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Sample records for anopheline divergence time

  1. A sensitive, specific and reproducible real-time polymerase chain reaction method for detection of Plasmodium vivax and Plasmodium falciparum infection in field-collected anophelines.

    Science.gov (United States)

    Bickersmith, Sara A; Lainhart, William; Moreno, Marta; Chu, Virginia M; Vinetz, Joseph M; Conn, Jan E

    2015-06-01

    We describe a simple method for detection of Plasmodium vivax and Plasmodium falciparum infection in anophelines using a triplex TaqMan real-time polymerase chain reaction (PCR) assay (18S rRNA). We tested the assay on Anopheles darlingi and Anopheles stephensi colony mosquitoes fed with Plasmodium-infected blood meals and in duplicate on field collected An. darlingi. We compared the real-time PCR results of colony-infected and field collected An. darlingi, separately, to a conventional PCR method. We determined that a cytochrome b-PCR method was only 3.33% as sensitive and 93.38% as specific as our real-time PCR assay with field-collected samples. We demonstrate that this assay is sensitive, specific and reproducible.

  2. Comparison of the Performances of Five Primer Sets for the Detection and Quantification of Plasmodium in Anopheline Vectors by Real-Time PCR.

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    V Chaumeau

    Full Text Available Quantitative real-time polymerase chain reaction (qrtPCR has made a significant improvement for the detection of Plasmodium in anopheline vectors. A wide variety of primers has been used in different assays, mostly adapted from molecular diagnosis of malaria in human. However, such an adaptation can impact the sensitivity of the PCR. Therefore we compared the sensitivity of five primer sets with different molecular targets on blood stages, sporozoites and oocysts standards of Plasmodium falciparum (Pf and P. vivax (Pv. Dilution series of standard DNA were used to discriminate between methods at low concentrations of parasite and to generate standard curves suitable for the absolute quantification of Plasmodium sporozoites. Our results showed that the best primers to detect blood stages were not necessarily the best ones to detect sporozoites. Absolute detection threshold of our qrtPCR assay varied between 3.6 and 360 Pv sporozoites and between 6 and 600 Pf sporozoites per mosquito according to the primer set used in the reaction mix. In this paper, we discuss the general performance of each primer set and highlight the need to use efficient detection methods for transmission studies.

  3. Comparison of the Performances of Five Primer Sets for the Detection and Quantification of Plasmodium in Anopheline Vectors by Real-Time PCR.

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    Chaumeau, V; Andolina, C; Fustec, B; Tuikue Ndam, N; Brengues, C; Herder, S; Cerqueira, D; Chareonviriyaphap, T; Nosten, F; Corbel, V

    2016-01-01

    Quantitative real-time polymerase chain reaction (qrtPCR) has made a significant improvement for the detection of Plasmodium in anopheline vectors. A wide variety of primers has been used in different assays, mostly adapted from molecular diagnosis of malaria in human. However, such an adaptation can impact the sensitivity of the PCR. Therefore we compared the sensitivity of five primer sets with different molecular targets on blood stages, sporozoites and oocysts standards of Plasmodium falciparum (Pf) and P. vivax (Pv). Dilution series of standard DNA were used to discriminate between methods at low concentrations of parasite and to generate standard curves suitable for the absolute quantification of Plasmodium sporozoites. Our results showed that the best primers to detect blood stages were not necessarily the best ones to detect sporozoites. Absolute detection threshold of our qrtPCR assay varied between 3.6 and 360 Pv sporozoites and between 6 and 600 Pf sporozoites per mosquito according to the primer set used in the reaction mix. In this paper, we discuss the general performance of each primer set and highlight the need to use efficient detection methods for transmission studies.

  4. A Key to the Anophelines of Iran

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    Eugene R. Shahgudian

    1960-01-01

    Full Text Available Keys for identification of adult females and fourth instar larvae of Anopheline Mosquitoes of Iran with brief review of important literature on the Iranian Anopheline Fauna are given in this paper

  5. Carrier relaxation time divergence in single and double layer cuprates

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    Schneider, M. L.; Rast, S.; Onellion, M.; Demsar, J.; Taylor, A. J.; Glinka, Y.; Tolk, N. H.; Ren, Y. H.; Lüpke, G.; Klimov, A.; Xu, Y.; Sobolewski, R.; Si, W.; Zeng, X. H.; Soukiassian, A.; Xi, X. X.; Abrecht, M.; Ariosa, D.; Pavuna, D.; Krapf, A.; Manzke, R.; Printz, J. O.; Williamsen, M. S.; Downum, K. E.; Guptasarma, P.; Bozovic, I.

