools for feature-finding tasks in multi-spectral imagery (MSI) data sets. Our system uses an integrated spatio-spectral approach and is capable of combining suitably-registered data from different sensors. We investigate the speed-up obtained by parallelization of the evolutionary process via multiple processors (a workstation cluster) and develop a model for prediction of run-times for different numbers of processors. We demonstrate our system on Landsat Thematic Mapper MSI , covering the recent Cerro Grande fire at Los Alamos, NM, USA.

Chemodiversity in Selaginella: a reference system for parallel and convergent metabolic evolution in terrestrial plants

PubMed Central

Weng, Jing-Ke; Noel, Joseph P.

2013-01-01

Early plants began colonizing the terrestrial earth approximately 450 million years ago. Their success on land has been partially attributed to the evolution of specialized metabolic systems from core metabolic pathways, the former yielding structurally and functionally diverse chemicals to cope with a myriad of biotic and abiotic ecological pressures. Over the past two decades, functional genomics, primarily focused on flowering plants, has begun cataloging the biosynthetic players underpinning assorted classes of plant specialized metabolites. However, the molecular mechanisms enriching specialized metabolic pathways during land plant evolution remain largely unexplored. Selaginella is an extant lycopodiophyte genus representative of an ancient lineage of tracheophytes. Notably, the lycopodiophytes diverged from euphyllophytes over 400 million years ago. The recent completion of the whole-genome sequence of an extant lycopodiophyte, S. moellendorffii, provides new genomic and biochemical resources for studying metabolic evolution in vascular plants. 400 million years of independent evolution of lycopodiophytes and euphyllophytes resulted in numerous metabolic traits confined to each lineage. Surprisingly, a cadre of specialized metabolites, generally accepted to be restricted to seed plants, have been identified in Selaginella. Initial work suggested that Selaginella lacks obvious catalytic homologs known to be involved in the biosynthesis of well-studied specialized metabolites in seed plants. Therefore, these initial functional analyses suggest that the same chemical phenotypes arose independently more commonly than anticipated from our conventional understanding of the evolution of metabolism. Notably, the emergence of analogous and homologous catalytic machineries through convergent and parallel evolution, respectively, seems to have occurred repeatedly in different plant lineages. PMID:23717312

Long waves in parallel flow in Hele-Shaw cells

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

Zeybek, M.; Yortsos, Y.C.

1991-09-09

The evolution of fluid interfaces in parallel flow in Hele-Shaw cells is studied theoretically and experimentally in the limit of large capillary number. It is shown that such interfaces support wave motion, the amplitude of which for long waves is governed by a set of Korteweg--de Vries and Airy equations. Experiments conducted in a long Hele-Shaw cell validate the theory in the symmetric case.

Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback.

PubMed

Conte, Gina L; Arnegard, Matthew E; Best, Jacob; Chan, Yingguang Frank; Jones, Felicity C; Kingsley, David M; Schluter, Dolph; Peichel, Catherine L

2015-11-01

How predictable is the genetic basis of phenotypic adaptation? Answering this question begins by estimating the repeatability of adaptation at the genetic level. Here, we provide a comprehensive estimate of the repeatability of the genetic basis of adaptive phenotypic evolution in a natural system. We used quantitative trait locus (QTL) mapping to discover genomic regions controlling a large number of morphological traits that have diverged in parallel between pairs of threespine stickleback (Gasterosteus aculeatus species complex) in Paxton and Priest lakes, British Columbia. We found that nearly half of QTL affected the same traits in the same direction in both species pairs. Another 40% influenced a parallel phenotypic trait in one lake but not the other. The remaining 10% of QTL had phenotypic effects in opposite directions in the two species pairs. Similarity in the proportional contributions of all QTL to parallel trait differences was about 0.4. Surprisingly, QTL reuse was unrelated to phenotypic effect size. Our results indicate that repeated use of the same genomic regions is a pervasive feature of parallel phenotypic adaptation, at least in sticklebacks. Identifying the causes of this pattern would aid prediction of the genetic basis of phenotypic evolution. Copyright © 2015 by the Genetics Society of America.

Three-dimensional Hybrid Simulation Study of Anisotropic Turbulence in the Proton Kinetic Regime

NASA Astrophysics Data System (ADS)

Vasquez, Bernard J.; Markovskii, Sergei A.; Chandran, Benjamin D. G.

2014-06-01

Three-dimensional numerical hybrid simulations with particle protons and quasi-neutralizing fluid electrons are conducted for a freely decaying turbulence that is anisotropic with respect to the background magnetic field. The turbulence evolution is determined by both the combined root-mean-square (rms) amplitude for fluctuating proton bulk velocity and magnetic field and by the ratio of perpendicular to parallel wavenumbers. This kind of relationship had been considered in the past with regard to interplanetary turbulence. The fluctuations nonlinearly evolve to a turbulent phase whose net wave vector anisotropy is usually more perpendicular than the initial one, irrespective of the initial ratio of perpendicular to parallel wavenumbers. Self-similar anisotropy evolution is found as a function of the rms amplitude and parallel wavenumber. Proton heating rates in the turbulent phase vary strongly with the rms amplitude but only weakly with the initial wave vector anisotropy. Even in the limit where wave vectors are confined to the plane perpendicular to the background magnetic field, the heating rate remains close to the corresponding case with finite parallel wave vector components. Simulation results obtained as a function of proton plasma to background magnetic pressure ratio β p in the range 0.1-0.5 show that the wave vector anisotropy also weakly depends on β p .

Musical emotions: Functions, origins, evolution

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid

2010-03-01

Theories of music origins and the role of musical emotions in the mind are reviewed. Most existing theories contradict each other, and cannot explain mechanisms or roles of musical emotions in workings of the mind, nor evolutionary reasons for music origins. Music seems to be an enigma. Nevertheless, a synthesis of cognitive science and mathematical models of the mind has been proposed describing a fundamental role of music in the functioning and evolution of the mind, consciousness, and cultures. The review considers ancient theories of music as well as contemporary theories advanced by leading authors in this field. It addresses one hypothesis that promises to unify the field and proposes a theory of musical origin based on a fundamental role of music in cognition and evolution of consciousness and culture. We consider a split in the vocalizations of proto-humans into two types: one less emotional and more concretely-semantic, evolving into language, and the other preserving emotional connections along with semantic ambiguity, evolving into music. The proposed hypothesis departs from other theories in considering specific mechanisms of the mind-brain, which required the evolution of music parallel with the evolution of cultures and languages. Arguments are reviewed that the evolution of language toward becoming the semantically powerful tool of today required emancipation from emotional encumbrances. The opposite, no less powerful mechanisms required a compensatory evolution of music toward more differentiated and refined emotionality. The need for refined music in the process of cultural evolution is grounded in fundamental mechanisms of the mind. This is why today's human mind and cultures cannot exist without today's music. The reviewed hypothesis gives a basis for future analysis of why different evolutionary paths of languages were paralleled by different evolutionary paths of music. Approaches toward experimental verification of this hypothesis in psychological and neuroimaging research are reviewed.

Using hybridization networks to retrace the evolution of Indo-European languages.

PubMed

Willems, Matthieu; Lord, Etienne; Laforest, Louise; Labelle, Gilbert; Lapointe, François-Joseph; Di Sciullo, Anna Maria; Makarenkov, Vladimir

2016-09-06

Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics. Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods. We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.

Influence of equilibrium shear flow in the parallel magnetic direction on edge localized mode crash

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

Luo, Y.; Xiong, Y. Y.; Chen, S. Y., E-mail: sychen531@163.com

2016-04-15

The influence of the parallel shear flow on the evolution of peeling-ballooning (P-B) modes is studied with the BOUT++ four-field code in this paper. The parallel shear flow has different effects in linear simulation and nonlinear simulation. In the linear simulations, the growth rate of edge localized mode (ELM) can be increased by Kelvin-Helmholtz term, which can be caused by the parallel shear flow. In the nonlinear simulations, the results accord with the linear simulations in the linear phase. However, the ELM size is reduced by the parallel shear flow in the beginning of the turbulence phase, which is recognizedmore » as the P-B filaments' structure. Then during the turbulence phase, the ELM size is decreased by the shear flow.« less

Convergent Evolution of Human-Isolated H7N9 Avian Influenza A Viruses.

PubMed

Xiang, Dan; Shen, Xuejuan; Pu, Zhiqing; Irwin, David M; Liao, Ming; Shen, Yongyi

2018-05-05

Avian influenza A virus H7N9 has caused 5 epidemic waves of human infections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human). We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses. Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.

Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces

NASA Astrophysics Data System (ADS)

Ferrando, N.; Gosálvez, M. A.; Cerdá, J.; Gadea, R.; Sato, K.

2011-03-01

Presently, dynamic surface-based models are required to contain increasingly larger numbers of points and to propagate them over longer time periods. For large numbers of surface points, the octree data structure can be used as a balance between low memory occupation and relatively rapid access to the stored data. For evolution rules that depend on neighborhood states, extended simulation periods can be obtained by using simplified atomistic propagation models, such as the Cellular Automata (CA). This method, however, has an intrinsic parallel updating nature and the corresponding simulations are highly inefficient when performed on classical Central Processing Units (CPUs), which are designed for the sequential execution of tasks. In this paper, a series of guidelines is presented for the efficient adaptation of octree-based, CA simulations of complex, evolving surfaces into massively parallel computing hardware. A Graphics Processing Unit (GPU) is used as a cost-efficient example of the parallel architectures. For the actual simulations, we consider the surface propagation during anisotropic wet chemical etching of silicon as a computationally challenging process with a wide-spread use in microengineering applications. A continuous CA model that is intrinsically parallel in nature is used for the time evolution. Our study strongly indicates that parallel computations of dynamically evolving surfaces simulated using CA methods are significantly benefited by the incorporation of octrees as support data structures, substantially decreasing the overall computational time and memory usage.

A systemic approach for modeling biological evolution using Parallel DEVS.

PubMed

Heredia, Daniel; Sanz, Victorino; Urquia, Alfonso; Sandín, Máximo

2015-08-01

A new model for studying the evolution of living organisms is proposed in this manuscript. The proposed model is based on a non-neodarwinian systemic approach. The model is focused on considering several controversies and open discussions about modern evolutionary biology. Additionally, a simplification of the proposed model, named EvoDEVS, has been mathematically described using the Parallel DEVS formalism and implemented as a computer program using the DEVSLib Modelica library. EvoDEVS serves as an experimental platform to study different conditions and scenarios by means of computer simulations. Two preliminary case studies are presented to illustrate the behavior of the model and validate its results. EvoDEVS is freely available at http://www.euclides.dia.uned.es. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Crack classification and evolution in anisotropic shale during cyclic loading tests by acoustic emission

NASA Astrophysics Data System (ADS)

Wang, Miaomiao; Tan, Chengxuan; Meng, Jing; Yang, Baicun; Li, Yuan

2017-08-01

Characterization and evolution of the cracking mode in shale formation is significant, as fracture networks are an important element in shale gas exploitation. In this study we determine the crack modes and evolution in anisotropic shale under cyclic loading using the acoustic emission (AE) parameter-analysis method based on the average frequency and RA (rise-time/amplitude) value. Shale specimens with bedding-plane orientations parallel and perpendicular to the axial loading direction were subjected to loading cycles with increasing peak values until failure occurred. When the loading was parallel to the bedding plane, most of the cracks at failure were shear cracks, while tensile cracks were dominant in the specimens that were loaded normal to the bedding direction. The evolution of the crack mode in the shale specimens observed in the loading-unloading sequence except for the first cycle can be divided into three stages: (I) no or several cracks (AE events) form as a result of the Kaiser effect, (II) tensile and shear cracks increase steadily at nearly equal proportions, (III) tensile cracks and shear cracks increase abruptly, with more cracks forming in one mode than in the other. As the dominant crack motion is influenced by the bedding, the failure mechanism is discussed based on the evolution of the different crack modes. Our conclusions can increase our understanding of the formation mechanism of fracture networks in the field.

Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions.

PubMed

Lee, Carol Eunmi; Kiergaard, Michael; Gelembiuk, Gregory William; Eads, Brian Donovan; Posavi, Marijan

2011-08-01

Marine to freshwater colonizations constitute among the most dramatic evolutionary transitions in the history of life. This study examined evolution of ionic regulation following saline-to-freshwater transitions in an invasive species. In recent years, the copepod Eurytemora affinis has invaded freshwater habitats multiple times independently. We found parallel evolutionary shifts in ion-motive enzyme activity (V-type H(+) ATPase, Na(+) /K(+) -ATPase) across independent invasions and in replicate laboratory selection experiments. Freshwater populations exhibited increased V-type H(+) ATPase activity in fresh water (0 PSU) and declines at higher salinity (15 PSU) relative to saline populations. This shift represented marked evolutionary increases in plasticity. In contrast, freshwater populations displayed reduced Na(+) /K(+) -ATPase activity across all salinities. Most notably, modifying salinity alone during laboratory selection experiments recapitulated the evolutionary shifts in V-type H(+) ATPase activity observed in nature. Maternal and embryonic acclimation could not account for the observed shifts in enzyme activity. V-type H(+) ATPase function has been hypothesized to be critical for freshwater and terrestrial adaptations, but evolution of this enzyme function had not been previously demonstrated in the context of habitat transitions. Moreover, the speed of these evolutionary shifts was remarkable, within a few generations in the laboratory and a few decades in the wild. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Storm Time Evolution of Outer Radiation Belt Relativistic Electrons by a Nearly Continuous Distribution of Chorus

NASA Astrophysics Data System (ADS)

Yang, Chang; Xiao, Fuliang; He, Yihua; Liu, Si; Zhou, Qinghua; Guo, Mingyue; Zhao, Wanli

2018-03-01

During the 13-14 November 2012 storm, Van Allen Probe A simultaneously observed a 10 h period of enhanced chorus (including quasi-parallel and oblique propagation components) and relativistic electron fluxes over a broad range of L = 3-6 and magnetic local time = 2-10 within a complete orbit cycle. By adopting a Gaussian fit to the observed wave spectra, we obtain the wave parameters and calculate the bounce-averaged diffusion coefficients. We solve the Fokker-Planck diffusion equation to simulate flux evolutions of relativistic (1.8-4.2 MeV) electrons during two intervals when Probe A passed the location L = 4.3 along its orbit. The simulating results show that chorus with combined quasi-parallel and oblique components can produce a more pronounced flux enhancement in the pitch angle range ˜45°-80°, consistent well with the observation. The current results provide the first evidence on how relativistic electron fluxes vary under the drive of almost continuously distributed chorus with both quasi-parallel and oblique components within a complete orbit of Van Allen Probe.

Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis.

PubMed

McGlothlin, Joel W; Chuckalovcak, John P; Janes, Daniel E; Edwards, Scott V; Feldman, Chris R; Brodie, Edmund D; Pfrender, Michael E; Brodie, Edmund D

2014-11-01

Members of a gene family expressed in a single species often experience common selection pressures. Consequently, the molecular basis of complex adaptations may be expected to involve parallel evolutionary changes in multiple paralogs. Here, we use bacterial artificial chromosome library scans to investigate the evolution of the voltage-gated sodium channel (Nav) family in the garter snake Thamnophis sirtalis, a predator of highly toxic Taricha newts. Newts possess tetrodotoxin (TTX), which blocks Nav's, arresting action potentials in nerves and muscle. Some Thamnophis populations have evolved resistance to extremely high levels of TTX. Previous work has identified amino acid sites in the skeletal muscle sodium channel Nav1.4 that confer resistance to TTX and vary across populations. We identify parallel evolution of TTX resistance in two additional Nav paralogs, Nav1.6 and 1.7, which are known to be expressed in the peripheral nervous system and should thus be exposed to ingested TTX. Each paralog contains at least one TTX-resistant substitution identical to a substitution previously identified in Nav1.4. These sites are fixed across populations, suggesting that the resistant peripheral nerves antedate resistant muscle. In contrast, three sodium channels expressed solely in the central nervous system (Nav1.1-1.3) showed no evidence of TTX resistance, consistent with protection from toxins by the blood-brain barrier. We also report the exon-intron structure of six Nav paralogs, the first such analysis for snake genes. Our results demonstrate that the molecular basis of adaptation may be both repeatable across members of a gene family and predictable based on functional considerations. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The evolution of vision.

PubMed

Gehring, Walter J

2014-01-01

In this review, the evolution of vision is retraced from its putative origins in cyanobacteria to humans. Circadian oscillatory clocks, phototropism, and phototaxis require the capability to detect light. Photosensory proteins allow us to reconstruct molecular phylogenetic trees. The evolution of animal eyes leading from an ancestral prototype to highly complex image forming eyes can be deciphered on the basis of evolutionary developmental genetic experiments and comparative genomics. As all bilaterian animals share the same master control gene, Pax6, and the same retinal and pigment cell determination genes, we conclude that the different eye-types originated monophyletically and subsequently diversified by divergent, parallel, or convergent evolution. © 2012 Wiley Periodicals, Inc.

Evolution: bats, radar, and science (The Remote Sensing Award Lecture)

NASA Technical Reports Server (NTRS)

Atlas, David

1991-01-01

A parallel is drawn between the evolution of the bat and the evolution of the science and technology of radar and remote sensing to illustrate the importance of the role of Darwinian processes in the culture and practice of science and technology, and thus in the survival of their vitality. The lecture touches on several themes of interest to the science community, such as the relation between basic and applied science and engineering; research in academia, industry, and government laboratories; elite scientists; and the survival of a scientific institution.

The science of computing - The evolution of parallel processing

NASA Technical Reports Server (NTRS)

Denning, P. J.

1985-01-01

The present paper is concerned with the approaches to be employed to overcome the set of limitations in software technology which impedes currently an effective use of parallel hardware technology. The process required to solve the arising problems is found to involve four different stages. At the present time, Stage One is nearly finished, while Stage Two is under way. Tentative explorations are beginning on Stage Three, and Stage Four is more distant. In Stage One, parallelism is introduced into the hardware of a single computer, which consists of one or more processors, a main storage system, a secondary storage system, and various peripheral devices. In Stage Two, parallel execution of cooperating programs on different machines becomes explicit, while in Stage Three, new languages will make parallelism implicit. In Stage Four, there will be very high level user interfaces capable of interacting with scientists at the same level of abstraction as scientists do with each other.

Phylogenetic analyses of mode of larval development.

PubMed

Hart, M

2000-12-01

Phylogenies based on morphological or molecular characters have been used to provide an evolutionary context for analysis of larval evolution. Studies of gastropods, bivalves, tunicates, sea stars, sea urchins, and polychaetes have revealed massive parallel evolution of similar larval forms. Some of these studies were designed to test, and have rejected, the species selection hypothesis for evolutionary trends in the frequency of derived larvae or life history traits. However, the lack of well supported models of larval character evolution leave some doubt about the quality of inferences of larval evolution from phylogenies of living taxa. Better models based on maximum likelihood methods and known prior probabilities of larval character state changes will improve our understanding of the history of larval evolution. Copyright 2000 Academic Press.

Local and nonlocal parallel heat transport in general magnetic fields

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

Del-Castillo-Negrete, Diego B; Chacon, Luis

2011-01-01

A novel approach for the study of parallel transport in magnetized plasmas is presented. The method avoids numerical pollution issues of grid-based formulations and applies to integrable and chaotic magnetic fields with local or nonlocal parallel closures. In weakly chaotic fields, the method gives the fractal structure of the devil's staircase radial temperature profile. In fully chaotic fields, the temperature exhibits self-similar spatiotemporal evolution with a stretched-exponential scaling function for local closures and an algebraically decaying one for nonlocal closures. It is shown that, for both closures, the effective radial heat transport is incompatible with the quasilinear diffusion model.

Cortical organization in insectivora: the parallel evolution of the sensory periphery and the brain.

PubMed

Catania, K C

2000-06-01

Insectivores are traditionally described as a primitive group that has not changed much in the course of mammalian evolution. In contrast, recent studies reveal a great diversity of sensorimotor specializations among insectivores adapted to a number of different ecological niches, indicating that there has been significant diversification and change in the course of their evolution. Here the organization of sensory cortex is compared in the African hedgehog (Atelerix albiventris), the masked shrew (Sorex cinereus), the eastern mole (Scalopus aquaticus), and the star-nosed mole (Condylura cristata). Each of these four closely related species lives in a unique ecological niche, exhibits a different repertoire of behaviors, and has a different configuration of peripheral sensory receptors. Corresponding specializations of cortical sensory areas reveal a number of ways in which the cortex has evolved in parallel with changes to the sensory periphery. These specializations include expansion of cortical representations (cortical magnification), the addition or loss of cortical areas in the processing network, and the subdivision of areas into modules (barrels and stripes). Copyright 2000 S. Karger AG, Basel

Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1

PubMed Central

Carroll, Sean Michael; Chubiz, Lon M.; Agashe, Deepa; Marx, Christopher J.

2015-01-01

Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been “rationalized” by the bioengineer, plus other “illogical” mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods. PMID:27682084

Yardang evolution from maturity to demise

NASA Astrophysics Data System (ADS)

Barchyn, Thomas E.; Hugenholtz, Chris H.

2015-07-01

Yardangs are enigmatic wind-parallel ridges sculpted by aeolian processes that are found extensively in arid environments on Earth and Mars. No general theory exists to explain the long-term evolution of yardangs, curtailing modeling of landscape evolution and dynamics of suspended sediment release. We present a hypothesis of yardang evolution using relative rates of sediment flux, interyardang corridor downcutting, yardang denudation, substrate erodibility, and substrate clast content. To develop and sustain yardangs, corridor downcutting must exceed yardang vertical denudation and deflation. However, erosion of substrate yields considerable quantities of sediment that shelters corridors, slowing downcutting. We model the evolution of yardangs through various combinations of rates and substrate compositions, demonstrating the life span, suspended sediment release, and resulting landscape evolution. We find that yardangs have a distinct and predictable evolution, with inevitable demise and unexpectedly dynamic and autogenic erosion rates driven by subtle differences in substrate clast composition.

Evolution of Kelvin-Helmholtz instability at Venus in the presence of the parallel magnetic field

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

Lu, H. Y.; Key Laboratory of Planetary Sciences, Chinese Academy of Sciences, Nanjing 210008; Cao, J. B.

2015-06-15

Two-dimensional MHD simulations were performed to study the evolution of the Kelvin-Helmholtz (KH) instability at the Venusian ionopause in response to the strong flow shear in presence of the in-plane magnetic field parallel to the flow direction. The physical behavior of the KH instability as well as the triggering and occurrence conditions for highly rolled-up vortices are characterized through several physical parameters, including Alfvén Mach number on the upper side of the layer, the density ratio, and the ratio of parallel magnetic fields between two sides of the layer. Using these parameters, the simulations show that both the high densitymore » ratio and the parallel magnetic field component across the boundary layer play a role of stabilizing the instability. In the high density ratio case, the amount of total magnetic energy in the final quasi-steady status is much more than that in the initial status, which is clearly different from the case with low density ratio. We particularly investigate the nonlinear development of the case that has a high density ratio and uniform magnetic field. Before the instability saturation, a single magnetic island is formed and evolves into two quasi-steady islands in the non-linear phase. A quasi-steady pattern eventually forms and is embedded within a uniform magnetic field and a broadened boundary layer. The estimation of loss rates of ions from Venus indicates that the stabilizing effect of the parallel magnetic field component on the KH instability becomes strong in the case of high density ratio.« less

Multicore: Fallout from a Computing Evolution

ScienceCinema

Yelick, Kathy [Director, NERSC

2017-12-09

July 22, 2008 Berkeley Lab lecture: Parallel computing used to be reserved for big science and engineering projects, but in two years that's all changed. Even laptops and hand-helds use parallel processors. Unfortunately, the software hasn't kept pace. Kathy Yelick, Director of the National Energy Research Scientific Computing Center at Berkeley Lab, describes the resulting chaos and the computing community's efforts to develop exciting applications that take advantage of tens or hundreds of processors on a single chip.

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity.

PubMed

Hipp, Andrew L; Manos, Paul S; González-Rodríguez, Antonio; Hahn, Marlene; Kaproth, Matthew; McVay, John D; Avalos, Susana Valencia; Cavender-Bares, Jeannine

2018-01-01

Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

PubMed Central

Schrider, Daniel R.; Hahn, Matthew W.; Begun, David J.

2016-01-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster. In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

Parallel Evolution in Science: The Historical Roots and Central Concepts of General Systems Theory; and "General Systems Theory,""Modern Organizational Theory," and Organizational Communication.

ERIC Educational Resources Information Center

Lederman, Linda Costigan; Rogers, Don

The two papers in this document focus on general systems theory. In her paper, Linda Lederman discusses the emergence and evolution of general systems theory, defines its central concepts, and draws some conclusions regarding the nature of the theory and its value as an epistemology. Don Rogers, in his paper, relates some of the important features…

Gravitational field calculations on a dynamic lattice by distributed computing.

NASA Astrophysics Data System (ADS)

Mähönen, P.; Punkka, V.

A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing

NASA Astrophysics Data System (ADS)

Mähönen, Petri; Punkka, Veikko

A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

On the consequences of bi-Maxwellian plasma distributions for parallel electric fields

NASA Technical Reports Server (NTRS)

Olsen, Richard C.

1992-01-01

The objective is to use the measurements of the equatorial particle distributions to obtain the parallel electric field structure and the evolution of the plasma distribution function along the field line. Appropriate uses of kinetic theory allows us to use the measured ( and inferred) particle distributions to obtain the electric field, and hence the variation on plasma density along the magnetic field line. The approach, here, is to utilize the adiabatic invariants, and assume the plasma distributions are in equilibrium.

Parallel ridge pattern on dermoscopy: observation in non-melanoma cases*

PubMed Central

Fracaroli, Tainá Scalfoni; Lavorato, Fernanda Guedes; Maceira, Juan Piñeiro; Barcaui, Carlos

2013-01-01

The acral melanoma is the most prevalent type of melanoma in the non-Caucasian population, and dermoscopy is a useful tool for earlier diagnosis and differentiation from benign lesions. The dermoscopic pattern often associated with melanoma on the volar skin is the parallel ridge, with 99% specificity according to the literature. However, this pattern can also occur in several benign acral lesions, so it is important to make a good interpretation of this pattern, along with the clinical history and evolution. PMID:24068145

a Predator-Prey Model Based on the Fully Parallel Cellular Automata

NASA Astrophysics Data System (ADS)

He, Mingfeng; Ruan, Hongbo; Yu, Changliang

We presented a predator-prey lattice model containing moveable wolves and sheep, which are characterized by Penna double bit strings. Sexual reproduction and child-care strategies are considered. To implement this model in an efficient way, we build a fully parallel Cellular Automata based on a new definition of the neighborhood. We show the roles played by the initial densities of the populations, the mutation rate and the linear size of the lattice in the evolution of this model.

Multicore: Fallout From a Computing Evolution (LBNL Summer Lecture Series)

ScienceCinema

Yelick, Kathy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

2018-05-07

Summer Lecture Series 2008: Parallel computing used to be reserved for big science and engineering projects, but in two years that's all changed. Even laptops and hand-helds use parallel processors. Unfortunately, the software hasn't kept pace. Kathy Yelick, Director of the National Energy Research Scientific Computing Center at Berkeley Lab, describes the resulting chaos and the computing community's efforts to develop exciting applications that take advantage of tens or hundreds of processors on a single chip.

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

PubMed

Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

2014-03-20

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

PubMed Central

Payen, Celia; Di Rienzi, Sara C.; Ong, Giang T.; Pogachar, Jamie L.; Sanchez, Joseph C.; Sunshine, Anna B.; Raghuraman, M. K.; Brewer, Bonita J.; Dunham, Maitreya J.

2014-01-01

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another. PMID:24368781

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

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

Zamora, Richard James; Voter, Arthur F.; Perez, Danny

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

DOE PAGES

Zamora, Richard James; Voter, Arthur F.; Perez, Danny; ...

2016-12-01

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less

Anisotropic heat transport in reversed shear configurations: shearless Cantori barriers and nonlocal transport

NASA Astrophysics Data System (ADS)

Blasevski, D.; Del-Castillo-Negrete, D.

2012-10-01

Heat transport in magnetized plasmas is a problem of fundamental interest in controlled fusion. In Ref.footnotetext D. del-Castillo-Negrete, and L. Chac'on, Phys. Rev. Lett., 106, 195004 (2011); Phys. Plasmas 19, 056112 (2012). we proposed a Lagrangian-Green's function (LG) method to study this problem in the strongly anisotropic (χ=0) regime. The LG method bypasses the need to discretize the transport operators on a grid and it is applicable to general parallel flux closures and 3-D magnetic fields. Here we apply the LG method to parallel transport (with local and nonlocal parallel flux closures) in reversed shear magnetic field configurations known to exhibit robust transport barriers in the vicinity of the extrema of the q-profile. By shearless Cantori (SC) we mean the invariant Cantor sets remaining after the destruction of toroidal flux surfaces with zero magnetic shear, q^'=0. We provide numerical evidence of the role of SC in the anomalously slow relaxation of radial temperature gradients in chaotic magnetic fields with no transport barriers. The spatio-temporal evolution of temperature pulses localized in the reversed shear region exhibits non-diffusive self-similar evolution and nonlocal effective radial transport.

Construction and comparison of parallel implicit kinetic solvers in three spatial dimensions

NASA Astrophysics Data System (ADS)

Titarev, Vladimir; Dumbser, Michael; Utyuzhnikov, Sergey

2014-01-01

The paper is devoted to the further development and systematic performance evaluation of a recent deterministic framework Nesvetay-3D for modelling three-dimensional rarefied gas flows. Firstly, a review of the existing discretization and parallelization strategies for solving numerically the Boltzmann kinetic equation with various model collision integrals is carried out. Secondly, a new parallelization strategy for the implicit time evolution method is implemented which improves scaling on large CPU clusters. Accuracy and scalability of the methods are demonstrated on a pressure-driven rarefied gas flow through a finite-length circular pipe as well as an external supersonic flow over a three-dimensional re-entry geometry of complicated aerodynamic shape.

Radiation-MHD Simulations of Pillars and Globules in HII Regions

NASA Astrophysics Data System (ADS)

Mackey, J.

2012-07-01

Implicit and explicit raytracing-photoionisation algorithms have been implemented in the author's radiation-magnetohydrodynamics code. The algorithms are described briefly and their efficiency and parallel scaling are investigated. The implicit algorithm is more efficient for calculations where ionisation fronts have very supersonic velocities, and the explicit algorithm is favoured in the opposite limit because of its better parallel scaling. The implicit method is used to investigate the effects of initially uniform magnetic fields on the formation and evolution of dense pillars and cometary globules at the boundaries of HII regions. It is shown that for weak and medium field strengths an initially perpendicular field is swept into alignment with the pillar during its dynamical evolution, matching magnetic field observations of the ‘Pillars of Creation’ in M16. A strong perpendicular magnetic field remains in its initial configuration and also confines the photoevaporation flow into a bar-shaped, dense, ionised ribbon which partially shields the ionisation front.

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

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

Arampatzis, Giorgos, E-mail: garab@math.uoc.gr; Katsoulakis, Markos A., E-mail: markos@math.umass.edu; Plechac, Petr, E-mail: plechac@math.udel.edu

2012-10-01

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decompositionmore » corresponds to a decomposition of the Markov generator into a hierarchy of operators and can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). Based on this operator decomposition, we formulate parallel Fractional step kinetic Monte Carlo algorithms by employing the Trotter Theorem and its randomized variants; these schemes, (a) are partially asynchronous on each fractional step time-window, and (b) are characterized by their communication schedule between processors. The proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules. We carry out a detailed benchmarking of the parallel KMC schemes using available exact solutions, for example, in Ising-type systems and we demonstrate the capabilities of the method to simulate complex spatially distributed reactions at very large scales on GPUs. Finally, we discuss work load balancing between processors and propose a re-balancing scheme based on probabilistic mass transport methods.« less

Darwinian perspectives on the evolution of human languages.

PubMed

Pagel, Mark

2017-02-01

Human languages evolve by a process of descent with modification in which parent languages give rise to daughter languages over time and in a manner that mimics the evolution of biological species. Descent with modification is just one of many parallels between biological and linguistic evolution that, taken together, offer up a Darwinian perspective on how languages evolve. Combined with statistical methods borrowed from evolutionary biology, this Darwinian perspective has brought new opportunities to the study of the evolution of human languages. These include the statistical inference of phylogenetic trees of languages, the study of how linguistic traits evolve over thousands of years of language change, the reconstruction of ancestral or proto-languages, and using language change to date historical events.

Social Cognition and the Evolution of Language: Constructing Cognitive Phylogenies

PubMed Central

Fitch, W. Tecumseh; Huber, Ludwig; Bugnyar, Thomas

2015-01-01

Human language and social cognition are closely linked: advanced social cognition is necessary for children to acquire language, and language allows forms of social understanding (and, more broadly, culture) that would otherwise be impossible. Both “language” and “social cognition” are complex constructs, involving many independent cognitive mechanisms, and the comparative approach provides a powerful route to understanding the evolution of such mechanisms. We provide a broad comparative review of mechanisms underlying social intelligence in vertebrates, with the goal of determining which human mechanisms are broadly shared, which have evolved in parallel in other clades, and which, potentially, are uniquely developed in our species. We emphasize the importance of convergent evolution for testing hypotheses about neural mechanisms and their evolution. PMID:20346756

Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers | Office of Cancer Genomics

Cancer.gov

Human tumors show a high level of genetic heterogeneity, but the processes that influence the timing and route of metastatic dissemination of the subclones are unknown. Here we have used whole-exome sequencing of 103 matched benign, malignant and metastatic skin tumors from genetically heterogeneous mice to demonstrate that most metastases disseminate synchronously from the primary tumor, supporting parallel rather than linear evolution as the predominant model of metastasis.

Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine.

PubMed

Diogo, Rui; Smith, Christopher M; Ziermann, Janine M

2015-11-01

We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications. © 2015 Wiley Periodicals, Inc.

Clonal origins and parallel evolution of regionally synchronous colorectal adenoma and carcinoma.

PubMed

Kim, Tae-Min; An, Chang Hyeok; Rhee, Je-Keun; Jung, Seung-Hyun; Lee, Sung Hak; Baek, In-Pyo; Kim, Min Sung; Lee, Sug Hyung; Chung, Yeun-Jun

2015-09-29

Although the colorectal adenoma-to-carcinoma sequence represents a classical cancer progression model, the evolution of the mutational landscape underlying this model is not fully understood. In this study, we analyzed eight synchronous pairs of colorectal high-grade adenomas and carcinomas, four microsatellite-unstable (MSU) and four-stable (MSS) pairs, using whole-exome sequencing. In the MSU adenoma-carcinoma pairs, we observed no subclonal mutations in adenomas that became fixed in paired carcinomas, suggesting a 'parallel' evolution of synchronous adenoma-to-carcinoma, rather than a 'stepwise' evolution. The abundance of indel (in MSU and MSS pairs) and microsatellite instability (in MSU pairs) was noted in the later adenoma- or carcinoma-specific mutations, indicating that the mutational processes and functional constraints operative in early and late colorectal carcinogenesis are different. All MSU cases exhibited clonal, truncating mutations in ACVR2A, TGFBR2, and DNA mismatch repair genes, but none were present in APC or KRAS. In three MSS pairs, both APC and KRAS mutations were identified as both early and clonal events, often accompanying clonal copy number changes. An MSS case uniquely exhibited clonal ERBB2 amplification, followed by APC and TP53 mutations as carcinoma-specific events. Along with the previously unrecognized clonal origins of synchronous colorectal adenoma-carcinoma pairs, our study revealed that the preferred sequence of mutational events during colorectal carcinogenesis can be context-dependent.

Hidden and cryptic species reflect parallel and correlated evolution in the phylogeny of the genus Callyntra (Coleoptera: Tenebrionidae) of Central Chile.

PubMed

Zúñiga-Reinoso, Álvaro; Méndez, Marco A

2018-04-24

The origin of cryptic species has traditionally been associated with events of recent speciation, genetic constraints, selection of an adaptive character, sexual selection and/or convergent evolution. Species of the genus Callyntra inhabit coastal terraces, mountain slopes, and peaks; their elytral designs are associated with each of these habitats. However, cryptic species have been described within each of these habitats; the taxonomy of this group has been problematic, thus establishing the phylogenetic relationships in this group is fundamental to clarify the systematics and evolutionary patterns of Callyntra. We reconstructed the phylogeny of this group using two mitochondrial genes (COI, 16S) and one nuclear gene (Mp20). We also performed species delimitation using PTP based methods (PTP, mlPTP, bPTP) and GMYC, and evaluated the evolution of the elytral design related to habitat preference. The results showed a tree with five clades, that together with the different methods of species delimitation recovered the described species and suggested at least five new species. The elytral design and habitat preference showed phylogenetic signals. We propose a new classification based on monophyletic groups recovered by phylogenetic analyses. We also suggest that parallel evolution in different habitats and later stasis in the elytral design would be the cause of the origin of cryptic species in this group from central Chile. Copyright © 2018 Elsevier Inc. All rights reserved.

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

PubMed

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

2011-02-10

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

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

PubMed Central

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

2011-01-01

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

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids.

PubMed

Meier, Joana Isabel; Marques, David Alexander; Wagner, Catherine Elise; Excoffier, Laurent; Seehausen, Ole

2018-06-01

The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case is blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through "hybrid parallel speciation". Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new "nyererei-like" and "pundamilia-like" species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two-thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.

Vanadium Nitrogenase Reduces CO*

PubMed Central

Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W.

2011-01-01

Vanadium nitrogenase not only reduces dinitrogen to ammonia but also reduces carbon monoxide to ethylene, ethane, and propane. The parallelism between the two reactions suggests a potential link in mechanism and evolution between the carbon and nitrogen cycles on Earth. PMID:20689010

Parallel evolution of storage roots in morning glories (Convolvulaceae).

PubMed

Eserman, Lauren A; Jarret, Robert L; Leebens-Mack, James H

2018-05-29

Storage roots are an ecologically and agriculturally important plant trait that have evolved numerous times in angiosperms. Storage roots primarily function to store carbohydrates underground as reserves for perennial species. In morning glories, storage roots are well characterized in the crop species sweetpotato, where starch accumulates in storage roots. This starch-storage tissue proliferates, and roots thicken to accommodate the additional tissue. In morning glories, storage roots have evolved numerous times. The primary goal of this study is to understand whether this was through parallel evolution, where species use a common genetic mechanism to achieve storage root formation, or through convergent evolution, where storage roots in distantly related species are formed using a different set of genes. Pairs of species where one forms storage roots and the other does not were sampled from two tribes in the morning glory family, the Ipomoeeae and Merremieae. Root anatomy in storage roots and fine roots was examined. Furthermore, we sequenced total mRNA from storage roots and fine roots in these species and analyzed differential gene expression. Anatomical results reveal that storage roots of species in the Ipomoeeae tribe, such as sweetpotato, accumulate starch similar to species in the Merremieae tribe but differ in vascular tissue organization. In both storage root forming species, more genes were found to be upregulated in storage roots compared to fine roots. Further, we find that fifty-seven orthologous genes were differentially expressed between storage roots and fine roots in both storage root forming species. These genes are primarily involved in starch biosynthesis, regulation of starch biosynthesis, and transcription factor activity. Taken together, these results demonstrate that storage roots of species from both morning glory tribes are anatomically different but utilize a common core set of genes in storage root formation. This is consistent with a pattern of parallel evolution, thus highlighting the importance of examining anatomy together with gene expression to understand the evolutionary origins of ecologically and economically important plant traits.

Mammalian bone palaeohistology: a survey and new data with emphasis on island forms

PubMed Central

Scheyer, Torsten M.; Veitschegger, Kristof; Forasiepi, Analia M.; Amson, Eli; Van der Geer, Alexandra A.E.; Van den Hoek Ostende, Lars W.; Hayashi, Shoji; Sánchez-Villagra, Marcelo R.

2015-01-01

The interest in mammalian palaeohistology has increased dramatically in the last two decades. Starting in 1849 via descriptive approaches, it has been demonstrated that bone tissue and vascularisation types correlate with several biological variables such as ontogenetic stage, growth rate, and ecology. Mammalian bone displays a large variety of bone tissues and vascularisation patterns reaching from lamellar or parallel-fibred to fibrolamellar or woven-fibred bone, depending on taxon and individual age. Here we systematically review the knowledge and methods on cynodont and mammalian bone microstructure as well as palaeohistology and discuss potential future research fields and techniques. We present new data on the bone microstructure of two extant marsupial species and of several extinct continental and island placental mammals. Extant marsupials display mainly parallel-fibred primary bone with radial and oblique but mainly longitudinal vascular canals. Three juvenile specimens of the dwarf island hippopotamid Hippopotamus minor from the Late Pleistocene of Cyprus show reticular to plexiform fibrolamellar bone. The island murid Mikrotia magna from the Late Miocene of Gargano, Italy displays parallel-fibred primary bone with reticular vascularisation and strong remodelling in the middle part of the cortex. Leithia sp., the dormouse from the Pleistocene of Sicily, is characterised by a primary bone cortex consisting of lamellar bone and a high amount of compact coarse cancellous bone. The bone cortex of the fossil continental lagomorph Prolagus oeningensis and three fossil species of insular Prolagus displays mainly parallel-fibred primary bone and reticular, radial as well as longitudinal vascularisation. Typical for large mammals, secondary bone in the giant rhinocerotoid Paraceratherium sp. from the Late Oligocene of Turkey is represented by dense Haversian bone. The skeletochronological features of Sinomegaceros yabei, a large-sized deer from the Pleistocene of Japan closely related to Megaloceros, indicate a high growth rate. These examples and the synthesis of existing data show the potential of bone microstructure to reveal essential information on life history evolution. The bone tissue and the skeletochronological data of the sampled island species suggest the presence of various modes of bone histological modification and mammalian life history evolution on islands to depend on factors of island evolution such as island size, distance from mainland, climate, phylogeny, and time of evolution. PMID:26528418

Nonlinear Evolution of Counter-Propagating Whistler Mode Waves Excited by Anisotropic Electrons Within the Equatorial Source Region: 1-D PIC Simulations

NASA Astrophysics Data System (ADS)

Chen, Huayue; Gao, Xinliang; Lu, Quanming; Sun, Jicheng; Wang, Shui

2018-02-01

Nonlinear physical processes related to whistler mode waves are attracting more and more attention for their significant role in reshaping whistler mode spectra in the Earth's magnetosphere. Using a 1-D particle-in-cell simulation model, we have investigated the nonlinear evolution of parallel counter-propagating whistler mode waves excited by anisotropic electrons within the equatorial source region. In our simulations, after the linear phase of whistler mode instability, the strong electrostatic standing structures along the background magnetic field will be formed, resulting from the coupling between excited counter-propagating whistler mode waves. The wave numbers of electrostatic standing structures are about twice those of whistler mode waves generated by anisotropic hot electrons. Moreover, these electrostatic standing structures can further be coupled with either parallel or antiparallel propagating whistler mode waves to excite high-k modes in this plasma system. Compared with excited whistler mode waves, these high-k modes typically have 3 times wave number, same frequency, and about 2 orders of magnitude smaller amplitude. Our study may provide a fresh view on the evolution of whistler mode waves within their equatorial source regions in the Earth's magnetosphere.

An Airway Network Flow Assignment Approach Based on an Efficient Multiobjective Optimization Framework

PubMed Central

Zhang, Xuejun; Lei, Jiaxing

2015-01-01

Considering reducing the airspace congestion and the flight delay simultaneously, this paper formulates the airway network flow assignment (ANFA) problem as a multiobjective optimization model and presents a new multiobjective optimization framework to solve it. Firstly, an effective multi-island parallel evolution algorithm with multiple evolution populations is employed to improve the optimization capability. Secondly, the nondominated sorting genetic algorithm II is applied for each population. In addition, a cooperative coevolution algorithm is adapted to divide the ANFA problem into several low-dimensional biobjective optimization problems which are easier to deal with. Finally, in order to maintain the diversity of solutions and to avoid prematurity, a dynamic adjustment operator based on solution congestion degree is specifically designed for the ANFA problem. Simulation results using the real traffic data from China air route network and daily flight plans demonstrate that the proposed approach can improve the solution quality effectively, showing superiority to the existing approaches such as the multiobjective genetic algorithm, the well-known multiobjective evolutionary algorithm based on decomposition, and a cooperative coevolution multiobjective algorithm as well as other parallel evolution algorithms with different migration topology. PMID:26180840

Parallel evolution of facial stripe patterns in the Neolamprologus brichardi/pulcher species complex endemic to Lake Tanganyika.

PubMed

Duftner, Nina; Sefc, Kristina M; Koblmüller, Stephan; Salzburger, Walter; Taborsky, Michael; Sturmbauer, Christian

2007-11-01

Colour pattern diversity can be due to random processes or to natural or sexual selection. Consequently, similarities in colour patterns are not always correlated with common ancestry, but may result from convergent evolution under shared selection pressures or drift. Neolamprologus brichardi and Neolamprologus pulcher have been described as two distinct species based on differences in the arrangement of two dark bars on the operculum. Our study uses DNA sequences of the mitochondrial control region to show that relatedness of haplotypes disagrees with species assignment based on head colour pattern. This suggests repeated parallel evolution of particular stripe patterns. The complete lack of shared haplotypes between populations of the same or different phenotypes reflects strong philopatric behaviour, possibly induced by the cooperative breeding mode in which offspring remain in their natal territory and serve as helpers until they disperse to nearby territories or take over a breeding position. Concordant phylogeographic patterns between N. brichardi/N. pulcher populations and other rock-dwelling cichlids suggest that the same colonization routes have been taken by sympatric species and that these routes were affected by lake level fluctuations in the past.

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies.

PubMed

Daane, Jacob M; Rohner, Nicolas; Konstantinidis, Peter; Djuranovic, Sergej; Harris, Matthew P

2016-01-01

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Predator-induced phenotypic plasticity of shape and behavior: parallel and unique patterns across sexes and species

PubMed Central

Kinnison, Michael T.

2017-01-01

Abstract Phenotypic plasticity is often an adaptation of organisms to cope with temporally or spatially heterogenous landscapes. Like other adaptations, one would predict that different species, populations, or sexes might thus show some degree of parallel evolution of plasticity, in the form of parallel reaction norms, when exposed to analogous environmental gradients. Indeed, one might even expect parallelism of plasticity to repeatedly evolve in multiple traits responding to the same gradient, resulting in integrated parallelism of plasticity. In this study, we experimentally tested for parallel patterns of predator-mediated plasticity of size, shape, and behavior of 2 species and sexes of mosquitofish. Examination of behavioral trials indicated that the 2 species showed unique patterns of behavioral plasticity, whereas the 2 sexes in each species showed parallel responses. Fish shape showed parallel patterns of plasticity for both sexes and species, albeit males showed evidence of unique plasticity related to reproductive anatomy. Moreover, patterns of shape plasticity due to predator exposure were broadly parallel to what has been depicted for predator-mediated population divergence in other studies (slender bodies, expanded caudal regions, ventrally located eyes, and reduced male gonopodia). We did not find evidence of phenotypic plasticity in fish size for either species or sex. Hence, our findings support broadly integrated parallelism of plasticity for sexes within species and less integrated parallelism for species. We interpret these findings with respect to their potential broader implications for the interacting roles of adaptation and constraint in the evolutionary origins of parallelism of plasticity in general. PMID:29491997

Utilization of PD modalities: evolution.

PubMed

Venkataraman, Vijaya; Nolph, Karl D

2002-01-01

In the early 1960s, peritoneal dialysis (PD) was introduced as a form of long-term maintenance therapy in patients with end-stage renal disease (ESRD). We have come a long way since. Increasing understanding of peritoneal kinetic behavior, its innovative manipulation to meet patient needs, critical monitoring of clinical outcomes, and parallel development in technology have all contributed to the worldwide success of the therapy over the past four decades. In this article we review the evolution of the various PD modalities in the context of these factors.

A non-linear theory of the parallel firehose and gyrothermal instabilities in a weakly collisional plasma

NASA Astrophysics Data System (ADS)

Rosin, M. S.; Schekochihin, A. A.; Rincon, F.; Cowley, S. C.

2011-05-01

Weakly collisional magnetized cosmic plasmas have a dynamical tendency to develop pressure anisotropies with respect to the local direction of the magnetic field. These anisotropies trigger plasma instabilities at scales just above the ion Larmor radius ρi and much below the mean free path λmfp. They have growth rates of a fraction of the ion cyclotron frequency, which is much faster than either the global dynamics or even local turbulence. Despite their microscopic nature, these instabilities dramatically modify the transport properties and, therefore, the macroscopic dynamics of the plasma. The non-linear evolution of these instabilities is expected to drive pressure anisotropies towards marginal stability values, controlled by the plasma beta βi. Here this non-linear evolution is worked out in an ab initio kinetic calculation for the simplest analytically tractable example - the parallel (k⊥= 0) firehose instability in a high-beta plasma. An asymptotic theory is constructed, based on a particular physical ordering and leading to a closed non-linear equation for the firehose turbulence. In the non-linear regime, both the analytical theory and the numerical solution predict secular (∝t) growth of magnetic fluctuations. The fluctuations develop a k-3∥ spectrum, extending from scales somewhat larger than ρi to the maximum scale that grows secularly with time (∝t1/2); the relative pressure anisotropy (p⊥-p∥)/p∥ tends to the marginal value -2/βi. The marginal state is achieved via changes in the magnetic field, not particle scattering. When a parallel ion heat flux is present, the parallel firehose mutates into the new gyrothermal instability (GTI), which continues to exist up to firehose-stable values of pressure anisotropy, which can be positive and are limited by the magnitude of the ion heat flux. The non-linear evolution of the GTI also features secular growth of magnetic fluctuations, but the fluctuation spectrum is eventually dominated by modes around a maximal scale ˜ρilT/λmfp, where lT is the scale of the parallel temperature variation. Implications for momentum and heat transport are speculated about. This study is motivated by our interest in the dynamics of galaxy cluster plasmas (which are used as the main astrophysical example), but its relevance to solar wind and accretion flow plasmas is also briefly discussed.

Long-time dynamics through parallel trajectory splicing

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

Perez, Danny; Cubuk, Ekin D.; Waterland, Amos

2015-11-24

Simulating the atomistic evolution of materials over long time scales is a longstanding challenge, especially for complex systems where the distribution of barrier heights is very heterogeneous. Such systems are difficult to investigate using conventional long-time scale techniques, and the fact that they tend to remain trapped in small regions of configuration space for extended periods of time strongly limits the physical insights gained from short simulations. We introduce a novel simulation technique, Parallel Trajectory Splicing (ParSplice), that aims at addressing this problem through the timewise parallelization of long trajectories. The computational efficiency of ParSplice stems from a speculation strategymore » whereby predictions of the future evolution of the system are leveraged to increase the amount of work that can be concurrently performed at any one time, hence improving the scalability of the method. ParSplice is also able to accurately account for, and potentially reuse, a substantial fraction of the computational work invested in the simulation. We validate the method on a simple Ag surface system and demonstrate substantial increases in efficiency compared to previous methods. As a result, we then demonstrate the power of ParSplice through the study of topology changes in Ag 42Cu 13 core–shell nanoparticles.« less

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.

PubMed

Samis, Karen E; Murren, Courtney J; Bossdorf, Oliver; Donohue, Kathleen; Fenster, Charles B; Malmberg, Russell L; Purugganan, Michael D; Stinchcombe, John R

2012-06-01

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150-200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.

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.

Generation and evolution of anisotropic turbulence and related energy transfer in drifting proton-alpha plasmas

NASA Astrophysics Data System (ADS)

Maneva, Y. G.; Poedts, S.

2018-05-01

The power spectra of magnetic field fluctuations in the solar wind typically follow a power-law dependence with respect to the observed frequencies and wave-numbers. The background magnetic field often influences the plasma properties, setting a preferential direction for plasma heating and acceleration. At the same time the evolution of the solar-wind turbulence at the ion and electron scales is influenced by the plasma properties through local micro-instabilities and wave-particle interactions. The solar-wind-plasma temperature and the solar-wind turbulence at sub- and sup-ion scales simultaneously show anisotropic features, with different components and fluctuation power in parallel with and perpendicular to the orientation of the background magnetic field. The ratio between the power of the magnetic field fluctuations in parallel and perpendicular direction at the ion scales may vary with the heliospheric distance and depends on various parameters, including the local wave properties and nonthermal plasma features, such as temperature anisotropies and relative drift speeds. In this work we have performed two-and-a-half-dimensional hybrid simulations to study the generation and evolution of anisotropic turbulence in a drifting multi-ion species plasma. We investigate the evolution of the turbulent spectral slopes along and across the background magnetic field for the cases of initially isotropic and anisotropic turbulence. Finally, we show the effect of the various turbulent spectra for the local ion heating in the solar wind.

Parallel Evolution of Cold Tolerance within Drosophila melanogaster

PubMed Central

Braun, Dylan T.; Lack, Justin B.

2017-01-01

Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation. PMID:27777283

A heterogeneous computing accelerated SCE-UA global optimization method using OpenMP, OpenCL, CUDA, and OpenACC.

PubMed

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Liang, Ke; Hong, Yang

2017-10-01

The shuffled complex evolution optimization developed at the University of Arizona (SCE-UA) has been successfully applied in various kinds of scientific and engineering optimization applications, such as hydrological model parameter calibration, for many years. The algorithm possesses good global optimality, convergence stability and robustness. However, benchmark and real-world applications reveal the poor computational efficiency of the SCE-UA. This research aims at the parallelization and acceleration of the SCE-UA method based on powerful heterogeneous computing technology. The parallel SCE-UA is implemented on Intel Xeon multi-core CPU (by using OpenMP and OpenCL) and NVIDIA Tesla many-core GPU (by using OpenCL, CUDA, and OpenACC). The serial and parallel SCE-UA were tested based on the Griewank benchmark function. Comparison results indicate the parallel SCE-UA significantly improves computational efficiency compared to the original serial version. The OpenCL implementation obtains the best overall acceleration results however, with the most complex source code. The parallel SCE-UA has bright prospects to be applied in real-world applications.

Parallel evolution of storage roots in Morning Glories (Convolvulaceae)

USDA-ARS?s Scientific Manuscript database

Storage roots are an ecologically and agriculturally important plant trait. In morning glories, storage roots are well characterized in the crop species sweetpotato. Storage roots have evolved numerous times across the morning glory family. This study aims to understand whether this was through para...

Parallel and convergent evolution of the dim-light vision gene RH1 in bats (Order: Chiroptera).

PubMed

Shen, Yong-Yi; Liu, Jie; Irwin, David M; Zhang, Ya-Ping

2010-01-21

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

PubMed Central

Shen, Yong-Yi; Liu, Jie; Irwin, David M.; Zhang, Ya-Ping

2010-01-01

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats. PMID:20098620

Efficient solution of parabolic equations by Krylov approximation methods

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Y.

1990-01-01

Numerical techniques for solving parabolic equations by the method of lines is addressed. The main motivation for the proposed approach is the possibility of exploiting a high degree of parallelism in a simple manner. The basic idea of the method is to approximate the action of the evolution operator on a given state vector by means of a projection process onto a Krylov subspace. Thus, the resulting approximation consists of applying an evolution operator of a very small dimension to a known vector which is, in turn, computed accurately by exploiting well-known rational approximations to the exponential. Because the rational approximation is only applied to a small matrix, the only operations required with the original large matrix are matrix-by-vector multiplications, and as a result the algorithm can easily be parallelized and vectorized. Some relevant approximation and stability issues are discussed. We present some numerical experiments with the method and compare its performance with a few explicit and implicit algorithms.

Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

PubMed Central

Moreno-Letelier, Alejandra; Olmedo, Gabriela; Eguiarte, Luis E.; Martinez-Castilla, Leon; Souza, Valeria

2011-01-01

The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events. PMID:21461370

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies

PubMed Central

Daane, Jacob M.; Rohner, Nicolas; Konstantinidis, Peter; Djuranovic, Sergej; Harris, Matthew P.

2016-01-01

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes. PMID:26452532

Parameter Estimation of Fractional-Order Chaotic Systems by Using Quantum Parallel Particle Swarm Optimization Algorithm

PubMed Central

Huang, Yu; Guo, Feng; Li, Yongling; Liu, Yufeng

2015-01-01

Parameter estimation for fractional-order chaotic systems is an important issue in fractional-order chaotic control and synchronization and could be essentially formulated as a multidimensional optimization problem. A novel algorithm called quantum parallel particle swarm optimization (QPPSO) is proposed to solve the parameter estimation for fractional-order chaotic systems. The parallel characteristic of quantum computing is used in QPPSO. This characteristic increases the calculation of each generation exponentially. The behavior of particles in quantum space is restrained by the quantum evolution equation, which consists of the current rotation angle, individual optimal quantum rotation angle, and global optimal quantum rotation angle. Numerical simulation based on several typical fractional-order systems and comparisons with some typical existing algorithms show the effectiveness and efficiency of the proposed algorithm. PMID:25603158

EUPDF-II: An Eulerian Joint Scalar Monte Carlo PDF Module : User's Manual

NASA Technical Reports Server (NTRS)

Raju, M. S.; Liu, Nan-Suey (Technical Monitor)

2004-01-01

EUPDF-II provides the solution for the species and temperature fields based on an evolution equation for PDF (Probability Density Function) and it is developed mainly for application with sprays, combustion, parallel computing, and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase CFD and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with an understanding of the various models involved in the PDF formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers. The source code of EUPDF-II will be available with National Combustion Code (NCC) as a complete package.

Parallel Grand Canonical Monte Carlo (ParaGrandMC) Simulation Code

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.

2016-01-01

This report provides an overview of the Parallel Grand Canonical Monte Carlo (ParaGrandMC) simulation code. This is a highly scalable parallel FORTRAN code for simulating the thermodynamic evolution of metal alloy systems at the atomic level, and predicting the thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces.

A Parallel Genetic Algorithm for Automated Electronic Circuit Design

NASA Technical Reports Server (NTRS)

Long, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris

2000-01-01

Parallelized versions of genetic algorithms (GAs) are popular primarily for three reasons: the GA is an inherently parallel algorithm, typical GA applications are very compute intensive, and powerful computing platforms, especially Beowulf-style computing clusters, are becoming more affordable and easier to implement. In addition, the low communication bandwidth required allows the use of inexpensive networking hardware such as standard office ethernet. In this paper we describe a parallel GA and its use in automated high-level circuit design. Genetic algorithms are a type of trial-and-error search technique that are guided by principles of Darwinian evolution. Just as the genetic material of two living organisms can intermix to produce offspring that are better adapted to their environment, GAs expose genetic material, frequently strings of 1s and Os, to the forces of artificial evolution: selection, mutation, recombination, etc. GAs start with a pool of randomly-generated candidate solutions which are then tested and scored with respect to their utility. Solutions are then bred by probabilistically selecting high quality parents and recombining their genetic representations to produce offspring solutions. Offspring are typically subjected to a small amount of random mutation. After a pool of offspring is produced, this process iterates until a satisfactory solution is found or an iteration limit is reached. Genetic algorithms have been applied to a wide variety of problems in many fields, including chemistry, biology, and many engineering disciplines. There are many styles of parallelism used in implementing parallel GAs. One such method is called the master-slave or processor farm approach. In this technique, slave nodes are used solely to compute fitness evaluations (the most time consuming part). The master processor collects fitness scores from the nodes and performs the genetic operators (selection, reproduction, variation, etc.). Because of dependency issues in the GA, it is possible to have idle processors. However, as long as the load at each processing node is similar, the processors are kept busy nearly all of the time. In applying GAs to circuit design, a suitable genetic representation 'is that of a circuit-construction program. We discuss one such circuit-construction programming language and show how evolution can generate useful analog circuit designs. This language has the desirable property that virtually all sets of combinations of primitives result in valid circuit graphs. Our system allows circuit size (number of devices), circuit topology, and device values to be evolved. Using a parallel genetic algorithm and circuit simulation software, we present experimental results as applied to three analog filter and two amplifier design tasks. For example, a figure shows an 85 dB amplifier design evolved by our system, and another figure shows the performance of that circuit (gain and frequency response). In all tasks, our system is able to generate circuits that achieve the target specifications.

Ecological transition predictably associated with gene degeneration.

PubMed

Wessinger, Carolyn A; Rausher, Mark D

2015-02-01

Gene degeneration or loss can significantly contribute to phenotypic diversification, but may generate genetic constraints on future evolutionary trajectories, potentially restricting phenotypic reversal. Such constraints may manifest as directional evolutionary trends when parallel phenotypic shifts consistently involve gene degeneration or loss. Here, we demonstrate that widespread parallel evolution in Penstemon from blue to red flowers predictably involves the functional inactivation and degeneration of the enzyme flavonoid 3',5'-hydroxylase (F3'5'H), an anthocyanin pathway enzyme required for the production of blue floral pigments. Other types of genetic mutations do not consistently accompany this phenotypic shift. This pattern may be driven by the relatively large mutational target size of degenerative mutations to this locus and the apparent lack of associated pleiotropic effects. The consistent degeneration of F3'5'H may provide a mechanistic explanation for the observed asymmetry in the direction of flower color evolution in Penstemon: Blue to red transitions are common, but reverse transitions have not been observed. Although phenotypic shifts in this system are likely driven by natural selection, internal constraints may generate predictable genetic outcomes and may restrict future evolutionary trajectories. © 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.

Turbulence Evolution and Shock Acceleration of Solar Energetic Particles

NASA Technical Reports Server (NTRS)

Chee, Ng K.

2007-01-01

We model the effects of self-excitation/damping and shock transmission of Alfven waves on solar-energetic-particle (SEP) acceleration at a coronal-mass-ejection (CME) driven parallel shock. SEP-excited outward upstream waves speedily bootstrap acceleration. Shock transmission further raises the SEP-excited wave intensities at high wavenumbers but lowers them at low wavenumbers through wavenumber shift. Downstream, SEP excitation of inward waves and damping of outward waves tend to slow acceleration. Nevertheless, > 2000 km/s parallel shocks at approx. 3.5 solar radii can accelerate SEPs to 100 MeV in < 5 minutes.

Application of computational physics within Northrop

NASA Technical Reports Server (NTRS)

George, M. W.; Ling, R. T.; Mangus, J. F.; Thompkins, W. T.

1987-01-01

An overview of Northrop programs in computational physics is presented. These programs depend on access to today's supercomputers, such as the Numerical Aerodynamical Simulator (NAS), and future growth on the continuing evolution of computational engines. Descriptions here are concentrated on the following areas: computational fluid dynamics (CFD), computational electromagnetics (CEM), computer architectures, and expert systems. Current efforts and future directions in these areas are presented. The impact of advances in the CFD area is described, and parallels are drawn to analagous developments in CEM. The relationship between advances in these areas and the development of advances (parallel) architectures and expert systems is also presented.

Linguistic Ambiguity in a Connectionist Model for Grammatical Studies.

ERIC Educational Resources Information Center

Angelica, Julia; Ney, James W.

1995-01-01

Discusses the evolution of the connectionist model of language processing, focusing on the parallel distributed processing (PDP) model proposed by Rumelhart and others (1986) that explains the microstructure of cognition in terms of interactive activation between elementary input, output, and intermediate processing units linked by weighted…

Modern Science and Conservative Islam: An Uneasy Relationship

ERIC Educational Resources Information Center

Edis, Taner

2009-01-01

Familiar Western debates about religion, science, and science education have parallels in the Islamic world. There are difficulties reconciling conservative, traditional versions of Islam with modern science, particularly theories such as evolution. As a result, many conservative Muslim thinkers are drawn toward creationism, hopes of Islamizing…

Long waves in parallel flow in Hele-Shaw cells

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

Zeybek, M.; Yortsos, Y.C.

During the past several years the flow of immiscible flow in Hele-Shaw cells and porous media has been investigated extensively. Of particular interest to most studies has been frontal displacement, specifically viscous fingering instabilities and finger growth. The practical ramifications regarding oil recovery, as well as many other industrial processes in porous media, have served as the primary driving force for most of these investigations. By contrast, little attention has been paid to the motion of lateral fluid interface, which are parallel to the main flow direction. Parallel flow is an often encountered, although much overlooked regime. The evolution ofmore » fluid interfaces in parallel flow in Hele-Shaw cells is studied both theoretically and experimentally in the large capillary number limit. It is shown that such interfaces support wave motion, the amplitude of which for long waves is governed by the KdV equation. Experiments are conducted in a long Hele-Shaw cell that validate the theory in the symmetric case. 35 refs., 16 figs.« less

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

Reimberg, Paulo; Bernardeau, Francis; Pitrou, Cyril, E-mail: paulo.flose-reimberg@cea.fr, E-mail: francis.bernardeau@cea.fr, E-mail: pitrou@iap.fr

Redshift-space distortions are generally considered in the plane parallel limit, where the angular separation between the two sources can be neglected. Given that galaxy catalogues now cover large fractions of the sky, it becomes necessary to consider them in a formalism which takes into account the wide angle separations. In this article we derive an operational formula for the matter correlators in the Newtonian limit to be used in actual data sets. In order to describe the geometrical nature of the wide angle RSD effect on Fourier space, we extend the formalism developed in configuration space to Fourier space withoutmore » relying on a plane-parallel approximation, but under the extra assumption of no bias evolution. We then recover the plane-parallel limit not only in configuration space where the geometry is simpler, but also in Fourier space, and we exhibit the first corrections that should be included in large surveys as a perturbative expansion over the plane-parallel results. We finally compare our results to existing literature, and show explicitly how they are related.« less

The parallel-antiparallel signal difference in double-wave-vector diffusion-weighted MR at short mixing times: A phase evolution perspective

NASA Astrophysics Data System (ADS)

Finsterbusch, Jürgen

2011-01-01

Experiments with two diffusion weightings applied in direct succession in a single acquisition, so-called double- or two-wave-vector diffusion-weighting (DWV) experiments at short mixing times, have been shown to be a promising tool to estimate cell or compartment sizes, e.g. in living tissue. The basic theory for such experiments predicts that the signal decays for parallel and antiparallel wave vector orientations differ by a factor of three for small wave vectors. This seems to be surprising because in standard, single-wave-vector experiments the polarity of the diffusion weighting has no influence on the signal attenuation. Thus, the question how this difference can be understood more pictorially is often raised. In this rather educational manuscript, the phase evolution during a DWV experiment for simple geometries, e.g. diffusion between parallel, impermeable planes oriented perpendicular to the wave vectors, is considered step-by-step and demonstrates how the signal difference develops. Considering the populations of the phase distributions obtained, the factor of three between the signal decays which is predicted by the theory can be reproduced. Furthermore, the intermediate signal decay for orthogonal wave vector orientations can be derived when investigating diffusion in a box. Thus, the presented “phase gymnastics” approach may help to understand the signal modulation observed in DWV experiments at short mixing times.

Efficient Parallel Algorithms for Landscape Evolution Modelling

NASA Astrophysics Data System (ADS)

Moresi, L. N.; Mather, B.; Beucher, R.

2017-12-01

Landscape erosion and the deposition of sediments by river systems are strongly controlled bytopography, rainfall patterns, and the susceptibility of the basement to the action ofrunning water. It is well understood that each of these processes depends on the other, for example:topography results from active tectonic processes; deformation, metamorphosis andexhumation alter the competence of the basement; rainfall patterns depend on topography;uplift and subsidence in response to tectonic stress can be amplified by erosionand sediment deposition. We typically gain understanding of such coupled systems through forward models which capture theessential interactions of the various components and attempt parameterise those parts of the individual systemthat are unresolvable at the scale of the interaction. Here we address the problem of predicting erosion and deposition rates at a continental scalewith a resolution of tens to hundreds of metres in a dynamic, Lagrangian framework. This isa typical requirement for a code to interface with a mantle / lithosphere dynamics model anddemands an efficient, unstructured, parallel implementation. We address this through a very general algorithm that treats all parts of the landscape evolution equationsin sparse-matrix form including those for stream-flow accumulation, dam-filling and catchment determination. This givesus considerable flexibility in developing unstructured, parallel code, and in creating a modular packagethat can be configured by users to work at different temporal and spatial scales, but is also has potential advantagesin treating the non-linear parts of the problem in a general manner.

The Development of the Mathematical Mind.

ERIC Educational Resources Information Center

Scott, Judith

1995-01-01

Draws parallels between Montessori's mathematical curriculum and the evolution of numbers and counting. Suggests that children share with ancient Sumerians a basic human tendency to develop "the mathematical mind." Argues that children do not need to be surrounded by math; rather, the classroom must supply them with the means to explore…

Educational preparation of black nurses: a historical perspective.

PubMed

Carnegie, M Elizabeth

2005-01-01

To where minority nursing needs to proceed, the minority nursing community must understand where we have been. This historical perspective traces our roots through every level of nursing education. Parallels are drawn between minority nurse educational evolution and the historical events occurring in the greater society in the United States.

Using Coarrays to Parallelize Legacy Fortran Applications: Strategy and Case Study

DOE PAGES

Radhakrishnan, Hari; Rouson, Damian W. I.; Morris, Karla; ...

2015-01-01

This paper summarizes a strategy for parallelizing a legacy Fortran 77 program using the object-oriented (OO) and coarray features that entered Fortran in the 2003 and 2008 standards, respectively. OO programming (OOP) facilitates the construction of an extensible suite of model-verification and performance tests that drive the development. Coarray parallel programming facilitates a rapid evolution from a serial application to a parallel application capable of running on multicore processors and many-core accelerators in shared and distributed memory. We delineate 17 code modernization steps used to refactor and parallelize the program and study the resulting performance. Our initial studies were donemore » using the Intel Fortran compiler on a 32-core shared memory server. Scaling behavior was very poor, and profile analysis using TAU showed that the bottleneck in the performance was due to our implementation of a collective, sequential summation procedure. We were able to improve the scalability and achieve nearly linear speedup by replacing the sequential summation with a parallel, binary tree algorithm. We also tested the Cray compiler, which provides its own collective summation procedure. Intel provides no collective reductions. With Cray, the program shows linear speedup even in distributed-memory execution. We anticipate similar results with other compilers once they support the new collective procedures proposed for Fortran 2015.« less

What Pinnipeds Have to Say about Human Speech, Music, and the Evolution of Rhythm.

PubMed

Ravignani, Andrea; Fitch, W Tecumseh; Hanke, Frederike D; Heinrich, Tamara; Hurgitsch, Bettina; Kotz, Sonja A; Scharff, Constance; Stoeger, Angela S; de Boer, Bart

2016-01-01

Research on the evolution of human speech and music benefits from hypotheses and data generated in a number of disciplines. The purpose of this article is to illustrate the high relevance of pinniped research for the study of speech, musical rhythm, and their origins, bridging and complementing current research on primates and birds. We briefly discuss speech, vocal learning, and rhythm from an evolutionary and comparative perspective. We review the current state of the art on pinniped communication and behavior relevant to the evolution of human speech and music, showing interesting parallels to hypotheses on rhythmic behavior in early hominids. We suggest future research directions in terms of species to test and empirical data needed.

What Pinnipeds Have to Say about Human Speech, Music, and the Evolution of Rhythm

PubMed Central

Ravignani, Andrea; Fitch, W. Tecumseh; Hanke, Frederike D.; Heinrich, Tamara; Hurgitsch, Bettina; Kotz, Sonja A.; Scharff, Constance; Stoeger, Angela S.; de Boer, Bart

2016-01-01

Research on the evolution of human speech and music benefits from hypotheses and data generated in a number of disciplines. The purpose of this article is to illustrate the high relevance of pinniped research for the study of speech, musical rhythm, and their origins, bridging and complementing current research on primates and birds. We briefly discuss speech, vocal learning, and rhythm from an evolutionary and comparative perspective. We review the current state of the art on pinniped communication and behavior relevant to the evolution of human speech and music, showing interesting parallels to hypotheses on rhythmic behavior in early hominids. We suggest future research directions in terms of species to test and empirical data needed. PMID:27378843

Silencing, positive selection and parallel evolution: busy history of primate cytochromes C.

PubMed

Pierron, Denis; Opazo, Juan C; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.

Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

PubMed Central

Pierron, Denis; Opazo, Juan C.; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E.; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I.

2011-01-01

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades. PMID:22028846

Detecting regular sound changes in linguistics as events of concerted evolution

DOE PAGES

Hruschka, Daniel  J.; Branford, Simon; Smith, Eric  D.; ...

2014-12-18

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular soundmore » change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.« less

Detecting regular sound changes in linguistics as events of concerted evolution.

PubMed

Hruschka, Daniel J; Branford, Simon; Smith, Eric D; Wilkins, Jon; Meade, Andrew; Pagel, Mark; Bhattacharya, Tanmoy

2015-01-05

Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Why Africa matters: evolution of Old World Salvia (Lamiaceae) in Africa

PubMed Central

Will, Maria; Claßen-Bockhoff, Regine

2014-01-01

Background and Aims Salvia is the largest genus in Lamiaceae and it has recently been found to be non-monophyletic. Molecular data on Old World Salvia are largely lacking. In this study, we present data concerning Salvia in Africa. The focus is on the colonization of the continent, character evolution and the switch of pollination systems in the genus. Methods Maximum likelihood and Bayesian inference were used for phylogenetic reconstruction. Analyses were based on two nuclear markers [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and one plastid marker (rpl32-trnL). Sequence data were generated for 41 of the 62 African taxa (66 %). Mesquite was used to reconstruct ancestral character states for distribution, life form, calyx shape, stamen type and pollination syndrome. Key Results Salvia in Africa is non-monophyletic. Each of the five major regions in Africa, except Madagascar, was colonized at least twice, and floristic links between North African, south-west Asian and European species are strongly supported. The large radiation in Sub-Saharan Africa (23 species) can be traced back to dispersal from North Africa via East Africa to the Cape Region. Adaptation to bird pollination in southern Africa and Madagascar reflects parallel evolution. Conclusions The phenotypic diversity in African Salvia is associated with repeated introductions to the continent. Many important evolutionary processes, such as colonization, adaptation, parallelism and character transformation, are reflected in this comparatively small group. The data presented in this study can help to understand the evolution of Salvia sensu lato and other large genera. PMID:24966353

Detecting regular sound changes in linguistics as events of concerted evolution

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

Hruschka, Daniel  J.; Branford, Simon; Smith, Eric  D.

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular soundmore » change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.« less

Experimental evolution in biofilm populations

PubMed Central

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

Experimental evolution in biofilm populations.

PubMed

Steenackers, Hans P; Parijs, Ilse; Dubey, Akanksha; Foster, Kevin R; Vanderleyden, Jozef

2016-05-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. © FEMS 2016.

Temporal evolution of surface ripples on a finite plasma slab subject to the magneto-Rayleigh-Taylor instability

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

Weis, M. R.; Zhang, P.; Lau, Y. Y., E-mail: yylau@umich.edu

2014-12-15

Using the ideal magnetohydrodynamic model, we calculate the temporal evolution of initial ripples on the boundaries of a planar plasma slab that is subjected to the magneto-Rayleigh-Taylor instability. The plasma slab consists of three regions. We assume that in each region the plasma density is constant with an arbitrary value and the magnetic field is also constant with an arbitrary magnitude and an arbitrary direction parallel to the interfaces. Thus, the instability may be driven by a combination of magnetic pressure and kinetic pressure. The general dispersion relation is derived, together with the feedthrough factor between the two interfaces. Themore » temporal evolution is constructed from the superposition of the eigenmodes. Previously established results are recovered in the various limits. Numerical examples are given on the temporal evolution of ripples on the interfaces of the finite plasma slab.« less

Dynamically correlated mutations drive human Influenza A evolution.

PubMed

Tria, F; Pompei, S; Loreto, V

2013-01-01

Human Influenza A virus undergoes recurrent changes in the hemagglutinin (HA) surface protein, primarily involved in the human antibody recognition. Relevant antigenic changes, enabling the virus to evade host immune response, have been recognized to occur in parallel to multiple mutations at antigenic sites in HA. Yet, the role of correlated mutations (epistasis) in driving the molecular evolution of the virus still represents a challenging puzzle. Further, though circulation at a global geographic level is key for the survival of Influenza A, its role in shaping the viral phylodynamics remains largely unexplored. Here we show, through a sequence based epidemiological model, that epistatic effects between amino acids substitutions, coupled with a reservoir that mimics worldwide circulating viruses, are key determinants that drive human Influenza A evolution. Our approach explains all the up-to-date observations characterizing the evolution of H3N2 subtype, including phylogenetic properties, nucleotide fixation patterns, and composition of antigenic clusters.

Giant hub Src and Syk tyrosine kinase thermodynamic profiles recapitulate evolution

NASA Astrophysics Data System (ADS)

Phillips, J. C.

2017-10-01

Thermodynamic scaling theory, previously applied mainly to small proteins, here analyzes quantitative evolution of the titled functional network giant hub enzymes. The broad domain structure identified homologically is confirmed hydropathically using amino acid sequences only. The most surprising results concern the evolution of the tyrosine kinase globular surface roughness from avians to mammals, which is first order, compared to the evolution within mammals from rodents to humans, which is second order. The mystery of the unique amide terminal region of proto oncogene tyrosine protein kinase is resolved by the discovery there of a rare hydroneutral septad targeting cluster, which is paralleled by an equally rare octad catalytic cluster in tyrosine kinase in humans and a few other species (cat and dog). These results, which go far towards explaining why these proteins are among the largest giant hubs in protein interaction networks, use no adjustable parameters.

Temporal evolution of surface ripples on a finite plasma slab subject to the magneto-Rayleigh-Taylor instability

DOE PAGES

Weis, Matthew Robert; Zhang, Peng; Lau, Yue Ying; ...

2014-12-17

Using the ideal magnetohydrodynamic model, we calculate the temporal evolution of initial ripples on the boundaries of a planar plasma slab that is subjected to the magneto-Rayleigh-Taylor instability. The plasma slab consists of three regions. We assume that in each region the plasma density is constant with an arbitrary value and the magnetic field is also constant with an arbitrary magnitude and an arbitrary direction parallel to the interfaces. Then, the instability may be driven by a combination of magnetic pressure and kinetic pressure. Thus the general dispersion relation is derived, together with the feedthrough factor between the two interfaces.more » The temporal evolution is constructed from the superposition of the eigenmodes. Those previously established results are recovered in the various limits. Numerical examples are given on the temporal evolution of ripples on the interfaces of the finite plasma slab.« less

Cultural evolutionary theory: How culture evolves and why it matters

PubMed Central

Creanza, Nicole; Kolodny, Oren; Feldman, Marcus W.

2017-01-01

Human cultural traits—behaviors, ideas, and technologies that can be learned from other individuals—can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene–culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment. PMID:28739941

Cultural evolutionary theory: How culture evolves and why it matters.

PubMed

Creanza, Nicole; Kolodny, Oren; Feldman, Marcus W

2017-07-24

Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

A case study in evolutionary contingency.

PubMed

Blount, Zachary D

2016-08-01

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

Multi-Physics Modelling of Fault Mechanics Using REDBACK: A Parallel Open-Source Simulator for Tightly Coupled Problems

NASA Astrophysics Data System (ADS)

Poulet, Thomas; Paesold, Martin; Veveakis, Manolis

2017-03-01

Faults play a major role in many economically and environmentally important geological systems, ranging from impermeable seals in petroleum reservoirs to fluid pathways in ore-forming hydrothermal systems. Their behavior is therefore widely studied and fault mechanics is particularly focused on the mechanisms explaining their transient evolution. Single faults can change in time from seals to open channels as they become seismically active and various models have recently been presented to explain the driving forces responsible for such transitions. A model of particular interest is the multi-physics oscillator of Alevizos et al. (J Geophys Res Solid Earth 119(6), 4558-4582, 2014) which extends the traditional rate and state friction approach to rate and temperature-dependent ductile rocks, and has been successfully applied to explain spatial features of exposed thrusts as well as temporal evolutions of current subduction zones. In this contribution we implement that model in REDBACK, a parallel open-source multi-physics simulator developed to solve such geological instabilities in three dimensions. The resolution of the underlying system of equations in a tightly coupled manner allows REDBACK to capture appropriately the various theoretical regimes of the system, including the periodic and non-periodic instabilities. REDBACK can then be used to simulate the drastic permeability evolution in time of such systems, where nominally impermeable faults can sporadically become fluid pathways, with permeability increases of several orders of magnitude.

Extended computational kernels in a massively parallel implementation of the Trotter-Suzuki approximation

NASA Astrophysics Data System (ADS)

Wittek, Peter; Calderaro, Luca

2015-12-01

We extended a parallel and distributed implementation of the Trotter-Suzuki algorithm for simulating quantum systems to study a wider range of physical problems and to make the library easier to use. The new release allows periodic boundary conditions, many-body simulations of non-interacting particles, arbitrary stationary potential functions, and imaginary time evolution to approximate the ground state energy. The new release is more resilient to the computational environment: a wider range of compiler chains and more platforms are supported. To ease development, we provide a more extensive command-line interface, an application programming interface, and wrappers from high-level languages.

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Collisionless dissipation processes in quasi-parallel shocks. [in solar wind

NASA Technical Reports Server (NTRS)

Quest, K. B.; Forslund, D. W.; Brackbill, J. U.; Lee, K.

1983-01-01

The evolution of collisionless, quasi-parallel shocks (the angle between the shock normal and the upstream magnetic field being less than 45 deg) is examined using two dimensional particle simulations. Reflected ions upstream from the shock are observed with average guiding center velocity and gyrational energy which agree well with the prediction of simple specular reflection. Strong ion heating through the shock ramp is apparently caused by large amplitude whistler turbulence. A flux of suprathermal electrons is also the magnetic field direction. Much stronger ion heating occurs in the shock than electron heating. The relevance of this work to the earth's bow shock is discussed.

High-rate serial interconnections for embedded and distributed systems with power and resource constraints

NASA Astrophysics Data System (ADS)

Sheynin, Yuriy; Shutenko, Felix; Suvorova, Elena; Yablokov, Evgenej

2008-04-01

High rate interconnections are important subsystems in modern data processing and control systems of many classes. They are especially important in prospective embedded and on-board systems that used to be multicomponent systems with parallel or distributed architecture, [1]. Modular architecture systems of previous generations were based on parallel busses that were widely used and standardised: VME, PCI, CompactPCI, etc. Busses evolution went in improvement of bus protocol efficiency (burst transactions, split transactions, etc.) and increasing operation frequencies. However, due to multi-drop bus nature and multi-wire skew problems the parallel bussing speedup became more and more limited. For embedded and on-board systems additional reason for this trend was in weight, size and power constraints of an interconnection and its components. Parallel interfaces have become technologically more challenging as their respective clock frequencies have increased to keep pace with the bandwidth requirements of their attached storage devices. Since each interface uses a data clock to gate and validate the parallel data (which is normally 8 bits or 16 bits wide), the clock frequency need only be equivalent to the byte rate or word rate being transmitted. In other words, for a given transmission frequency, the wider the data bus, the slower the clock. As the clock frequency increases, more high frequency energy is available in each of the data lines, and a portion of this energy is dissipated in radiation. Each data line not only transmits this energy but also receives some from its neighbours. This form of mutual interference is commonly called "cross-talk," and the signal distortion it produces can become another major contributor to loss of data integrity unless compensated by appropriate cable designs. Other transmission problems such as frequency-dependent attenuation and signal reflections, while also applicable to serial interfaces, are more troublesome in parallel interfaces due to the number of additional cable conductors involved. In order to compensate for these drawbacks, higher quality cables, shorter cable runs and fewer devices on the bus have been the norm. Finally, the physical bulk of the parallel cables makes them more difficult to route inside an enclosure, hinders cooling airflow and is incompatible with the trend toward smaller form-factor devices. Parallel busses worked in systems during the past 20 years, but the accumulated problems dictate the need for change and the technology is available to spur the transition. The general trend in high-rate interconnections turned from parallel bussing to scalable interconnections with a network architecture and high-rate point-to-point links. Analysis showed that data links with serial information transfer could achieve higher throughput and efficiency and it was confirmed in various research and practical design. Serial interfaces offer an improvement over older parallel interfaces: better performance, better scalability, and also better reliability as the parallel interfaces are at their limits of speed with reliable data transfers and others. The trend was implemented in major standards' families evolution: e.g. from PCI/PCI-X parallel bussing to PCIExpress interconnection architecture with serial lines, from CompactPCI parallel bus to ATCA (Advanced Telecommunications Architecture) specification with serial links and network topologies of an interconnection, etc. In the article we consider a general set of characteristics and features of serial interconnections, give a brief overview of serial interconnections specifications. In more details we present the SpaceWire interconnection technology. Have been developed for space on-board systems applications the SpaceWire has important features and characteristics that make it a prospective interconnection for wide range of embedded systems.

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

PubMed Central

Spang, Anja; Saw, Jimmy H.; Lind, Anders E.; Ettema, Thijs J. G.

2013-01-01

The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. PMID:24348093

[The diffusion of the human evolution in Spain and the JAE (1907-1939)].

PubMed

Pelayo, Francisco

2007-01-01

During the first decades of the 20th century important findings of hominids fossil remains were made, enlarging the knowledge on Human Evolution. This period runs parallel to the activity of the Junta para Ampliación de Estudios e Investigaciones Científicas (JAE), an institution that helped to spread the new paleontological facts in Spain by providing funds for further studies and research, by the foundation of the Comisión de Investigaciones Paleontológicas y Prehistóricas (CIPP) and the promotion of publications on Human Paleontology.

The petrographic microscope: Evolution of a mineralogical research instrument

USGS Publications Warehouse

Kile, D.E.

2003-01-01

The petrographic microscope, designed to observe and measure the optical properties of minerals as a means of identifying them, has provided a foundation for mineralogical and petrological research for more than 120 years. Much of what is known today in these fields is attributable to this instrument, the development of which paralleled an evolution of fundamental optical theory and its correlation with mineral structure and composition. This instrument and its related accessories have evolved through a range of models and designs, which are in themselves distinctive for their scientific function and elegant construction, and are today prized by collectors of scientific instruments.

Modeling evolution of crosstalk in noisy signal transduction networks

NASA Astrophysics Data System (ADS)

Tareen, Ammar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2018-02-01

Signal transduction networks can form highly interconnected systems within cells due to crosstalk between constituent pathways. To better understand the evolutionary design principles underlying such networks, we study the evolution of crosstalk for two parallel signaling pathways that arise via gene duplication. We use a sequence-based evolutionary algorithm and evolve the network based on two physically motivated fitness functions related to information transmission. We find that one fitness function leads to a high degree of crosstalk while the other leads to pathway specificity. Our results offer insights on the relationship between network architecture and information transmission for noisy biomolecular networks.

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

ERIC Educational Resources Information Center

Ha, Minsu; Nehm, Ross H.