    2003-12-01

    We report the transient optical pump-probe reflectivity measurements on single and double layer cuprate single crystals and thin films of ten different stoichiometries. We find that with sufficiently low fluence the relaxation time (tauR) of all samples exhibits a power law divergence with temperature (T): tauR ∝ T^{-3 ± 0.5}. Further, the divergence has an onset temperature above the superconducting transition temperature for all superconducting samples. Possible causes of this divergence are discussed.

  6. Carrier Rexlaxation Time Divergence in Single and Double Layer Cuprates.

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, M.; Rast, S.; Onellion, M.; Demsar, J.; Taylor, A. J.; Glinka, Y.; Tolk, N. H.; Ren, Y. H.; Lupke, G.; Klimov, A.; Sobolewski, R.; Xu, Y.; Si, Weidong; Zeng, X. H.; Soukiassian, A.; Xi, X. X.; Abrecht, M.; Ariosa, D.; Pavuna, D.; Drapf, A.; Manzke, R.; Printz, J. O.; Williamsen, M. S.; Downum, K. E.; Guptasarma, P.

    2003-06-20

    We report the transient optical pump-probe reflectivity measurements on single and double layer cuprate single crystals and thin films of ten different stoichiometries. We find that with sufficiently low fluence the relaxation time (tau [sub R] of all samples exhibits a power law divergence with temperature (T): tau [sub R] [proportional to] T[sup -3 [plus or minus] 0.5]. Further, the divergence has an onset temperature above the superconducting transition temperature for all superconducting samples. Possible causes of this divergence are discussed.

  7. Estimating Divergence Times and Substitution Rates in Rhizobia.

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    Chriki-Adeeb, Rim; Chriki, Ali

    2016-01-01

    Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.

  8. Determining divergence times with a protein clock: update and reevaluation

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    Feng, D. F.; Cho, G.; Doolittle, R. F.; Bada, J. L. (Principal Investigator)

    1997-01-01

    A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

  9. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

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    Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

  10. The unbearable uncertainty of Bayesian divergence time estimation

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    Mario DOS REIS; Ziheng YANG

    2013-01-01

    Divergence time estimation using molecular sequence data relying on uncertain fossil calibrations is an unconventional statistical estimation problem.As the sequence data provide information about the distances only,estimation of absolute times and rates has to rely on information in the prior,so that the model is only semiidentifiable.In this paper,we use a combination of mathematical analysis,computer simulation,and real data analysis to examine the uncertainty in posterior time estimates when the amount of sequence data increases.The analysis extends the infinite-sites theory of Yang and Rannala,which predicts the posterior distribution of divergence times and rate when the amount of data approaches infinity.We found that the posterior credibility interval in general decreases and reaches a non-zero limit when the data size increases.However,for the node with the most precise fossil calibration (as measured by the interval width divided by the mid value),sequence data do not really make the time estimate any more precise.We propose a finite-sites theory which predicts that the square of the posterior interval width approaches its infinite-data limit at the rate 1/n,where n is the sequence length.We suggest a procedure to partition the uncertainty of posterior time estimates into that due to uncertainties in fossil calibrations and that due to sampling errors in the sequence data.We evaluate the impact of conflicting fossil calibrations on posterior time estimation and point out that narrow credibility intervals or overly precise time estimates can be produced by conflicting or erroneous fossil calibrations.

  11. A survey of adult anophelines in French Guiana: enhanced descriptions of species distribution and biting responses.

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    Dusfour, Isabelle; Carinci, Romuald; Issaly, Jean; Gaborit, Pascal; Girod, Romain

    2013-12-01

    In French Guiana, Anopheles darlingi is considered the main malaria vector. However, several reports have hypothesized the implication of other anopheline species in malaria transmission for the territory. Data on the ecology of these other potential vectors is rare or even unexplored in French Guiana. The aim of this study was to describe the biting habits of several anopheline species in multiple localities in French Guiana. Six sampling sites yielded 1,083 anopheline adults. Results indicated the presence of An. darlingi in all study locations and it was the only species to be collected inside villages. Other anophelines collected included An. aquasalis, An. braziliensis, An. intermedius, An. mediopunctatus, An. nuneztovari, An. oswaldoi, and An. triannulatus, all of which were associated with open areas and forests. The environment and time, at which biting behavior was recorded, varied for each species. It was noted that An. oswaldoi showed a daytime rhythm in open areas. This study is the first to report on the biting habits of a range of anophelines in French Guiana that may play a role in malaria transmission. This information is vital to fully describe the risk of malaria transmission and thereby design appropriate vector control measures and malaria prevention programs.

  12. Consequences of Secondary Calibrations on Divergence Time Estimates.

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    John J Schenk

    Full Text Available Secondary calibrations (calibrations based on the results of previous molecular dating studies are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.