2014-01-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or…

The "Three Doctrines Discussions" of Tang China: Religious Debate as a Rhetorical Strategy.

ERIC Educational Resources Information Center

Garrett, Mary M.

1994-01-01

Reports on the origins and importance of the "Three Doctrines Discussions" of the Chinese Tang dynasty (618-960). Shows how their evolution and decline parallel shifts in the balance of political power. Argues that these debates functioned rhetorically to enhance and legitimate the emperor's political power. (HB)

Experiences in Teaching a Graduate Course on Model-Driven Software Development

ERIC Educational Resources Information Center

Tekinerdogan, Bedir

2011-01-01

Model-driven software development (MDSD) aims to support the development and evolution of software intensive systems using the basic concepts of model, metamodel, and model transformation. In parallel with the ongoing academic research, MDSD is more and more applied in industrial practices. After being accepted both by a broad community of…

Interuniversal entanglement in a cyclic multiverse

NASA Astrophysics Data System (ADS)

Robles-Pérez, Salvador; Balcerzak, Adam; Dąbrowski, Mariusz P.; Krämer, Manuel

2017-04-01

We study scenarios of parallel cyclic multiverses which allow for a different evolution of the physical constants, while having the same geometry. These universes are classically disconnected, but quantum-mechanically entangled. Applying the thermodynamics of entanglement, we calculate the temperature and the entropy of entanglement. It emerges that the entropy of entanglement is large at big bang and big crunch singularities of the parallel universes as well as at the maxima of the expansion of these universes. The latter seems to confirm earlier studies that quantum effects are strong at turning points of the evolution of the universe performed in the context of the timeless nature of the Wheeler-DeWitt equation and decoherence. On the other hand, the entropy of entanglement at big rip singularities is going to zero despite its presumably quantum nature. This may be an effect of total dissociation of the universe structures into infinitely separated patches violating the null energy condition. However, the temperature of entanglement is large/infinite at every classically singular point and at maximum expansion and seems to be a better measure of quantumness.

Pulsating Magnetic Reconnection Driven by Three-Dimensional Flux-Rope Interactions.

PubMed

Gekelman, W; De Haas, T; Daughton, W; Van Compernolle, B; Intrator, T; Vincena, S

2016-06-10

The dynamics of magnetic reconnection is investigated in a laboratory experiment consisting of two magnetic flux ropes, with currents slightly above the threshold for the kink instability. The evolution features periodic bursts of magnetic reconnection. To diagnose this complex evolution, volumetric three-dimensional data were acquired for both the magnetic and electric fields, allowing key field-line mapping quantities to be directly evaluated for the first time with experimental data. The ropes interact by rotating about each other and periodically bouncing at the kink frequency. During each reconnection event, the formation of a quasiseparatrix layer (QSL) is observed in the magnetic field between the flux ropes. Furthermore, a clear correlation is demonstrated between the quasiseparatrix layer and enhanced values of the quasipotential computed by integrating the parallel electric field along magnetic field lines. These results provide clear evidence that field lines passing through the quasiseparatrix layer are undergoing reconnection and give a direct measure of the nonlinear reconnection rate. The measurements suggest that the parallel electric field within the QSL is supported predominantly by electron pressure; however, resistivity may play a role.

Full-field drift Hamiltonian particle orbits in 3D geometry

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Brunner, S.; Isaev, M. Yu

2011-02-01

A Hamiltonian/Lagrangian theory to describe guiding centre orbit drift motion which is canonical in the Boozer coordinate frame has been extended to include full electromagnetic perturbed fields in anisotropic pressure 3D equilibria with nested magnetic flux surfaces. A redefinition of the guiding centre velocity to eliminate the motion due to finite equilibrium radial magnetic fields and the choice of a gauge condition that sets the radial component of the electromagnetic vector potential to zero are invoked to guarantee that the Boozer angular coordinates retain the canonical structure. The canonical momenta are identified and the guiding centre particle radial drift motion and parallel gyroradius evolution are derived. The particle coordinate position is linearly modified by wave-particle interactions. All the nonlinear wave-wave interactions appear explicitly only in the evolution of the parallel gyroradius. The radial variation of the electrostatic potential is related to the binormal component of the displacement vector for MHD-type perturbations. The electromagnetic vector potential projections can then be determined from the electrostatic potential and the radial component of the MHD displacement vector.

The effect of plastic strain on the evolution of crystallographic texture in Zircaloy-2

NASA Astrophysics Data System (ADS)

Ballinger, R. G.; Lucas, G. E.; Pelloux, R. M.

1984-09-01

The evolution of crystallographic texture during plastic deformation was investigated in Zircaloy-2 using X-ray and metallographic techniques. Inverse pole figures, the resolved fraction of basal poles, and the volume fraction of twinned material, were determined as a function of plastic strain for several strain paths and initial textures at 298 K and 623 K. Incremental transverse platic strain ratios ( R) were mesured as a function of plastic strain. Texture rotation occurs early in the deformation process, after as little as 1.5% plastic strain. For compressive plastic strains, the resolved fraction of basal poles increases in the direction parallel to the strain axis. For tensile plastic strains, the resolved fraction of basal poles decreases in the direction parallel to the strain axis. The rate of change of the resolved fraction of basal poles with plastic strain is a function of the initial resolved fraction of basal poles. The texture rotation can be explained by considering the operation of the principal tensile twinning systems, {101¯2}<1¯011>.

Parallel evolution of Nitric Oxide signaling: Diversity of synthesis & memory pathways

PubMed Central

Moroz, Leonid L.; Kohn, Andrea B.

2014-01-01

The origin of NO signaling can be traceable back to the origin of life with the large scale of parallel evolution of NO synthases (NOSs). Inducible-like NOSs may be the most basal prototype of all NOSs and that neuronal-like NOS might have evolved several times from this prototype. Other enzymatic and non-enzymatic pathways for NO synthesis have been discovered using reduction of nitrites, an alternative source of NO. Diverse synthetic mechanisms can co-exist within the same cell providing a complex NO-oxygen microenvironment tightly coupled with cellular energetics. The dissection of multiple sources of NO formation is crucial in analysis of complex biological processes such as neuronal integration and learning mechanisms when NO can act as a volume transmitter within memory-forming circuits. In particular, the molecular analysis of learning mechanisms (most notably in insects and gastropod molluscs) opens conceptually different perspectives to understand the logic of recruiting evolutionarily conserved pathways for novel functions. Giant uniquely identified cells from Aplysia and related species precent unuque opportunities for integrative analysis of NO signaling at the single cell level. PMID:21622160

General trends of chromosomal evolution in Aphidococca (Insecta, Homoptera, Aphidinea + Coccinea)

PubMed Central

Gavrilov-Zimin, Ilya A.; Stekolshchikov, Andrey V.; Gautam, D.C.

2015-01-01

Abstract Parallel trends of chromosomal evolution in Aphidococca are discussed, based on the catalogue of chromosomal numbers and genetic systems of scale insects by Gavrilov (2007) and the new catalogue for aphids provided in the present paper. To date chromosome numbers have been reported for 482 species of scale insects and for 1039 species of aphids, thus respectively comprising about 6% and 24% of the total number of species. Such characters as low modal numbers of chromosomes, heterochromatinization of part of chromosomes, production of only two sperm instead of four from each primary spermatocyte, physiological sex determination, "larval" meiosis, wide distribution of parthenogenesis and chromosomal races are considered as a result of homologous parallel changes of the initial genotype of Aphidococca ancestors. From a cytogenetic point of view, these characters separate Aphidococca from all other groups of Paraneoptera insects and in this sense can be considered as additional taxonomic characters. In contrast to available paleontological data the authors doubt that Coccinea with their very diverse (and partly primitive) genetic systems may have originated later then Aphidinea with their very specialised and unified genetic system. PMID:26312130

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

NASA Astrophysics Data System (ADS)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

Experiments with a Parallel Multi-Objective Evolutionary Algorithm for Scheduling

NASA Technical Reports Server (NTRS)

Brown, Matthew; Johnston, Mark D.

2013-01-01

Evolutionary multi-objective algorithms have great potential for scheduling in those situations where tradeoffs among competing objectives represent a key requirement. One challenge, however, is runtime performance, as a consequence of evolving not just a single schedule, but an entire population, while attempting to sample the Pareto frontier as accurately and uniformly as possible. The growing availability of multi-core processors in end user workstations, and even laptops, has raised the question of the extent to which such hardware can be used to speed up evolutionary algorithms. In this paper we report on early experiments in parallelizing a Generalized Differential Evolution (GDE) algorithm for scheduling long-range activities on NASA's Deep Space Network. Initial results show that significant speedups can be achieved, but that performance does not necessarily improve as more cores are utilized. We describe our preliminary results and some initial suggestions from parallelizing the GDE algorithm. Directions for future work are outlined.

Feynman’s clock, a new variational principle, and parallel-in-time quantum dynamics

PubMed Central

McClean, Jarrod R.; Parkhill, John A.; Aspuru-Guzik, Alán

2013-01-01

We introduce a discrete-time variational principle inspired by the quantum clock originally proposed by Feynman and use it to write down quantum evolution as a ground-state eigenvalue problem. The construction allows one to apply ground-state quantum many-body theory to quantum dynamics, extending the reach of many highly developed tools from this fertile research area. Moreover, this formalism naturally leads to an algorithm to parallelize quantum simulation over time. We draw an explicit connection between previously known time-dependent variational principles and the time-embedded variational principle presented. Sample calculations are presented, applying the idea to a hydrogen molecule and the spin degrees of freedom of a model inorganic compound, demonstrating the parallel speedup of our method as well as its flexibility in applying ground-state methodologies. Finally, we take advantage of the unique perspective of this variational principle to examine the error of basis approximations in quantum dynamics. PMID:24062428

Quantum statistics and squeezing for a microwave-driven interacting magnon system.

PubMed

Haghshenasfard, Zahra; Cottam, Michael G

2017-02-01

Theoretical studies are reported for the statistical properties of a microwave-driven interacting magnon system. Both the magnetic dipole-dipole and the exchange interactions are included and the theory is developed for the case of parallel pumping allowing for the inclusion of the nonlinear processes due to the four-magnon interactions. The method of second quantization is used to transform the total Hamiltonian from spin operators to boson creation and annihilation operators. By using the coherent magnon state representation we have studied the magnon occupation number and the statistical behavior of the system. In particular, it is shown that the nonlinearities introduced by the parallel pumping field and the four-magnon interactions lead to non-classical quantum statistical properties of the system, such as magnon squeezing. Also control of the collapse-and-revival phenomena for the time evolution of the average magnon number is demonstrated by varying the parallel pumping amplitude and the four-magnon coupling.

A laboratory study of ion energization by EIC waves and subsequent upstreaming along diverging magnetic field lines

NASA Technical Reports Server (NTRS)

Cartier, S. L.; Dangelo, N.; Merlino, R. L.

1986-01-01

A laboratory study related to energetic upstreaming ions in the ionosphere-magnetosphere system is described. The experiment was carried out in a cesium Q machine plasma with a region of nonuniform magnetic field. Electrostatic ion cyclotron waves were excited by drawing an electron current to a small biased exciter electrode. In the presence of the instability, ions are heated in the direction perpendicular to B. Using a gridded retarding potential ion energy analyzer, the evolution of the ion velocity distribution was followed as the ions passed through the heating region and subsequently flowed out along the diverging B field lines. As expected, the heated ions transfer their energy from perpendicular to parallel motion as they move through the region of diverging B field. Both their parallel thermal energy and the parallel drift energy increase at the expense of the perpendicular energy.

Convergent evolution of marine mammals is associated with distinct substitutions in common genes

PubMed Central

Zhou, Xuming; Seim, Inge; Gladyshev, Vadim N.

2015-01-01

Phenotypic convergence is thought to be driven by parallel substitutions coupled with natural selection at the sequence level. Multiple independent evolutionary transitions of mammals to an aquatic environment offer an opportunity to test this thesis. Here, whole genome alignment of coding sequences identified widespread parallel amino acid substitutions in marine mammals; however, the majority of these changes were not unique to these animals. Conversely, we report that candidate aquatic adaptation genes, identified by signatures of likelihood convergence and/or elevated ratio of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few parallel substitutions and exhibit distinct sequence changes in each group. Moreover, no significant positive correlation was found between likelihood convergence and positive selection in all three marine lineages. These results suggest that convergence in protein coding genes associated with aquatic lifestyle is mainly characterized by independent substitutions and relaxed negative selection. PMID:26549748

Milestones in Software Engineering and Knowledge Engineering History: A Comparative Review

PubMed Central

del Águila, Isabel M.; Palma, José; Túnez, Samuel

2014-01-01

We present a review of the historical evolution of software engineering, intertwining it with the history of knowledge engineering because “those who cannot remember the past are condemned to repeat it.” This retrospective represents a further step forward to understanding the current state of both types of engineerings; history has also positive experiences; some of them we would like to remember and to repeat. Two types of engineerings had parallel and divergent evolutions but following a similar pattern. We also define a set of milestones that represent a convergence or divergence of the software development methodologies. These milestones do not appear at the same time in software engineering and knowledge engineering, so lessons learned in one discipline can help in the evolution of the other one. PMID:24624046

Milestones in software engineering and knowledge engineering history: a comparative review.

PubMed

del Águila, Isabel M; Palma, José; Túnez, Samuel

2014-01-01

We present a review of the historical evolution of software engineering, intertwining it with the history of knowledge engineering because "those who cannot remember the past are condemned to repeat it." This retrospective represents a further step forward to understanding the current state of both types of engineerings; history has also positive experiences; some of them we would like to remember and to repeat. Two types of engineerings had parallel and divergent evolutions but following a similar pattern. We also define a set of milestones that represent a convergence or divergence of the software development methodologies. These milestones do not appear at the same time in software engineering and knowledge engineering, so lessons learned in one discipline can help in the evolution of the other one.

Convergent or parallel molecular evolution of momilactone A and B: potent allelochemicals, momilactones have been found only in rice and the moss Hypnum plumaeforme.

PubMed

Kato-Noguchi, Hisashi

2011-09-01

Plant second metabolites momilactone A and B, which act as potent phytoalexins and allelochemicals, have been found thus far only in rice and the moss Hypnum plumaeforme, although both plants are taxonomically quite distinct. The concentrations of momilactone A and B, respectively, in rice plants were 4.5-140 and 2.9-85μg/g, and those in H. plumaeforme were 8.4-58.7 and 4.2-23.4μg/g. Momilactone A and B concentrations in rice and H. plumaeforme plants were increased by UV irradiation, elicitor and jasmonic acid treatments. Rice and H. plumaeforme plants secrete momilactone A and B into the rhizosphere, and the secretion level was also increased by UV irradiation, elicitor and jasmonic acid treatments. In addition, although endogenous concentrations of momilactone A in rice and H. plumaeforme were greater than those of momilactone B, the secretion levels of momilactone B were greater than those of momilactone A in rice and H. plumaeforme, which suggests that momilactone B may be selectively secreted by both rice and H. plumaeforme. As momilactone A and B exert potent antifungal and growth inhibitory activities, momilactone A and B may play an important role in the defense responses in H. plumaeforme and rice against pathogen infections and in allelopathy. The secretion of momilactone A and B into the rhizosphere may also prevent bacterial and fungal infections and provide a competitive advantage for nutrients through the inhibition of invading root systems of neighboring plants as allelochemicals. Therefore, both plants, despite their evolutionary distance, may use same defense strategy with respect to the momilactone A and B production and secretion, which resulting from convergent or parallel evolutionary processes. In the case of parallel evolution, there may be plant species providing the missing link in molecular evolution of momilactones between H. plumaeforme and rice. Copyright © 2011 Elsevier GmbH. All rights reserved.

Kinetic and energy production analysis of pyrolysis of lignocellulosic biomass using a three-parallel Gaussian reaction model.

PubMed

Chen, Tianju; Zhang, Jinzhi; Wu, Jinhu

2016-07-01

The kinetic and energy productions of pyrolysis of a lignocellulosic biomass were investigated using a three-parallel Gaussian distribution method in this work. The pyrolysis experiment of the pine sawdust was performed using a thermogravimetric-mass spectroscopy (TG-MS) analyzer. A three-parallel Gaussian distributed activation energy model (DAEM)-reaction model was used to describe thermal decomposition behaviors of the three components, hemicellulose, cellulose and lignin. The first, second and third pseudocomponents represent the fractions of hemicellulose, cellulose and lignin, respectively. It was found that the model is capable of predicting the pyrolysis behavior of the pine sawdust. The activation energy distribution peaks for the three pseudo-components were centered at 186.8, 197.5 and 203.9kJmol(-1) for the pine sawdust, respectively. The evolution profiles of H2, CH4, CO, and CO2 were well predicted using the three-parallel Gaussian distribution model. In addition, the chemical composition of bio-oil was also obtained by pyrolysis-gas chromatography/mass spectrometry instrument (Py-GC/MS). Copyright © 2016 Elsevier Ltd. All rights reserved.

ColDICE: A parallel Vlasov–Poisson solver using moving adaptive simplicial tessellation

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

Sousbie, Thierry, E-mail: tsousbie@gmail.com; Department of Physics, The University of Tokyo, Tokyo 113-0033; Research Center for the Early Universe, School of Science, The University of Tokyo, Tokyo 113-0033

2016-09-15

Resolving numerically Vlasov–Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm consisting in representing the phase-space sheet with a conforming, self-adaptive simplicial tessellation of which the vertices follow the Lagrangian equations of motion. The algorithm is implemented both in six- and four-dimensional phase-space. Refinement of the tessellation mesh is performed using the bisection method and a local representation of the phase-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the bestmore » way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincaré invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli [65–67] generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a “warm” dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.« less

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

PubMed

Copetti, Dario; Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L M; Childs, Kevin L; Eguiarte, Luis E; Lee, Seunghee; Liu, Tiffany L; McMahon, Michelle M; Whiteman, Noah K; Wing, Rod A; Wojciechowski, Martin F; Sanderson, Michael J

2017-11-07

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus ( Carnegiea gigantea ) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae ( Pachycereus , Lophocereus , and Stenocereus ) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti. Published under the PNAS license.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

PubMed Central

Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L. M.; Childs, Kevin L.; Eguiarte, Luis E.; Lee, Seunghee; Liu, Tiffany L.; McMahon, Michelle M.; Whiteman, Noah K.; Wing, Rod A.; Wojciechowski, Martin F.; Sanderson, Michael J.

2017-01-01

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia. We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed “hemiplasy.” The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti. PMID:29078296

Different evolutionary pathways underlie the morphology of wrist bones in hominoids

PubMed Central

2013-01-01

Background The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context. We identify morphological features that principally characterize primate – and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones – the scaphoid, lunate, triquetrum, capitate and hamate – are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Result Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Conclusions Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist bones. These results exemplify a degree of evolutionary and functional independence across different wrist bones, the potential evolvability of skeletal morphology, and help to contextualize the postcranial mosaicism observed in the hominin fossil record. PMID:24148262

Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella.

PubMed

Harms, Alexander; Segers, Francisca H I D; Quebatte, Maxime; Mistl, Claudia; Manfredi, Pablo; Körner, Jonas; Chomel, Bruno B; Kosoy, Michael; Maruyama, Soichi; Engel, Philipp; Dehio, Christoph

2017-03-01

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Why Africa matters: evolution of Old World Salvia (Lamiaceae) in Africa.

PubMed

Will, Maria; Claßen-Bockhoff, Regine

2014-07-01

Salvia is the largest genus in Lamiaceae and it has recently been found to be non-monophyletic. Molecular data on Old World Salvia are largely lacking. In this study, we present data concerning Salvia in Africa. The focus is on the colonization of the continent, character evolution and the switch of pollination systems in the genus. Maximum likelihood and Bayesian inference were used for phylogenetic reconstruction. Analyses were based on two nuclear markers [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and one plastid marker (rpl32-trnL). Sequence data were generated for 41 of the 62 African taxa (66 %). Mesquite was used to reconstruct ancestral character states for distribution, life form, calyx shape, stamen type and pollination syndrome. Salvia in Africa is non-monophyletic. Each of the five major regions in Africa, except Madagascar, was colonized at least twice, and floristic links between North African, south-west Asian and European species are strongly supported. The large radiation in Sub-Saharan Africa (23 species) can be traced back to dispersal from North Africa via East Africa to the Cape Region. Adaptation to bird pollination in southern Africa and Madagascar reflects parallel evolution. The phenotypic diversity in African Salvia is associated with repeated introductions to the continent. Many important evolutionary processes, such as colonization, adaptation, parallelism and character transformation, are reflected in this comparatively small group. The data presented in this study can help to understand the evolution of Salvia sensu lato and other large genera. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Morphological Evolution of Gyroid-Forming Block Copolymer Thin Films with Varying Solvent Evaporation Rate.

PubMed

Wu, Yi-Hsiu; Lo, Ting-Ya; She, Ming-Shiuan; Ho, Rong-Ming

2015-08-05

In this study, we aim to examine the morphological evolution of block copolymer (BCP) nanostructured thin films through solvent evaporation at different rates for solvent swollen polystyrene-block-poly(l-lactide) (PS-PLLA). Interesting phase transitions from disorder to perpendicular cylinder and then gyroid can be found while using a partially selective solvent for PS to swell PS-PLLA thin film followed by solvent evaporation. During the transitions, gyroid-forming BCP thin film with characteristic crystallographic planes of (111)G, (110)G, and (211)G parallel to air surface can be observed, and will gradually transform into coexisting (110)G and (211)G planes, and finally transforms to (211)G plane due to the preferential segregation of constituted block to the surface (i.e., the thermodynamic origin for self-assembly) that affects the relative amount of each component at the air surface. With the decrease on the evaporation rate, the disorder phase will transform to parallel cylinder and then directly to (211)G without transition to perpendicular cylinder phase. Most importantly, the morphological evolution of PS-PLLA thin films is strongly dependent upon the solvent removal rate only in the initial stage of the evaporation process due to the anisotropy of cylinder structure. Once the morphology is transformed back to the isotropic gyroid structure after long evaporation, the morphological evolution will only relate to the variation of the surface composition. Similar phase transitions at the substrate can also be obtained by controlling the ratio of PLLA-OH to PS-OH homopolymers to functionalize the substrate. As a result, the fabrication of well-defined nanostructured thin films with controlled orientation can be achieved by simple swelling and deswelling with controlled evaporation rate.

Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella

PubMed Central

Harms, Alexander; Segers, Francisca H.I.D.; Quebatte, Maxime; Mistl, Claudia; Manfredi, Pablo; Körner, Jonas; Chomel, Bruno B.; Kosoy, Michael; Maruyama, Soichi; Engel, Philipp

2017-01-01

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation. PMID:28338931

Evolution of allowable stresses in shear for lumber

Treesearch

Robert L. Ethington; William L. Galligan; Henry M. Montrey; Alan D. Freas

1979-01-01

This paper surveys research leading to allowable shear stress parallel to grain for lumber. In early flexure tests of lumber, some pieces failed in shear. The estimated shear stress at time of failure was generally lower than shear strength measured on small, clear, straight-grained specimens. This and other engineering observations gave rise to adjustments that...

Parallel evolution of early and late feathering in turkey and chicken, same gene, different mutation

USDA-ARS?s Scientific Manuscript database

The sex-linked slow (SF) and fast (FF) feathering rate at hatch has been widely used in poultry breeding for autosexing at hatching. In chicken, the sex-linked K (SF), and k+ (FF) alleles are responsible for the feathering rate phenotype in chicken. The K allele is dominant and a partial duplication...

Triticum mosaic virus exhibits limited population variation yet shows evidence of parallel evolution after replicated serial passage in wheat

USDA-ARS?s Scientific Manuscript database

An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed ...

Monetizing French Distance Education: A Field Enquiry on Higher Education Value(s)

ERIC Educational Resources Information Center

Olivier, Marty

2014-01-01

A field enquiry in French distance education allows us to analyze the evolution of a specific institution towards new public management: Parallel to a trend of free courseware and open education, there is a paradoxical reality of distance education monetization. Whereas history shows how traditional French education is a state controlled public…

Parallel heat transport in integrable and chaotic magnetic fields

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

Del-Castillo-Negrete, Diego B; Chacon, Luis

2012-01-01

The study of transport in magnetized plasmas is a problem of fundamental interest in controlled fusion, space plasmas, and astrophysics research. Three issues make this problem particularly chal- lenging: (i) The extreme anisotropy between the parallel (i.e., along the magnetic field), , and the perpendicular, , conductivities ( / may exceed 1010 in fusion plasmas); (ii) Magnetic field lines chaos which in general complicates (and may preclude) the construction of magnetic field line coordinates; and (iii) Nonlocal parallel transport in the limit of small collisionality. Motivated by these issues, we present a Lagrangian Green s function method to solve themore » local and non-local parallel transport equation applicable to integrable and chaotic magnetic fields in arbitrary geom- etry. The method avoids by construction the numerical pollution issues of grid-based algorithms. The potential of the approach is demonstrated with nontrivial applications to integrable (magnetic island chain), weakly chaotic (devil s staircase), and fully chaotic magnetic field configurations. For the latter, numerical solutions of the parallel heat transport equation show that the effective radial transport, with local and non-local closures, is non-diffusive, thus casting doubts on the appropriateness of the applicability of quasilinear diffusion descriptions. General conditions for the existence of non-diffusive, multivalued flux-gradient relations in the temperature evolution are derived.« less

Competitive Dominance among Strains of Luminous Bacteria Provides an Unusual Form of Evidence for Parallel Evolution in Sepiolid Squid-Vibrio Symbioses

PubMed Central

Nishiguchi, Michele K.; Ruby, Edward G.; McFall-Ngai, Margaret J.

1998-01-01

One of the principal assumptions in symbiosis research is that associated partners have evolved in parallel. We report here experimental evidence for parallel speciation patterns among several partners of the sepiolid squid-luminous bacterial symbioses. Molecular phylogenies for 14 species of host squids were derived from sequences of both the nuclear internal transcribed spacer region and the mitochondrial cytochrome oxidase subunit I; the glyceraldehyde phosphate dehydrogenase locus was sequenced for phylogenetic determinations of 7 strains of bacterial symbionts. Comparisons of trees constructed for each of the three loci revealed a parallel phylogeny between the sepiolids and their respective symbionts. Because both the squids and their bacterial partners can be easily cultured independently in the laboratory, we were able to couple these phylogenetic analyses with experiments to examine the ability of the different symbiont strains to compete with each other during the colonization of one of the host species. Our results not only indicate a pronounced dominance of native symbiont strains over nonnative strains, but also reveal a hierarchy of symbiont competency that reflects the phylogenetic relationships of the partners. For the first time, molecular systematics has been coupled with experimental colonization assays to provide evidence for the existence of parallel speciation among a set of animal-bacterial associations. PMID:9726861

Parallel processing in the honeybee olfactory pathway: structure, function, and evolution.

PubMed

Rössler, Wolfgang; Brill, Martin F

2013-11-01

Animals face highly complex and dynamic olfactory stimuli in their natural environments, which require fast and reliable olfactory processing. Parallel processing is a common principle of sensory systems supporting this task, for example in visual and auditory systems, but its role in olfaction remained unclear. Studies in the honeybee focused on a dual olfactory pathway. Two sets of projection neurons connect glomeruli in two antennal-lobe hemilobes via lateral and medial tracts in opposite sequence with the mushroom bodies and lateral horn. Comparative studies suggest that this dual-tract circuit represents a unique adaptation in Hymenoptera. Imaging studies indicate that glomeruli in both hemilobes receive redundant sensory input. Recent simultaneous multi-unit recordings from projection neurons of both tracts revealed widely overlapping response profiles strongly indicating parallel olfactory processing. Whereas lateral-tract neurons respond fast with broad (generalistic) profiles, medial-tract neurons are odorant specific and respond slower. In analogy to "what-" and "where" subsystems in visual pathways, this suggests two parallel olfactory subsystems providing "what-" (quality) and "when" (temporal) information. Temporal response properties may support across-tract coincidence coding in higher centers. Parallel olfactory processing likely enhances perception of complex odorant mixtures to decode the diverse and dynamic olfactory world of a social insect.

Origin and evolution of chromosomal sperm proteins.

PubMed

Eirín-López, José M; Ausió, Juan

2009-10-01

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a "vertical" transition from a histone to a protamine-like and finally protamine types (H --> PL --> P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine-like (PL)- and protamine (P)-types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution.

Evolution of central pattern generators and rhythmic behaviours

PubMed Central

Katz, Paul S.

2016-01-01

Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization. PMID:26598733

Evolution of central pattern generators and rhythmic behaviours.

PubMed

Katz, Paul S

2016-01-05

Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization. © 2015 The Author(s).

Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia.

PubMed

Kearney, Michael; Blacket, Mark J; Strasburg, Jared L; Moritz, Craig

2006-06-01

The rarity of parthenogenesis, reproduction without sex, is a major evolutionary puzzle. To understand why sexual genetic systems are so successful in nature, we must understand why parthenogenesis sometimes evolves and persists. Here we use DNA sequence data to test for similarities in the tempo and mode of the evolution of parthenogenesis in a grasshopper and a lizard from the Australian desert. We find spectacular congruence between genetic and geographic patterns of parthenogenesis in these distantly related organisms. In each species, parthenogenesis evolved twice and appears to have expanded in parallel waves across the desert, suggesting a highly general selective force against sex.

Matrix Product Operator Simulations of Quantum Algorithms

DTIC Science & Technology

2015-02-01

parallel to the Grover subspace parametrically: (Zi|φ〉)‖ = s cos γ|α〉+ s sin γ|β〉, s = √ a(k)2 (N − 1)2 + b(k)2, γ = tan −1 ( b(k)(N − 1) a(k) ) (6.32) Each...of this vector parallel to the Grover subspace in parametric form: (XiZi|φ〉)‖ = s cos(γ)|α〉+ s sin(γ)|β〉, s = 1√ N − 1 , γ = tan −1 ( cot (( k + 1 2 ) θ...quant- ph/0001106, 2000. Bibliography 146 [30] Jérémie Roland and Nicolas J Cerf. Quantum search by local adiabatic evolution. Physical Review A, 65(4

Robust High-Resolution Cloth Using Parallelism, History-Based Collisions and Accurate Friction

PubMed Central

Selle, Andrew; Su, Jonathan; Irving, Geoffrey; Fedkiw, Ronald

2015-01-01

In this paper we simulate high resolution cloth consisting of up to 2 million triangles which allows us to achieve highly detailed folds and wrinkles. Since the level of detail is also influenced by object collision and self collision, we propose a more accurate model for cloth-object friction. We also propose a robust history-based repulsion/collision framework where repulsions are treated accurately and efficiently on a per time step basis. Distributed memory parallelism is used for both time evolution and collisions and we specifically address Gauss-Seidel ordering of repulsion/collision response. This algorithm is demonstrated by several high-resolution and high-fidelity simulations. PMID:19147895

Assembly of the cnidarian camera-type eye from vertebrate-like components.

PubMed

Kozmik, Zbynek; Ruzickova, Jana; Jonasova, Kristyna; Matsumoto, Yoshifumi; Vopalensky, Pavel; Kozmikova, Iryna; Strnad, Hynek; Kawamura, Shoji; Piatigorsky, Joram; Paces, Vaclav; Vlcek, Cestmir

2008-07-01

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution.

On Borders: From Ancient to Postmodern Times

NASA Astrophysics Data System (ADS)

Bellezza, G.

2013-11-01

The article deals with the evolution of the concept of borders between human groups and with its slow evolution from the initial no men's land zones to the ideal single-dimension linear borders. In ancient times the first borders were natural, such as mountain ranges or large rivers until, with the development of Geodesy, astronomical borders based on meridians and parallels became a favourite natural base. Actually, Modern States adopted these to fix limits in unknown conquered territories. The postmodern thought led give more importance to cultural borders until, in the most recent times, is becoming rather impossible to fix borders in the virtual cyberspace.

Evolution, brain, and the nature of language.

PubMed

Berwick, Robert C; Friederici, Angela D; Chomsky, Noam; Bolhuis, Johan J

2013-02-01

Language serves as a cornerstone for human cognition, yet much about its evolution remains puzzling. Recent research on this question parallels Darwin's attempt to explain both the unity of all species and their diversity. What has emerged from this research is that the unified nature of human language arises from a shared, species-specific computational ability. This ability has identifiable correlates in the brain and has remained fixed since the origin of language approximately 100 thousand years ago. Although songbirds share with humans a vocal imitation learning ability, with a similar underlying neural organization, language is uniquely human. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolution of Query Optimization Methods

NASA Astrophysics Data System (ADS)

Hameurlain, Abdelkader; Morvan, Franck

Query optimization is the most critical phase in query processing. In this paper, we try to describe synthetically the evolution of query optimization methods from uniprocessor relational database systems to data Grid systems through parallel, distributed and data integration systems. We point out a set of parameters to characterize and compare query optimization methods, mainly: (i) size of the search space, (ii) type of method (static or dynamic), (iii) modification types of execution plans (re-optimization or re-scheduling), (iv) level of modification (intra-operator and/or inter-operator), (v) type of event (estimation errors, delay, user preferences), and (vi) nature of decision-making (centralized or decentralized control).

Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

NASA Astrophysics Data System (ADS)

Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

2017-11-01

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

NASA Astrophysics Data System (ADS)

Moreau, P.; César de Sá, J.; Grégoire, S.; Lochegnies, D.

2007-05-01

Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication…). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutive contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.

Efficient Analysis of Simulations of the Sun's Magnetic Field

NASA Astrophysics Data System (ADS)

Scarborough, C. W.; Martínez-Sykora, J.

2014-12-01

Dynamics in the solar atmosphere, including solar flares, coronal mass ejections, micro-flares and different types of jets, are powered by the evolution of the sun's intense magnetic field. 3D Radiative Magnetohydrodnamics (MHD) computer simulations have furthered our understanding of the processes involved: When non aligned magnetic field lines reconnect, the alteration of the magnetic topology causes stored magnetic energy to be converted into thermal and kinetic energy. Detailed analysis of this evolution entails tracing magnetic field lines, an operation which is not time-efficient on a single processor. By utilizing a graphics card (GPU) to trace lines in parallel, conducting such analysis is made feasible. We applied our GPU implementation to the most advanced 3D Radiative-MHD simulations (Bifrost, Gudicksen et al. 2011) of the solar atmosphere in order to better understand the evolution of the modeled field lines.

Networks of Learning

NASA Astrophysics Data System (ADS)

Bettencourt, Luis; Kaiser, David

2004-03-01

Based on an a historically documented example of scientific discovery - Feynman diagrams as the main calculational tool of theoretical high energy Physics - we map the time evolution of the social network of early adopters through in the US, UK, Japan and the USSR. The spread of the technique for total number of users in each region is then modelled in terms of epidemic models, highlighting parallel and divergent aspects of this analogy. We also show that transient social arrangements develop as the idea is introduced and learned, which later disappear as the technique becomes common knowledge. Such early transient is characterized by abnormally low connectivity distribution powers and by high clustering. This interesting early non-equilibrium stage of network evolution is captured by a new dynamical model for network evolution, which coincides in its long time limit with familiar preferential aggregation dynamics.

Understanding protein evolution: from protein physics to Darwinian selection.

PubMed

Zeldovich, Konstantin B; Shakhnovich, Eugene I

2008-01-01

Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

Visualizing tumor evolution with the fishplot package for R.

PubMed

Miller, Christopher A; McMichael, Joshua; Dang, Ha X; Maher, Christopher A; Ding, Li; Ley, Timothy J; Mardis, Elaine R; Wilson, Richard K

2016-11-07

Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visualizations, such as scatterplots, can be difficult to interpret. Current data visualization methods are also typically manual and laborious, and often only approximate subclonal fractions. We have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. The simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. The fishplot package is available at https://github.com/chrisamiller/fishplot .

Reduce, reuse, and recycle: developmental evolution of trait diversification.

PubMed

Preston, Jill C; Hileman, Lena C; Cubas, Pilar

2011-03-01

A major focus of evolutionary developmental (evo-devo) studies is to determine the genetic basis of variation in organismal form and function, both of which are fundamental to biological diversification. Pioneering work on metazoan and flowering plant systems has revealed conserved sets of genes that underlie the bauplan of organisms derived from a common ancestor. However, the extent to which variation in the developmental genetic toolkit mirrors variation at the phenotypic level is an active area of research. Here we explore evidence from the angiosperm evo-devo literature supporting the frugal use of genes and genetic pathways in the evolution of developmental patterning. In particular, these examples highlight the importance of genetic pleiotropy in different developmental modules, thus reducing the number of genes required in growth and development, and the reuse of particular genes in the parallel evolution of ecologically important traits.

Nothing in the History of Spanish Anís Makes Sense, Except in the Light of Evolution

NASA Astrophysics Data System (ADS)

Delgado, Juan Antonio; Palma, Ricardo Luis

2011-02-01

We describe, discuss and illustrate a metaphoric parallel between the history of the most famous Spanish liqueur, " Anís del Mono" ( Anís of the Monkey), and the evolution of living organisms in the light of Darwinian theory and other biological hypotheses published subsequent to Charles Darwin's Origin of Species. Also, we report the use of a caricature of a simian Darwin with a positive connotation, perhaps the only one ever produced. We conclude that, like some species in the natural world, Anís of the Monkey has evolved, adapted, survived and become the fittest and most successful anís in the Spanish market and possibly the world. We hope this paper will contribute a new useful metaphor for the teaching of biological evolution.

Development and Evaluation of an Online CO2 Evolution Test and a Multicomponent Biodegradation Test System

PubMed Central

Strotmann, Uwe; Reuschenbach, Peter; Schwarz, Helmut; Pagga, Udo

2004-01-01

Well-established biodegradation tests use biogenously evolved carbon dioxide (CO2) as an analytical parameter to determine the ultimate biodegradability of substances. A newly developed analytical technique based on the continuous online measurement of conductivity showed its suitability over other techniques. It could be demonstrated that the method met all criteria of established biodegradation tests, gave continuous biodegradation curves, and was more reliable than other tests. In parallel experiments, only small variations in the biodegradation pattern occurred. When comparing the new online CO2 method with existing CO2 evolution tests, growth rates and lag periods were similar and only the final degree of biodegradation of aniline was slightly lower. A further test development was the unification and parallel measurement of all three important summary parameters for biodegradation—i.e., CO2 evolution, determination of the biochemical oxygen demand (BOD), and removal of dissolved organic carbon (DOC)—in a multicomponent biodegradation test system (MCBTS). The practicability of this test method was demonstrated with aniline. This test system had advantages for poorly water-soluble and highly volatile compounds and allowed the determination of the carbon fraction integrated into biomass (heterotrophic yield). The integrated online measurements of CO2 and BOD systems produced continuous degradation curves, which better met the stringent criteria of ready biodegradability (60% biodegradation in a 10-day window). Furthermore the data could be used to calculate maximal growth rates for the modeling of biodegradation processes. PMID:15294794

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza.

PubMed

Huang, Zhongyun; Young, Nelson D; Reagon, Michael; Hyma, Katie E; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

2017-06-01

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the 'agricultural weed syndrome', making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed-crop pairs, but are not shared among all weed-crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms. © 2017 John Wiley & Sons Ltd.

Conflicting character distribution within different data sets on cardueline finches: artifact or history?

PubMed

Fehrer, J

1996-01-01

Cardueline finches (Passeriformes: Fringillidae, Carduelinae) provide an example of unresolved species relationships despite decades of extensive study of the group. Existing morphological studies suffer from numerous cases of assumed parallel evolution due to a conflicting character distribution in different lineages. In this study, results of assumed parallel evolution due to a conflicting character distribution in different lineages. In this study, results of cytochrome b sequence analysis are compared with species relationships suggested by morphological and behavioral evidence. In the molecular analyses, species clusters mutually excluding each other were observed, lowering the statistical support of the internodes, i.e., the branches could not be resolved convincingly. Despite these difficulties, some phylogenetic signal was present in the molecular data as well as in the other approaches. In particular, any species or genus relationship suggested by cytochrome b sequence analysis was reflected by some other evidence. Based on this general congruence of the different data sets and on a considerable cytochrome b tree stability observed independent of species combination, choice of outgroup and tree-generating method, the short internodes are interpreted to reflect a historical reality. A model of cardueline evolution is proposed which assumes a population of cardueline ancestors with considerable polymorphism concerning the mitochondrial DNA and morphological characters alike. Retention of ancestral character states in different lineages and a subsequent rapid radiation are suggested to explain the conflicting character distributions observed in different fields of investigation.

Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces.

PubMed

Hong, Ie-Hong; Liao, Yung-Cheng; Tsai, Yung-Feng

2013-11-05

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process.

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces

PubMed Central

2013-01-01

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process. PMID:24188092

Comprehensive School Reform at the Helm: The North Carolina Instructional Leadership Reform Program. Benchmark. Volume 5, Issue 4, Fall 2004

ERIC Educational Resources Information Center

Janc, Helen; Appelbaum, Deborah

2004-01-01

This newsletter discusses how in many ways the development of the school reform concept parallels with the evolution of thinking about principal leadership over the past decade. Under Comprehensive School Reform (CSR), schools are increasingly being asked to use data to plan for improvement and to fortify instruction and professional development…

The evolution of concepts of vestibular peripheral information processing: toward the dynamic, adaptive, parallel processing macular model

NASA Technical Reports Server (NTRS)

Ross, Muriel D.

2003-01-01

In a letter to Robert Hooke, written on 5 February, 1675, Isaac Newton wrote "If I have seen further than certain other men it is by standing upon the shoulders of giants." In his context, Newton was referring to the work of Galileo and Kepler, who preceded him. However, every field has its own giants, those men and women who went before us and, often with few tools at their disposal, uncovered the facts that enabled later researchers to advance knowledge in a particular area. This review traces the history of the evolution of views from early giants in the field of vestibular research to modern concepts of vestibular organ organization and function. Emphasis will be placed on the mammalian maculae as peripheral processors of linear accelerations acting on the head. This review shows that early, correct findings were sometimes unfortunately disregarded, impeding later investigations into the structure and function of the vestibular organs. The central themes are that the macular organs are highly complex, dynamic, adaptive, distributed parallel processors of information, and that historical references can help us to understand our own place in advancing knowledge about their complicated structure and functions.

Rapid parallel evolution overcomes global honey bee parasite.

PubMed

Oddie, Melissa; Büchler, Ralph; Dahle, Bjørn; Kovacic, Marin; Le Conte, Yves; Locke, Barbara; de Miranda, Joachim R; Mondet, Fanny; Neumann, Peter

2018-05-16

In eusocial insect colonies nestmates cooperate to combat parasites, a trait called social immunity. However, social immunity failed for Western honey bees (Apis mellifera) when the ectoparasitic mite Varroa destructor switched hosts from Eastern honey bees (Apis cerana). This mite has since become the most severe threat to A. mellifera world-wide. Despite this, some isolated A. mellifera populations are known to survive infestations by means of natural selection, largely by supressing mite reproduction, but the underlying mechanisms of this are poorly understood. Here, we show that a cost-effective social immunity mechanism has evolved rapidly and independently in four naturally V. destructor-surviving A. mellifera populations. Worker bees of all four 'surviving' populations uncapped/recapped worker brood cells more frequently and targeted mite-infested cells more effectively than workers in local susceptible colonies. Direct experiments confirmed the ability of uncapping/recapping to reduce mite reproductive success without sacrificing nestmates. Our results provide striking evidence that honey bees can overcome exotic parasites with simple qualitative and quantitative adaptive shifts in behaviour. Due to rapid, parallel evolution in four host populations this appears to be a key mechanism explaining survival of mite infested colonies.

The Effect of Surface Induced Flows on Bubble and Particle Aggregation

NASA Technical Reports Server (NTRS)

Guelcher, Scott A.; Solomentsev, Yuri E.; Anderson, John L.; Boehmer, Marcel; Sides, Paul J.

1999-01-01

Almost 20 years have elapsed since a phenomenon called "radial specific coalescence" was identified. During studies of electrolytic oxygen evolution from the back side of a vertically oriented, transparent tin oxide electrode in alkaline electrolyte, one of the authors (Sides) observed that large "collector" bubbles appeared to attract smaller bubbles. The bubbles moved parallel to the surface of the electrode, while the electric field was normal to the electrode surface. The phenomenon was reported but not explained. More recently self ordering of latex particles was observed during electrophoretic deposition at low DC voltages likewise on a transparent tin oxide electrode. As in the bubble work, the field was normal to the electrode while the particles moved parallel to it. Fluid convection caused by surface induced flows (SIF) can explain these two apparently different experimental observations: the aggregation of particles on an electrode during electrophoretic deposition, and a radial bubble coalescence pattern on an electrode during electrolytic gas evolution. An externally imposed driving force (the gradient of electrical potential or temperature), interacting with the surface of particles or bubbles very near a planar conducting surface, drives the convection of fluid that causes particles and bubbles to approach each other on the electrode.

Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization.

PubMed

Ettensohn, Charles A

2014-05-01

It is widely accepted that biomineralized structures appeared independently in many metazoan clades during the Cambrian. How this occurred, and whether it involved the parallel co-option of a common set of biochemical and developmental pathways (i.e., a shared biomineralization "toolkit"), are questions that remain unanswered. Here, I provide evidence that horizontal gene transfer supported the evolution of biomineralization in some metazoans. I show that Msp130 proteins, first described as proteins expressed selectively by the biomineral-forming primary mesenchyme cells of the sea urchin embryo, have a much wider taxonomic distribution than was previously appreciated. Msp130 proteins are present in several invertebrate deuterostomes and in one protostome clade (molluscs). Surprisingly, closely related proteins are also present in many bacteria and several algae, and I propose that msp130 genes were introduced into metazoan lineages via multiple, independent horizontal gene transfer events. Phylogenetic analysis shows that the introduction of an ancestral msp130 gene occurred in the sea urchin lineage more than 250 million years ago and that msp130 genes underwent independent, parallel duplications in each of the metazoan phyla in which these genes are found. © 2014 Wiley Periodicals, Inc.

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses.

PubMed

van Velzen, Robin; Holmer, Rens; Bu, Fengjiao; Rutten, Luuk; van Zeijl, Arjan; Liu, Wei; Santuari, Luca; Cao, Qingqin; Sharma, Trupti; Shen, Defeng; Roswanjaya, Yuda; Wardhani, Titis A K; Kalhor, Maryam Seifi; Jansen, Joelle; van den Hoogen, Johan; Güngör, Berivan; Hartog, Marijke; Hontelez, Jan; Verver, Jan; Yang, Wei-Cai; Schijlen, Elio; Repin, Rimi; Schilthuizen, Menno; Schranz, M Eric; Heidstra, Renze; Miyata, Kana; Fedorova, Elena; Kohlen, Wouter; Bisseling, Ton; Smit, Sandra; Geurts, Rene

2018-05-15

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION ( NIN ) and RHIZOBIUM-DIRECTED POLAR GROWTH ( RPG ). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN , RPG , and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants. Copyright © 2018 the Author(s). Published by PNAS.

Nonlinear Evolution of Short-wavelength Torsional Alfvén Waves

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

Shestov, S. V.; Nakariakov, V. M.; Ulyanov, A. S.

2017-05-10

We analyze nonlinear evolution of torsional Alfvén waves in a straight magnetic flux tube filled in with a low- β plasma, and surrounded with a plasma of lower density. Such magnetic tubes model, in particular, a segment of a coronal loop or a polar plume. The wavelength is taken comparable to the tube radius. We perform a numerical simulation of the wave propagation using ideal magnetohydrodynamics. We find that a torsional wave nonlinearly induces three kinds of compressive flows: the parallel flow at the Alfvén speed, which constitutes a bulk plasma motion along the magnetic field, the tube wave, andmore » also transverse flows in the radial direction, associated with sausage fast magnetoacoustic modes. In addition, the nonlinear torsional wave steepens and its propagation speed increases. The latter effect leads to the progressive distortion of the torsional wave front, i.e., nonlinear phase mixing. Because of the intrinsic non-uniformity of the torsional wave amplitude across the tube radius, the nonlinear effects are more pronounced in regions with higher wave amplitudes. They are always absent at the axes of the flux tube. In the case of a linear radial profile of the wave amplitude, the nonlinear effects are localized in an annulus region near the tube boundary. Thus, the parallel compressive flows driven by torsional Alfvén waves in the solar and stellar coronae, are essentially non-uniform in the perpendicular direction. The presence of additional sinks for the wave energy reduces the efficiency of the nonlinear parallel cascade in torsional Alfvén waves.« less

Evolution Born of Moisture: Analogies and Parallels Between Anaximander's Ideas on Origin of Life and Man and Later Pre-Darwinian and Darwinian Evolutionary Concepts.

PubMed

Kočandrle, Radim; Kleisner, Karel

2013-01-01

This study focuses on the origin of life as presented in the thought of Anaximander of Miletus but also points to some parallel motifs found in much later conceptions of both the pre-Darwinian German romantic science and post-Darwinian biology. According to Anaximander, life originated in the moisture associated with earth (mud). This moist environment hosted the first living creatures that later populated the dry land. In these descriptions, one can trace the earliest hints of the notion of environmental adaptation. The origin of humans was seen as connected in some way with fish: ancient humans were supposed to have developed inside fish-like animals. Anaximander took into account changes in the development of living creatures (adaptations) and speculated on the origins of humans. Similar ideas are found also in the writings of much later, eighteenth and nineteenth century authors who were close to the tradition of German romantic science. We do not argue that these later concepts are in any way directly linked with those of the pre-Socratics, but they show surprising parallels in, e.g., the hypothesis that life originated in a moist environment or the supposition that human developed from fish-like ancestors. These transformations are seen as a consequence of timeless logic rather than as evolution in historical terms. Despite the accent on the origin of living things, both Anaximander and the later Naturphilosophen lack in their notions the element most characteristic of Darwin's thought, that is, the emphasis on historicity and uniqueness of all that comes into being.

Nonlinear Evolution of Short-wavelength Torsional Alfvén Waves

NASA Astrophysics Data System (ADS)

Shestov, S. V.; Nakariakov, V. M.; Ulyanov, A. S.; Reva, A. A.; Kuzin, S. V.

2017-05-01

We analyze nonlinear evolution of torsional Alfvén waves in a straight magnetic flux tube filled in with a low-β plasma, and surrounded with a plasma of lower density. Such magnetic tubes model, in particular, a segment of a coronal loop or a polar plume. The wavelength is taken comparable to the tube radius. We perform a numerical simulation of the wave propagation using ideal magnetohydrodynamics. We find that a torsional wave nonlinearly induces three kinds of compressive flows: the parallel flow at the Alfvén speed, which constitutes a bulk plasma motion along the magnetic field, the tube wave, and also transverse flows in the radial direction, associated with sausage fast magnetoacoustic modes. In addition, the nonlinear torsional wave steepens and its propagation speed increases. The latter effect leads to the progressive distortion of the torsional wave front, I.e., nonlinear phase mixing. Because of the intrinsic non-uniformity of the torsional wave amplitude across the tube radius, the nonlinear effects are more pronounced in regions with higher wave amplitudes. They are always absent at the axes of the flux tube. In the case of a linear radial profile of the wave amplitude, the nonlinear effects are localized in an annulus region near the tube boundary. Thus, the parallel compressive flows driven by torsional Alfvén waves in the solar and stellar coronae, are essentially non-uniform in the perpendicular direction. The presence of additional sinks for the wave energy reduces the efficiency of the nonlinear parallel cascade in torsional Alfvén waves.

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

PubMed Central

Holmer, Rens; Bu, Fengjiao; Rutten, Luuk; van Zeijl, Arjan; Liu, Wei; Santuari, Luca; Cao, Qingqin; Sharma, Trupti; Shen, Defeng; Roswanjaya, Yuda; Wardhani, Titis A. K.; Kalhor, Maryam Seifi; Jansen, Joelle; van den Hoogen, Johan; Güngör, Berivan; Hartog, Marijke; Hontelez, Jan; Verver, Jan; Schijlen, Elio; Repin, Rimi; Schilthuizen, Menno; Heidstra, Renze; Miyata, Kana; Fedorova, Elena; Kohlen, Wouter; Bisseling, Ton; Smit, Sandra

2018-01-01

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants. PMID:29717040

Gravitational spreading, bookshelf faulting, and tectonic evolution of the South Polar Terrain of Saturn's moon Enceladus

NASA Astrophysics Data System (ADS)

Yin, An; Pappalardo, Robert T.

2015-11-01

Despite a decade of intense research the mechanical origin of the tiger-stripe fractures (TSF) and their geologic relationship to the hosting South Polar Terrain (SPT) of Enceladus remain poorly understood. Here we show via systematic photo-geological mapping that the semi-squared SPT is bounded by right-slip, left-slip, extensional, and contractional zones on its four edges. Discrete deformation along the edges in turn accommodates translation of the SPT as a single sheet with its transport direction parallel to the regional topographic gradient. This parallel relationship implies that the gradient of gravitational potential energy drove the SPT motion. In map view, internal deformation of the SPT is expressed by distributed right-slip shear parallel to the SPT transport direction. The broad right-slip shear across the whole SPT was facilitated by left-slip bookshelf faulting along the parallel TSF. We suggest that the flow-like tectonics, to the first approximation across the SPT on Enceladus, is best explained by the occurrence of a transient thermal event, which allowed the release of gravitational potential energy via lateral viscous flow within the thermally weakened ice shell.

Implementation of Multivariable Logic Functions in Parallel by Electrically Addressing a Molecule of Three Dopants in Silicon.

PubMed

Fresch, Barbara; Bocquel, Juanita; Hiluf, Dawit; Rogge, Sven; Levine, Raphael D; Remacle, Françoise

2017-07-05

To realize low-power, compact logic circuits, one can explore parallel operation on single nanoscale devices. An added incentive is to use multivalued (as distinct from Boolean) logic. Here, we theoretically demonstrate that the computation of all the possible outputs of a multivariate, multivalued logic function can be implemented in parallel by electrical addressing of a molecule made up of three interacting dopant atoms embedded in Si. The electronic states of the dopant molecule are addressed by pulsing a gate voltage. By simulating the time evolution of the non stationary electronic density built by the gate voltage, we show that one can implement a molecular decision tree that provides in parallel all the outputs for all the inputs of the multivariate, multivalued logic function. The outputs are encoded in the populations and in the bond orders of the dopant molecule, which can be measured using an STM tip. We show that the implementation of the molecular logic tree is equivalent to a spectral function decomposition. The function that is evaluated can be field-programmed by changing the time profile of the pulsed gate voltage. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parallel and orthogonal stimulus in ultradiluted neural networks

NASA Astrophysics Data System (ADS)

Sobral, G. A., Jr.; Vieira, V. M.; Lyra, M. L.; da Silva, C. R.

2006-10-01

Extending a model due to Derrida, Gardner, and Zippelius, we have studied the recognition ability of an extreme and asymmetrically diluted version of the Hopfield model for associative memory by including the effect of a stimulus in the dynamics of the system. We obtain exact results for the dynamic evolution of the average network superposition. The stimulus field was considered as proportional to the overlapping of the state of the system with a particular stimulated pattern. Two situations were analyzed, namely, the external stimulus acting on the initialization pattern (parallel stimulus) and the external stimulus acting on a pattern orthogonal to the initialization one (orthogonal stimulus). In both cases, we obtained the complete phase diagram in the parameter space composed of the stimulus field, thermal noise, and network capacity. Our results show that the system improves its recognition ability for parallel stimulus. For orthogonal stimulus two recognition phases emerge with the system locking at the initialization or stimulated pattern. We confront our analytical results with numerical simulations for the noiseless case T=0 .

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

PubMed

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

PubMed Central

2010-01-01

Background Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. Results The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conclusions Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution. PMID:20565927

Integrated 3-D vision system for autonomous vehicles

NASA Astrophysics Data System (ADS)

Hou, Kun M.; Shawky, Mohamed; Tu, Xiaowei

1992-03-01

Nowadays, autonomous vehicles have become a multidiscipline field. Its evolution is taking advantage of the recent technological progress in computer architectures. As the development tools became more sophisticated, the trend is being more specialized, or even dedicated architectures. In this paper, we will focus our interest on a parallel vision subsystem integrated in the overall system architecture. The system modules work in parallel, communicating through a hierarchical blackboard, an extension of the 'tuple space' from LINDA concepts, where they may exchange data or synchronization messages. The general purpose processing elements are of different skills, built around 40 MHz i860 Intel RISC processors for high level processing and pipelined systolic array processors based on PLAs or FPGAs for low-level processing.

Parallel proton fire hose instability in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Matteini, Lorenzo; Landi, Simone; Hellinger, Petr; Velli, Marco

2006-10-01

We report a study of the properties of the parallel proton fire hose instability comparing the results obtained by the linear analysis, from one-dimensional (1-D) standard hybrid simulations and 1-D hybrid expanding box simulations. The three different approaches converge toward the same instability threshold condition which is in good agreement with in situ observations, suggesting that such instability is relevant in the solar wind context. We investigate also the effect of the wave-particle interactions on shaping the proton distribution function and on the evolution of the spectrum of the magnetic fluctuations during the expansion. We find that the resonant interaction can provide the proton distribution function to depart from the bi-Maxwellian form.

Hypersonic Boundary Layer Instability Over a Corner

NASA Technical Reports Server (NTRS)

Balakumar, Ponnampalam; Zhao, Hong-Wu; McClinton, Charles (Technical Monitor)

2001-01-01

A boundary-layer transition study over a compression corner was conducted under a hypersonic flow condition. Due to the discontinuities in boundary layer flow, the full Navier-Stokes equations were solved to simulate the development of disturbance in the boundary layer. A linear stability analysis and PSE method were used to get the initial disturbance for parallel and non-parallel flow respectively. A 2-D code was developed to solve the full Navier-stokes by using WENO(weighted essentially non-oscillating) scheme. The given numerical results show the evolution of the linear disturbance for the most amplified disturbance in supersonic and hypersonic flow over a compression ramp. The nonlinear computations also determined the minimal amplitudes necessary to cause transition at a designed location.

Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation.

PubMed

Jin, Biao; Nijenhuis, Ivonne; Rolle, Massimo

2018-06-01

We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

The overview effect: the impact of space exploration on the evolution of nursing science.

PubMed

Butcher, H K; Forchuk, C

1992-01-01

The purpose of this article is to explore the overview effect, an experience evoked by space travel that has the capacity to transform all patterns of human existence and evolution toward greater potentials in human diversity and creativity. As nurses migrate with humanity into the solar system and beyond, they will experience the overview effect. The core components of the effect include changed perceptions of space, time, sound, and weight which have the potential to transform the evolution of nursing science. Nursing paradigms will encompass a view of humanity as integral with an infinite evolutionary universe. After generations of living in space in a diversity of new environments, the physical body will undergo radical changes, and the meaning of health will be transformed. The article concludes with a discussion on the parallels between Rogers' science of unitary human beings and the overview effect.

Clonal evolution in hematologic malignancies and therapeutic implications

PubMed Central

Landau, Dan A.; Carter, Scott L.; Getz, Gad; Wu, Catherine J.

2014-01-01

The ability of cancer to evolve and adapt is a principal challenge to therapy in general, and to the paradigm of targeted therapy in particular. This ability is fueled by the co-existence of multiple, genetically heterogeneous subpopulations within the cancer cell population. Increasing evidence has supported the idea that these subpopulations are selected in a Darwinian fashion, by which the genetic landscape of the tumor is continuously reshaped. Massively parallel sequencing has enabled a recent surge in our ability to study this process, adding to previous efforts using cytogenetic methods and targeted sequencing. Altogether, these studies reveal the complex evolutionary trajectories occurring across individual hematological malignancies. They also suggest that while clonal evolution may contribute to resistance to therapy, treatment may also hasten the evolutionary process. New insights into this process challenge us to understand the impact of treatment on clonal evolution, and inspire the development of novel prognostic and therapeutic strategies. PMID:23979521

Tempo and mode in human evolution.

PubMed Central

McHenry, H M

1994-01-01

The quickening pace of paleontological discovery is matched by rapid developments in geochronology. These new data show that the pattern of morphological change in the hominid lineage was mosaic. Adaptations essential to bipedalism appeared early, but some locomotor features changed much later. Relative to the highly derived postcrania of the earliest hominids, the craniodental complex was quite primitive (i.e., like the reconstructed last common ancestor with the African great apes). The pattern of craniodental change among successively younger species of Hominidae implies extensive parallel evolution between at least two lineages in features related to mastication. Relative brain size increased slightly among successively younger species of Australopithecus, expanded significantly with the appearance of Homo, but within early Homo remained at about half the size of Homo sapiens for almost a million years. Many apparent trends in human evolution may actually be due to the accumulation of relatively rapid shifts in successive species. PMID:8041697

Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness

PubMed Central

Bozek, Katarzyna; Wei, Yuning; Yan, Zheng; Liu, Xiling; Xiong, Jieyi; Sugimoto, Masahiro; Tomita, Masaru; Pääbo, Svante; Pieszek, Raik; Sherwood, Chet C.; Hof, Patrick R.; Ely, John J.; Steinhauser, Dirk; Willmitzer, Lothar; Bangsbo, Jens; Hansson, Ola; Call, Josep; Giavalisco, Patrick; Khaitovich, Philipp

2014-01-01

Metabolite concentrations reflect the physiological states of tissues and cells. However, the role of metabolic changes in species evolution is currently unknown. Here, we present a study of metabolome evolution conducted in three brain regions and two non-neural tissues from humans, chimpanzees, macaque monkeys, and mice based on over 10,000 hydrophilic compounds. While chimpanzee, macaque, and mouse metabolomes diverge following the genetic distances among species, we detect remarkable acceleration of metabolome evolution in human prefrontal cortex and skeletal muscle affecting neural and energy metabolism pathways. These metabolic changes could not be attributed to environmental conditions and were confirmed against the expression of their corresponding enzymes. We further conducted muscle strength tests in humans, chimpanzees, and macaques. The results suggest that, while humans are characterized by superior cognition, their muscular performance might be markedly inferior to that of chimpanzees and macaque monkeys. PMID:24866127

Mirror neurons and the evolution of language.

PubMed

Corballis, Michael C

2010-01-01

The mirror system provided a natural platform for the subsequent evolution of language. In nonhuman primates, the system provides for the understanding of biological action, and possibly for imitation, both prerequisites for language. I argue that language evolved from manual gestures, initially as a system of pantomime, but with gestures gradually "conventionalizing" to assume more symbolic form. The evolution of episodic memory and mental time travel, probably beginning with the genus Homo during the Pleistocene, created pressure for the system to "grammaticalize," involving the increased vocabulary necessary to refer to episodes separated in time and place from the present, constructions such as tense to refer to time itself, and the generativity to construct future (and fictional) episodes. In parallel with grammaticalization, the language medium gradually incorporated facial and then vocal elements, culminating in autonomous speech (albeit accompanied still by manual gesture) in our own species, Homo sapiens. 2009 Elsevier Inc. All rights reserved.

Apollo and the geology of the moon /Twenty-eighth William Smith Lecture/

NASA Technical Reports Server (NTRS)

Schmitt, H. H.

1975-01-01

Lunar geology evidence is examined for clues to the origin and evolution of the moon and earth. Seven evolutionary episodes, the last covering three billion years to the present day, are constructed for the moon. Parallel episodes in the earth's evolution are masked by the dynamic continuing evolution of the earth over a 4.5 billion year span, in contrast to the moon's quiescence and inability to retain fluids. Comparisons are drawn between the geochemistry and tectonics of the lunar basaltic maria and the earth's ocean basins. Lunar maria rocks differ strikingly in chemical composition from meteoritic matter and solar material. Inundation of frontside lunar maria basins by vast oceans of dark basalt mark the last of the major internally generated evolutionary episodes, and is attributed to consequences of meltdown of the lunar mantle and crust by radioisotope decay from below. Data are drawn primarily from Apollo missions 11-17, supplemented by other sources.

Kinetic theory of turbulence for parallel propagation revisited: Low-to-intermediate frequency regime

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

Yoon, Peter H., E-mail: yoonp@umd.edu; School of Space Research, Kyung Hee University, Yongin, Gyeonggi 446-701

2015-09-15

A previous paper [P. H. Yoon, “Kinetic theory of turbulence for parallel propagation revisited: Formal results,” Phys. Plasmas 22, 082309 (2015)] revisited the second-order nonlinear kinetic theory for turbulence propagating in directions parallel/anti-parallel to the ambient magnetic field, in which the original work according to Yoon and Fang [Phys. Plasmas 15, 122312 (2008)] was refined, following the paper by Gaelzer et al. [Phys. Plasmas 22, 032310 (2015)]. The main finding involved the dimensional correction pertaining to discrete-particle effects in Yoon and Fang's theory. However, the final result was presented in terms of formal linear and nonlinear susceptibility response functions. Inmore » the present paper, the formal equations are explicitly written down for the case of low-to-intermediate frequency regime by making use of approximate forms for the response functions. The resulting equations are sufficiently concrete so that they can readily be solved by numerical means or analyzed by theoretical means. The derived set of equations describe nonlinear interactions of quasi-parallel modes whose frequency range covers the Alfvén wave range to ion-cyclotron mode, but is sufficiently lower than the electron cyclotron mode. The application of the present formalism may range from the nonlinear evolution of whistler anisotropy instability in the high-beta regime, and the nonlinear interaction of electrons with whistler-range turbulence.« less

Dynamic imaging in electrical impedance tomography of the human chest with online transition matrix identification.

PubMed

Moura, Fernando Silva; Aya, Julio Cesar Ceballos; Fleury, Agenor Toledo; Amato, Marcelo Britto Passos; Lima, Raul Gonzalez

2010-02-01

One of the electrical impedance tomography objectives is to estimate the electrical resistivity distribution in a domain based only on electrical potential measurements at its boundary generated by an imposed electrical current distribution into the boundary. One of the methods used in dynamic estimation is the Kalman filter. In biomedical applications, the random walk model is frequently used as evolution model and, under this conditions, poor tracking ability of the extended Kalman filter (EKF) is achieved. An analytically developed evolution model is not feasible at this moment. The paper investigates the identification of the evolution model in parallel to the EKF and updating the evolution model with certain periodicity. The evolution model transition matrix is identified using the history of the estimated resistivity distribution obtained by a sensitivity matrix based algorithm and a Newton-Raphson algorithm. To numerically identify the linear evolution model, the Ibrahim time-domain method is used. The investigation is performed by numerical simulations of a domain with time-varying resistivity and by experimental data collected from the boundary of a human chest during normal breathing. The obtained dynamic resistivity values lie within the expected values for the tissues of a human chest. The EKF results suggest that the tracking ability is significantly improved with this approach.

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns

PubMed Central

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E.

2016-01-01

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this ‘ancient’ fern lineage across the tropics. PMID:27412279

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns.

PubMed

Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E

2016-07-13

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics. © 2016 The Author(s).

Runaway tails in magnetized plasmas

NASA Technical Reports Server (NTRS)

Moghaddam-Taaheri, E.; Vlahos, L.; Rowland, H. L.; Papadopoulos, K.

1985-01-01

The evolution of a runaway tail driven by a dc electric field in a magnetized plasma is analyzed. Depending on the strength of the electric field and the ratio of plasma to gyrofrequency, there are three different regimes in the evolution of the tail. The tail can be (1) stable with electrons accelerated to large parallel velocities, (2) unstable to Cerenkov resonance because of the depletion of the bulk and the formation of a positive slope, (3) unstable to the anomalous Doppler resonance instability driven by the large velocity anisotropy in the tail. Once an instability is triggered (Cerenkov or anomalous Doppler resonance) the tail relaxes into an isotropic distribution. The role of a convection type loss term is also discussed.

Evolution and coevolution of developmental programs

NASA Astrophysics Data System (ADS)

Jacob, Christian

1999-09-01

The developmental processes of single organisms, such as growth and structure formation, can be described by parallel rewrite systems in the form of Lindenmayer systems, which also allow one to generate geometrical structures in 3D space using turtle interpretation. We present examples of L-systems for growth programs of plant-like structures. Evolution-based programming techniques are applied to design L-systems by Genetic L-system Programming (GLP), demonstrating how developmental programs for plants, exhibiting specific morphogenetic properties can be interactively bred or automatically evolved. Finally, we demonstrate coevolutionary effects among plant populations consisting of different species, interacting with each other, competing for resources like sunlight and nutrients, and evolving successful reproduction strategies in their specific environments.

Structure and evolution of cereal genomes.

PubMed

Paterson, Andrew H; Bowers, John E; Peterson, Daniel G; Estill, James C; Chapman, Brad A

2003-12-01

The cereal species, of central importance to our diet, began to diverge 50-70 million years ago. For the past few thousand years, these species have undergone largely parallel selection regimes associated with domestication and improvement. The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both the shared and the independent dimensions of cereal evolution. New data and population-based approaches are identifying genes that have been involved in cereal improvement. Reduced-representation sequencing promises to accelerate gene discovery in many large-genome cereals, and to better link the under-explored genomes of 'orphan' cereals with state-of-the-art knowledge.

Host switch during evolution of a genetically distinct hantavirus in the American shrew mole (Neurotrichus gibbsii)

PubMed Central

Kang, Hae Ji; Bennett, Shannon N.; Dizney, Laurie; Sumibcay, Laarni; Arai, Satoru; Ruedas, Luis A.; Song, Jin-Won; Yanagihara, Richard

2009-01-01

A genetically distinct hantavirus, designated Oxbow virus (OXBV), was detected in tissues of an American shrew mole (Neurotrichus gibbsii), captured in Gresham, Oregon, in September 2003. Pairwise analysis of full-length S- and M- and partial L-segment nucleotide and amino acid sequences of OXBV indicated low sequence similarity with rodent-borne hantaviruses. Phylogenetic analyses using maximum-likelihood and Bayesian methods, and host-parasite evolutionary comparisons, showed that OXBV and Asama virus, a hantavirus recently identified from the Japanese shrew mole (Urotrichus talpoides), were related to soricine shrew-borne hantaviruses from North America and Eurasia, respectively, suggesting parallel evolution associated with cross-species transmission. PMID:19394994

The contribution of statistical physics to evolutionary biology.

PubMed

de Vladar, Harold P; Barton, Nicholas H

2011-08-01

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time. Copyright © 2011 Elsevier Ltd. All rights reserved.

A highly efficient 3D level-set grain growth algorithm tailored for ccNUMA architecture

NASA Astrophysics Data System (ADS)

Mießen, C.; Velinov, N.; Gottstein, G.; Barrales-Mora, L. A.

2017-12-01

A highly efficient simulation model for 2D and 3D grain growth was developed based on the level-set method. The model introduces modern computational concepts to achieve excellent performance on parallel computer architectures. Strong scalability was measured on cache-coherent non-uniform memory access (ccNUMA) architectures. To achieve this, the proposed approach considers the application of local level-set functions at the grain level. Ideal and non-ideal grain growth was simulated in 3D with the objective to study the evolution of statistical representative volume elements in polycrystals. In addition, microstructure evolution in an anisotropic magnetic material affected by an external magnetic field was simulated.

Assembly of the cnidarian camera-type eye from vertebrate-like components

PubMed Central

Kozmik, Zbynek; Ruzickova, Jana; Jonasova, Kristyna; Matsumoto, Yoshifumi; Vopalensky, Pavel; Kozmikova, Iryna; Strnad, Hynek; Kawamura, Shoji; Piatigorsky, Joram; Paces, Vaclav; Vlcek, Cestmir

2008-01-01

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution. PMID:18577593

Causal evidence between monsoon and evolution of rhizomyine rodents

PubMed Central

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J.

2015-01-01

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence. PMID:25759260

Causal evidence between monsoon and evolution of rhizomyine rodents.

PubMed

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J

2015-03-11

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

PubMed Central

Woltering, Joost M.; Duboule, Denis

2015-01-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. PMID:26238020

Phase space analysis in anisotropic optical systems

NASA Technical Reports Server (NTRS)

Rivera, Ana Leonor; Chumakov, Sergey M.; Wolf, Kurt Bernardo

1995-01-01

From the minimal action principle follows the Hamilton equations of evolution for geometric optical rays in anisotropic media. As in classical mechanics of velocity-dependent potentials, the velocity and the canonical momentum are not parallel, but differ by an anisotropy vector potential, similar to that of linear electromagnetism. Descartes' well known diagram for refraction is generalized and a factorization theorem holds for interfaces between two anisotropic media.

On computational methods for crashworthiness

NASA Technical Reports Server (NTRS)

Belytschko, T.

1992-01-01

The evolution of computational methods for crashworthiness and related fields is described and linked with the decreasing cost of computational resources and with improvements in computation methodologies. The latter includes more effective time integration procedures and more efficient elements. Some recent developments in methodologies and future trends are also summarized. These include multi-time step integration (or subcycling), further improvements in elements, adaptive meshes, and the exploitation of parallel computers.

Using parallel evolutionary development for a biologically-inspired computer vision system for mobile robots.

PubMed

Wright, Cameron H G; Barrett, Steven F; Pack, Daniel J

2005-01-01

We describe a new approach to attacking the problem of robust computer vision for mobile robots. The overall strategy is to mimic the biological evolution of animal vision systems. Our basic imaging sensor is based upon the eye of the common house fly, Musca domestica. The computational algorithms are a mix of traditional image processing, subspace techniques, and multilayer neural networks.

Applying Massively Parallel Kinetic Monte Carlo Methods to Simulate Grain Growth and Sintering in Powdered Metals

DTIC Science & Technology

2011-09-01

Structure Evolution During Sintering From [19]. ...................................20 Figure 10. Ising Model Configuration With Eight Nearest Neighbors...INTRODUCTION A. MOTIVATION The ability to fabricate structural components from metals with a fine (micron- sized), controlled grain size is one of the...hallmarks of modern, structural metallurgy. Powder metallurgy, in particular, consists of powder manufacture, powder blending, compacting, and sintering

Numerical Modeling of Internal Flow Aerodynamics. Part 2: Unsteady Flows

DTIC Science & Technology

2004-01-01

fluid- structure coupling, ...). • • • • • Prediction: in this simulation, we want to assess the effect of a change in SRM geometry, propellant...surface reaches the structure ). The third characteristic time describes the slow evolution of the internal geometry. The last characteristic time...incorporates fluid- structure coupling facility, and is parallel. MOPTI® manages exchanges between two principal computational modules: • • A varying

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms.

PubMed

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P; Feltus, F Alex; Paterson, Andrew H

2011-01-01

Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

PubMed Central

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P.; Feltus, F. Alex; Paterson, Andrew H.

2011-01-01

Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution. PMID:22164235

PARALLEL RACE FORMATION AND THE EVOLUTION OF MIMICRY IN HELICONIUS BUTTERFLIES: A PHYLOGENETIC HYPOTHESIS FROM MITOCHONDRIAL DNA SEQUENCES.

PubMed

Brower, Andrew V Z

1996-02-01

Mimicry has been a fundamental focus of research since the birth of evolutionary biology yet rarely has been studied from a phylogenetic perspective beyond the simple recognition that mimics are not similar due to common descent. The difficulty of finding characters to discern relationships among closely related and convergent taxa has challenged systematists for more than a century. The phenotypic diversity of wing pattens among mimetic Heliconius adds an additional twist to the problem, because single species contain more than a dozen radically different-looking geographical races even though the mimetic advantage is theoretically highest when all individuals within and between species appear the same. Mitochondrial DNA (mtDNA) offers an independent way to address these issues. In this study, Cytochrome Oxidase I and II sequences from multiple, parallel races of Heliconius erato and Heliconius melpomene are examined, to estimate intraspecific phylogeny and gauge sequence divergence and ages of clades among races within each species. Although phenotypes of sympatric races exhibit remarkable concordance between the two species, the mitochondrial cladograms show that the species have not shared a common evolutionary history. H. erato exhibits a basal split between trans- and cis-Andean groups of races, whereas H. melpomene originates in the Guiana Shield. Diverse races in either species appear to have evolved within the last 200,000 yr, and convergent phenotypes have evolved independently within as well as between species. These results contradict prior theories of the evolution of mimicry based on analysis of wing-pattern genetics. © 1996 The Society for the Study of Evolution.

Two-dimensional global hybrid simulation of pressure evolution and waves in the magnetosheath

NASA Astrophysics Data System (ADS)

Lin, Y.; Denton, R. E.; Lee, L. C.; Chao, J. K.

2001-06-01

A two-dimensional hybrid simulation is carried out for the global structure of the magnetosheath. Quasi-perpendicular magnetosonic/fast mode waves with large-amplitude in-phase oscillations of the magnetic field and the ion density are seen near the bow shock transition. Alfvén/ion-cyclotron waves are observed along the streamlines in the magnetosheath, and the wave power peaks in the middle magnetosheath. Antiphase oscillations in the magnetic field and density are present away from the shock transition. Transport ratio analysis suggests that these oscillations result from mirror mode waves. Since fluid simulations are currently best able to model the global magnetosphere and the pressure in the magnetosphere is inherently anisotropic (parallel pressure p∥≠perpendicular pressure p⊥), it is of some interest to see if a fluid model can be used to predict the anisotropic pressure evolution of a plasma. Here the predictions of double adiabatic theory, the bounded anisotropy model, and the double polytropic model are tested using the two-dimensional hybrid simulation of the magnetosheath. Inputs to the models from the hybrid simulation are the initial post bow shock pressures and the time-dependent density and magnetic field strength along streamlines of the plasma. The success of the models is evaluated on the basis of how well they predict the subsequent evolution of p∥ and p⊥. The bounded anisotropy model, which encorporates a bound on p⊥/p∥ due to the effect of ion cyclotron pitch angle scattering, does a very good job of predicting the evolution of p⊥ this is evidence that local transfer of energy due to waves is occurring. Further evidence is the positive identification of ion-cyclotron waves in the simulation. The lack of such a good prediction for the evolution of p∥ appears to be due to the model's lack of time dependence for the wave-particle interaction and its neglect of the parallel heat flux. Estimates indicate that these effects will be less significant in the real magnetosheath, though perhaps not negligible.

Fracture patterns of the drainage basin of Wadi Dahab in relation to tectonic-landscape evolution of the Gulf of Aqaba - Dead Sea transform fault

NASA Astrophysics Data System (ADS)

Shalaby, Ahmed

2017-10-01

Crustal rifting of the Arabian-Nubian Shield and formation of the Afro-Arabian rifts since the Miocene resulted in uplifting and subsequent terrain evolution of Sinai landscapes; including drainage systems and fault scarps. Geomorphic evolution of these landscapes in relation to tectonic evolution of the Afro-Arabian rifts is the prime target of this study. The fracture patterns and landscape evolution of the Wadi Dahab drainage basin (WDDB), in which its landscape is modeled by the tectonic evolution of the Gulf of Aqaba-Dead Sea transform fault, are investigated as a case study of landscape modifications of tectonically-controlled drainage systems. The early developed drainage system of the WDDB was achieved when the Sinai terrain subaerially emerged in post Eocene and initiation of the Afro-Arabian rifts in the Oligo-Miocene. Conjugate shear fractures, parallel to trends of the Afro-Arabian rifts, are synthesized with tensional fracture arrays to adapt some of inland basins, which represent the early destination of the Sinai drainage systems as paleolakes trapping alluvial sediments. Once the Gulf of Aqaba rift basin attains its deeps through sinistral movements on the Gulf of Aqaba-Dead Sea transform fault in the Pleistocene and the consequent rise of the Southern Sinai mountainous peaks, relief potential energy is significantly maintained through time so that it forced the Pleistocene runoffs to flow via drainage systems externally into the Gulf of Aqaba. Hence the older alluvial sediments are (1) carved within the paleolakes by a new generation of drainage systems; followed up through an erosional surface by sandy- to silty-based younger alluvium; and (2) brought on footslopes of fault scarps reviving the early developed scarps and inselbergs. These features argue for crustal uplifting of Sinai landscapes syn-rifting of the Gulf of Aqaba rift basin. Oblique orientation of the Red Sea-Gulf of Suez rift relative to the WNW-trending Precambrian Najd faults; and extrusion of volcanic rocks in directions parallel to the rift boundaries geometrically suggest rifting on tensional fractures that mutually bridge the Najd fault-related shear fractures. These aspects might envisage reactivation of the preexisting Precambrian fracture patterns in the Arabian-Nubian shield by the Oligo-Miocene to Pleistocene rift-controlled stress field.

Two Parallel Olfactory Pathways for Processing General Odors in a Cockroach

PubMed Central

Watanabe, Hidehiro; Nishino, Hiroshi; Mizunami, Makoto; Yokohari, Fumio

2017-01-01

In animals, sensory processing via parallel pathways, including the olfactory system, is a common design. However, the mechanisms that parallel pathways use to encode highly complex and dynamic odor signals remain unclear. In the current study, we examined the anatomical and physiological features of parallel olfactory pathways in an evolutionally basal insect, the cockroach Periplaneta americana. In this insect, the entire system for processing general odors, from olfactory sensory neurons to higher brain centers, is anatomically segregated into two parallel pathways. Two separate populations of secondary olfactory neurons, type1 and type2 projection neurons (PNs), with dendrites in distinct glomerular groups relay olfactory signals to segregated areas of higher brain centers. We conducted intracellular recordings, revealing olfactory properties and temporal patterns of both types of PNs. Generally, type1 PNs exhibit higher odor-specificities to nine tested odorants than type2 PNs. Cluster analyses revealed that odor-evoked responses were temporally complex and varied in type1 PNs, while type2 PNs exhibited phasic on-responses with either early or late latencies to an effective odor. The late responses are 30–40 ms later than the early responses. Simultaneous intracellular recordings from two different PNs revealed that a given odor activated both types of PNs with different temporal patterns, and latencies of early and late responses in type2 PNs might be precisely controlled. Our results suggest that the cockroach is equipped with two anatomically and physiologically segregated parallel olfactory pathways, which might employ different neural strategies to encode odor information. PMID:28529476

Dermatologic Surgical Instruments: A History and Review.

PubMed

Gandhi, Sumul A; Kampp, Jeremy T

2017-01-01

Dermatologic surgery requires precision and accuracy given the delicate nature of procedures performed. The use of the most appropriate instrument for each action helps optimize both functionality and cosmetic outcome. To review the history of surgical instruments used in dermatology, with a focus on mechanism and evolution to the instruments that are used in current practice. A comprehensive literature search was conducted via textbook and journal research for historic references while review of current references was conducted online using multiple search engines and PubMed. There are a number of articles that review instruments in dermatology, but this article adds a unique perspective in classifying their evolution, while also presenting them as levers that serve to increase human dexterity during the course of surgery. Surgical instruments allow fine manipulation of tissue, which in turn produces optimal outcomes. Surgical tools have been around since the dawn of man, and their evolution parallels the extent to which human civilization has specialized over time. This article describes the evolution of instruments from the general surgical armamentaria to the specialized tools that are used today.

The evolution of eyes and visually guided behaviour

PubMed Central

Nilsson, Dan-Eric

2009-01-01

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes. PMID:19720648

Adaptive Molecular Evolution for 13,000 Phage Generations

PubMed Central

Wichman, Holly A.; Millstein, Jack; Bull, J. J.

2005-01-01

Bacteriophage φX174 was evolved on a continuous supply of sensitive hosts for 180 days (∼13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell. PMID:15687276

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

PubMed

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects.

Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses

PubMed Central

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Background Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. Methodology/Principal Findings We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Conclusions/Significance Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects. PMID:22272330

Influence of Magnesium Content on the Local Structure of Amorphous Calcium Carbonate (ACC): Real Time Determination by In Situ PDF Analysis

NASA Astrophysics Data System (ADS)

Mergelsberg, S. T.; Ulrich, R. N.; Michel, F. M.; Dove, P. M.

2016-12-01

Calcium carbonate minerals are an essential component in the exoskeletons of crustaceans and mollusks. The onset of exoskeleton mineralization includes the precipitation of amorphous calcium carbonate (ACC) as a reactive intermediate that later transforms to produce diverse structures. Despite the importance of ACC as a critical phase during skeleton formation, the chemical and physical properties are not well characterized at conditions that approximate biological environments. Of particular interest are the solubility of ACC, the short-range structure at the time of formation, and the evolution of ACC structure to final products. Recent advances showing the widespread occurrence of multistep pathways to mineralization in biological and geological settings (De Yoreo et al., 2015) underline the importance of understanding amorphous intermediates. Using quantitative laboratory techniques developed by our research group (Blue et al., 2013; Blue and Dove, 2015; Blue et al., in press), this experimental study quantifies the solubility of ACC in parallel with the physical characterization of the corresponding structure. We measured ACC solubility at specific time points during the precipitation and during its subsequent evolution under the mild pH conditions that approximate biological and environmental conditions. In parallel experiments, structural data were collected from in situ pair distribution function (PDF) analyses were conducted to follow the evolution of individual samples from initial precipitation to final product. The measurements are leading to a quantitative solubility function for ACC with variable Mg contents and an x-ray based understanding of ACC structure in the same particles. We are also finding temporal changes in the short-range order of ACC after precipitation and this order is dependent upon Mg content. Moreover, the data show Mg distribution through the ACC particles is dependent upon total alkalinity. Insights from this study hold promise for better understanding the nature of the initial ACC that forms and factors that influence its structural evolution to final products.

Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.).

PubMed

Remigereau, Marie-Stanislas; Lakis, Ghayas; Rekima, Samah; Leveugle, Magalie; Fontaine, Michaël C; Langin, Thierry; Sarr, Aboubakry; Robert, Thierry

2011-01-01

During the Neolithic revolution, early farmers altered plant development to domesticate crops. Similar traits were often selected independently in different wild species; yet the genetic basis of this parallel phenotypic evolution remains elusive. Plant architecture ranks among these target traits composing the domestication syndrome. We focused on the reduction of branching which occurred in several cereals, an adaptation known to rely on the major gene Teosinte-branched1 (Tb1) in maize. We investigate the role of the Tb1 orthologue (Pgtb1) in the domestication of pearl millet (Pennisetum glaucum), an African outcrossing cereal. Gene cloning, expression profiling, QTL mapping and molecular evolution analysis were combined in a comparative approach between pearl millet and maize. Our results in pearl millet support a role for PgTb1 in domestication despite important differences in the genetic basis of branching adaptation in that species compared to maize (e.g. weaker effects of PgTb1). Genetic maps suggest this pattern to be consistent in other cereals with reduced branching (e.g. sorghum, foxtail millet). Moreover, although the adaptive sites underlying domestication were not formerly identified, signatures of selection pointed to putative regulatory regions upstream of both Tb1 orthologues in maize and pearl millet. However, the signature of human selection in the pearl millet Tb1 is much weaker in pearl millet than in maize. Our results suggest that some level of parallel evolution involved at least regions directly upstream of Tb1 for the domestication of pearl millet and maize. This was unanticipated given the multigenic basis of domestication traits and the divergence of wild progenitor species for over 30 million years prior to human selection. We also hypothesized that regular introgression of domestic pearl millet phenotypes by genes from the wild gene pool could explain why the selective sweep in pearl millet is softer than in maize.

Cereal Domestication and Evolution of Branching: Evidence for Soft Selection in the Tb1 Orthologue of Pearl Millet (Pennisetum glaucum [L.] R. Br.)

PubMed Central

Remigereau, Marie-Stanislas; Lakis, Ghayas; Rekima, Samah; Leveugle, Magalie; Fontaine, Michaël C.; Langin, Thierry; Sarr, Aboubakry; Robert, Thierry

2011-01-01

Background During the Neolithic revolution, early farmers altered plant development to domesticate crops. Similar traits were often selected independently in different wild species; yet the genetic basis of this parallel phenotypic evolution remains elusive. Plant architecture ranks among these target traits composing the domestication syndrome. We focused on the reduction of branching which occurred in several cereals, an adaptation known to rely on the major gene Teosinte-branched1 (Tb1) in maize. We investigate the role of the Tb1 orthologue (Pgtb1) in the domestication of pearl millet (Pennisetum glaucum), an African outcrossing cereal. Methodology/Principal Findings Gene cloning, expression profiling, QTL mapping and molecular evolution analysis were combined in a comparative approach between pearl millet and maize. Our results in pearl millet support a role for PgTb1 in domestication despite important differences in the genetic basis of branching adaptation in that species compared to maize (e.g. weaker effects of PgTb1). Genetic maps suggest this pattern to be consistent in other cereals with reduced branching (e.g. sorghum, foxtail millet). Moreover, although the adaptive sites underlying domestication were not formerly identified, signatures of selection pointed to putative regulatory regions upstream of both Tb1 orthologues in maize and pearl millet. However, the signature of human selection in the pearl millet Tb1 is much weaker in pearl millet than in maize. Conclusions/Significance Our results suggest that some level of parallel evolution involved at least regions directly upstream of Tb1 for the domestication of pearl millet and maize. This was unanticipated given the multigenic basis of domestication traits and the divergence of wild progenitor species for over 30 million years prior to human selection. We also hypothesized that regular introgression of domestic pearl millet phenotypes by genes from the wild gene pool could explain why the selective sweep in pearl millet is softer than in maize. PMID:21799845

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies.

PubMed

Sullam, Karen E; Rubin, Benjamin E R; Dalton, Christopher M; Kilham, Susan S; Flecker, Alexander S; Russell, Jacob A

2015-07-01

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

PubMed Central

Sullam, Karen E; Rubin, Benjamin ER; Dalton, Christopher M; Kilham, Susan S; Flecker, Alexander S; Russell, Jacob A

2015-01-01

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation. PMID:25575311

Parallel evolution of circulating FABP4 and NT-proBNP in heart failure patients

PubMed Central

2013-01-01

Background Circulating adipocyte fatty acid-binding protein (FABP4) levels are considered to be a link between obesity, insulin resistance, diabetes, and cardiovascular (CV) diseases. In vitro, FABP4 has exhibited cardiodepressant activity by suppressing cardiomyocyte contraction. We have explored the relationship between FABP4 and the N-terminal fragment of pro-B-type natriuretic peptide (NT-proBNP) as a clinical parameter of heart failure (HF). Methods We included 179 stable HF patients who were referred to a specialized HF unit, 108 of whom were prospectively followed for up to 6 months. A group of 163 non-HF patients attending a CV risk unit was used as the non-HF control group for the FABP4 comparisons. Results In the HF patients, FABP4 and NT-proBNP were assayed, along with a clinical and functional assessment of the heart at baseline and after 6 months of specialized monitoring. The FABP4 levels were higher in the patients with HF than in the non-HF high CV risk control group (p<0.001). The FABP4 levels were associated with the NT-proBNP levels in patients with HF (r=0.601, p<0.001), and this association was stronger in the diabetic patients. FABP4 was also associated with heart rate and the results of the 6-minute walk test. After the follow-up period, FABP4 decreased in parallel to NT-proBNP and to the clinical parameters of HF. Conclusions FABP4 is associated with the clinical manifestations and biomarkers of HF. It exhibits a parallel evolution with the circulating levels of NT-proBNP in HF patients. PMID:23642261

Parallel evolution of circulating FABP4 and NT-proBNP in heart failure patients.

PubMed

Cabré, Anna; Valdovinos, Pilar; Lázaro, Iolanda; Bonet, Gil; Bardají, Alfredo; Masana, Lluís

2013-05-04

Circulating adipocyte fatty acid-binding protein (FABP4) levels are considered to be a link between obesity, insulin resistance, diabetes, and cardiovascular (CV) diseases. In vitro, FABP4 has exhibited cardiodepressant activity by suppressing cardiomyocyte contraction. We have explored the relationship between FABP4 and the N-terminal fragment of pro-B-type natriuretic peptide (NT-proBNP) as a clinical parameter of heart failure (HF). We included 179 stable HF patients who were referred to a specialized HF unit, 108 of whom were prospectively followed for up to 6 months. A group of 163 non-HF patients attending a CV risk unit was used as the non-HF control group for the FABP4 comparisons. In the HF patients, FABP4 and NT-proBNP were assayed, along with a clinical and functional assessment of the heart at baseline and after 6 months of specialized monitoring. The FABP4 levels were higher in the patients with HF than in the non-HF high CV risk control group (p<0.001). The FABP4 levels were associated with the NT-proBNP levels in patients with HF (r=0.601, p<0.001), and this association was stronger in the diabetic patients. FABP4 was also associated with heart rate and the results of the 6-minute walk test. After the follow-up period, FABP4 decreased in parallel to NT-proBNP and to the clinical parameters of HF. FABP4 is associated with the clinical manifestations and biomarkers of HF. It exhibits a parallel evolution with the circulating levels of NT-proBNP in HF patients.

The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains.

PubMed

Hughes, Colin E; Atchison, Guy W

2015-07-01

Alpine plant radiations are compared across the world's major mountain ranges and shown to be overwhelmingly young and fast, largely confined to the Pliocene and Pleistocene, and some of them apparently in the early explosive phase of radiation. Accelerated diversification triggered by island-like ecological opportunities following the final phases of mountain uplift, and in many cases enabled by the key adaptation of perennial habit, provides a general model for alpine plant radiations. Accelerated growth form evolution facilitated by perenniality provides compelling evidence of ecological release and suggests striking parallels between island-like alpine, and especially tropicalpine radiations, and island radiations more generally. These parallels suggest that the world's mountains offer an excellent comparative system for explaining evolutionary radiation. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Phase space simulation of collisionless stellar systems on the massively parallel processor

NASA Technical Reports Server (NTRS)

White, Richard L.

1987-01-01

A numerical technique for solving the collisionless Boltzmann equation describing the time evolution of a self gravitating fluid in phase space was implemented on the Massively Parallel Processor (MPP). The code performs calculations for a two dimensional phase space grid (with one space and one velocity dimension). Some results from calculations are presented. The execution speed of the code is comparable to the speed of a single processor of a Cray-XMP. Advantages and disadvantages of the MPP architecture for this type of problem are discussed. The nearest neighbor connectivity of the MPP array does not pose a significant obstacle. Future MPP-like machines should have much more local memory and easier access to staging memory and disks in order to be effective for this type of problem.

Genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia cell line

PubMed Central

STOCZYNSKA-FIDELUS, EWELINA; PIASKOWSKI, SYLWESTER; PAWLOWSKA, ROZA; SZYBKA, MALGORZATA; PECIAK, JOANNA; HULAS-BIGOSZEWSKA, KRYSTYNA; WINIECKA-KLIMEK, MARTA; RIESKE, PIOTR

2016-01-01

Thorough examination of genetic heterogeneity of cell lines is uncommon. In order to address this issue, the present study analyzed the genetic heterogeneity of RPMI-8402, a T-acute lymphoblastic leukemia (T-ALL) cell line. For this purpose, traditional techniques such as fluorescence in situ hybridization and immunocytochemistry were used, in addition to more advanced techniques, including cell sorting, Sanger sequencing and massive parallel sequencing. The results indicated that the RPMI-8402 cell line consists of several genetically different cell subpopulations. Furthermore, massive parallel sequencing of RPMI-8402 provided insight into the evolution of T-ALL carcinogenesis, since this cell line exhibited the genetic heterogeneity typical of T-ALL. Therefore, the use of cell lines for drug testing in future studies may aid the progress of anticancer drug research. PMID:26870252

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

Effect of regional slope on drainage networks

NASA Astrophysics Data System (ADS)

Phillips, Loren F.; Schumm, S. A.

1987-09-01

Drainage networks that develop under conditions of no structural control and homogeneous lithology are generally dendritic, depending upon the shape and inclination of the surface on which they form. An experimental study was designed to investigate the effect of an increase of slope on the evolution and development of dendritic drainage patterns. As slope steepens, the pattern changes from dendritic at 1% slope, to subdendritic at 2%, to subparallel at 3%, to parallel at 5% and higher. The change from a dendritic-type pattern to a parallel-type pattern occurs at a low slope, between 2% and 3%, and primary channel junction angles decrease abruptly from about 60° to 43°. *Present address: U.S. Army Environmental Hygiene Agency, Attn: HSHB-ME-WM, Aberdeen Proving Ground, Maryland 21010-5422

Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

PubMed

Yesylevskyy, Semen O

2015-07-15

Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

Spontaneous Hot Flow Anomalies at Quasi-Parallel Shocks: 2. Hybrid Simulations

NASA Technical Reports Server (NTRS)

Omidi, N.; Zhang, H.; Sibeck, D.; Turner, D.

2013-01-01

Motivated by recent THEMIS observations, this paper uses 2.5-D electromagnetic hybrid simulations to investigate the formation of Spontaneous Hot Flow Anomalies (SHFA) upstream of quasi-parallel bow shocks during steady solar wind conditions and in the absence of discontinuities. The results show the formation of a large number of structures along and upstream of the quasi-parallel bow shock. Their outer edges exhibit density and magnetic field enhancements, while their cores exhibit drops in density, magnetic field, solar wind velocity and enhancements in ion temperature. Using virtual spacecraft in the simulation, we show that the signatures of these structures in the time series data are very similar to those of SHFAs seen in THEMIS data and conclude that they correspond to SHFAs. Examination of the simulation data shows that SHFAs form as the result of foreshock cavitons interacting with the bow shock. Foreshock cavitons in turn form due to the nonlinear evolution of ULF waves generated by the interaction of the solar wind with the backstreaming ions. Because foreshock cavitons are an inherent part of the shock dissipation process, the formation of SHFAs is also an inherent part of the dissipation process leading to a highly non-uniform plasma in the quasi-parallel magnetosheath including large scale density and magnetic field cavities.

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

PubMed

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

2018-05-16

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

From chemotaxis to the cognitive map: The function of olfaction

PubMed Central

Jacobs, Lucia F.

2012-01-01

A paradox of vertebrate brain evolution is the unexplained variability in the size of the olfactory bulb (OB), in contrast to other brain regions, which scale predictably with brain size. Such variability appears to be the result of selection for olfactory function, yet there is no obvious concordance that would predict the causal relationship between OB size and behavior. This discordance may derive from assuming the primary function of olfaction is odorant discrimination and acuity. If instead the primary function of olfaction is navigation, i.e., predicting odorant distributions in time and space, variability in absolute OB size could be ascribed and explained by variability in navigational demand. This olfactory spatial hypothesis offers a single functional explanation to account for patterns of olfactory system scaling in vertebrates, the primacy of olfaction in spatial navigation, even in visual specialists, and proposes an evolutionary scenario to account for the convergence in olfactory structure and function across protostomes and deuterostomes. In addition, the unique percepts of olfaction may organize odorant information in a parallel map structure. This could have served as a scaffold for the evolution of the parallel map structure of the mammalian hippocampus, and possibly the arthropod mushroom body, and offers an explanation for similar flexible spatial navigation strategies in arthropods and vertebrates. PMID:22723365

Osmotic/ionic status of body fluids in the euryhaline cephalopod suggest possible parallel evolution of osmoregulation

PubMed Central

Sakamoto, Tatsuya; Ogawa, Satoshi; Nishiyama, Yudai; Akada, Chiaki; Takahashi, Hideya; Watanabe, Taro; Minakata, Hiroyuki; Sakamoto, Hirotaka

2015-01-01

Acclimation from marine to dilute environments constitutes among the dramatic evolutionary transitions in the history of life. Such adaptations have evolved in multiple lineages, but studies of the blood/hemolymph homeostasis mechanisms are limited to those using evolutionarily advanced Deuterostome (chordates) and Ecdysozoa (crustaceans). Here, we examined hemolymph homeostasis in the advanced Lophotrochozoa/mollusc, the other unexplored taxa, and its possible regulation by the vasopressin/oxytocin superfamily peptides known to be implicated in fluid homeostasis in Chordata and Arthropoda. The hemolymph osmotic and ionic status in the euryhaline cephalopod (Octopus ocellatus) following transfer from 30-ppt normal seawater to 20 ppt salinity indicate hyperosmo- and hyperionoregulatory abilities for more than 1 week, as in crustaceans and teleost fish. While ventilation frequency decreased by 1 day, Na+/K+-ATPase activity, which has been generally implicated in ion transport, was induced in two of the eight posterior gills after 1 week. In addition, the octopuses were intravenously injected with 1 or 100 ng/g octopressin or cephalotocin, which are Octopus vasopressin/oxytocin orthologs. After 1 day, octopressin, but not cephalotocin, decreased the hemolymph osmolality and Ca concentrations, as well as urinary Na concentrations. These data provide evidence for possible parallel evolution in hyperionoregulatory mechanisms and coordination by conserved peptides. PMID:26403952

Effect of Gold on the Microstructural Evolution and Integrity of a Sintered Silver Joint

NASA Astrophysics Data System (ADS)

Muralidharan, Govindarajan; Leonard, Donovan N.; Meyer, Harry M.

2017-07-01

There is a need for next-generation, high-performance power electronic packages and systems employing wide-bandgap devices to operate at high temperatures in automotive and electric grid applications. Sintered silver joints are currently being evaluated as an alternative to Pb-free solder joints. Of particular interest is the development of joints based on silver paste consisting of nano- or micron-scale particles that can be processed without application of external pressure. The microstructural evolution at the interface of a pressureless-sintered silver joint formed between a SiC die with Ti/Ni/Au metallization and an active metal brazed (AMB) substrate with Ag metallization at 250°C has been evaluated using scanning electron microscopy (SEM), x-ray microanalysis, and x-ray photoelectron spectroscopy (XPS). Results from focused ion beam (FIB) cross-sections show that, during sintering, pores in the sintered region near to the Au layer tend to be narrow and elongated with long axis oriented parallel to the interface. Further densification results in formation of many small, relatively equiaxed pores aligned parallel to the interface, creating a path for easy crack propagation. X-ray microanalysis results confirm interdiffusion between Au and Ag and that a region with poor mechanical strength is formed at the edge of this region of interdiffusion.

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

PubMed Central

Fuller, Dorian Q; Denham, Tim; Arroyo-Kalin, Manuel; Lucas, Leilani; Stevens, Chris J.; Qin, Ling; Allaby, Robin G.; Purugganan, Michael D.

2014-01-01

Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers. PMID:24753577

Measuring Low Mass Galaxies In The WFC3 Infrared Spectroscopic Parallels Survey

NASA Astrophysics Data System (ADS)

Colbert, James; Teplitz, Harry; Scarlata, Claudia; Siana, Brian; Malkan, Matt; McCarthy, Patrick; Henry, Alaina; Atek, Hakim; Fosbury, Robert; Ross, Nathanial; Hathi, Nimish; Bridge, Carrie; Bunker, Andrew; Dressler, Alan; Shim, Hyunjin; Bedregal, Alejandro; Dominguez, Alberto; Rafelski, Marc; Masters, Dan; Martin, Crystal; Dai, Sophia

2015-10-01

The WFC3 Infrared Spectroscopic Parallel (WISP) Survey uses over 1800 HST orbits to study galaxy evolution over a majority of cosmic history. Its slitless grism spectroscopy over a wide, continuous spectral range (0.8-1.7 micron) provides an unbiased selection of thousands of emission line galaxies over 0.5 < z < 2.5. Hundreds of these galaxies are detected in multiple emission lines, allowing for important diagnostics of metallicity and dust extinction. We propose deep 3.6 micron imaging (5 sigma, 0.9 micro-Jy) of 60 of the deepest WISP fields observed with the combination of G102+G141 grisms, in order to detect emission-line galaxies down to 0.1 L* and masses below 10^8 Mo. Combined with our HST optical and near-IR photometry, these IRAC data will be critical to determining accurate stellar masses for both passive and active galaxies in our survey. We will determine the evolution of the faint end slope of the stellar mass function and the mass-metallicity relation down to low-mass galaxies. The addition of the IRAC photometry will also provide much stronger constraints on dust extinction and star formation history, especially when combined with information available from the emission lines themselves.

A high-order time-parallel scheme for solving wave propagation problems via the direct construction of an approximate time-evolution operator

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

Haut, T. S.; Babb, T.; Martinsson, P. G.

2015-06-16

Our manuscript demonstrates a technique for efficiently solving the classical wave equation, the shallow water equations, and, more generally, equations of the form ∂u/∂t=Lu∂u/∂t=Lu, where LL is a skew-Hermitian differential operator. The idea is to explicitly construct an approximation to the time-evolution operator exp(τL)exp(τL) for a relatively large time-step ττ. Recently developed techniques for approximating oscillatory scalar functions by rational functions, and accelerated algorithms for computing functions of discretized differential operators are exploited. Principal advantages of the proposed method include: stability even for large time-steps, the possibility to parallelize in time over many characteristic wavelengths and large speed-ups over existingmore » methods in situations where simulation over long times are required. Numerical examples involving the 2D rotating shallow water equations and the 2D wave equation in an inhomogenous medium are presented, and the method is compared to the 4th order Runge–Kutta (RK4) method and to the use of Chebyshev polynomials. The new method achieved high accuracy over long-time intervals, and with speeds that are orders of magnitude faster than both RK4 and the use of Chebyshev polynomials.« less

Parallel or convergent evolution in human population genomic data revealed by genotype networks.

PubMed

R Vahdati, Ali; Wagner, Andreas

2016-08-02

Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite a shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. For 42 genes, the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. When analyzing possible explanations, we discovered evidence for positive selection in 21 of these genes and, in addition, a potential role for constrained variation and purifying selection. Balancing selection plays at most a small role. The 42 genes with excess cycles are enriched in functions related to immunity and response to pathogens. Genotype networks are representations of genetic variation data that can help understand unusual patterns of genomic variation.

DNA sequence transfer between two high-cysteine chorion gene families in the silkmoth Bombyx mori.

PubMed Central

Iatrou, K; Tsitilou, S G; Kafatos, F C

1984-01-01

We have previously shown that one type of high-cysteine silkmoth chorion protein (Hc-A) has evolved from the A family of chorion proteins by radical modifications of the NH2-terminal and COOH-terminal polypeptide arms: most of the arm sequences have been deleted, while short cysteine- and glycine-containing repeats have expanded into long arrays. Strikingly similar modifications of the arms have led to the evolution of a second type of high-cysteine protein (Hc-B) from the B family of chorion proteins. It appears that the parallel evolution of these high-cysteine-encoding gene families has not been entirely independent: examination of 3' untranslated regions shows evidence of information transfer between the two families. PMID:6589605

Implementation of a 3D version of ponderomotive guiding center solver in particle-in-cell code OSIRIS

NASA Astrophysics Data System (ADS)

Helm, Anton; Vieira, Jorge; Silva, Luis; Fonseca, Ricardo

2016-10-01

Laser-driven accelerators gained an increased attention over the past decades. Typical modeling techniques for laser wakefield acceleration (LWFA) are based on particle-in-cell (PIC) simulations. PIC simulations, however, are very computationally expensive due to the disparity of the relevant scales ranging from the laser wavelength, in the micrometer range, to the acceleration length, currently beyond the ten centimeter range. To minimize the gap between these despair scales the ponderomotive guiding center (PGC) algorithm is a promising approach. By describing the evolution of the laser pulse envelope separately, only the scales larger than the plasma wavelength are required to be resolved in the PGC algorithm, leading to speedups in several orders of magnitude. Previous work was limited to two dimensions. Here we present the implementation of the 3D version of a PGC solver into the massively parallel, fully relativistic PIC code OSIRIS. We extended the solver to include periodic boundary conditions and parallelization in all spatial dimensions. We present benchmarks for distributed and shared memory parallelization. We also discuss the stability of the PGC solver.

Electron acceleration in a secondary magnetic island formed during magnetic reconnection with a guide field

NASA Astrophysics Data System (ADS)

Wang, Huanyu; Lu, Quanming; Huang, Can; Wang, Shui

2017-05-01

Secondary magnetic islands may be generated in the vicinity of an X line during magnetic reconnection. In this paper, by performing two-dimensional (2-D) particle-in-cell simulations, we investigate the role of a secondary magnetic island in electron acceleration during magnetic reconnection with a guide field. The electron motions are found to be adiabatic, and we analyze the contributions of the parallel electric field and Fermi and betatron mechanisms to electron acceleration in the secondary island during the evolution of magnetic reconnection. When the secondary island is formed, electrons are accelerated by the parallel electric field due to the existence of the reconnection electric field in the electron current sheet. Electrons can be accelerated by both the parallel electric field and Fermi mechanism when the secondary island begins to merge with the primary magnetic island, which is formed simultaneously with the appearance of X lines. With the increase in the guide field, the contributions of the Fermi mechanism to electron acceleration become less and less important. When the guide field is sufficiently large, the contribution of the Fermi mechanism is almost negligible.

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

Alignment between Protostellar Outflows and Filamentary Structure

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Vorobyov, Eduard I.; Tobin, John J.; Pineda, Jaime E.; Offner, Stella S. R.; Lee, Katherine I.; Kristensen, Lars E.; Jørgensen, Jes K.; Goodman, Alyssa A.; Bourke, Tyler L.; Arce, Héctor G.; Plunkett, Adele L.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2-1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ˜3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

Similar Genetic Mechanisms Underlie the Parallel Evolution of Floral Phenotypes

PubMed Central

Zhang, Wenheng; Kramer, Elena M.; Davis, Charles C.

2012-01-01

The repeated origin of similar phenotypes is invaluable for studying the underlying genetics of adaptive traits; molecular evidence, however, is lacking for most examples of such similarity. The floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to result from specialization on oil-bee pollinators. We recently demonstrated that CYCLOIDEA2–like genes (CYC2A and CYC2B) are associated with the development of the stereotypical floral zygomorphy that is critical to this plant–pollinator mutualism. Here, we build on this developmental framework to characterize floral symmetry in three clades of Malpighiaceae that have independently lost their oil bee association and experienced parallel shifts in their floral morphology, especially in regard to symmetry. We show that in each case these species exhibit a loss of CYC2B function, and a strikingly similar shift in the expression of CYC2A that is coincident with their shift in floral symmetry. These results indicate that similar floral phenotypes in this large angiosperm clade have evolved via parallel genetic changes from an otherwise highly conserved developmental program. PMID:22558314

A parallel reaction-transport model applied to cement hydration and microstructure development

NASA Astrophysics Data System (ADS)

Bullard, Jeffrey W.; Enjolras, Edith; George, William L.; Satterfield, Steven G.; Terrill, Judith E.

2010-03-01

A recently described stochastic reaction-transport model on three-dimensional lattices is parallelized and is used to simulate the time-dependent structural and chemical evolution in multicomponent reactive systems. The model, called HydratiCA, uses probabilistic rules to simulate the kinetics of diffusion, homogeneous reactions and heterogeneous phenomena such as solid nucleation, growth and dissolution in complex three-dimensional systems. The algorithms require information only from each lattice site and its immediate neighbors, and this localization enables the parallelized model to exhibit near-linear scaling up to several hundred processors. Although applicable to a wide range of material systems, including sedimentary rock beds, reacting colloids and biochemical systems, validation is performed here on two minerals that are commonly found in Portland cement paste, calcium hydroxide and ettringite, by comparing their simulated dissolution or precipitation rates far from equilibrium to standard rate equations, and also by comparing simulated equilibrium states to thermodynamic calculations, as a function of temperature and pH. Finally, we demonstrate how HydratiCA can be used to investigate microstructure characteristics, such as spatial correlations between different condensed phases, in more complex microstructures.

Comparing wave shoaling methods used in large-scale coastal evolution modeling

NASA Astrophysics Data System (ADS)

Limber, P. W.; Adams, P. N.; Murray, A.

2013-12-01

A variety of methods are available to simulate wave propagation from the deep ocean to the surf zone. They range from simple and computationally fast (e.g. linear wave theory applied to shore-parallel bathymetric contours) to complicated and computationally intense (e.g., Delft's ';Simulating WAves Nearshore', or SWAN, model applied to complex bathymetry). Despite their differences, the goal of each method is the same with respect to coastline evolution modeling: to link offshore waves with rates of (and gradients in) alongshore sediment transport. Choosing a shoaling technique for modeling coastline evolution should be partly informed by the spatial and temporal scales of the model, as well as the model's intent (is it simulating a specific coastline, or exploring generic coastline dynamics?). However, the particular advantages and disadvantages of each technique, and how the advantages/disadvantages vary over different model spatial and temporal scales, are not always clear. We present a wave shoaling model that simultaneously computes breaking wave heights and angles using three increasingly complex wave shoaling routines: the most basic approach assuming shore-parallel bathymetric contours, a wave ray tracing method that includes wave energy convergence and divergence and non-shore-parallel contours, and a spectral wave model (SWAN). Initial results show reasonable agreement between wave models along a flat shoreline for small (1 m) wave heights, low wave angles (0 to 10 degrees), and simple bathymetry. But, as wave heights and angles increase, bathymetry becomes more variable, and the shoreline shape becomes sinuous, the model results begin to diverge. This causes different gradients in alongshore sediment transport between model runs employing different shoaling techniques and, therefore, different coastline behavior. Because SWAN does not approximate wave breaking (which drives alongshore sediment transport) we use a routine to extract grid cells from SWAN output where wave height is approximately one-half of the water depth (a standard wave breaking threshold). The goal of this modeling exercise is to understand under what conditions a simple wave model is sufficient for simulating coastline evolution, and when using a more complex shoaling routine can optimize a coastline model. The Coastline Evolution Model (CEM; Ashton and Murray, 2006) is used to show how different shoaling routines affect modeled coastline behavior. The CEM currently includes the most basic wave shoaling approach to simulate cape and spit formation. We will instead couple it to SWAN, using the insight from the comprehensive wave model (above) to guide its application. This will allow waves transformed over complex bathymetry, such as cape-associated shoals and ridges, to be input for the CEM so that large-scale coastline behavior can be addressed in less idealized environments. Ashton, A., and Murray, A.B., 2006, High-angle wave instability and emergent shoreline shapes: 1. Modeling of sand waves, flying spits, and capes: Journal of Geophysical Research, v. 111, p. F04011, doi:10.1029/2005JF000422.

Evolution of stress and strain during 3D folding: application to orthogonal fracture systems in folded turbidites, SW Portugal

NASA Astrophysics Data System (ADS)

Reber, J. E.; Schmalholz, S. M.; Lechmann, S. M.

2009-04-01

We present field data and numerical modeling results which show the evolution of stress and strain patterns during 3D folding resulting in an orthogonal fracture system. The field area is located near Almograve, SW Portugal. The area is part of the Mira Formation which itself is part of the South Portuguese Zone (SPZ). The structural development of the SPZ is characterized by southwest vergent folding and thrust displacement. The metamorphism in the SPZ increases from diagenetic conditions in the southwest to greenschist-facies conditions to the northeast. The Mira Formation is composed of turbiditic layers of Carboniferous age with low sandstone to shale ratio. The data was gathered at three outcrops which show structures similar to chocolate tablet structures in the folded sandstone layers. Chocolate tablet structures are generated under simultaneous extension in two directions and show two fracture systems of the same age which are perpendicular to each other. However, the Mira Formation is located in a convergent area. Also, the outcrops near Almograve show two fracture systems of different age. The fractures orthogonal to the fold axis and the bedding are crosscut by fractures parallel to the fold axis and orthogonal to the bedding. Our hypothesis for the evolution of the observed fracture systems is as follows; the older fractures which are now orthogonal to the fold axis and to the bedding plane were generated during compression while the layers were still approximately horizontal. They are parallel to σ1(i.e. mode 1 fractures). The second and younger fracture family was generated in a phase where there is local extension in the fold limbs. These fractures are orthogonal to the far-field σ1, parallel to the fold axis and perpendicular to the bedding. The shortening direction is constant during the entire folding process. We test our hypothesis with numerical modeling. We use 2D and 3D finite element codes with a mixed formulation for incompressible flow and a viscous rheology. The stress and strain tensor components are calculated at each numerical nodal point. The stress and strain fields are visualized through ellipses and ellipsoids which are calculated using the eigenvalues of the respective tensors. The shortest main axis represents the direction of the smallest stress σ3 and the longest main axis represents the direction of the largest stress σ1. To generate two orthogonal fracture systems in the fold limbs we expect a relatively rapid change of the stress field in the fold limbs during folding. With a relatively slow change of the stress field we would expect to see more than two fracture systems with a wide range of fracture orientation which we did not observe in the field. The preliminary 2D results show, as expected, a sudden flip of the main axes of the stress ellipse which corresponds to a change from limb-parallel compression to extension. For the 3D model we expect similar results and we will investigate the impact of different deformation boundary conditions on the evolution of the 3D stress and strain fields.

Natural selection in chemical evolution.

PubMed

Fernando, Chrisantha; Rowe, Jonathan

2007-07-07

We propose that chemical evolution can take place by natural selection if a geophysical process is capable of heterotrophic formation of liposomes that grow at some base rate, divide by external agitation, and are subject to stochastic chemical avalanches, in the absence of nucleotides or any monomers capable of modular heredity. We model this process using a simple hill-climbing algorithm, and an artificial chemistry that is unique in exhibiting conservation of mass and energy in an open thermodynamic system. Selection at the liposome level results in the stabilization of rarely occurring molecular autocatalysts that either catalyse or are consumed in reactions that confer liposome level fitness; typically they contribute in parallel to an increasingly conserved intermediary metabolism. Loss of competing autocatalysts can sometimes be adaptive. Steady-state energy flux by the individual increases due to the energetic demands of growth, but also of memory, i.e. maintaining variations in the chemical network. Self-organizing principles such as those proposed by Kauffman, Fontana, and Morowitz have been hypothesized as an ordering principle in chemical evolution, rather than chemical evolution by natural selection. We reject those notions as either logically flawed or at best insufficient in the absence of natural selection. Finally, a finite population model without elitism shows the practical evolutionary constraints for achieving chemical evolution by natural selection in the lab.

Social evolution in multispecies biofilms

PubMed Central

Mitri, Sara; Xavier, João B.; Foster, Kevin R.

2011-01-01

Microbial ecology is revealing the vast diversity of strains and species that coexist in many environments, ranging from free-living communities to the symbionts that compose the human microbiome. In parallel, there is growing evidence of the importance of cooperative phenotypes for the growth and behavior of microbial groups. Here we ask: How does the presence of multiple species affect the evolution of cooperative secretions? We use a computer simulation of spatially structured cellular groups that captures key features of their biology and physical environment. When nutrient competition is strong, we find that the addition of new species can inhibit cooperation by eradicating secreting strains before they can become established. When nutrients are abundant and many species mix in one environment, however, our model predicts that secretor strains of any one species will be surrounded by other species. This “social insulation” protects secretors from competition with nonsecretors of the same species and can improve the prospects of within-species cooperation. We also observe constraints on the evolution of mutualistic interactions among species, because it is difficult to find conditions that simultaneously favor both within- and among-species cooperation. Although relatively simple, our model reveals the richness of interactions between the ecology and social evolution of multispecies microbial groups, which can be critical for the evolution of cooperation. PMID:21690380

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model.

PubMed

Woltering, Joost M; Duboule, Denis

2015-11-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Insights into hominid evolution from the gorilla genome sequence

PubMed Central

Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Greg E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H.; Schwalie, Petra C.; Tang, Y. Amy; Ward, Michelle C.; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N.; Ayub, Qasim; Ball, Edward V.; Beal, Kathryn; Bradley, Brenda J.; Chen, Yuan; Clee, Chris M.; Fitzgerald, Stephen; Graves, Tina A.; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K.; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C.; Munch, Kasper; O’Connor, Timothy D.; Phillips, Andrew D.; Prado-Martinez, Javier; Rogers, Anthony S.; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T.; Stenson, Peter D.; Turner, Daniel J.; Vigilant, Linda; Vilella, Albert J.; Whitener, Weldon; Zhu, Baoli; Cooper, David N.; de Jong, Pieter; Dermitzakis, Emmanouil T.; Eichler, Evan E.; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I.; Ning, Zemin; Odom, Duncan T.; Ponting, Chris P.; Quail, Michael A.; Ryder, Oliver A.; Searle, Stephen M.; Warren, Wesley C.; Wilson, Richard K.; Schierup, Mikkel H.; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard

2012-01-01

Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. PMID:22398555

Parallel Tracks as Quasi-steady States for the Magnetic Boundary Layers in Neutron-star Low-mass X-Ray Binaries

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

Erkut, M. Hakan; Çatmabacak, Onur, E-mail: mherkut@gmail.com

The neutron stars in low-mass X-ray binaries (LMXBs) are usually thought to be weakly magnetized objects accreting matter from their low-mass companions in the form of a disk. Albeit weak compared to those in young neutron-star systems, the neutron-star magnetospheres in LMXBs can play an important role in determining the correlations between spectral and temporal properties. Parallel tracks appearing in the kilohertz (kHz) quasi-periodic oscillation (QPO) frequency versus X-ray flux plane can be used as a tool to study the magnetosphere–disk interaction in neutron-star LMXBs. For dynamically important weak fields, the formation of a non-Keplerian magnetic boundary layer at themore » innermost disk truncated near the surface of the neutron star is highly likely. Such a boundary region may harbor oscillatory modes of frequencies in the kHz range. We generate parallel tracks using the boundary region model of kHz QPOs. We also present the direct application of our model to the reproduction of the observed parallel tracks of individual sources such as 4U 1608–52, 4U 1636–53, and Aql X-1. We reveal how the radial width of the boundary layer must vary in the long-term flux evolution of each source to regenerate the parallel tracks. The run of the radial width looks similar for different sources and can be fitted by a generic model function describing the average steady behavior of the boundary region over the long term. The parallel tracks then correspond to the possible quasi-steady states the source can occupy around the average trend.« less

Bioinformatics algorithm based on a parallel implementation of a machine learning approach using transducers

NASA Astrophysics Data System (ADS)

Roche-Lima, Abiel; Thulasiram, Ruppa K.

2012-02-01

Finite automata, in which each transition is augmented with an output label in addition to the familiar input label, are considered finite-state transducers. Transducers have been used to analyze some fundamental issues in bioinformatics. Weighted finite-state transducers have been proposed to pairwise alignments of DNA and protein sequences; as well as to develop kernels for computational biology. Machine learning algorithms for conditional transducers have been implemented and used for DNA sequence analysis. Transducer learning algorithms are based on conditional probability computation. It is calculated by using techniques, such as pair-database creation, normalization (with Maximum-Likelihood normalization) and parameters optimization (with Expectation-Maximization - EM). These techniques are intrinsically costly for computation, even worse when are applied to bioinformatics, because the databases sizes are large. In this work, we describe a parallel implementation of an algorithm to learn conditional transducers using these techniques. The algorithm is oriented to bioinformatics applications, such as alignments, phylogenetic trees, and other genome evolution studies. Indeed, several experiences were developed using the parallel and sequential algorithm on Westgrid (specifically, on the Breeze cluster). As results, we obtain that our parallel algorithm is scalable, because execution times are reduced considerably when the data size parameter is increased. Another experience is developed by changing precision parameter. In this case, we obtain smaller execution times using the parallel algorithm. Finally, number of threads used to execute the parallel algorithm on the Breezy cluster is changed. In this last experience, we obtain as result that speedup is considerably increased when more threads are used; however there is a convergence for number of threads equal to or greater than 16.

Parallel Tracks as Quasi-steady States for the Magnetic Boundary Layers in Neutron-star Low-mass X-Ray Binaries

NASA Astrophysics Data System (ADS)

Erkut, M. Hakan; Çatmabacak, Onur

2017-11-01

The neutron stars in low-mass X-ray binaries (LMXBs) are usually thought to be weakly magnetized objects accreting matter from their low-mass companions in the form of a disk. Albeit weak compared to those in young neutron-star systems, the neutron-star magnetospheres in LMXBs can play an important role in determining the correlations between spectral and temporal properties. Parallel tracks appearing in the kilohertz (kHz) quasi-periodic oscillation (QPO) frequency versus X-ray flux plane can be used as a tool to study the magnetosphere-disk interaction in neutron-star LMXBs. For dynamically important weak fields, the formation of a non-Keplerian magnetic boundary layer at the innermost disk truncated near the surface of the neutron star is highly likely. Such a boundary region may harbor oscillatory modes of frequencies in the kHz range. We generate parallel tracks using the boundary region model of kHz QPOs. We also present the direct application of our model to the reproduction of the observed parallel tracks of individual sources such as 4U 1608-52, 4U 1636-53, and Aql X-1. We reveal how the radial width of the boundary layer must vary in the long-term flux evolution of each source to regenerate the parallel tracks. The run of the radial width looks similar for different sources and can be fitted by a generic model function describing the average steady behavior of the boundary region over the long term. The parallel tracks then correspond to the possible quasi-steady states the source can occupy around the average trend.

PARALLEL EVOLUTION OF QUASI-SEPARATRIX LAYERS AND ACTIVE REGION UPFLOWS

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

Mandrini, C. H.; Cristiani, G. D.; Nuevo, F. A.

2015-08-10

Persistent plasma upflows were observed with Hinode’s EUV Imaging Spectrometer (EIS) at the edges of active region (AR) 10978 as it crossed the solar disk. We analyze the evolution of the photospheric magnetic and velocity fields of the AR, model its coronal magnetic field, and compute the location of magnetic null-points and quasi-sepratrix layers (QSLs) searching for the origin of EIS upflows. Magnetic reconnection at the computed null points cannot explain all of the observed EIS upflow regions. However, EIS upflows and QSLs are found to evolve in parallel, both temporarily and spatially. Sections of two sets of QSLs, calledmore » outer and inner, are found associated to EIS upflow streams having different characteristics. The reconnection process in the outer QSLs is forced by a large-scale photospheric flow pattern, which is present in the AR for several days. We propose a scenario in which upflows are observed, provided that a large enough asymmetry in plasma pressure exists between the pre-reconnection loops and lasts as long as a photospheric forcing is at work. A similar mechanism operates in the inner QSLs; in this case, it is forced by the emergence and evolution of the bipoles between the two main AR polarities. Our findings provide strong support for the results from previous individual case studies investigating the role of magnetic reconnection at QSLs as the origin of the upflowing plasma. Furthermore, we propose that persistent reconnection along QSLs does not only drive the EIS upflows, but is also responsible for the continuous metric radio noise-storm observed in AR 10978 along its disk transit by the Nançay Radio Heliograph.« less

Grasping convergent evolution in syngnathids: a unique tale of tails.

PubMed

Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

2014-06-01

Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be concluded from this study. © 2014 Anatomical Society.

Grasping convergent evolution in syngnathids: a unique tale of tails

PubMed Central

Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

2014-01-01

Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be concluded from this study. PMID:24697519

Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors.

PubMed

Saber, Ali; Hiltermann, T Jeroen N; Kok, Klaas; Terpstra, M Martijn; de Lange, Kim; Timens, Wim; Groen, Harry J M; van den Berg, Anke

2017-02-01

Several studies have shown heterogeneity in lung cancer, with parallel existence of multiple subclones characterized by their own specific mutational landscape. The extent to which minor clones become dominant in distinct metastasis is not clear. The aim of our study was to gain insight in the evolution pattern of lung cancer by investigating genomic heterogeneity between primary tumor and its distant metastases. Whole exome sequencing (WES) was performed on 24 tumor and five normal samples of two small cell lung carcinoma (SCLC) and three non-SCLC (NSCLC) patients. Validation of somatic variants in these 24 and screening of 33 additional samples was done by single primer enrichment technology. For each of the three NSCLC patients, about half of the mutations were shared between all tumor samples, whereas for SCLC patients, this percentage was around 95. Independent validation of the non-ubiquitous mutations confirmed the WES data for the vast majority of the variants. Phylogenetic trees indicated more distance between the tumor samples of the NSCLC patients as compared to the SCLC patients. Analysis of 30 independent DNA samples of 16 biopsies used for WES revealed a low degree of intra-tumor heterogeneity of the selected sets of mutations. In the primary tumors of all five patients, variable percentages (19-67%) of the seemingly metastases-specific mutations were present albeit at low read frequencies. Patients with advanced NSCLC have a high percentage of non-ubiquitous mutations indicative of branched evolution. In contrast, the low degree of heterogeneity in SCLC suggests a parallel and linear model of evolution. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

PubMed

Miller, Christopher A; White, Brian S; Dees, Nathan D; Griffith, Malachi; Welch, John S; Griffith, Obi L; Vij, Ravi; Tomasson, Michael H; Graubert, Timothy A; Walter, Matthew J; Ellis, Matthew J; Schierding, William; DiPersio, John F; Ley, Timothy J; Mardis, Elaine R; Wilson, Richard K; Ding, Li

2014-08-01

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.

Environment determines evolutionary trajectory in a constrained phenotypic space

PubMed Central

Fraebel, David T; Mickalide, Harry; Schnitkey, Diane; Merritt, Jason; Kuhlman, Thomas E; Kuehn, Seppe

2017-01-01

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory. DOI: http://dx.doi.org/10.7554/eLife.24669.001 PMID:28346136

Niche construction, sources of selection and trait coevolution.

PubMed

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

Orthologs, paralogs and genome comparisons

NASA Technical Reports Server (NTRS)

Gogarten, J. P.; Olendzenski, L.

1999-01-01

During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.

Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards.

PubMed

Kamath, Ambika; Losos, Jonathan B

2017-03-01

Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the extent of habitat use specialization among individuals is comparable to the extent of specialization in the same traits among ten sympatric Anolis habitat specialist species in Cuba. However, the adaptive correlations between habitat use and morphology commonly seen across species of Anolis were not observed across individuals in the sampled population. Our results therefore suggest that while patterns of ecological specialization can transcend scale, these parallels are the consequence of distinct ecological processes acting at microevolutionary and macroevolutionary scales. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

PubMed Central

Dees, Nathan D.; Griffith, Malachi; Welch, John S.; Griffith, Obi L.; Vij, Ravi; Tomasson, Michael H.; Graubert, Timothy A.; Walter, Matthew J.; Ellis, Matthew J.; Schierding, William; DiPersio, John F.; Ley, Timothy J.; Mardis, Elaine R.; Wilson, Richard K.; Ding, Li

2014-01-01

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy. PMID:25102416

Creationism as a Misconception: Socio-cognitive conflict in the teaching of evolution

NASA Astrophysics Data System (ADS)

Foster, Colin

2012-09-01

This position paper argues that students' understanding and acceptance of evolution may be supported, rather than hindered, by classroom discussion of creationism. Parallels are drawn between creationism and other scientific misconceptions, both of the scientific community in the past and of students in the present. Science teachers frequently handle their students' misconceptions as they arise by offering appropriate socio-cognitive conflict, which highlights reasons to disbelieve one idea and to believe another. It is argued that this way of working, rather than outlawing discussion, is more scientific and more honest. Scientific truth does not win the day by attempting to deny its opponents a voice but by engaging them with evidence. Teachers can be confident that evolution has nothing to fear from a free and frank discussion in which claims can be rebutted with evidence. Such an approach is accessible to children of all ages and is ultimately more likely to drive out pre-scientific superstitions. It also models the scientific process more authentically and develops students' ability to think critically.

Evolving phenotypic networks in silico.

PubMed

François, Paul

2014-11-01

Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

Numerical Modeling of S-Wave Generation by Fracture Damage in Underground Nuclear Explosions

DTIC Science & Technology

2009-09-30

Element Package, ABAQUS. A user -defined subroutine , VUMAT, was written that incorporates the micro-mechanics based damage constitutive law described...dynamic damage evolution on the elastic and anelastic response. 2) whereas the Ashby/Sammis model was only applicable to the case where the initial cracks ...are all parallel and the same size, we can now include a specified distribution of initial crack sizes with random azimuthal orientation about the

The intercrater plains of Mercury and the Moon: Their nature, origin and role in terrestrial planet evolution. Crater statistical data. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Leake, M. A.

1982-01-01

The total number of craters within a bin of mean diameter, and the number of craters of each degradational type within that bin are tabulated. Rim-to-rim diameters were measured at arbitrary azimuths for rectified photos or photos taken at vertical incidence (most lunar photos), and at azimuths paralleling a local tangent to the limb for oblique images.

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

Coeval emplacement and orogen-parallel transport of gold in oblique convergent orogens

NASA Astrophysics Data System (ADS)

Upton, Phaedra; Craw, Dave

2016-12-01

Varying amounts of gold mineralisation is occurring in all young and active collisional mountain belts. Concurrently, these syn-orogenic hydrothermal deposits are being eroded and transported to form placer deposits. Local extension occurs in convergent orogens, especially oblique orogens, and facilitates emplacement of syn-orogenic gold-bearing deposits with or without associated magmatism. Numerical modelling has shown that extension results from directional variations in movement rates along the rock transport trajectory during convergence, and is most pronounced for highly oblique convergence with strong crustal rheology. On-going uplift during orogenesis exposes gold deposits to erosion, transport, and localised placer concentration. Drainage patterns in variably oblique convergent orogenic belts typically have an orogen-parallel or sub-parallel component; the details of which varies with convergence obliquity and the vagaries of underlying geological controls. This leads to lateral transport of eroded syn-orogenic gold on a range of scales, up to > 100 km. The presence of inherited crustal blocks with contrasting rheology in oblique orogenic collision zones can cause perturbations in drainage patterns, but numerical modelling suggests that orogen-parallel drainage is still a persistent and robust feature. The presence of an inherited block of weak crust enhances the orogen-parallel drainage by imposition of localised subsidence zones elongated along a plate boundary. Evolution and reorientation of orogen-parallel drainage can sever links between gold placer deposits and their syn-orogenic sources. Many of these modelled features of syn-orogenic gold emplacement and varying amounts of orogen-parallel detrital gold transport can be recognised in the Miocene to Recent New Zealand oblique convergent orogen. These processes contribute little gold to major placer goldfields, which require more long-term recycling and placer gold concentration. Most eroded syn-orogenic gold becomes diluted by abundant lithic debris in rivers and sedimentary basins except where localised concentration occurs, especially on beaches.

Evolution of a minimal parallel programming model

DOE PAGES

Lusk, Ewing; Butler, Ralph; Pieper, Steven C.

2017-04-30

Here, we take a historical approach to our presentation of self-scheduled task parallelism, a programming model with its origins in early irregular and nondeterministic computations encountered in automated theorem proving and logic programming. We show how an extremely simple task model has evolved into a system, asynchronous dynamic load balancing (ADLB), and a scalable implementation capable of supporting sophisticated applications on today’s (and tomorrow’s) largest supercomputers; and we illustrate the use of ADLB with a Green’s function Monte Carlo application, a modern, mature nuclear physics code in production use. Our lesson is that by surrendering a certain amount of generalitymore » and thus applicability, a minimal programming model (in terms of its basic concepts and the size of its application programmer interface) can achieve extreme scalability without introducing complexity.« less

Structure and function of SemiSWEET and SWEET sugar transporters.

PubMed

Feng, Liang; Frommer, Wolf B

2015-08-01

SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure-function relations in this new class of transporters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Longitudinal train dynamics: an overview

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin

2016-12-01

This paper discusses the evolution of longitudinal train dynamics (LTD) simulations, which covers numerical solvers, vehicle connection systems, air brake systems, wagon dumper systems and locomotives, resistance forces and gravitational components, vehicle in-train instabilities, and computing schemes. A number of potential research topics are suggested, such as modelling of friction, polymer, and transition characteristics for vehicle connection simulations, studies of wagon dumping operations, proper modelling of vehicle in-train instabilities, and computing schemes for LTD simulations. Evidence shows that LTD simulations have evolved with computing capabilities. Currently, advanced component models that directly describe the working principles of the operation of air brake systems, vehicle connection systems, and traction systems are available. Parallel computing is a good solution to combine and simulate all these advanced models. Parallel computing can also be used to conduct three-dimensional long train dynamics simulations.

Application of morphological synthesis for understanding electrode microstructure evolution as a function of applied charge/discharge cycles

DOE PAGES

Glazoff, Michael V.; Dufek, Eric J.; Shalashnikov, Egor V.

2016-09-15

Morphological analysis and synthesis operations were employed for analysis of electrode microstructure transformations and evolution accompanying the application of charge/discharge cycles to electrochemical storage systems (batteries). Using state-of-the-art morphological algorithms, it was possible to predict microstructure evolution in porous Si electrodes for Li-ion batteries with sufficient accuracy. Algorithms for image analyses (segmentation, feature extraction, and 3D-reconstructions using 2D-images) were also developed. Altogether, these techniques could be considered supplementary to phase-field mesoscopic approach to microstructure evolution that is based upon clear and definitive changes in the appearance of microstructure. However, unlike in phase-field, the governing equations for morphological approach are geometry-,more » not physics-based. Similar non-physics based approach to understanding different phenomena was attempted with the introduction of cellular automata. It is anticipated that morphological synthesis and analysis will represent a useful supplementary tool to phase-field and will render assistance to unraveling the underlying microstructure-property relationships. The paper contains data on electrochemical characterization of different electrode materials that was conducted in parallel to morphological study.« less

Friction-induced nano-structural evolution of graphene as a lubrication additive

NASA Astrophysics Data System (ADS)

Zhao, Jun; Mao, Junyuan; Li, Yingru; He, Yongyong; Luo, Jianbin

2018-03-01

Graphene has attracted enormous attention in the field of lubrication based on its excellent physical and chemical properties. Although many studies have obtained thermally or chemically- exfoliated graphene and investigated their wide and important application, few studies have reported their physical nano-structural evolution under friction. In this study, we investigated the lubrication properties of graphene additives with different layer numbers and interlayer spacing by exfoliating. The additives with a higher degrees of exfoliation changed to ordering under friction, and had better lubrication properties, while that with a lower degrees exhibited obvious structural defects and high friction. Therefore, the original degrees of exfoliation plays a key role in the structural evolution of graphene and superior lubrication can be achieved through the physical nano-structure changing to ordering, even graphitization. Furthermore, the ordered tribofilm on the frictional interfaces was parallel to the sliding direction, meaning the highly exfoliated graphene indeed reaching slippage between its layers, which wasn't experimentally discovered in previous studies. This work provides a new understanding of the relationship between friction-induced nano-structural evolution and lubrication properties of graphene as a lubrication additive, and has great potential for the structural design of graphene as a lubrication additive.

Rapid biological speciation driven by tectonic evolution in New Zealand

NASA Astrophysics Data System (ADS)

Craw, Dave; Upton, Phaedra; Burridge, Christopher P.; Wallis, Graham P.; Waters, Jonathan M.

2016-02-01

Collisions between tectonic plates lead to the rise of new mountain ranges that can separate biological populations and ultimately result in new species. However, the identification of links between tectonic mountain-building and biological speciation is confounded by environmental and ecological factors. Thus, there are surprisingly few well-documented examples of direct tectonic controls on terrestrial biological speciation. Here we present examples from New Zealand, where the rapid evolution of 18 species of freshwater fishes has resulted from parallel tectonic landscape evolution. We use numerical models to reconstruct changes in the deep crustal structure and surface drainage catchments of the southern island of New Zealand over the past 25 million years. We show that the island and mountain topography evolved in six principal tectonic zones, which have distinct drainage catchments that separated fish populations. We use new and existing phylogenetic analyses of freshwater fish populations, based on over 1,000 specimens from more than 400 localities, to show that fish genomes can retain evidence of this tectonic landscape development, with a clear correlation between geologic age and extent of DNA sequence divergence. We conclude that landscape evolution has controlled on-going biological diversification over the past 25 million years.

A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.

PubMed

Wagner, Andreas

2014-07-07

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Evolution of speech and evolution of language.

PubMed

de Boer, Bart

2017-02-01

Speech is the physical signal used to convey spoken language. Because of its physical nature, speech is both easier to compare with other species' behaviors and easier to study in the fossil record than other aspects of language. Here I argue that convergent fossil evidence indicates adaptations for complex vocalizations at least as early as the common ancestor of Neanderthals and modern humans. Furthermore, I argue that it is unlikely that language evolved separately from speech, but rather that gesture, speech, and song coevolved to provide both a multimodal communication system and a musical system. Moreover, coevolution must also have played a role by allowing both cognitive and anatomical adaptations to language and speech to evolve in parallel. Although such a coevolutionary scenario is complex, it is entirely plausible from a biological point of view.

Social behavioural epistemology and the scientific community.

PubMed

Watve, Milind

2017-07-01

The progress of science is influenced substantially by social behaviour of and social interactions within the scientific community. Similar to innovations in primate groups, the social acceptance of an innovation depends not only upon the relevance of the innovation but also on the social dominance and connectedness of the innovator. There are a number of parallels between many well-known phenomena in behavioural evolution and various behavioural traits observed in the scientific community. It would be useful, therefore, to use principles of behavioural evolution as hypotheses to study the social behaviour of the scientific community. I argue in this paper that a systematic study of social behavioural epistemology is likely to boost the progress of science by addressing several prevalent biases and other problems in scientific communication and by facilitating appropriate acceptance/rejection of novel concepts.

Evolution of microstructure, strain and physical properties in oxide nanocomposite films

DOE PAGES

Chen, Aiping; Weigand, Marcus; Bi, Zhenxing; ...

2014-06-24

Using LSMO:ZnO nanocomposite films as a model system, we have researched the effect of film thickness on the physical properties of nanocomposites. It shows that strain, microstructure, as well as magnetoresistance strongly rely on film thickness. The magnetotransport properties have been fitted by a modified parallel connection channel model, which is in agreement with the microstructure evolution as a function of film thickness in nanocomposite films on sapphire substrates. The strain analysis indicates that the variation of physical properties in nanocomposite films on LAO is dominated by strain effect. These results confirm the critical role of film thickness on microstructures,more » strain states, and functionalities. Furthermore, it shows that one can use film thickness as a key parameter to design nanocomposites with optimum functionalities.« less

Plasma dynamics on current-carrying magnetic flux tubes

NASA Technical Reports Server (NTRS)

Swift, Daniel W.

1992-01-01

A 1D numerical simulation is used to investigate the evolution of a plasma in a current-carrying magnetic flux tube of variable cross section. A large potential difference, parallel to the magnetic field, is applied across the domain. The result is that density minimum tends to deepen, primarily in the cathode end, and the entire potential drop becomes concentrated across the region of density minimum. The evolution of the simulation shows some sensitivity to particle boundary conditions, but the simulations inevitably evolve into a final state with a nearly stationary double layer near the cathode end. The simulation results are at sufficient variance with observations that it appears unlikely that auroral electrons can be explained by a simple process of acceleration through a field-aligned potential drop.

Reduced swimming performance repeatedly evolves upon loss of migration in landlocked populations of Alewife

USGS Publications Warehouse

Velotta, Jonathan P.; McCormick, Stephen; Jones, Andrew W.; Schultz, Eric T.

2018-01-01

Whole-organism performance tasks are accomplished by the integration of morphological traits and physiological functions. Understanding how evolutionary change in morphology and physiology influences whole-organism performance will yield insight into the factors that shape its own evolution. We demonstrate that nonmigratory populations of alewife (Alosa pseudoharengus) have evolved reduced swimming performance in parallel, compared with their migratory ancestor. In contrast to theoretically and empirically based predictions, poor swimming among nonmigratory populations is unrelated to the evolution of osmoregulation and occurs despite the fact that nonmigratory alewives have a more fusiform (torpedo-like) body shape than their ancestor. Our results suggest that elimination of long-distance migration from the life cycle has shaped performance more than changes in body shape and physiological regulatory capacity.

Neuronal Control of Swimming Behavior: Comparison of Vertebrate and Invertebrate Model Systems

PubMed Central

Mullins, Olivia J.; Hackett, John T.; Buchanan, James T.; Friesen, W. Otto

2010-01-01

Swimming movements in the leech and lamprey are highly analogous, and lack homology. Thus, similarities in mechanisms must arise from convergent evolution rather than from common ancestry. Despite over forty years of parallel investigations into this annelid and primitive vertebrate, a close comparison of the approaches and results of this research is lacking. The present review evaluates the neural mechanisms underlying swimming in these two animals and describes the many similarities that provide intriguing examples of convergent evolution. Specifically, we discuss swim initiation, maintenance and termination, isolated nervous system preparations, neural-circuitry, central oscillators, intersegmental coupling, phase lags, cycle periods and sensory feedback. Comparative studies between species highlight mechanisms that optimize behavior and allow us a broader understanding of nervous system function. PMID:21093529

Spatial and temporal clonal evolution of intrahepatic cholangiocarcinoma.

PubMed

Dong, Liang-Qing; Shi, Yang; Ma, Li-Jie; Yang, Liu-Xiao; Wang, Xiao-Ying; Zhang, Shu; Wang, Zhi-Chao; Duan, Meng; Zhang, Zhao; Liu, Long-Zi; Zheng, Bo-Hao; Ding, Zhen-Bin; Ke, Ai-Wu; Gao, Da-Ming; Yuan, Ke; Zhou, Jian; Fan, Jia; Xi, Ruibin; Gao, Qiang

2018-07-01

Intrahepatic cholangiocarcinoma (ICC) is the second-most lethal primary liver cancer. Little is known about intratumoral heterogeneity (ITH) and its impact on ICC progression. We aimed to investigate the ITH of ICC in the hope of helping to develop new therapeutic strategies. We obtained 69 spatially distinct regions from six operable ICCs. Patient-derived primary cancer cells (PDPCs) were established for each region, followed by whole-exome sequencing (WES) and multi-level validation. We observed widespread ITH for both somatic mutations and clonal architecture, shaped by multiple mechanisms, like clonal "illusion", parallel evolution and chromosome instability. A median of 60.3% of mutations were heterogeneous, among which 85% of the driver mutations were located on the branches of tumor phylogenetic trees. Many truncal and clonal driver mutations occurred in tumor suppressor genes, such as TP53, SMARCB1 and PBRM1 that are involved in DNA repair and chromatin-remodeling. Genome doubling occurred in most cases (5/6) after the accumulation of truncal mutations and was shared by all intratumoral sub-regions. In all cases, ongoing chromosomal instability is evident throughout the evolutionary trajectory of ICC. The recurrence of ICC1239 provided evidence to support the polyclonal metastatic seeding in ICC. The change of mutation landscape and internal diversity among subclones during metastasis, such as the loss of chemoresistance mediator, can be used for new treatment strategies. Targeted therapy against truncal alterations, such as IDH1, JAK1, and KRAS mutations and EGFR amplification, was developed in 5/6 patients. Integrated investigations of spatial ITH and clonal evolution may provide an important molecular foundation for enhanced understanding of tumorigenesis and progression in ICC. We applied multiregional whole-exome sequencing to investigate the evolution of intrahepatic cholangiocarcinoma (ICC). The results revealed that many factors, such as parallel evolution and chromosome instability, may participate and promote the branch diversity of ICC. Interestingly, in one patient with primary and recurrent metastatic tumors, we found evidence of polyclonal metastatic seeding, indicating that symbiotic communities of multiple clones existed and were maintained during metastasis. More realistically, some truncal alterations, such as IDH1, JAK1, and KRAS mutations and EGFR amplification, could be promising treatment targets in patients with ICC. Copyright © 2018 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

New Insights From Whole Rock and Mineral Data on the Magmatic and Tectonic Evolution of the Columbia River Basalt Group (USA)

NASA Astrophysics Data System (ADS)

Caprarelli, G.; Reidel, S. P.

2004-12-01

The Miocene Columbia River Basalt Group (CRBG) of north-western USA was emplaced in a geologically dynamic setting characterized by a close association between magmatism and lithospheric thinning and rifting. We present and discuss electron probe microanalysis and XRFA data obtained from samples spanning the entire sequence of the CRBG. The examined basalts have near-aphyric textures. No glass is present, and plagioclase and augitic clinopyroxene are dominant matrix and groundmass phases. Plagioclase microcrysts are labradoritic to bytownitic. Whole rock compositions were taken as proxies of the liquid compositions. Application of plagioclase / melt and clinopyroxene / melt geothermobarometers indicated that during crustal ascent the magmas were dry, and that pre-eruptive pressures and temperatures ranged from 0 to 0.66 GPa and 1393 to 1495 K, respectively. In a P-T diagram most of the samples are distributed along a general CRBG trend, while some samples plot along a parallel higher temperature trend. The calculated P-T values, the positive correlation between calculated P and T, and no horizontal alignment of the data, exclude the presence of upper crustal solidification fronts, and indicate that magma aggregation zones were located deeper than 25 km, plausibly immediately below the Moho, that in this region is at a depth of approximately 35 km. Episodic stretching of the lithosphere best explains the observed parallel P-T trends. Whole rock major element abundances resulted from fractional crystallization of the magmas during ascent. To retrieve the compositions of the primitive melts we added to the bulk rock compositions variable amounts of magnesian olivine [Mg/(Mg+Fe) = 0.88], and derived the evolution of olivine fractionating magmas in equilibrium with mantle harzburgite. Two groups of samples were found, corresponding to the parallel P-T trends obtained from mineral / melt calculations. The highest temperature trend corresponds to samples whose calculated primitive compositions are in agreement with those obtained from peridotite melting experiments (as published in the relevant literature). Interpretation of results for rocks belonging to the general CRBG trend suggests, either: (a) that higher forsteritic content olivine should be used in the calculations; or, (b) that melt / ol / opx reactions occurred. Investigation of the CRBG primitive compositions has relevance with regard to the geodynamic evolution models of this region. We are currently undertaking melt inclusion studies of suitable CRBG samples.

The evolution of slip surface roughness during earthquake propagation in carbonate faults

NASA Astrophysics Data System (ADS)

Zhu, B.; De Paola, N.; Llewellin, E. W.; Holdsworth, R.

2014-12-01

Slip surface roughness is understood to control the dynamics of earthquake propagation. Quantifying the micro- and nano-scale roughness of slip surfaces can give insight into the grain-scale processes controlling the strength of faults during earthquake propagation. Friction experiments were performed on fine-grained calcite gouges, at speed 1 ms-1, normal stress 18 MPa, displacements 0.009-1.46 m, and room temperature and humidity. Results show a two stage-evolution (S1-2) of the fault strength, with an initial increase up to peak value 0.82 (S1), followed by a sudden decrease to a low, steady-state value 0.18 (S2). Samples retrieved at the end of S1 show the development of a cohesive slip zone (SZ), made of micron-scale, angular clasts formed by brittle fracturing and cataclasis. The SZ of samples deformed up to S2, is composed of nanograin aggregates which exhibit polygonal grain boundaries indicating high temperature grain boundary sliding creep deformation. In both cases, the SZ is bounded by a sharply defined slip surface. The 3-D geometry of seven experimental slip surfaces (40μm×40μm) has been reconstructed by digital processing of sets of 1800 images of SZ cross sections acquired at 20 nm intervals perpendicular to the slip direction, using a slicing (Focussed Ion Beam) and viewing (Field Emission Scanning Electron Microscope) technique. Spectrum power density analyses show that nano- and micron-scale slip surface roughness is anisotropic for both S1 and S2 slip surfaces. At the nano- and micron-scale, root mean square values decrease with length for S1 slip surfaces, but only slightly for S2 surfaces, and are anisotropic in the slip-normal and slip-parallel directions. The anisotropy is reduced at the nano-scale, although S2 slip surfaces are still smoother parallel to slip than normal to slip. Hurst exponents vary through scales, and are anisotropic in the directions parallel and normal to slip. Variable Hurst exponents indicate that slip surface roughness is scale-dependent with anisotropic, not self-affine behaviour at the micro/nano-scale, in contrast to the self-affine behaviour inferred at the mm to km scales. Dynamic weakening and creep deformation, observed during S2, coincide with an evolution towards less anisotropic and scale-dependent slip surface roughness at the nanoscale.

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

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

Moreland, Kenneth; Geveci, Berk

2014-11-01

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipelinemore » model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.« less

Task-switching costs promote the evolution of division of labor and shifts in individuality

PubMed Central

Goldsby, Heather J.; Dornhaus, Anna; Kerr, Benjamin; Ofria, Charles

2012-01-01

From microbes to humans, the success of many organisms is achieved by dividing tasks among specialized group members. The evolution of such division of labor strategies is an important aspect of the major transitions in evolution. As such, identifying specific evolutionary pressures that give rise to group-level division of labor has become a topic of major interest among biologists. To overcome the challenges associated with studying this topic in natural systems, we use actively evolving populations of digital organisms, which provide a unique perspective on the de novo evolution of division of labor in an open-ended system. We provide experimental results that address a fundamental question regarding these selective pressures: Does the ability to improve group efficiency through the reduction of task-switching costs promote the evolution of division of labor? Our results demonstrate that as task-switching costs rise, groups increasingly evolve division of labor strategies. We analyze the mechanisms by which organisms coordinate their roles and discover strategies with striking biological parallels, including communication, spatial patterning, and task-partitioning behaviors. In many cases, under high task-switching costs, individuals cease to be able to perform tasks in isolation, instead requiring the context of other group members. The simultaneous loss of functionality at a lower level and emergence of new functionality at a higher level indicates that task-switching costs may drive both the evolution of division of labor and also the loss of lower-level autonomy, which are both key components of major transitions in evolution. PMID:22872867

Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli.

PubMed

Alvarez-Ponce, David; Sabater-Muñoz, Beatriz; Toft, Christina; Ruiz-González, Mario X; Fares, Mario A

2016-09-26

The Neutral Theory of Molecular Evolution is considered the most powerful theory to understand the evolutionary behavior of proteins. One of the main predictions of this theory is that essential proteins should evolve slower than dispensable ones owing to increased selective constraints. Comparison of genomes of different species, however, has revealed only small differences between the rates of evolution of essential and nonessential proteins. In some analyses, these differences vanish once confounding factors are controlled for, whereas in other cases essentiality seems to have an independent, albeit small, effect. It has been argued that comparing relatively distant genomes may entail a number of limitations. For instance, many of the genes that are dispensable in controlled lab conditions may be essential in some of the conditions faced in nature. Moreover, essentiality can change during evolution, and rates of protein evolution are simultaneously shaped by a variety of factors, whose individual effects are difficult to isolate. Here, we conducted two parallel mutation accumulation experiments in Escherichia coli, during 5,500-5,750 generations, and compared the genomes at different points of the experiments. Our approach (a short-term experiment, under highly controlled conditions) enabled us to overcome many of the limitations of previous studies. We observed that essential proteins evolved substantially slower than nonessential ones during our experiments. Strikingly, rates of protein evolution were only moderately affected by expression level and protein length. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

The effect of electrodes on 11 acene molecular spin valve: Semi-empirical study

NASA Astrophysics Data System (ADS)

Aadhityan, A.; Preferencial Kala, C.; John Thiruvadigal, D.

2017-10-01

A new revolution in electronics is molecular spintronics, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. The key point is the creation of molecular spin valve which consists of a diamagnetic molecule in between two magnetic leads. In this paper, non-equilibrium Green's function (NEGF) combined with Extended Huckel Theory (EHT); a semi-empirical approach is used to analyse the electron transport characteristics of 11 acene molecular spin valve. We examine the spin-dependence transport on 11 acene molecular junction with various semi-infinite electrodes as Iron, Cobalt and Nickel. To analyse the spin-dependence transport properties the left and right electrodes are joined to the central region in parallel and anti-parallel configurations. We computed spin polarised device density of states, projected device density of states of carbon and the electrode element, and transmission of these devices. The results demonstrate that the effect of electrodes modifying the spin-dependence behaviours of these systems in a controlled way. In Parallel and anti-parallel configuration the separation of spin up and spin down is lager in the case of iron electrode than nickel and cobalt electrodes. It shows that iron is the best electrode for 11 acene spin valve device. Our theoretical results are reasonably impressive and trigger our motivation for comprehending the transport properties of these molecular-sized contacts.

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

PubMed

Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

2015-09-17

Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively little attention; however, our results suggest that it may be an important mechanism that predicts evolutionary responses to new environments.

The Role of Environmental Shear and Thermodynamic Conditions in Determining the Structure and Evolution of Mesoscale Convective Systems during TOGA COARE.

NASA Astrophysics Data System (ADS)

Lemone, Margaret A.; Zipser, Edward J.; Trier, Stanley B.

1998-12-01

A collection of case studies is used to elucidate the influence of environmental soundings on the structure and evolution of the convection in the mesoscale convective systems sampled by the turboprop aircraft in the Tropical Ocean Global Atmosphere (TOGA) Coupled Ocean-Atmosphere Response Experiment (COARE). The soundings were constructed primarily from aircraft data below 5-6 km and primarily from radiosonde data at higher altitudes.The well-documented role of the vertical shear of the horizontal wind in determining the mesoscale structure of tropical convection is confirmed and extended. As noted by earlier investigators, nearly all convective bands occurring in environments with appreciable shear below a low-level wind maximum are oriented nearly normal to the shear beneath the wind maximum and propagate in the direction of the low-level shear at a speed close to the wind maximum; when there is appreciable shear at middle levels (800-400 mb), convective bands form parallel to the shear. With appreciable shear at both levels, the lower-level shear determines the orientation of the primary convective bands. If the midlevel shear is opposite the low-level shear, secondary bands parallel to the midlevel shear will extend rearward from the primary band in later stages of its evolution; if the midlevel shear is 90 degrees to the low-level shear, the primary band will retain its two-dimensional mesoscale structure. Convection has no obvious mesoscale organization on days with little shear or days with widespread convection.Environmental temperatures and humidities have no obvious effect on the mesoscale convective pattern, but they affect COARE convection in other ways. The high tops of COARE convection are related to high parcel equilibrium levels, which approach 100 mb in some cases. Convective available potential energies are larger than those in the GARP (Global Atmospheric Research Program) Atlantic Tropical Experiment (GATE) mainly because of the higher equilibrium levels. The buoyancy integrated over the lowest 500 mb is similar for the two experiments. Convective inihibitions are small, enabling convection to propagate with only weak forcing. Comparison of slow-moving shear-parallel bands in COARE and GATE suggests that lower relative humidities between the top of the mixed layer and 500 mb can shorten their lifetimes significantly.COARE mesoscale organization and evolution differs from what was observed in GATE. Less-organized convection is more common in COARE. Of the convective bands observed, a greater fraction in COARE are faster-moving, shear-perpendicular squall lines. GATE slow-moving lines tend to be longer lived than those for COARE. The differences are probably traceable to differences in environmental shear and relative humidity, respectively.

Development of a parallel FE simulator for modeling the whole trans-scale failure process of rock from meso- to engineering-scale

NASA Astrophysics Data System (ADS)

Li, Gen; Tang, Chun-An; Liang, Zheng-Zhao

2017-01-01

Multi-scale high-resolution modeling of rock failure process is a powerful means in modern rock mechanics studies to reveal the complex failure mechanism and to evaluate engineering risks. However, multi-scale continuous modeling of rock, from deformation, damage to failure, has raised high requirements on the design, implementation scheme and computation capacity of the numerical software system. This study is aimed at developing the parallel finite element procedure, a parallel rock failure process analysis (RFPA) simulator that is capable of modeling the whole trans-scale failure process of rock. Based on the statistical meso-damage mechanical method, the RFPA simulator is able to construct heterogeneous rock models with multiple mechanical properties, deal with and represent the trans-scale propagation of cracks, in which the stress and strain fields are solved for the damage evolution analysis of representative volume element by the parallel finite element method (FEM) solver. This paper describes the theoretical basis of the approach and provides the details of the parallel implementation on a Windows - Linux interactive platform. A numerical model is built to test the parallel performance of FEM solver. Numerical simulations are then carried out on a laboratory-scale uniaxial compression test, and field-scale net fracture spacing and engineering-scale rock slope examples, respectively. The simulation results indicate that relatively high speedup and computation efficiency can be achieved by the parallel FEM solver with a reasonable boot process. In laboratory-scale simulation, the well-known physical phenomena, such as the macroscopic fracture pattern and stress-strain responses, can be reproduced. In field-scale simulation, the formation process of net fracture spacing from initiation, propagation to saturation can be revealed completely. In engineering-scale simulation, the whole progressive failure process of the rock slope can be well modeled. It is shown that the parallel FE simulator developed in this study is an efficient tool for modeling the whole trans-scale failure process of rock from meso- to engineering-scale.

Programming cells by multiplex genome engineering and accelerated evolution.

PubMed

Wang, Harris H; Isaacs, Farren J; Carr, Peter A; Sun, Zachary Z; Xu, George; Forest, Craig R; Church, George M

2009-08-13

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems

PubMed Central

Yoshida, M. A.; Ogura, A.; Ikeo, K.; Shigeno, S.; Moritaki, T.; Winters, G. C.; Kohn, A. B.; Moroz, L. L.

2015-01-01

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called “evolutionary tinkering” or “co-option”, and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the “camera” eye from nautilus’ “pinhole” eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids’ opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. PMID:26002349

Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli

PubMed Central

Alvarez-Ponce, David; Sabater-Muñoz, Beatriz; Toft, Christina; Ruiz-González, Mario X.; Fares, Mario A.

2016-01-01

Abstract The Neutral Theory of Molecular Evolution is considered the most powerful theory to understand the evolutionary behavior of proteins. One of the main predictions of this theory is that essential proteins should evolve slower than dispensable ones owing to increased selective constraints. Comparison of genomes of different species, however, has revealed only small differences between the rates of evolution of essential and nonessential proteins. In some analyses, these differences vanish once confounding factors are controlled for, whereas in other cases essentiality seems to have an independent, albeit small, effect. It has been argued that comparing relatively distant genomes may entail a number of limitations. For instance, many of the genes that are dispensable in controlled lab conditions may be essential in some of the conditions faced in nature. Moreover, essentiality can change during evolution, and rates of protein evolution are simultaneously shaped by a variety of factors, whose individual effects are difficult to isolate. Here, we conducted two parallel mutation accumulation experiments in Escherichia coli, during 5,500–5,750 generations, and compared the genomes at different points of the experiments. Our approach (a short-term experiment, under highly controlled conditions) enabled us to overcome many of the limitations of previous studies. We observed that essential proteins evolved substantially slower than nonessential ones during our experiments. Strikingly, rates of protein evolution were only moderately affected by expression level and protein length. PMID:27566759

Roles of density-dependent growth and life history evolution in accounting for fisheries-induced trait changes.

PubMed

Eikeset, Anne Maria; Dunlop, Erin S; Heino, Mikko; Storvik, Geir; Stenseth, Nils C; Dieckmann, Ulf

2016-12-27

The relative roles of density dependence and life history evolution in contributing to rapid fisheries-induced trait changes remain debated. In the 1930s, northeast Arctic cod (Gadus morhua), currently the world's largest cod stock, experienced a shift from a traditional spawning-ground fishery to an industrial trawl fishery with elevated exploitation in the stock's feeding grounds. Since then, age and length at maturation have declined dramatically, a trend paralleled in other exploited stocks worldwide. These trends can be explained by demographic truncation of the population's age structure, phenotypic plasticity in maturation arising through density-dependent growth, fisheries-induced evolution favoring faster-growing or earlier-maturing fish, or a combination of these processes. Here, we use a multitrait eco-evolutionary model to assess the capacity of these processes to reproduce 74 y of historical data on age and length at maturation in northeast Arctic cod, while mimicking the stock's historical harvesting regime. Our results show that model predictions critically depend on the assumed density dependence of growth: when this is weak, life history evolution might be necessary to prevent stock collapse, whereas when a stronger density dependence estimated from recent data is used, the role of evolution in explaining fisheries-induced trait changes is diminished. Our integrative analysis of density-dependent growth, multitrait evolution, and stock-specific time series data underscores the importance of jointly considering evolutionary and ecological processes, enabling a more comprehensive perspective on empirically observed stock dynamics than previous studies could provide.

Not different, Just Better: The Adaptive Evolution of an Enzyme

DTIC Science & Technology

2015-12-20

ELEMENT NUMBER 5b. GRANT NUMBER 5a. CONTRACT NUMBER Form Approved OMB NO. 0704-0188 3 . DATES COVERED (From - To) - UU UU UU UU 20-12-2015 1-Oct-2011 30...is precisely regulated by allostery and the adaptation of allostery is unknown, and 3 ) multiple experiments by others have demonstrated that adaptive...mutations in the same gene, but replicate populations, functionally parallel? • Aim 3 ) Expression, purification and functional analysis of evolved pyruvate

A Collection of Technical Studies Completed for the Computer-Aided Acquisition and Logistic Support (CALS) Program Fiscal Year 1988. Volume 2. Graphics, CGM MIL SPEC

DTIC Science & Technology

1991-03-01

test cases are gathered, studied, and evaluated; industry and other national European programs are studied; and experience is gained. This evolution ...application callable layer. The CGM Generator can be used to record device-independent picture descriptions. conceptually in parallel with the...contributors: I Organization Peter R. Bono Associates, Inc. Secretarial Support Susan Bonde , Diane Bono, E!aine Bono, Brenda Carson, Gillian Hall

Protocol Interoperability Between DDN and ISO (Defense Data Network and International Organization for Standardization) Protocols

DTIC Science & Technology

1988-08-01

Interconnection (OSI) in years. It is felt even more urgent in the past few years, with the rapid evolution of communication technologies and the...services and protocols above the transport layer are usually implemented as user- callable utilities on the host computers, it is desirable to offer them...Networks, Prentice-hall, New Jersey, 1987 [ BOND 87] Bond , John, "Parallel-Processing Concepts Finally Come together in Real Systems", Computer Design

Evolutionary Genetics of Hypoxia Tolerance in Cetaceans during Diving

PubMed Central

Tian, Ran; Wang, Zhengfei; Niu, Xu; Zhou, Kaiya; Xu, Shixia; Yang, Guang

2016-01-01

Hypoxia was a major challenge faced by cetaceans during the course of secondary aquatic adaptation. Although physiological traits of hypoxia tolerance in cetaceans have been well characterized, the underlying molecular mechanisms remain unknown. We investigated the sequences of 17 hypoxia-tolerance-related genes in representative cetaceans to provide a comprehensive insight into the genetic basis of hypoxia tolerance in these animals. Genes involved in carrying and transporting oxygen in the blood and muscle (hemoglobin-α and β, myoglobin), and genes involved in the regulation of vasoconstriction (endothelin-1, -2, and -3; endothelin receptor type A and B; adrenergic receptor α-1D; and arginine vasopressin) appear to have undergone adaptive evolution, evidence for positive selection on their particular sites, and radical physiochemical property changes of selected condons. Interestingly, “long-diving” cetaceans had relatively higher ω (dN/dS) values than “short-diving” cetaceans for the hemoglobin β gene, indicating divergent selective pressure presented in cetacean lineages with different diving abilities. Additionally, parallel positive selection or amino acid changes (ADRA1D: P50A, A53G, AVPR1B: I/V270T) among animals exposed to different hypoxia habitats reflect functional convergence or similar genetic mechanisms of hypoxia tolerance. In summary, positive selection, divergent selective pressures, and parallel evolution at the molecular level provided some new insights into the genetic adaptation of hypoxia tolerance. PMID:26912402

SAChES: Scalable Adaptive Chain-Ensemble Sampling.

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

Swiler, Laura Painton; Ray, Jaideep; Ebeida, Mohamed Salah

We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the usemore » of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.« less

Spatial evolution of Zagros collision zone in Kurdistan - NW Iran, constraints for Arabia-Eurasia oblique convergence

NASA Astrophysics Data System (ADS)

Sadeghi, S.; Yassaghi, A.

2015-09-01

Stratigraphy, detailed structural mapping and crustal scale cross section of the NW Zagros collision zone evolved during convergence of the Arabian and Eurasian plates were conducted to constrain the spatial evolution of the belt oblique convergence since Late Cretaceous. Zagros orogeny in NW Iran consists of the Sanandaj-Sirjan, Gaveh Rud and ophiolite zones as internal, and Bisotoun, Radiolarite and High Zagros zones as external parts. The Main Zagros Thrust is known as major structures of the Zagros suture zone. Two stages of deformation are recognized in the external parts of Zagros. In the early stage, presence of dextrally deformed domains beside the reversely deformed domains in the Radiolarite zone as well as dextral-reverse faults in both Bisotoun and Radiolarite zones demonstrates partitioning of the dextral transpression. In the late stage, southeastward propagation of the Zagros orogeny towards its foreland resulted in synchronous development of orogen-parallel strike-slip and pure thrust faults. It is proposed that the first stage related to the late Cretaceous oblique obduction, and the second stage is resulted from Cenozoic collision. Cenozoic orogen-parallel strike-slip component of Zagros oblique faulting is not confined to the Zagros suture zone (Main Recent) but also occurred in the more external part (Marekhil-Ravansar fault system). Thus, it is proposed that oblique convergence of Arabia-Eurasia plates occurred in Zagros collision zone since the Late Cretaceous.

Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron.

PubMed

Sohm, Jill A; Ahlgren, Nathan A; Thomson, Zachary J; Williams, Cheryl; Moffett, James W; Saito, Mak A; Webb, Eric A; Rocap, Gabrielle

2016-02-01

Marine picocyanobacteria, comprised of the genera Synechococcus and Prochlorococcus, are the most abundant and widespread primary producers in the ocean. More than 20 genetically distinct clades of marine Synechococcus have been identified, but their physiology and biogeography are not as thoroughly characterized as those of Prochlorococcus. Using clade-specific qPCR primers, we measured the abundance of 10 Synechococcus clades at 92 locations in surface waters of the Atlantic and Pacific Oceans. We found that Synechococcus partition the ocean into four distinct regimes distinguished by temperature, macronutrients and iron availability. Clades I and IV were prevalent in colder, mesotrophic waters; clades II, III and X dominated in the warm, oligotrophic open ocean; clades CRD1 and CRD2 were restricted to sites with low iron availability; and clades XV and XVI were only found in transitional waters at the edges of the other biomes. Overall, clade II was the most ubiquitous clade investigated and was the dominant clade in the largest biome, the oligotrophic open ocean. Co-occurring clades that occupy the same regime belong to distinct evolutionary lineages within Synechococcus, indicating that multiple ecotypes have evolved independently to occupy similar niches and represent examples of parallel evolution. We speculate that parallel evolution of ecotypes may be a common feature of diverse marine microbial communities that contributes to functional redundancy and the potential for resiliency.

Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron

PubMed Central

Sohm, Jill A; Ahlgren, Nathan A; Thomson, Zachary J; Williams, Cheryl; Moffett, James W; Saito, Mak A; Webb, Eric A; Rocap, Gabrielle

2016-01-01

Marine picocyanobacteria, comprised of the genera Synechococcus and Prochlorococcus, are the most abundant and widespread primary producers in the ocean. More than 20 genetically distinct clades of marine Synechococcus have been identified, but their physiology and biogeography are not as thoroughly characterized as those of Prochlorococcus. Using clade-specific qPCR primers, we measured the abundance of 10 Synechococcus clades at 92 locations in surface waters of the Atlantic and Pacific Oceans. We found that Synechococcus partition the ocean into four distinct regimes distinguished by temperature, macronutrients and iron availability. Clades I and IV were prevalent in colder, mesotrophic waters; clades II, III and X dominated in the warm, oligotrophic open ocean; clades CRD1 and CRD2 were restricted to sites with low iron availability; and clades XV and XVI were only found in transitional waters at the edges of the other biomes. Overall, clade II was the most ubiquitous clade investigated and was the dominant clade in the largest biome, the oligotrophic open ocean. Co-occurring clades that occupy the same regime belong to distinct evolutionary lineages within Synechococcus, indicating that multiple ecotypes have evolved independently to occupy similar niches and represent examples of parallel evolution. We speculate that parallel evolution of ecotypes may be a common feature of diverse marine microbial communities that contributes to functional redundancy and the potential for resiliency. PMID:26208139

A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry

PubMed Central

Salas-Gismondi, Rodolfo; Flynn, John J.; Baby, Patrice; Tejada-Lara, Julia V.; Claude, Julien; Antoine, Pierre-Olivier

2016-01-01

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region. PMID:27097031

Adaptive dynamics of cuticular hydrocarbons in Drosophila

PubMed Central

Rajpurohit, Subhash; Hanus, Robert; Vrkoslav, Vladimír; Behrman, Emily L.; Bergland, Alan O.; Petrov, Dmitri; Cvačka, Josef; Schmidt, Paul S.

2016-01-01

Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore, we also characterized spatial and temporal change in allele frequencies for SNPs in genes that are associated with the production and chemical profile of CHCs. Our data demonstrate a striking degree of parallelism for clinal and seasonal variation in CHCs in this taxon; CHC profiles also demonstrate significant plasticity in response to rearing temperature, and the observed patterns of plasticity parallel the spatiotemporal patterns observed in nature. We find that these congruent shifts in CHC profiles across time and space are also mirrored by predictable shifts in allele frequencies at SNPs associated with CHC chain length. Finally, we observed rapid and predictable evolution of CHC profiles in experimental mesocosms in the field. Together, these data strongly suggest that CHC profiles respond rapidly and adaptively to environmental parameters that covary with latitude and season, and that this response reflects the process of local adaptation in natural populations of D. melanogaster. PMID:27718537

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

PubMed Central

Elmer, Kathryn R.; Kusche, Henrik; Lehtonen, Topi K.; Meyer, Axel

2010-01-01

The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection. PMID:20439280

The formation mechanism and evolution of ps-laser-induced high-spatial-frequency periodic surface structures on titanium

NASA Astrophysics Data System (ADS)

Pan, A. F.; Wang, W. J.; Mei, X. S.; Yang, H. Z.; Sun, X. F.

2017-01-01

We report the formation and evolution mechanisms of HSFLs (high-spatial-frequency laser-induced periodic surface structures) on the commercial pure titanium under 10-ps 532-nm-wavelength laser irradiation. At a lower peak laser fluence, HSFLs in the rough zone are first formed along the surface texture. Subsequently, HSFLs in the flat zone are formed with an orientation parallel to the laser polarization direction. The formation of HSFLs can be attributed to the parallel orientation of the initial periodic modulation of the electron plasma concentration to the laser polarization direction. In particular, the formation of HSFLs along the surface texture occurs because the absorbed laser energy density is along the surface texture. At a higher peak laser fluence, two types of HSFLs appear together with LSFLs. The first type involves HSFLs that initially cover the concave part of the LSFL (low-spatial-frequency laser-induced periodic surface structures) and penetrate inward as the number of spot overlaps increases. This formation mechanism can be attributed to cavitation instability. The second type involves HSFLs that are initially in the convex part of the LSFL, and they are transformed into oxidized nanodots as the number of spot overlaps increases. The oxidized nanodots increase the absorption of laser energy in titanium, which leads to the ablation and removal of the oxidized material. Therefore, the surface of the LSFL becomes smooth.

Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

PubMed Central

Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

2003-01-01

We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

Effect of Gold on the Microstructural Evolution and Integrity of a Sintered Silver Joint

DOE PAGES

Muralidharan, Govindarajan; Leonard, Donovan N.; Meyer, Harry M.

2017-01-05

There is a need for next-generation, high-performance power electronic packages and systems employing wide band gap devices to operate at high temperatures in automotive and electric grid applications. Sintered silver joints are currently being evaluated as an alternative to Pb-free solder joints. Of particular interest is the development of joints based on silver paste consisting of nanoscale or micron scale particles that can be processed without the application of an external pressure. Microstructural evolution at the interface of a pressureless sintered silver joint formed between a SiC die with a Ti/Ni/Au metallization and an Active Metal Brazed substrate with Agmore » metallization at 250 °C was evaluated using Scanning Electron Microscopy, X-ray microanalysis, and X-ray Photo Electron Spectroscopy. Results from Focused Ion Beam cross-sections show that during sintering, the pores in the sintered region close to the Au layer tend to be smaller and are oriented predominantly with their longer dimension oriented parallel to the interface. With further densification, this results in the alignment of small pores parallel to the interface, creating a path for easy crack propagation. Lastly, X-ray microchemical analyses results confirm interdiffusion between Au and Ag and that a region with poor mechanical strength is formed at the edge of this region of interdiffusion.« less

A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry.

PubMed

Salas-Gismondi, Rodolfo; Flynn, John J; Baby, Patrice; Tejada-Lara, Julia V; Claude, Julien; Antoine, Pierre-Olivier

2016-01-01

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region.

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

PubMed Central

2015-01-01

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses. PMID:26683838

Evolution and hydration of the Juan de Fuca crust and uppermost mantle: a plate-scale seismic investigation from ridge to trench

NASA Astrophysics Data System (ADS)

Carbotte, S. M.; Canales, J.; Carton, H. D.; Nedimovic, M. R.; Han, S.; Marjanovic, M.; Gibson, J. C.; Janiszewski, H. A.; Horning, G.; Delescluse, M.; Watremez, L.; Farkas, A.; Biescas Gorriz, B.; Bornstein, G.; Childress, L. B.; Parker, B.

2012-12-01

The evolution of oceanic lithosphere involves incorporation of water into the physical and chemical structure of the crust and shallow mantle through fluid circulation, which initiates at the mid-ocean ridge and continues on the ridge flanks long after crustal formation. At subduction zones, water stored and transported with the descending plate is gradually released at depth, strongly influencing subduction zone processes. Cascadia is a young-lithosphere end member of the global subduction system where relatively little hydration of the downgoing Juan de Fuca (JdF) plate is expected due to its young age and presumed warm thermal state. However, numerous observations support the abundant presence of water within the subduction zone, suggesting that the JdF plate is significantly hydrated prior to subduction. Knowledge of the state of hydration of the JdF plate is limited, with few constraints on crustal and upper mantle structure. During the Cascadia Ridge-to-Trench experiment conducted in June-July 2012 over 4000 km of active source seismic data were acquired as part of a study of the evolution and state of hydration of the crust and shallow mantle of the JdF plate prior to subduction at the Cascadia margin. Coincident long-streamer (8 km) multi-channel seismic (MCS) and wide-angle ocean bottom seismometer (OBS) data were acquired in a two-ship program with the R/V Langseth (MGL1211), and R/V Oceanus (OC1206A). Our survey included two ridge-perpendicular transects across the full width of the JdF plate, a long trench-parallel line ~10 km seaward of the Cascadia deformation front, as well as three fan lines to study mantle anisotropy. The plate transects were chosen to provide reference sections of JdF plate evolution over the maximum range of JdF plate ages (8-9 Ma), offshore two contrasting regions of the Cascadia Subduction zone, and provide the first continuous ridge-to-trench images acquired at any oceanic plate. The trench-parallel line was designed to characterize variations in plate structure and hydration linked to JdF plate segmentation for over 450 km along the margin. Shipboard brute stacks of the MCS data reveal evidence for reactivation of abyssal hill faulting in the plate interior far from the trench. Ridgeward-dipping lower crustal reflectors are observed, similar to those observed in mature Pacific crust elsewhere, as well as conjugate reflectivity near the deformation front along the Oregon transect. Bright intracrustal reflectivity is also observed along the trench-parallel transect with marked changes in reflectivity along the Oregon and Washington margins. Initial inspection of the OBS record sections indicate good quality data with the expected oceanic crustal and upper mantle P-wave arrivals: Ps and Pg refractions through sedimentary and igneous layers, respectively, PmP wide-angle reflections from the crust-mantle transition zone, and Pn upper mantle refractions. The Pg-PmP-Pn triplication is typically observed at 40-50 km source-receiver offsets. Pn characteristics show evidence for upper mantle azimuthal anisotropic propagation: along the plate transects Pn is typically weaker and difficult to observe beyond ~80 km offsets, while along the trench-parallel transect Pn arrivals have higher amplitude and are easily observed up to source-receiver offsets of 160-180 km. An overview on the Cascadia Ridge to Trench data acquisition program and preliminary results will be presented.

Alignment between Protostellar Outflows and Filamentary Structure

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

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mixmore » of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.« less

Host shifts result in parallel genetic changes when viruses evolve in closely related species

PubMed Central

Day, Jonathan P.; Smith, Sophia C. L.; Houslay, Thomas M.; Tagliaferri, Lucia

2018-01-01

Host shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease. PMID:29649296

Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations

PubMed Central

Tobler, Ray; Hermisson, Joachim; Schlötterer, Christian

2015-01-01

Thermal stress is a pervasive selective agent in natural populations that impacts organismal growth, survival, and reproduction. Drosophila melanogaster exhibits a variety of putatively adaptive phenotypic responses to thermal stress in natural and experimental settings; however, accompanying assessments of fitness are typically lacking. Here, we quantify changes in fitness and known thermal tolerance traits in replicated experimental D. melanogaster populations following more than 40 generations of evolution to either cyclic cold or hot temperatures. By evaluating fitness for both evolved populations alongside a reconstituted starting population, we show that the evolved populations were the best adapted within their respective thermal environments. More strikingly, the evolved populations exhibited increased fitness in both environments and improved resistance to both acute heat and cold stress. This unexpected parallel response appeared to be an adaptation to the rapid temperature changes that drove the cycling thermal regimes, as parallel fitness changes were not observed when tested in a constant thermal environment. Our results add to a small, but growing group of studies that demonstrate the importance of fluctuating temperature changes for thermal adaptation and highlight the need for additional work in this area. PMID:26080903

Testing convergent and parallel adaptations in talpids humeral mechanical performance by means of geometric morphometrics and finite element analysis.

PubMed

Piras, P; Sansalone, G; Teresi, L; Kotsakis, T; Colangelo, P; Loy, A

2012-07-01

The shape and mechanical performance in Talpidae humeri were studied by means of Geometric Morphometrics and Finite Element Analysis, including both extinct and extant taxa. The aim of this study was to test whether the ability to dig, quantified by humerus mechanical performance, was characterized by convergent or parallel adaptations in different clades of complex tunnel digger within Talpidae, that is, Talpinae+Condylura (monophyletic) and some complex tunnel diggers not belonging to this clade. Our results suggest that the pattern underlying Talpidae humerus evolution is evolutionary parallelism. However, this insight changed to true convergence when we tested an alternative phylogeny based on molecular data, with Condylura moved to a more basal phylogenetic position. Shape and performance analyses, as well as specific comparative methods, provided strong evidence that the ability to dig complex tunnels reached a functional optimum in distantly related taxa. This was also confirmed by the lower phenotypic variance in complex tunnel digger taxa, compared to non-complex tunnel diggers. Evolutionary rates of phenotypic change showed a smooth deceleration in correspondence with the most recent common ancestor of the Talpinae+Condylura clade. Copyright © 2012 Wiley Periodicals, Inc.

Laser-induced extreme magnetic field in nanorod targets

NASA Astrophysics Data System (ADS)

Lécz, Zsolt; Andreev, Alexander

2018-03-01

The application of nano-structured target surfaces in laser-solid interaction has attracted significant attention in the last few years. Their ability to absorb significantly more laser energy promises a possible route for advancing the currently established laser ion acceleration concepts. However, it is crucial to have a better understanding of field evolution and electron dynamics during laser-matter interactions before the employment of such exotic targets. This paper focuses on the magnetic field generation in nano-forest targets consisting of parallel nanorods grown on plane surfaces. A general scaling law for the self-generated quasi-static magnetic field amplitude is given and it is shown that amplitudes up to 1 MT field are achievable with current technology. Analytical results are supported by three-dimensional particle-in-cell simulations. Non-parallel arrangements of nanorods has also been considered which result in the generation of donut-shaped azimuthal magnetic fields in a larger volume.

Oscillatory electroosmotic flow in a parallel-plate microchannel under asymmetric zeta potentials

NASA Astrophysics Data System (ADS)

Peralta, M.; Arcos, J.; Méndez, F.; Bautista, O.

2017-06-01

In this work, we conduct a theoretical analysis of the start-up of an oscillatory electroosmotic flow (EOF) in a parallel-plate microchannel under asymmetric zeta potentials. It is found that the transient evolution of the flow field is controlled by the parameters {R}ω , {R}\\zeta , and \\bar{κ }, which represent the dimensionless frequency, the ratio of the zeta potentials of the microchannel walls, and the electrokinetic parameter, which is defined as the ratio of the microchannel height to the Debye length. The analysis is performed for both low and high zeta potentials; in the former case, an analytical solution is derived, whereas in the latter, a numerical solution is obtained. These solutions provide the fundamental characteristics of the oscillatory EOFs for which, with suitable adjustment of the zeta potential and the dimensionless frequency, the velocity profiles of the fluid flow exhibit symmetric or asymmetric shapes.

Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans

PubMed Central

Miller, Craig T.; Beleza, Sandra; Pollen, Alex A.; Schluter, Dolph; Kittles, Rick A.; Shriver, Mark D.; Kingsley, David M.

2010-01-01

SUMMARY Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue, and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans. PMID:18083106

The CAnadian NIRISS Unbiased Cluster Survey (CANUCS)

NASA Astrophysics Data System (ADS)

Ravindranath, Swara; NIRISS GTO Team

2017-06-01

CANUCS GTO program is a JWST spectroscopy and imaging survey of five massive galaxy clusters and ten parallel fields using the NIRISS low-resolution grisms, NIRCam imaging and NIRSpec multi-object spectroscopy. The primary goal is to understand the evolution of low mass galaxies across cosmic time. The resolved emission line maps and line ratios for many galaxies, with some at resolution of 100pc via the magnification by gravitational lensing will enable determining the spatial distribution of star formation, dust and metals. Other science goals include the detection and characterization of galaxies within the reionization epoch, using multiply-imaged lensed galaxies to constrain cluster mass distributions and dark matter substructure, and understanding star-formation suppression in the most massive galaxy clusters. In this talk I will describe the science goals of the CANUCS program. The proposed prime and parallel observations will be presented with details of the implementation of the observation strategy using JWST proposal planning tools.

NIRcam-NIRSpec GTO Observations of Galaxy Evolution

NASA Astrophysics Data System (ADS)

Rieke, Marcia J.; Ferruit, Pierre; Alberts, Stacey; Bunker, Andrew; Charlot, Stephane; Chevallard, Jacopo; Dressler, Alan; Egami, Eiichi; Eisenstein, Daniel; Endsley, Ryan; Franx, Marijn; Frye, Brenda L.; Hainline, Kevin; Jakobsen, Peter; Lake, Emma Curtis; Maiolino, Roberto; Rix, Hans-Walter; Robertson, Brant; Stark, Daniel; Williams, Christina; Willmer, Christopher; Willott, Chris J.

2017-06-01

The NIRSpec and and NIRCam GTO Teams are planning a joint imaging and spectroscopic study of the high redshift universe. By virtue of planning a joint program which includes medium and deep near- and mid-infrared imaging surveys and multi-object spectroscopy (MOS) of sources in the same fields, we have learned much about planning observing programs for each of the instruments and using them in parallel mode to maximize photon collection time. The design and rationale for our joint program will be explored in this talk with an emphasis on why we have chosen particular suites of filters and spectroscopic resolutions, why we have chosen particular exposure patterns, and how we have designed the parallel observations. The actual observations that we intend on executing will serve as examples of how to layout mosaics and MOS observations to maximize observing efficiency for surveys with JWST.

A hybrid dynamic harmony search algorithm for identical parallel machines scheduling

NASA Astrophysics Data System (ADS)

Chen, Jing; Pan, Quan-Ke; Wang, Ling; Li, Jun-Qing

2012-02-01

In this article, a dynamic harmony search (DHS) algorithm is proposed for the identical parallel machines scheduling problem with the objective to minimize makespan. First, an encoding scheme based on a list scheduling rule is developed to convert the continuous harmony vectors to discrete job assignments. Second, the whole harmony memory (HM) is divided into multiple small-sized sub-HMs, and each sub-HM performs evolution independently and exchanges information with others periodically by using a regrouping schedule. Third, a novel improvisation process is applied to generate a new harmony by making use of the information of harmony vectors in each sub-HM. Moreover, a local search strategy is presented and incorporated into the DHS algorithm to find promising solutions. Simulation results show that the hybrid DHS (DHS_LS) is very competitive in comparison to its competitors in terms of mean performance and average computational time.

Quantifying the origins of life on a planetary scale.

PubMed

Scharf, Caleb; Cronin, Leroy

2016-07-19

A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress can be made on parameter estimation for determining origins of life probabilities, based on constraints from Bayesian approaches. We discuss a variety of "microscale" factors and their role in determining "macroscale" abiogenesis probabilities on suitable planets. We also propose that impact ejecta exchange between planets with parallel chemistries and chemical evolution could in principle amplify the development of molecular complexity and abiogenesis probabilities. This amplification could be very significant, and both bias our conclusions about abiogenesis probabilities based on the Earth and provide a major source of variance in the probability of life arising in planetary systems. We use our heuristic formula to suggest a number of observational routes for improving constraints on origins of life probabilities.

Quantifying the origins of life on a planetary scale

NASA Astrophysics Data System (ADS)

Scharf, Caleb; Cronin, Leroy

2016-07-01

A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress can be made on parameter estimation for determining origins of life probabilities, based on constraints from Bayesian approaches. We discuss a variety of “microscale” factors and their role in determining “macroscale” abiogenesis probabilities on suitable planets. We also propose that impact ejecta exchange between planets with parallel chemistries and chemical evolution could in principle amplify the development of molecular complexity and abiogenesis probabilities. This amplification could be very significant, and both bias our conclusions about abiogenesis probabilities based on the Earth and provide a major source of variance in the probability of life arising in planetary systems. We use our heuristic formula to suggest a number of observational routes for improving constraints on origins of life probabilities.

Turbopump Performance Improved by Evolutionary Algorithms

NASA Technical Reports Server (NTRS)

Oyama, Akira; Liou, Meng-Sing

2002-01-01

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

Dielectric monitoring of carbon nanotube network formation in curing thermosetting nanocomposites

NASA Astrophysics Data System (ADS)

Battisti, A.; Skordos, A. A.; Partridge, I. K.

2009-08-01

This paper focuses on monitoring of carbon nanotube (CNT) network development during the cure of unsaturated polyester nanocomposites by means of electrical impedance spectroscopy. A phenomenological model of the dielectric response is developed using equivalent circuit analysis. The model comprises two parallel RC elements connected in series, each of them giving rise to a semicircular arc in impedance complex plane plots. An established inverse modelling methodology is utilized for the estimation of the parameters of the corresponding equivalent circuit. This allows a quantification of the evolution of two separate processes corresponding to the two parallel RC elements. The high frequency process, which is attributed to CNT aggregates, shows a monotonic decrease in characteristic time during the cure. In contrast, the low frequency process, which corresponds to inter-aggregate phenomena, shows a more complex behaviour explained by the interplay between conductive network development and the cross-linking of the polymer.

Worldwide patterns of bird colouration on islands.

PubMed

Doutrelant, Claire; Paquet, Matthieu; Renoult, Julien P; Grégoire, Arnaud; Crochet, Pierre-André; Covas, Rita

2016-05-01

Island environments share distinctive characteristics that offer unique opportunities to investigate parallel evolution. Previous research has produced evidence of an island syndrome for morphological traits, life-history strategies and ecological niches, but little is known about the response to insularity of other important traits such as animal signals. Here, we tested whether birds' plumage colouration is part of the island syndrome. We analysed with spectrophotometry the colouration of 116 species endemic to islands and their 116 closest mainland relatives. We found a pattern of reduced brightness and colour intensity for both sexes on islands. In addition, we found a decrease in the number of colour patches on islands that, in males, was associated with a decrease in the number of same-family sympatric species. These results demonstrate a worldwide pattern of parallel colour changes on islands and suggest that a relaxation of selection on species recognition may be one of the mechanisms involved. © 2016 John Wiley & Sons Ltd/CNRS.

DISSIPATION OF PARALLEL AND OBLIQUE ALFVÉN-CYCLOTRON WAVES—IMPLICATIONS FOR HEATING OF ALPHA PARTICLES IN THE SOLAR WIND

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

Maneva, Y. G.; Poedts, Stefaan; Viñas, Adolfo F.

2015-11-20

We perform 2.5D hybrid simulations with massless fluid electrons and kinetic particle-in-cell ions to study the temporal evolution of ion temperatures, temperature anisotropies, and velocity distribution functions in relation to the dissipation and turbulent evolution of a broadband spectrum of parallel and obliquely propagating Alfvén-cyclotron waves. The purpose of this paper is to study the relative role of parallel versus oblique Alfvén-cyclotron waves in the observed heating and acceleration of alpha particles in the fast solar wind. We consider collisionless homogeneous multi-species plasma, consisting of isothermal electrons, isotropic protons, and a minor component of drifting α particles in a finite-βmore » fast stream near the Earth. The kinetic ions are modeled by initially isotropic Maxwellian velocity distribution functions, which develop nonthermal features and temperature anisotropies when a broadband spectrum of low-frequency nonresonant, ω ≤ 0.34 Ω{sub p}, Alfvén-cyclotron waves is imposed at the beginning of the simulations. The initial plasma parameter values, such as ion density, temperatures, and relative drift speeds, are supplied by fast solar wind observations made by the Wind spacecraft at 1 AU. The imposed broadband wave spectra are left-hand polarized and resemble Wind measurements of Alfvénic turbulence in the solar wind. The imposed magnetic field fluctuations for all cases are within the inertial range of the solar wind turbulence and have a Kraichnan-type spectral slope α = −3/2. We vary the propagation angle from θ = 0° to θ = 30° and θ = 60°, and find that the heating of alpha particles is most efficient for the highly oblique waves propagating at 60°, whereas the protons exhibit perpendicular cooling at all propagation angles.« less

Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

PubMed

Olsen, Aaron M; Westneat, Mark W

2016-12-01

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570-1583, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Multiscale Monte Carlo equilibration: Pure Yang-Mills theory

DOE PAGES

Endres, Michael G.; Brower, Richard C.; Orginos, Kostas; ...

2015-12-29

In this study, we present a multiscale thermalization algorithm for lattice gauge theory, which enables efficient parallel generation of uncorrelated gauge field configurations. The algorithm combines standard Monte Carlo techniques with ideas drawn from real space renormalization group and multigrid methods. We demonstrate the viability of the algorithm for pure Yang-Mills gauge theory for both heat bath and hybrid Monte Carlo evolution, and show that it ameliorates the problem of topological freezing up to controllable lattice spacing artifacts.

Physical and Genetic Mechanisms Guiding the Evolution and Development of Dendritic, Flapping Insect-Wings

DTIC Science & Technology

2010-04-12

computer graphics, to music . Map L systems [2, 6, 7] extend the parallel rewriting in L systems to planar graphs with cycles, called maps [8]. The maps...carbon. For easy of reading , in the results below the mass is represented by the percentage carbon laminate coverage. As explained previously, the...previously, that value can be read in the left vertical axis. There are nine designs in the Pareto front. Depending on design goals any of these individuals

Automated video surveillance: teaching an old dog new tricks

NASA Astrophysics Data System (ADS)

McLeod, Alastair

1993-12-01

The automated video surveillance market is booming with new players, new systems, new hardware and software, and an extended range of applications. This paper reviews available technology, and describes the features required for a good automated surveillance system. Both hardware and software are discussed. An overview of typical applications is also given. A shift towards PC-based hybrid systems, use of parallel processing, neural networks, and exploitation of modern telecomms are introduced, highlighting the evolution modern video surveillance systems.

The Evolution of Military Officer Personnel Management Policies: A Preliminary Study with Parallels from Industry

DTIC Science & Technology

1978-08-01

Engineer School of Application in 1885; and the School for Cavalry and Light Artillery was established in 1892.10 This period of intellectual ferment has...one of tremendous ferment and dissatisfaction among the younger officers who had won a victory by the institution of the “plucking” boards. However...1954, pp. 637-646, and July 1954, pp. 761-771. Vinegar , J. W. (Manager of Training and Development for Xerox), “Personnel Development Through VERT

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. These approaches are implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Directional photofluidization lithography: micro/nanostructural evolution by photofluidic motions of azobenzene materials.

PubMed

Lee, Seungwoo; Kang, Hong Suk; Park, Jung-Ki

2012-04-24

This review demonstrates directional photofluidization lithography (DPL), which makes it possible to fabricate a generic and sophisticated micro/nanoarchitecture that would be difficult or impossible to attain with other methods. In particular, DPL differs from many of the existing micro/nanofabrication methods in that the post-treatment (i.e., photofluidization), after the preliminary fabrication process of the original micro/nanostructures, plays a pivotal role in the various micro/nanostructural evolutions including the deterministic reshaping of architectures, the reduction of structural roughness, and the dramatic enhancement of pattern resolution. Also, DPL techniques are directly compatible with a parallel and scalable micro/nanofabrication. Thus, DPL with such extraordinary advantages in micro/nanofabrication could provide compelling opportunities for basic micro/nanoscale science as well as for general technology applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The many shades of prion strain adaptation.

PubMed

Baskakov, Ilia V

2014-01-01

In several recent studies transmissible prion disease was induced in animals by inoculation with recombinant prion protein amyloid fibrils produced in vitro. Serial transmission of amyloid fibrils gave rise to a new class of prion strains of synthetic origin. Gradual transformation of disease phenotypes and PrP(Sc) properties was observed during serial transmission of synthetic prions, a process that resembled the phenomenon of prion strain adaptation. The current article discusses the remarkable parallels between phenomena of prion strain adaptation that accompanies cross-species transmission and the evolution of synthetic prions occurring within the same host. Two alternative mechanisms underlying prion strain adaptation and synthetic strain evolution are discussed. The current article highlights the complexity of the prion transmission barrier and strain adaptation and proposes that the phenomenon of prion adaptation is more common than previously thought.

Experimental observations of root growth in a controlled photoelastic granular material

NASA Astrophysics Data System (ADS)

Barés, Jonathan; Mora, Serge; Delenne, Jean-Yves; Fourcaud, Thierry

2017-06-01

We present a novel root observation apparatus capable of measuring the mechanical evolution of both the root network and the surrounding granular medium. The apparatus consists of 11 parallel growth frames, two of them being shearable, where the roots grow inside a photo-elastic or glass granular medium sandwiched between two pieces of glass. An automated system waters the plant and image each frame periodically in white light and between crossed polarisers. This makes it possible to follow (i) the root tips and (ii) the grain displacements as well as (iii) their inner pressure. We show how a root networks evolve in a granular medium and how it can mechanically stabilize it. This constitutes a model experiment to move forward in the understanding of the complex interaction between root growth and surrounding soil mechanical evolution.

Manual praxis in stone tool manufacture: implications for language evolution.

PubMed

Ruck, Lana

2014-12-01

Alternative functions of the left-hemisphere dominant Broca's region have induced hypotheses regarding the evolutionary parallels between manual praxis and language in humans. Many recent studies on Broca's area reveal several assumptions about the cognitive mechanisms that underlie both functions, including: (1) an accurate, finely controlled body schema, (2) increasing syntactical abilities, particularly for goal-oriented actions, and (3) bilaterality and fronto-parietal connectivity. Although these characteristics are supported by experimental paradigms, many researchers have failed to acknowledge a major line of evidence for the evolutionary development of these traits: stone tools. The neuroscience of stone tool manufacture is a viable proxy for understanding evolutionary aspects of manual praxis and language, and may provide key information for evaluating competing hypotheses on the co-evolution of these cognitive domains in our species. Copyright © 2014 Elsevier Inc. All rights reserved.

Evolution of the arginase fold and functional diversity

PubMed Central

Dowling, Daniel P.; Costanzo, Luigi Di; Gennadios, Heather A.; Christianson, David W.

2009-01-01

The large number of protein structures deposited in the Protein Data Bank allows for the identification of novel structural superfamilies based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique α/β fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel 8 stranded β-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core α/β fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes. PMID:18360740

Genome-wide signatures of convergent evolution in echolocating mammals

PubMed Central

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

Unexpected Convergent Evolution of Nasal Domes between Pleistocene Bovids and Cretaceous Hadrosaur Dinosaurs.

PubMed

O'Brien, Haley D; Faith, J Tyler; Jenkins, Kirsten E; Peppe, Daniel J; Plummer, Thomas W; Jacobs, Zenobia L; Li, Bo; Joannes-Boyau, Renaud; Price, Gilbert; Feng, Yue-Xing; Tryon, Christian A

2016-02-22

The fossil record provides tangible, historical evidence for the mode and operation of evolution across deep time. Striking patterns of convergence are some of the strongest examples of these operations, whereby, over time, similar environmental and/or behavioral pressures precipitate similarity in form and function between disparately related taxa. Here we present fossil evidence for an unexpected convergence between gregarious plant-eating mammals and dinosaurs. Recent excavations of Late Pleistocene deposits on Rusinga Island, Kenya, have uncovered a catastrophic assemblage of the wildebeest-like bovid Rusingoryx atopocranion. Previously known from fragmentary material, these new specimens reveal large, hollow, osseous nasal crests: a craniofacial novelty for mammals that is remarkably comparable to the nasal crests of lambeosaurine hadrosaur dinosaurs. Using adult and juvenile material from this assemblage, as well as computed tomographic imaging, we investigate this convergence from morphological, developmental, functional, and paleoenvironmental perspectives. Our detailed analyses reveal broad parallels between R. atopocranion and basal Lambeosaurinae, suggesting that osseous nasal crests may require a highly specific combination of ontogeny, evolution, and environmental pressures in order to develop. Copyright © 2016 Elsevier Ltd. All rights reserved.

The evolution of an ancient technology

PubMed Central

2017-01-01

We investigate pattern and process in the transmission of traditional weaving cultures in East and Southeast Asia. Our investigation covers a range of scales, from the experiences of individual weavers (‘micro’) to the broad-scale patterns of loom technologies across the region (‘macro’). Using published sources, we build an empirical model of cultural transmission (encompassing individual weavers, the household and the community), focussing on where cultural information resides and how it is replicated and how transmission errors are detected and eliminated. We compare this model with macro-level outcomes in the form of a new dataset of weaving loom technologies across a broad area of East and Southeast Asia. The lineages of technologies that we have uncovered display evidence for branching, hybridization (reticulation), stasis in some lineages, rapid change in others and the coexistence of both simple and complex forms. There are some striking parallels with biological evolution and information theory. There is sufficient detail and resolution in our findings to enable us to begin to critique theoretical models and assumptions that have been produced during the last few decades to describe the evolution of culture. PMID:28573032

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

PubMed

Wang, Yong; Waters, Jill; Leung, Marco L; Unruh, Anna; Roh, Whijae; Shi, Xiuqing; Chen, Ken; Scheet, Paul; Vattathil, Selina; Liang, Han; Multani, Asha; Zhang, Hong; Zhao, Rui; Michor, Franziska; Meric-Bernstam, Funda; Navin, Nicholas E

2014-08-14

Sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. Here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (ER(+)) breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. Using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.

Cyclic multiverses

NASA Astrophysics Data System (ADS)

Marosek, Konrad; Dąbrowski, Mariusz P.; Balcerzak, Adam

2016-09-01

Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (`non-singular' bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (`singular' bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two `parallel' universes with their physical evolution [physical coupling constants c(t) and G(t)] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion - the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans-Dicke theory where varying G(t) is replaced by the dynamical Brans-Dicke field φ(t) though these theories are slightly different.

The evolution of an ancient technology.

PubMed

Buckley, Christopher D; Boudot, Eric

2017-05-01

We investigate pattern and process in the transmission of traditional weaving cultures in East and Southeast Asia. Our investigation covers a range of scales, from the experiences of individual weavers ('micro') to the broad-scale patterns of loom technologies across the region ('macro'). Using published sources, we build an empirical model of cultural transmission (encompassing individual weavers, the household and the community), focussing on where cultural information resides and how it is replicated and how transmission errors are detected and eliminated. We compare this model with macro-level outcomes in the form of a new dataset of weaving loom technologies across a broad area of East and Southeast Asia. The lineages of technologies that we have uncovered display evidence for branching, hybridization (reticulation), stasis in some lineages, rapid change in others and the coexistence of both simple and complex forms. There are some striking parallels with biological evolution and information theory. There is sufficient detail and resolution in our findings to enable us to begin to critique theoretical models and assumptions that have been produced during the last few decades to describe the evolution of culture.

Signal design and perception in Hypocnemis antbirds: evidence for convergent evolution via social selection.

PubMed

Tobias, Joseph A; Seddon, Nathalie

2009-12-01

Natural selection is known to produce convergent phenotypes through mimicry or ecological adaptation. It has also been proposed that social selection--i.e., selection exerted by social competition--may drive convergent evolution in signals mediating interspecific communication, yet this idea remains controversial. Here, we use color spectrophotometry, acoustic analyses, and playback experiments to assess the hypothesis of adaptive signal convergence in two competing nonsister taxa, Hypocnemis peruviana and H. subflava (Aves: Thamnophilidae). We show that the structure of territorial songs in males overlaps in sympatry, with some evidence of convergent character displacement. Conversely, nonterritorial vocal and visual signals in males are strikingly diagnostic, in line with 6.8% divergence in mtDNA sequences. The same pattern of variation applies to females. Finally, we show that songs in both sexes elicit strong territorial responses within and between species, whereas songs of a third, allopatric and more closely related species (H. striata) are structurally divergent and elicit weaker responses. Taken together, our results provide compelling evidence that social selection can act across species boundaries to drive convergent or parallel evolution in taxa competing for space and resources.

Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

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

Moreau, P.; Gregoire, S.; Lochegnies, D.

2007-05-17

Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication...). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutivemore » contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.« less

[The Swiss archaeologist Otto Hauser. His skeletal findings and hypothesis on the evolution of man and his extensive activities in the development of prehistorical research and evolution].

PubMed

Drössler, Rudolf; Drössler, Sigrid; Freyberg, Manuela

2006-03-01

New investigations on Otto Hauser's skeleton findings and the excavations of this Swiss citizen in Southwest France from 1906 until 1914 placed the activities of this archaeologist again in the focus of scientific and public interest. This paper describes life and oeuvre of Otto Hauser and discusses the importance of the skeletons found by him and Hermann Klaatsch as well as the consequences of their discovery. The efforts of Otto Hauser to publish his discoveries, to present and spread his view concerning the evolution of man were remarkably manifold as well as the parallels between ancient man and contemporary ethnic groups living on a low technological level drawn by him and to wake and to promote the interest in prehistory. Many books, brochures, articles and public lectures contributed to this intention as well as co-operation with local historians and scientists of other disciplines, and also many films, teaching and illustrative materials. The scientific collection of the authors of this article comprises more than 6,500 written documents and photos.

Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution

PubMed Central

Kovac, Michal; Navas, Carolina; Horswell, Stuart; Salm, Max; Bardella, Chiara; Rowan, Andrew; Stares, Mark; Castro-Giner, Francesc; Fisher, Rosalie; de Bruin, Elza C.; Kovacova, Monika; Gorman, Maggie; Makino, Seiko; Williams, Jennet; Jaeger, Emma; Jones, Angela; Howarth, Kimberley; Larkin, James; Pickering, Lisa; Gore, Martin; Nicol, David L.; Hazell, Steven; Stamp, Gordon; O’Brien, Tim; Challacombe, Ben; Matthews, Nik; Phillimore, Benjamin; Begum, Sharmin; Rabinowitz, Adam; Varela, Ignacio; Chandra, Ashish; Horsfield, Catherine; Polson, Alexander; Tran, Maxine; Bhatt, Rupesh; Terracciano, Luigi; Eppenberger-Castori, Serenella; Protheroe, Andrew; Maher, Eamonn; El Bahrawy, Mona; Fleming, Stewart; Ratcliffe, Peter; Heinimann, Karl; Swanton, Charles; Tomlinson, Ian

2015-01-01

Papillary renal cell carcinoma (pRCC) is an important subtype of kidney cancer with a problematic pathological classification and highly variable clinical behaviour. Here we sequence the genomes or exomes of 31 pRCCs, and in four tumours, multi-region sequencing is undertaken. We identify BAP1, SETD2, ARID2 and Nrf2 pathway genes (KEAP1, NHE2L2 and CUL3) as probable drivers, together with at least eight other possible drivers. However, only ~10% of tumours harbour detectable pathogenic changes in any one driver gene, and where present, the mutations are often predicted to be present within cancer sub-clones. We specifically detect parallel evolution of multiple SETD2 mutations within different sub-regions of the same tumour. By contrast, large copy number gains of chromosomes 7, 12, 16 and 17 are usually early, monoclonal changes in pRCC evolution. The predominance of large copy number variants as the major drivers for pRCC highlights an unusual mode of tumorigenesis that may challenge precision medicine approaches. PMID:25790038

Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit

PubMed Central

Lawrie, David S.

2017-01-01

Forward Wright–Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright–Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called “embarrassingly parallel,” consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright–Fisher simulation, or “GO Fish” for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. PMID:28768689

Seismic anisotropy and mantle creep in young orogens

USGS Publications Warehouse

Meissner, R.; Mooney, W.D.; Artemieva, I.

2002-01-01

Seismic anisotropy provides evidence for the physical state and tectonic evolution of the lithosphere. We discuss the origin of anisotropy at various depths, and relate it to tectonic stress, geotherms and rheology. The anisotropy of the uppermost mantle is controlled by the orthorhombic mineral olivine, and may result from ductile deformation, dynamic recrystallization or annealing. Anisotropy beneath young orogens has been measured for the seismic phase Pn that propagates in the uppermost mantle. This anisotropy is interpreted as being caused by deformation during the most recent thermotectonic event, and thus provides information on the process of mountain building. Whereas tectonic stress and many structural features in the upper crust are usually orientated perpendicular to the structural axis of mountain belts, Pn anisotropy is aligned parallel to the structural axis. We interpret this to indicate mountain-parallel ductile (i.e. creeping) deformation in the uppermost mantle that is a consequence of mountain-perpendicular compressive stresses. The preferred orientation of the fast axes of some anisotropic minerals, such as olivine, is known to be in the creep direction, a consequence of the anisotropy of strength and viscosity of orientated minerals. In order to explain the anisotropy of the mantle beneath young orogens we extend the concept of crustal 'escape' (or 'extrusion') tectonics to the uppermost mantle. We present rheological model calculations to support this hypothesis. Mountain-perpendicular horizontal stress (determined in the upper crust) and mountain-parallel seismic anisotropy (in the uppermost mantle) require a zone of ductile decoupling in the middle or lower crust of young mountain belts. Examples for stress and mountain-parallel Pn anisotropy are given for Tibet, the Alpine chains, and young mountain ranges in the Americas. Finally, we suggest a simple model for initiating mountain parallel creep.

Synthesizing perspectives on the evolution of cooperation within and between species.

PubMed

Barker, Jessica L; Bronstein, Judith L; Friesen, Maren L; Jones, Emily I; Reeve, H Kern; Zink, Andrew G; Frederickson, Megan E

2017-04-01

Cooperation is widespread both within and between species, but are intraspecific and interspecific cooperation fundamentally similar or qualitatively different phenomena? This review evaluates this question, necessary for a general understanding of the evolution of cooperation. First, we outline three advantages of cooperation relative to noncooperation (acquisition of otherwise inaccessible goods and services, more efficient acquisition of resources, and buffering against variability), and predict when individuals should cooperate with a conspecific versus a heterospecific partner to obtain these advantages. Second, we highlight five axes along which heterospecific and conspecific partners may differ: relatedness and fitness feedbacks, competition and resource use, resource-generation abilities, relative evolutionary rates, and asymmetric strategy sets and outside options. Along all of these axes, certain asymmetries between partners are more common in, but not exclusive to, cooperation between species, especially complementary resource use and production. We conclude that cooperation within and between species share many fundamental qualities, and that differences between the two systems are explained by the various asymmetries between partners. Consideration of the parallels between intra- and interspecific cooperation facilitates application of well-studied topics in one system to the other, such as direct benefits within species and kin-selected cooperation between species, generating promising directions for future research. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Phylogeny-based comparative methods question the adaptive nature of sporophytic specializations in mosses.

PubMed

Huttunen, Sanna; Olsson, Sanna; Buchbender, Volker; Enroth, Johannes; Hedenäs, Lars; Quandt, Dietmar

2012-01-01

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized "epiphytic" traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.

Geological and petrologic evolution of seamounts near the EPR based on submersible and camera study

NASA Astrophysics Data System (ADS)

Batiza, Rodey; Smith, Terri L.; Niu, Yaoling

1989-09-01

Observations from 17 ALVIN dives and 14 ANGUS runs plus laboratory study of basalt samples collected with ALVIN help to constrain the morphologic, volcanic and petrologic evolution of four seamounts near the East Pacific Rise (EPR). Comparison among the four volcanoes provides evidence for a general pattern of near-EPR seamount evolution and shows the importance of sedimentation, mass wasting, hydrothermal activity and other geologic processes that occur on submerged oceanic volcanoes. Seamount 5, closest to the EPR (1.0 Ma) is the youngest seamount and may still be active. Its summit is covered by fresh lavas, recent faults and hydrothermal deposits. Seamount D is on crust 1.55 Ma and is inactive; like seamount 5, it has a breached caldera and is composed exclusively of N-MORB. Seamounts 5 and D represent the last stages of growth of typical N-MORB-only seamounts near the EPR axis. Seamounts 6 and 7 have bumpy, flattish summits composed of transitional and alkalic lavas. These lavas probably represent caldera fillings and caps overlying an edifice composed of N-MORB. Evolution from N-MORB-only cratered edifices to the alkalic stage does not occur on all near-EPR seamounts and may be favored by location on structures with relative-motion-parallel orientation.

In Situ Characterization of Ni and Ni/Fe Thin Film Electrodes for Oxygen Evolution in Alkaline Media by a Raman-Coupled Scanning Electrochemical Microscope Setup.

PubMed

Steimecke, Matthias; Seiffarth, Gerda; Bron, Michael

2017-10-17

We present a spectroelectrochemical setup, in which Raman microscopy is combined with scanning electrochemical microscopy (SECM) in order to provide both spectroscopic and electrochemical information on the very same location of an electrode at the same time. The setup is applied to a subject of high academic and practical interest, namely, the oxygen evolution reaction at Ni and Ni/Fe electrodes. It comprises a transparent substrate electrode, onto which Ni and Ni/Fe thin films are deposited. An ultramicroelectrode (UME) is placed closely above the substrate to obtain electrochemical information, while a Raman microscope probes the same sample spot from below. To obtain information on oxygen evolution activity and structural changes, increasingly positive potentials from 0.1 up to 0.7 V vs Hg|HgO|1 M KOH were applied to the Ni/Fe-electrodes in 0.1 M KOH solution. Evolved oxygen is detected by reduction at a Pt UME, allowing for the determination of onset potentials, while the substrate current, which is recorded in parallel, is due to both overlapping oxygen evolution and the oxidation of Ni(OH) 2 to NiOOH. An optimum of 15% Fe in Ni/Fe films with respect to oxygen evolution activity was determined. At the same time, the potential-dependent formation of γ-NiOOH characterized by the Raman double band at 475 and 557 cm -1 allows for the conclusion that a certain amount of disorder introduced by Fe atoms is necessary to obtain high oxygen evolution reaction (OER) activity.

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems.

PubMed

Yoshida, M A; Ogura, A; Ikeo, K; Shigeno, S; Moritaki, T; Winters, G C; Kohn, A B; Moroz, L L

2015-12-01

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called "evolutionary tinkering" or "co-option", and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the "camera" eye from nautilus' "pinhole" eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids' opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Roles of density-dependent growth and life history evolution in accounting for fisheries-induced trait changes

PubMed Central

Eikeset, Anne Maria; Dunlop, Erin S.; Heino, Mikko; Storvik, Geir; Stenseth, Nils C.; Dieckmann, Ulf

2016-01-01

The relative roles of density dependence and life history evolution in contributing to rapid fisheries-induced trait changes remain debated. In the 1930s, northeast Arctic cod (Gadus morhua), currently the world’s largest cod stock, experienced a shift from a traditional spawning-ground fishery to an industrial trawl fishery with elevated exploitation in the stock’s feeding grounds. Since then, age and length at maturation have declined dramatically, a trend paralleled in other exploited stocks worldwide. These trends can be explained by demographic truncation of the population’s age structure, phenotypic plasticity in maturation arising through density-dependent growth, fisheries-induced evolution favoring faster-growing or earlier-maturing fish, or a combination of these processes. Here, we use a multitrait eco-evolutionary model to assess the capacity of these processes to reproduce 74 y of historical data on age and length at maturation in northeast Arctic cod, while mimicking the stock’s historical harvesting regime. Our results show that model predictions critically depend on the assumed density dependence of growth: when this is weak, life history evolution might be necessary to prevent stock collapse, whereas when a stronger density dependence estimated from recent data is used, the role of evolution in explaining fisheries-induced trait changes is diminished. Our integrative analysis of density-dependent growth, multitrait evolution, and stock-specific time series data underscores the importance of jointly considering evolutionary and ecological processes, enabling a more comprehensive perspective on empirically observed stock dynamics than previous studies could provide. PMID:27940913

Parallel Selection Revealed by Population Sequencing in Chicken.

PubMed

Qanbari, Saber; Seidel, Michael; Strom, Tim-Mathias; Mayer, Klaus F X; Preisinger, Ruedi; Simianer, Henner

2015-11-13

Human-driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg-laying chicken along with pool sequences of three meat-type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or preimprovement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in "Ascites" in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement in chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to overconsumption of calcium in egg-laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution of CMS workload management towards multicore job support

NASA Astrophysics Data System (ADS)

Pérez-Calero Yzquierdo, A.; Hernández, J. M.; Khan, F. A.; Letts, J.; Majewski, K.; Rodrigues, A. M.; McCrea, A.; Vaandering, E.

2015-12-01

The successful exploitation of multicore processor architectures is a key element of the LHC distributed computing system in the coming era of the LHC Run 2. High-pileup complex-collision events represent a challenge for the traditional sequential programming in terms of memory and processing time budget. The CMS data production and processing framework is introducing the parallel execution of the reconstruction and simulation algorithms to overcome these limitations. CMS plans to execute multicore jobs while still supporting singlecore processing for other tasks difficult to parallelize, such as user analysis. The CMS strategy for job management thus aims at integrating single and multicore job scheduling across the Grid. This is accomplished by employing multicore pilots with internal dynamic partitioning of the allocated resources, capable of running payloads of various core counts simultaneously. An extensive test programme has been conducted to enable multicore scheduling with the various local batch systems available at CMS sites, with the focus on the Tier-0 and Tier-1s, responsible during 2015 of the prompt data reconstruction. Scale tests have been run to analyse the performance of this scheduling strategy and ensure an efficient use of the distributed resources. This paper presents the evolution of the CMS job management and resource provisioning systems in order to support this hybrid scheduling model, as well as its deployment and performance tests, which will enable CMS to transition to a multicore production model for the second LHC run.

Flows, Fields, and Forces in the Mars-Solar Wind Interaction

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Brain, D. A.; Luhmann, J. G.; DiBraccio, G. A.; Ruhunusiri, S.; Harada, Y.; Fowler, C. M.; Mitchell, D. L.; Connerney, J. E. P.; Espley, J. R.; Mazelle, C.; Jakosky, B. M.

2017-11-01

We utilize suprathermal ion and magnetic field measurements from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, organized by the upstream magnetic field, to investigate the morphology and variability of flows, fields, and forces in the Mars-solar wind interaction. We employ a combination of case studies and statistical investigations to characterize the interaction in both quasi-parallel and quasi-perpendicular regions and under high and low solar wind Mach number conditions. For the first time, we include a detailed investigation of suprathermal ion temperature and anisotropy. We find that the observed magnetic fields and suprathermal ion moments in the magnetosheath, bow shock, and upstream regions have observable asymmetries controlled by the interplanetary magnetic field, with particularly large asymmetries found in the ion parallel temperature and anisotropy. The greatest temperature anisotropies occur in quasi-perpendicular regions of the magnetosheath and under low Mach number conditions. These results have implications for the growth and evolution of wave-particle instabilities and their role in energy transport and dissipation. We utilize the measured parameters to estimate the average ion pressure gradient, J × B, and v × B macroscopic force terms. The pressure gradient force maintains nearly cylindrical symmetry, while the J × B force has larger asymmetries and varies in magnitude in comparison to the pressure gradient force. The v × B force felt by newly produced planetary ions exceeds the other forces in magnitude in the magnetosheath and upstream regions for all solar wind conditions.

The Evolution History of South China Sea: a Synthesis of Recent Geophysical, Geological, and Geochemical Results

NASA Astrophysics Data System (ADS)

Xue, M.; Li, L.; Chen, L.

2016-12-01

South China Sea (SCS) is located in the continental margin of Eurasia plate, where different geological blocks/tectonic plates interact. The dynamic mechanism of the formation of South China Sea (SCS) has been debated for decades. In this study, we first synthesize our geophysical results obtained in South China Sea, including an updated 3D velocity model from surface tomography using surrounding land stations and regional earthquakes, and shear wave splitting results obtained at surrounding land stations and OBS, using local, regional, and teleseismic earthquakes. The observed splitting results in South China Sea are complex: the fast polarization direction beneath the central basin is approximately NE-SW, nearly parallel to the extinct ridge in the central basin of SCS; however, the fast axis within the slab is trench-parallel outside the ridge subduction region. In 3D velocity models, subducting slabs are observed as dipping high velocity anomalies, and discontinuous low velocities are observed above the subduction slab, as well as in the basin. How the splitting observations are connected with the velocity models? How observations are linked to one another? How are the observations in central basin linked with surrounding region? We are aiming to link these observations themselves as well as with newly published results from geophysics, geochemistry, and geology in this region. Such a synthesis will improve our understanding about the evolution of South China Sea and facilitate new ideas.

Evolution of CMS Workload Management Towards Multicore Job Support

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

Perez-Calero Yzquierdo, A.; Hernández, J. M.; Khan, F. A.

The successful exploitation of multicore processor architectures is a key element of the LHC distributed computing system in the coming era of the LHC Run 2. High-pileup complex-collision events represent a challenge for the traditional sequential programming in terms of memory and processing time budget. The CMS data production and processing framework is introducing the parallel execution of the reconstruction and simulation algorithms to overcome these limitations. CMS plans to execute multicore jobs while still supporting singlecore processing for other tasks difficult to parallelize, such as user analysis. The CMS strategy for job management thus aims at integrating single andmore » multicore job scheduling across the Grid. This is accomplished by employing multicore pilots with internal dynamic partitioning of the allocated resources, capable of running payloads of various core counts simultaneously. An extensive test programme has been conducted to enable multicore scheduling with the various local batch systems available at CMS sites, with the focus on the Tier-0 and Tier-1s, responsible during 2015 of the prompt data reconstruction. Scale tests have been run to analyse the performance of this scheduling strategy and ensure an efficient use of the distributed resources. This paper presents the evolution of the CMS job management and resource provisioning systems in order to support this hybrid scheduling model, as well as its deployment and performance tests, which will enable CMS to transition to a multicore production model for the second LHC run.« less

Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium

DOE PAGES

Douglas, Sarah M.; Chubiz, Lon M.; Harcombe, William R.; ...

2016-09-12

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium,we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determinecommunity dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymousmutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator andmore » were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in termsof individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior.« less

Ion dynamics during the parametric instabilities of a left-hand polarized Alfvén wave in a proton-electron-alpha plasma

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

Gao, Xinliang; Lu, Quanming; Hao, Yufei

2014-01-01

The parametric instabilities of an Alfvén wave in a proton-electron plasma system are found to have great influence on proton dynamics, where part of the protons can be accelerated through the Landau resonance with the excited ion acoustic waves, and a beam component along the background magnetic field is formed. In this paper, with a one-dimensional hybrid simulation model, we investigate the evolution of the parametric instabilities of a monochromatic left-hand polarized Alfvén wave in a proton-electron-alpha plasma with a low beta. When the drift velocity between the protons and alpha particles is sufficiently large, the wave numbers of themore » backward daughter Alfvén waves can be cascaded toward higher values due to the modulational instability during the nonlinear evolution of the parametric instabilities, and the alpha particles are resonantly heated in both the parallel and perpendicular direction by the backward waves. On the other hand, when the drift velocity of alpha particles is small, the alpha particles are heated in the linear growth stage of the parametric instabilities due to the Landau resonance with the excited ion acoustic waves. Therefore, the heating occurs only in the parallel direction, and there is no obvious heating in the perpendicular direction. The relevance of our results to the preferential heating of heavy ions observed in the solar wind within 0.3 AU is also discussed in this paper.« less

Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium

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

Douglas, Sarah M.; Chubiz, Lon M.; Harcombe, William R.

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium,we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determinecommunity dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymousmutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator andmore » were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in termsof individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior.« less

Tectono-stratigraphic evolution of salt-controlled minibasins in a fold and thrust belt, the Oligo-Miocene central Sivas Basin

NASA Astrophysics Data System (ADS)

Kergaravat, Charlie; Ribes, Charlotte; Callot, Jean-Paul; Ringenbach, Jean-Claude

2017-09-01

The Central Sivas Basin (Turkey) provides an outcrop example of a minibasin province developed above a salt canopy within a foreland-fold and thrust belt. Several minibasins are examined to assess the influence of regional Oligo-Miocene shortening during the development of a minibasin province. The results are based on extensive field work, including regional and detailed outcrop mapping of at least 15 minibasin margins and analysis of the structural elements at all scales. This reveals a progressive increase in shortening and a decrease in salt tectonics during evolution of the province. The initiation of minibasins is driven mostly by the salt-induced accommodation forming a polygonal network of salt structures with mainly local halokinetic sequences (i.e. hooks and wedges). The initiation of shortening is marked by an abrupt increase in sedimentation rate within the flexural foreland basin causing burial of the preexisting salt structures. Subsequently, orogenic compression encourages the rejuvenation of linear salt structures oriented at right angle to the regional shortening direction. The influence of orogenic shortening during the last steps of the minibasin province evolution is clearly shown by: (i) the squeezing of salt structures to form welds which are developed both at right angle and oblique to the regional shortening direction, (ii) the emergence of thrust faults, (iii) the tilting and rotation of minibasins about vertical axis associated with the formation of strike-slip fault zones, and (iv) the extrusion of salt sheets. The pre-shortening geometry of the salt structures pattern, polygonal network of walls and diapirs versus linear and sub-parallel walls, influence the resultant structural style of the minibasin province subjected to shortening. Preexisting linear depocenter limited by sub-parallel walls accommodate preferentially the shortening compare to the preexisting sub-circular depocenter limited by polygonal network of salt walls and diapirs.

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

PubMed Central

Kümpers, Britta M. C.; Smith-Unna, Richard D.; Hibberd, Julian M.

2014-01-01

With at least 60 independent origins spanning monocotyledons and dicotyledons, the C4 photosynthetic pathway represents one of the most remarkable examples of convergent evolution. The recurrent evolution of this highly complex trait involving alterations to leaf anatomy, cell biology and biochemistry allows an increase in productivity by ∼50% in tropical and subtropical areas. The extent to which separate lineages of C4 plants use the same genetic networks to maintain C4 photosynthesis is unknown. We developed a new informatics framework to enable deep evolutionary comparison of gene expression in species lacking reference genomes. We exploited this to compare gene expression in species representing two independent C4 lineages (Cleome gynandra and Zea mays) whose last common ancestor diverged ∼140 million years ago. We define a cohort of 3,335 genes that represent conserved components of leaf and photosynthetic development in these species. Furthermore, we show that genes encoding proteins of the C4 cycle are recruited into networks defined by photosynthesis-related genes. Despite the wide evolutionary separation and independent origins of the C4 phenotype, we report that these species use homologous transcription factors to both induce C4 photosynthesis and to maintain the cell specific gene expression required for the pathway to operate. We define a core molecular signature associated with leaf and photosynthetic maturation that is likely shared by angiosperm species derived from the last common ancestor of the monocotyledons and dicotyledons. We show that deep evolutionary comparisons of gene expression can reveal novel insight into the molecular convergence of highly complex phenotypes and that parallel evolution of trans-factors underpins the repeated appearance of C4 photosynthesis. Thus, exploitation of extant natural variation associated with complex traits can be used to identify regulators. Moreover, the transcription factors that are shared by independent C4 lineages are key targets for engineering the C4 pathway into C3 crops such as rice. PMID:24901697

Comparison of fault-related folding algorithms to restore a fold-and-thrust-belt

NASA Astrophysics Data System (ADS)

Brandes, Christian; Tanner, David

2017-04-01

Fault-related folding means the contemporaneous evolution of folds as a consequence of fault movement. It is a common deformation process in the upper crust that occurs worldwide in accretionary wedges, fold-and-thrust belts, and intra-plate settings, in either strike-slip, compressional, or extensional regimes. Over the last 30 years different algorithms have been developed to simulate the kinematic evolution of fault-related folds. All these models of fault-related folding include similar simplifications and limitations and use the same kinematic behaviour throughout the model (Brandes & Tanner, 2014). We used a natural example of fault-related folding from the Limón fold-and-thrust belt in eastern Costa Rica to test two different algorithms and to compare the resulting geometries. A thrust fault and its hanging-wall anticline were restored using both the trishear method (Allmendinger, 1998; Zehnder & Allmendinger, 2000) and the fault-parallel flow approach (Ziesch et al. 2014); both methods are widely used in academia and industry. The resulting hanging-wall folds above the thrust fault are restored in substantially different fashions. This is largely a function of the propagation-to-slip ratio of the thrust, which controls the geometry of the related anticline. Understanding the controlling factors for anticline evolution is important for the evaluation of potential hydrocarbon reservoirs and the characterization of fault processes. References: Allmendinger, R.W., 1998. Inverse and forward numerical modeling of trishear fault propagation folds. Tectonics, 17, 640-656. Brandes, C., Tanner, D.C. 2014. Fault-related folding: a review of kinematic models and their application. Earth Science Reviews, 138, 352-370. Zehnder, A.T., Allmendinger, R.W., 2000. Velocity field for the trishear model. Journal of Structural Geology, 22, 1009-1014. Ziesch, J., Tanner, D.C., Krawczyk, C.M. 2014. Strain associated with the fault-parallel flow algorithm during kinematic fault displacement. Mathematical Geosciences, 46(1), 59-73.

Time to split Salvia s.l. (Lamiaceae) - New insights from Old World Salvia phylogeny.

PubMed

Will, Maria; Claßen-Bockhoff, Regine

2017-04-01

Salvia L. is widely known as the largest genus in the mint family. A morphological modification of the androecium (lever-like stamens) was used to support this genus. However, molecular data revealed that Salvia is polyphyletic. Since phylogenetic studies largely underrepresented Old World Salvia species, we filled this gap and combined new data with existing sequences. The aim of our study was the identification of well-supported clades that provide the basis for evolutionary and taxonomic conclusions. We included ITS data (internal transcribed spacer) from 220 Salvia species, 86 of which were sequenced for the first time. Additionally, the highly variable plastid marker rpl32-trnL was sequenced, providing new data for 100 Salvia species. These sequences were combined with the accessions available from GenBank. Old World Salvia is represented herein with 57% of its species. The two datasets were analyzed separately using BI and ML approaches. Our data confirm that Salvia is polyphyletic with four distinct evolutionary lineages (Clade I-IV), including five additional genera. The clades strongly reflect the geographical distribution, i.e., Clade IV (East Asia), Clade III (Southwest Asia to Northern Africa), and Clade II (America). The origin of Salvia s.s. (Clade I) is most likely Southwest Asia. A high degree of parallel character evolution was identified in most of the Old World sections. Based on our results, we reconstructed the evolution and biogeography of Salvia s.l. and propose to split this large group into six genera, each supported by geographical distribution, morphology, and karyology. Salvia s.l. is a polyphyletic group that was originally regarded as a genus because its species share a derived stamen structure. However, phylogenetic data clearly indicate that this floral trait and other morphological characters evolved in parallel. Our study illustrates that the combination of different data sets allows a comprehensive reconstruction of taxa and characteristic evolution, both of which are a precondition for future revision. Copyright © 2017 Elsevier Inc. All rights reserved.

Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic’s Era

PubMed Central

Moroz, Leonid L.

2015-01-01

The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570–600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the “omic” era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless “experiments” Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity. PMID:26163680

Morphometric and magmatic evolution at the Boset-Bericha Volcanic Complex in the Main Ethiopian Rift

NASA Astrophysics Data System (ADS)

Siegburg, Melanie; Gernon, Thomas; Bull, Jonathan; Keir, Derek; Taylor, Rex; Nixon, Casey; Abebe, Bekele; Ayele, Atalay

2017-04-01

Tectono-magmatic interactions are an intrinsic feature of continental rifting and break up in the Main Ethiopian Rift (MER). The Boset-Bericha volcanic complex (BBVC) is one of the largest stratovolcanoes in the MER (with a total area of ˜870 km2), with volcanism largely occurring over the last ˜2 Myr. Despite the fact that 4 million people live within 100 km of the volcano, little is known about its eruptive history and how the volcanic system interacts with rift valley tectonics. Here, we present a detailed relative eruption chronology combined with morphometric analyses of different elements of the volcanic complex and petrological analyses to constrain morphometric and magmatic evolution at the BBVC. Additionally, tectonic activity has been characterised around the BBVC, all based on field observations and mapping using high-resolution digital elevation data. The BBVC consists of the Gudda Volcano and the younger Bericha Volcano, two silicic eruption centres located along the NNE-SSW trending rift axis. The fault population predominantly comprises distributed extensional faults parallel to the rift axis, as well as localised discrete faults with displacements of up to 50 m in the rift centre, and up to 200 m in the NE-SW trending border fault system. Multiple cones, craters and fissure systems are also oriented parallel to the rift axis, i.e. perpendicular to the minimum compressive stress. The eruption history of BBVC can be differentiated into 5 main eruption stages, subdivided into at least 12 eruptive phases with a total of 128 mappable lava flows. Crosscutting relationships of lava flows provide a relative chronology of the eruptive history of the BBVC, starting with pre-BBVC rift floor basalts, pre-caldera and caldera activity, three post-caldera phases at the Gudda Volcano and two phases forming the Bericha Volcano. At least four fissure eruption phases occurred along the rift axis temporally in between the main eruptive phases. Morphometric analyses indicate a total corrected volume of eruptive material at the BBVC of ˜36 km3. The magmatic and morphometric evolution of the BBVC is spatially and temporally complex, showing a bimodal distribution of effusive basalts towards explosive peralkaline trachytic and rhyolitic lavas for the Gudda and Bericha Volcano, respectively, with rare intermediate lavas from fissure eruptions. Preliminary geochemical data suggest that fractional crystallisation may have played an important role in driving magmatic evolution the BBVC. This study emphasises the important role of tectono-magmatic interactions in the evolution of a continental rift system.

Three-Dimensional Structural and Hydrologic Evolution of Sant Corneli Anticline, a Fault-Cored Fold in the Central Spanish Pyrenees

NASA Astrophysics Data System (ADS)

Shackleton, J. R.; Cooke, M. L.

2005-12-01

The Sant Corneli Anticline is a well-exposed example of a fault-cored fold whose hydrologic evolution and structural development are directly linked. The E-W striking anticline is ~ 5 km wide with abrupt westerly plunge, and formed in response to thrusting associated with the upper Cretaceous to Miocene collision of Iberia with Europe. The fold's core of fractured carbonates contains a variety of west dipping normal faults with meter to decameter scale displacement and abundant calcite fill. This carbonate unit is capped by a marl unit with low angle, calcite filled normal faults. The marl unit is overlain by clastic syn-tectonic strata whose sedimentary architecture records limb rotation during the evolution of the fold. The syn-tectonic strata contain a variety of joint sets that record the stresses before, during, and possibly after fold growth. Faulting in the marl and calcite-filled joints in the syn-tectonic strata suggest that normal faults within the carbonate core of the fold eventually breached the overlying marl unit. This breach may have connected the joints of the syn-tectonic strata to the underlying carbonate reservoir and eliminated previous compartmentalization of fluids. Furthermore, breaching of the marl units probably enhanced joint formation in the overlying syn-tectonic strata. Future geochemical studies of calcite compositions in the three units will address this hypothesis. Preliminary mapping of joint sets in the syn-tectonic strata reveal a multistage history of jointing. Early bed-perpendicular joints healed by calcite strike NE-SW, parallel to normal faults in the underlying carbonates, and may be related to an early regional extensional event. Younger healed bed-perpendicular joints cross cut the NE-SW striking set, and are closer to N-S in strike: these joints are interpreted to represent the initial stages of folding. Decameter scale, bed perpendicular, unfilled fractures that are sub-parallel to strike probably represent small joints and faults that formed in response to outer arc extension during folding. Many filled, late stage joints strike sub-parallel to, and increase in frequency near, normal faults and transverse structures observed in the carbonate fold core. This suggests that faulting in the underlying carbonates and marls significantly affected the joint patterns in the syn-tectonic strata. Preliminary three-dimensional finite element restorations using Dynel have allowed us to test our hypotheses and constrain the timing of jointing and marl breach.

Assessment of Plio-Pleistocene Sea Surface Temperature Evolution Across Ocean Basins, Hemispheres, and Latitudes

NASA Astrophysics Data System (ADS)

Peterson, L.; Lawrence, K. T.; Mauriello, H.; Wilson, J.; Holte, L.

2015-12-01

New sea surface temperature (SST) records from the southern Pacific and southern Atlantic Oceans allow assessment of similarities and differences in climate evolution across ocean basins, hemispheres, and latitudes over the last 5 million years. Our high-resolution, alkenone-derived SST records from ODP Sites 1088 (South Atlantic, 41°S) and 1125 (South Pacific, 42°S) share strong structural similarities. When compared with SST records from the mid-latitudes of the northern hemisphere, these records provide compelling evidence for broadly hemispherically symmetrical open-ocean temperature evolution in both ocean basins as tropical warm pools contracted over the Plio-Pleistocene. This symmetry in temperature evolution occurs despite strong asymmetries in the development of the cryosphere over this interval, which was marked by extensive northern hemisphere ice sheet growth. Parallel SST evolution across ocean basins and hemispheres suggests that on longterm (>105 yr) timescales, many regions of the world ocean are more sensitive to the global energy budget than to local or regional climate dynamics, although important exceptions include coastal upwelling zone SSTs, high latitude SSTs, and benthic δ18O. Our analysis further reveals that throughout the last 5 Ma, temperature evolution in the extra-tropical Pacific of both hemispheres is very similar to the evolution of SST in the eastern equatorial Pacific upwelling zone, revealing tight coupling between the growth of meridional and equatorial Pacific zonal temperature gradients over this interval as both the extra-tropics and the eastern equatorial Pacific cold tongue underwent cooling. Finally, while long term temperature evolution is broadly consistent across latitudes and ocean basins throughout the entire Plio-Pleistocene, we see evidence that climate coupling on orbital timescales strengthened significantly at 2.7 Ma, at which point obliquity-band coherence emerges among diverse SST records. We attribute this emergence of coherence to a strengthened greenhouse gas feedback at the obliquity frequency that was initiated with the intensification of northern hemisphere glaciation, as proposed by Herbert et al. (2010).

Evolution of the axial electron cyclotron maser instability, with applications to solar microwave spikes

NASA Technical Reports Server (NTRS)

Vlahos, Loukas; Sprangle, Phillip

1987-01-01

The nonlinear evolution of cyclotron radiation from streaming and gyrating electrons in an external magnetic field is analyzed. The nonlinear dynamics of both the fields and the particles are treated fully relativistically and self-consistently. The model includes a background plasma and electrostatic effects. The analytical and numerical results show that a substantial portion of the beam particle energy can be converted to electromagnetic wave energy at frequencies far above the electron cyclotron frequency. In general, the excited radiation can propagate parallel to the magnetic field and, hence, escape gyrothermal absorption at higher cyclotron harmonics. The high-frequency Doppler-shifted cyclotron instability can have saturation efficiencies far higher than those associated with well-known instabilities of the electron cyclotron maser type. Although the analysis is general, the possibility of using this model to explain the intense radio emission observed from the sun is explored in detail.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been provEn effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. Several approaches that have proven effective for other evolutionary algorithms are modified and implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for standard test optimization problems and for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Sequence Memory Constraints Give Rise to Language-Like Structure through Iterated Learning

PubMed Central

Cornish, Hannah; Dale, Rick; Kirby, Simon; Christiansen, Morten H.

2017-01-01

Human language is composed of sequences of reusable elements. The origins of the sequential structure of language is a hotly debated topic in evolutionary linguistics. In this paper, we show that sets of sequences with language-like statistical properties can emerge from a process of cultural evolution under pressure from chunk-based memory constraints. We employ a novel experimental task that is non-linguistic and non-communicative in nature, in which participants are trained on and later asked to recall a set of sequences one-by-one. Recalled sequences from one participant become training data for the next participant. In this way, we simulate cultural evolution in the laboratory. Our results show a cumulative increase in structure, and by comparing this structure to data from existing linguistic corpora, we demonstrate a close parallel between the sets of sequences that emerge in our experiment and those seen in natural language. PMID:28118370

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

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.

Managing competing goals - a key role for the frontopolar cortex.

PubMed

Mansouri, Farshad Alizadeh; Koechlin, Etienne; Rosa, Marcello G P; Buckley, Mark J

2017-11-01

Humans are set apart from other animals by many elements of advanced cognition and behaviour, including language, judgement and reasoning. What is special about the human brain that gives rise to these abilities? Could the foremost part of the prefrontal cortex (the frontopolar cortex), which has become considerably enlarged in humans during evolution compared with other animals, be important in this regard, especially as, in primates, it contains a unique cytoarchitectural field, area 10? The first studies of the function of the frontopolar cortex in monkeys have now provided critical new insights about its precise role in monitoring the significance of current and alternative goals. In human evolution, the frontopolar cortex may have acquired a further role in enabling the monitoring of the significance of multiple goals in parallel, as well as switching between them. Here, we argue that many other forms of uniquely human behaviour may benefit from this cognitive ability mediated by the frontopolar cortex.

Parallel gradualistic evolution of Ordovician trilobites.

PubMed

Sheldon, P R

There are very few high-resolution studies of the fossil record from which to assess the relative frequency of gradualistic and punctuated evolution. Here I report some of the first detailed evidence of phyletic gradualism in benthic macroinvertebrates, based on a study of approximately 15,000 trilobites from central Wales. Over a period of about three million years, as many as eight lineages underwent a net increase in the number of pygidial ribs, a species-diagnostic character. The end members of most lineages have previously been assigned to different species and, in one case, to different genera. In view of intermediate morphologies and temporary trend reversals, however, practical taxonomic subdivision of each lineage proved impossible. The apparent success of earlier Linnean nomenclature (with its implications of discrete species) could easily have been misinterpreted as evidence of punctuation and stasis, and it is probable that detection of many other gradualistic patterns has been hindered by ready application of binominal taxonomy to fossils.

Continuing Evolution of Mars Sample Return

NASA Technical Reports Server (NTRS)

Mattingly, Richard; Matousek, Steve; Jordan, Frank

2004-01-01

This paper addresses the continued evolution of the Groundbreaking MSR concept over the last year. One of the tenets of the low-cost approach is to use substantial heritage from an earlier mission, Mars Science Laboratory (MSL). Recently, the MSL project developed and switched to a revolutionary landing approach, coined 'sky-crane' where the MSL, which is a rover, is lowered gently to the Martian surface from a hovering vehicle. MSR has adopted this approach, again continuing to capitalize on the heritage for a significant portion of the new lander. In parallel, a MSR Technology Board was formed to reexamine MSR technology needs and participate in a continuing refinement of architectural trades. While the focused technology program continues to be definitized through the remainder of this year, the current assessment of what technology development is required, is discussed in this paper. In addition, the results of new trade studies and considerations will be discussed.

[PRENATAL DIAGNOSIS: EVOLUTION OF CLINICAL INDICATIONS AND THE SOCIETY IN THE PAST 30 YEARS].

PubMed

Sagredo, José Miguel García

2014-01-01

Here we report the results of prenatal diagnosis at the Hospital Universitario Ramón y Cajal since its opening in 1979 to 2010, establishing a parallelism between the different methodologies for screening and prenatal diagnosis, clinical indications, and demographic changes. It shows how the indications have varied as to the structure of the population did. These changes have been possible thanks to the fact that the screening and prenatal diagnosis methods have allowed it. Demonstrating, once again, how procedures evolve with technology and adapt to the demography. This evolution has allowed to make a more effective prenatal diagnosis because the clinical indications have been more precise what has allowed to detect the same number of fetuses with chromosomal abnormalities by performing less invasive procedures, which has led to an optimization of prenatal diagnosis saving resources and personnel and, above all, avoiding unnecessary fetal losses.

Inhomogeneous cosmology and backreaction: Current status and future prospects

NASA Astrophysics Data System (ADS)

Bolejko, Krzysztof; Korzyński, Mikołaj

Astronomical observations reveal hierarchical structures in the universe, from galaxies, groups of galaxies, clusters and superclusters, to filaments and voids. On the largest scales, it seems that some kind of statistical homogeneity can be observed. As a result, modern cosmological models are based on spatially homogeneous and isotropic solutions of the Einstein equations, and the evolution of the universe is approximated by the Friedmann equations. In parallel to standard homogeneous cosmology, the field of inhomogeneous cosmology and backreaction is being developed. This field investigates whether small scale inhomogeneities via nonlinear effects can backreact and alter the properties of the universe on its largest scales, leading to a non-Friedmannian evolution. This paper presents the current status of inhomogeneous cosmology and backreaction. It also discusses future prospects of the field of inhomogeneous cosmology, which is based on a survey of 50 academics working in the field of inhomogeneous cosmology.

Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

NASA Technical Reports Server (NTRS)

Nakayama, S.; Kretsinger, R. H.

1993-01-01

In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

Epigenetics: Biology's Quantum Mechanics

PubMed Central

Jorgensen, Richard A.

2011-01-01

The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene – the molecular biological view and the epigenetic view – are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider. PMID:22639577

Hemimetabolous genomes reveal molecular basis of termite eusociality.

PubMed

Harrison, Mark C; Jongepier, Evelien; Robertson, Hugh M; Arning, Nicolas; Bitard-Feildel, Tristan; Chao, Hsu; Childers, Christopher P; Dinh, Huyen; Doddapaneni, Harshavardhan; Dugan, Shannon; Gowin, Johannes; Greiner, Carolin; Han, Yi; Hu, Haofu; Hughes, Daniel S T; Huylmans, Ann-Kathrin; Kemena, Carsten; Kremer, Lukas P M; Lee, Sandra L; Lopez-Ezquerra, Alberto; Mallet, Ludovic; Monroy-Kuhn, Jose M; Moser, Annabell; Murali, Shwetha C; Muzny, Donna M; Otani, Saria; Piulachs, Maria-Dolors; Poelchau, Monica; Qu, Jiaxin; Schaub, Florentine; Wada-Katsumata, Ayako; Worley, Kim C; Xie, Qiaolin; Ylla, Guillem; Poulsen, Michael; Gibbs, Richard A; Schal, Coby; Richards, Stephen; Belles, Xavier; Korb, Judith; Bornberg-Bauer, Erich

2018-03-01

Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.

Intergrannular strain evolution in a zircaloy-4 alloy with Widmanstatten microstructure

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

Clausen, Bjorn; Vogel, Sven C; Garlea, Eena

2009-01-01

A Zircaloy-4 alloy with Widmanstatten-Basketweave microstructure and random texture has been used to study the deformation systems responsible for the polycrystalline plasticity at the grain level. The evolution of internal strain and bulk texture is investigated using neutron diffraction and an elasto-plastic self-consistent (EPSC) modeling scheme. The macroscopic stress-strain behavior and intergranular (hkil-specific) strain development, parallel and perpendicular to the loading direction, were measured in-situ during uniaxial tensile loading. Then, the EPSC model was employed to simulate the experimental results. This modeling scheme accounts for the thermal anisotropy; elastic-plastic properties of the constituent grains; and activation, reorientation, and stress relaxationmore » associated with twinning. The agreement between the experiment and the model will be discussed as well as the critical resolved shear stresses (CRSS) and the hardening coefficients obtained from the model.« less

Parallel evolution of the make–accumulate–consume strategy in Saccharomyces and Dekkera yeasts

PubMed Central

Rozpędowska, Elżbieta; Hellborg, Linda; Ishchuk, Olena P.; Orhan, Furkan; Galafassi, Silvia; Merico, Annamaria; Woolfit, Megan; Compagno, Concetta; Piškur, Jure

2011-01-01

Saccharomyces yeasts degrade sugars to two-carbon components, in particular ethanol, even in the presence of excess oxygen. This characteristic is called the Crabtree effect and is the background for the 'make–accumulate–consume' life strategy, which in natural habitats helps Saccharomyces yeasts to out-compete other microorganisms. A global promoter rewiring in the Saccharomyces cerevisiae lineage, which occurred around 100 mya, was one of the main molecular events providing the background for evolution of this strategy. Here we show that the Dekkera bruxellensis lineage, which separated from the Saccharomyces yeasts more than 200 mya, also efficiently makes, accumulates and consumes ethanol and acetic acid. Analysis of promoter sequences indicates that both lineages independently underwent a massive loss of a specific cis-regulatory element from dozens of genes associated with respiration, and we show that also in D. bruxellensis this promoter rewiring contributes to the observed Crabtree effect. PMID:21556056

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel

PubMed Central

Kim, Young Bun; Oh, Jung Hun; McIver, Lauren J.; Rashkovetsky, Eugenia; Michalak, Katarzyna; Garner, Harold R.; Kang, Lin; Nevo, Eviatar; Korol, Abraham B.; Michalak, Pawel

2014-01-01

Repeat sequences, especially mobile elements, make up large portions of most eukaryotic genomes and provide enormous, albeit commonly underappreciated, evolutionary potential. We analyzed repeatomes of Drosophila melanogaster that have been diverging in response to a microclimate contrast in Evolution Canyon (Mount Carmel, Israel), a natural evolutionary laboratory with two abutting slopes at an average distance of only 200 m, which pose a constant ecological challenge to their local biotas. Flies inhabiting the colder and more humid north-facing slope carried about 6% more transposable elements than those from the hot and dry south-facing slope, in parallel to a suite of other genetic and phenotypic differences between the two populations. Nearly 50% of all mobile element insertions were slope unique, with many of them disrupting coding sequences of genes critical for cognition, olfaction, and thermotolerance, consistent with the observed patterns of thermotolerance differences and assortative mating. PMID:25006263

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel.

PubMed

Kim, Young Bun; Oh, Jung Hun; McIver, Lauren J; Rashkovetsky, Eugenia; Michalak, Katarzyna; Garner, Harold R; Kang, Lin; Nevo, Eviatar; Korol, Abraham B; Michalak, Pawel

2014-07-22

Repeat sequences, especially mobile elements, make up large portions of most eukaryotic genomes and provide enormous, albeit commonly underappreciated, evolutionary potential. We analyzed repeatomes of Drosophila melanogaster that have been diverging in response to a microclimate contrast in Evolution Canyon (Mount Carmel, Israel), a natural evolutionary laboratory with two abutting slopes at an average distance of only 200 m, which pose a constant ecological challenge to their local biotas. Flies inhabiting the colder and more humid north-facing slope carried about 6% more transposable elements than those from the hot and dry south-facing slope, in parallel to a suite of other genetic and phenotypic differences between the two populations. Nearly 50% of all mobile element insertions were slope unique, with many of them disrupting coding sequences of genes critical for cognition, olfaction, and thermotolerance, consistent with the observed patterns of thermotolerance differences and assortative mating.

Evolution of Nanowire Transmon Qubits and Their Coherence in a Magnetic Field

NASA Astrophysics Data System (ADS)

Luthi, F.; Stavenga, T.; Enzing, O. W.; Bruno, A.; Dickel, C.; Langford, N. K.; Rol, M. A.; Jespersen, T. S.; Nygârd, J.; Krogstrup, P.; DiCarlo, L.

2018-03-01

We present an experimental study of flux- and gate-tunable nanowire transmons with state-of-the-art relaxation time allowing quantitative extraction of flux and charge noise coupling to the Josephson energy. We evidence coherence sweet spots for charge, tuned by voltage on a proximal side gate, where first order sensitivity to switching two-level systems and background 1 /f noise is minimized. Next, we investigate the evolution of a nanowire transmon in a parallel magnetic field up to 70 mT, the upper bound set by the closing of the induced gap. Several features observed in the field dependence of qubit energy relaxation and dephasing times are not fully understood. Using nanowires with a thinner, partially covering Al shell will enable operation of these circuits up to 0.5 T, a regime relevant for topological quantum computation and other applications.

Cellular automaton model for molecular traffic jams

NASA Astrophysics Data System (ADS)

Belitsky, V.; Schütz, G. M.

2011-07-01

We consider the time evolution of an exactly solvable cellular automaton with random initial conditions both in the large-scale hydrodynamic limit and on the microscopic level. This model is a version of the totally asymmetric simple exclusion process with sublattice parallel update and thus may serve as a model for studying traffic jams in systems of self-driven particles. We study the emergence of shocks from the microscopic dynamics of the model. In particular, we introduce shock measures whose time evolution we can compute explicitly, both in the thermodynamic limit and for open boundaries where a boundary-induced phase transition driven by the motion of a shock occurs. The motion of the shock, which results from the collective dynamics of the exclusion particles, is a random walk with an internal degree of freedom that determines the jump direction. This type of hopping dynamics is reminiscent of some transport phenomena in biological systems.

Sequence Memory Constraints Give Rise to Language-Like Structure through Iterated Learning.

PubMed

Cornish, Hannah; Dale, Rick; Kirby, Simon; Christiansen, Morten H

2017-01-01

Human language is composed of sequences of reusable elements. The origins of the sequential structure of language is a hotly debated topic in evolutionary linguistics. In this paper, we show that sets of sequences with language-like statistical properties can emerge from a process of cultural evolution under pressure from chunk-based memory constraints. We employ a novel experimental task that is non-linguistic and non-communicative in nature, in which participants are trained on and later asked to recall a set of sequences one-by-one. Recalled sequences from one participant become training data for the next participant. In this way, we simulate cultural evolution in the laboratory. Our results show a cumulative increase in structure, and by comparing this structure to data from existing linguistic corpora, we demonstrate a close parallel between the sets of sequences that emerge in our experiment and those seen in natural language.

Evolutionary transitions towards eusociality in snapping shrimps.

PubMed

Chak, Solomon Tin Chi; Duffy, J Emmett; Hultgren, Kristin M; Rubenstein, Dustin R

2017-03-20

Animal social organization varies from complex societies where reproduction is dominated by a single individual (eusociality) to those where reproduction is more evenly distributed among group members (communal breeding). Yet, how simple groups transition evolutionarily to more complex societies remains unclear. Competing hypotheses suggest that eusociality and communal breeding are alternative evolutionary endpoints, or that communal breeding is an intermediate stage in the transition towards eusociality. We tested these alternative hypotheses in sponge-dwelling shrimps, Synalpheus spp. Although species varied continuously in reproductive skew, they clustered into pair-forming, communal and eusocial categories based on several demographic traits. Evolutionary transition models suggested that eusocial and communal species are discrete evolutionary endpoints that evolved independently from pair-forming ancestors along alternative paths. This 'family-centred' origin of eusociality parallels observations in insects and vertebrates, reinforcing the role of kin selection in the evolution of eusociality and suggesting a general model of animal social evolution.

Parallel Evolution of Larval Feeding Behavior, Morphology, and Habitat in the Snail-Kiling fly Genus Tetanocera

NASA Astrophysics Data System (ADS)

Chapman, E. G.; Foote, B. A.; Malukiewicz, J.; Hoeh, W. R.

2005-05-01

Sciomyzid larvae (Diptera: Acalyptratae) display a wide range of feeding behaviors, typically preying on a wide variety of gastropods. The genus Tetanocera is particularly interesting because its species occupy five larval feeding groups with each species' larvae living in one of two habitat types (aquatic or terrestrial). We constructed a molecular phylogeny for Tetanocera, estimated evolutionary transitions in larval feeding behaviors and habitats that occurred during Tetanocera phylogenesis, and investigated potential correlations among larval habitat and morphological characteristics. Approximately 3800 base pairs (both mitochondrial and nuclear) of sequence data were used to build the phylogeny. Larval feeding groups and habitat type were mapped onto the phylogeny and pair-wise comparisons were used to evaluate potential associations between habitat and morphology. Feeding and habitat groups within Tetanocera were usually not monophyletic and it was estimated that Tetanocera lineages made at least three independent aquatic to terrestrial transitions. These parallel habitat shifts were typically accompanied by parallel character state changes in four morphological characteristics (larval color and three posterior spiracular disc characters). These larval habitat-morphology associations were statistically significant and consistent with the action of natural selection in facilitating the morphological changes that occurred during aquatic to terrestrial habitat transitions in Tetanocera.

A Numerical Study of Scalable Cardiac Electro-Mechanical Solvers on HPC Architectures

PubMed Central

Colli Franzone, Piero; Pavarino, Luca F.; Scacchi, Simone

2018-01-01

We introduce and study some scalable domain decomposition preconditioners for cardiac electro-mechanical 3D simulations on parallel HPC (High Performance Computing) architectures. The electro-mechanical model of the cardiac tissue is composed of four coupled sub-models: (1) the static finite elasticity equations for the transversely isotropic deformation of the cardiac tissue; (2) the active tension model describing the dynamics of the intracellular calcium, cross-bridge binding and myofilament tension; (3) the anisotropic Bidomain model describing the evolution of the intra- and extra-cellular potentials in the deforming cardiac tissue; and (4) the ionic membrane model describing the dynamics of ionic currents, gating variables, ionic concentrations and stretch-activated channels. This strongly coupled electro-mechanical model is discretized in time with a splitting semi-implicit technique and in space with isoparametric finite elements. The resulting scalable parallel solver is based on Multilevel Additive Schwarz preconditioners for the solution of the Bidomain system and on BDDC preconditioned Newton-Krylov solvers for the non-linear finite elasticity system. The results of several 3D parallel simulations show the scalability of both linear and non-linear solvers and their application to the study of both physiological excitation-contraction cardiac dynamics and re-entrant waves in the presence of different mechano-electrical feedbacks. PMID:29674971

A parallel domain decomposition-based implicit method for the Cahn–Hilliard–Cook phase-field equation in 3D

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

Zheng, Xiang; Yang, Chao; State Key Laboratory of Computer Science, Chinese Academy of Sciences, Beijing 100190

2015-03-15

We present a numerical algorithm for simulating the spinodal decomposition described by the three dimensional Cahn–Hilliard–Cook (CHC) equation, which is a fourth-order stochastic partial differential equation with a noise term. The equation is discretized in space and time based on a fully implicit, cell-centered finite difference scheme, with an adaptive time-stepping strategy designed to accelerate the progress to equilibrium. At each time step, a parallel Newton–Krylov–Schwarz algorithm is used to solve the nonlinear system. We discuss various numerical and computational challenges associated with the method. The numerical scheme is validated by a comparison with an explicit scheme of high accuracymore » (and unreasonably high cost). We present steady state solutions of the CHC equation in two and three dimensions. The effect of the thermal fluctuation on the spinodal decomposition process is studied. We show that the existence of the thermal fluctuation accelerates the spinodal decomposition process and that the final steady morphology is sensitive to the stochastic noise. We also show the evolution of the energies and statistical moments. In terms of the parallel performance, it is found that the implicit domain decomposition approach scales well on supercomputers with a large number of processors.« less

Role of interbranch pumping on the quantum-statistical behavior of multi-mode magnons in ferromagnetic nanowires

NASA Astrophysics Data System (ADS)

Haghshenasfard, Zahra; Cottam, M. G.

2018-01-01

Theoretical studies are reported for the quantum-statistical properties of microwave-driven multi-mode magnon systems as represented by ferromagnetic nanowires with a stripe geometry. Effects of both the exchange and the dipole-dipole interactions, as well as a Zeeman term for an external applied field, are included in the magnetic Hamiltonian. The model also contains the time-dependent nonlinear effects due to parallel pumping with an electromagnetic field. Using a coherent magnon state representation in terms of creation and annihilation operators, we investigate the effects of parallel pumping on the temporal evolution of various nonclassical properties of the system. A focus is on the interbranch mixing produced by the pumping field when there are three or more modes. In particular, the occupation magnon number and the multi-mode cross correlations between magnon modes are studied. Manipulation of the collapse and revival phenomena of the average magnon occupation number and the control of the cross correlation between the magnon modes are demonstrated through tuning of the parallel pumping field amplitude and appropriate choices for the coherent magnon states. The cross correlations are a direct consequence of the interbranch pumping effects and do not appear in the corresponding one- or two-mode magnon systems.

Range-wide parallel climate-associated genomic clines in Atlantic salmon

PubMed Central

Stanley, Ryan R. E.; Wringe, Brendan F.; Guijarro-Sabaniel, Javier; Bourret, Vincent; Bernatchez, Louis; Bentzen, Paul; Beiko, Robert G.; Gilbey, John; Clément, Marie; Bradbury, Ian R.

2017-01-01

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change. PMID:29291123