  13. Proterozoic microfossils revealing the time of algal divergences

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    Moczydlowska-Vidal, Malgorzata

    2010-05-01

    Proterozoic microfossils revealing the time of algal divergences Małgorzata Moczydłowska-Vidal Uppsala University, Department of Earth Sciences, Palaeobiology, Villavägen 16, SE 752 36 Uppsala, Sweden (malgo.vidal@pal.uu.se) Morphological and reproductive features and cell wall ultrastructure and biochemistry of Proterozoic acritarchs are used to determine their affinity to modern algae. The first appearance datum of these microbiota is traced to infer a minimum age of the divergence of the algal classes to which they may belong. The chronological appearance of microfossils that represent phycoma-like and zygotic cysts and vegetative cells and/or aplanospores, respectively interpreted as prasinophyceaen and chlorophyceaen microalgae, is related to the Viridiplantae phylogeny. These divergence times differ from molecular clock estimates, and the palaeontological evidence suggests that they are older. The best examples of unicellular, organic-walled microfossils (acritarchs) from the Mesoproterozoic to Early Ordovician are reviewed to demonstrate features, which are indicative of their affinity to photosynthetic microalgae. The first indication that a microfossil may be algal is a decay- and acid-resistant cell wall, which reflects its biochemistry and ultrastructure, and probably indicates the ability to protect a resting/reproductive cyst. The biopolymers synthesized in the cell walls of algae and in land plants ("plant cells"), such as sporopollenin/algaenan, are diagnostic for photosynthetic taxa and were inherited from early unicellular ancestors. These preservable cell walls are resistant to acetolysis, hydrolysis and acids, and show diagnostic ultrastructures such as the trilaminar sheath structure (TLS). "Plant cell" walls differ in terms of chemical compounds, which give high preservation potential, from fungal and animal cell walls. Fungal and animal cells are fossilized only by syngenetic permineralization, whereas "plant cells" are fossilized as body

  14. Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times.

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    Gómez-Acevedo, Sandra; Rico-Arce, Lourdes; Delgado-Salinas, Alfonso; Magallón, Susana; Eguiarte, Luis E

    2010-07-01

    The interaction between Acacia and Pseudomyrmex is a textbook example of mutualism between ants and plants, nevertheless aspects of its evolutionary biology have not been formally explored. In this paper we analyze primarily the phylogenies of both New World Acacia and of their associated species of ants, and the geographic origin of this mutualism. Until now, there has been no molecular analysis of this relationship in terms of its origin and age. We analyzed three chloroplast markers (matK, psaB-rps14, and trnL-trnF) on a total of 70 taxa of legumes from the subfamily Mimosoideae, and two nuclear regions (long-wavelength rhodopsine and wingless) on a total of 43 taxa of ants from subfamily Pseudomyrmecinae. The monophyly of subgenus Acacia and within the New World lineages that of the myrmecophilous Acacia group was established. In addition, our results supported the monophyly of the genus Pseudomyrmex and of the associated acacia-ants P. ferrugineus group. Using Bayesian methods and calibration data, the estimated divergence times for the groups involved in the mutualism are: 5.44+/-1.93 My for the myrmecophilous acacias and 4.58+/-0.82 My for their associated ant species, implying that their relationship originated in Mesoamerica between the late Miocene to the middle Pliocene, with eventual diversification of both groups in Mexico.

  15. Wind, METOP ASCAT, 0.25 degrees, Global, Near Real Time, Divergence

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    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA CoastWatch distributes near real time wind divergence data originating with wind velocity measurements from the ASCAT instrument onboard EUMETSAT's ASCAT...

  16. Why are anopheline mosquitoes not present in the Seychelles?

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    Goodman Steven M

    2011-02-01

    Full Text Available Abstract Background Species of anopheline mosquitoes are largely distributed over emerged lands around the world and, within the tropics, few areas are without these insects, which are vectors of malaria parasites. Among the exceptions is the Seychelles archipelago in the western Indian Ocean. However, in the Aldabra island group, located in the extreme western portion of the archipelago, Anopheles gambiae s.l. was introduced, leading to massive proliferation and then elimination, with the most recent autochthonous malaria cases recorded in 1931. Methods In order to re-examine the absence of anopheline mosquitoes in the Seychelles, an entomological field survey was conducted in December 2008 at 17 sites on four granitic islands, including Mahé and Praslin, and ten sites on coralline atolls in the extreme west, including Aldabra. Results No evidence of larval or adult anophelines was found at the surveyed sites, which supports their absence in the Seychelles. Conclusions In the granitic islands of the Seychelles, the climate is favourable for anophelines. However, these islands are protected by their remoteness and prevailing seasonal winds. In addition, stagnant freshwater, required in anopheline larval development, is relatively uncommon on the granitic islands because of the steep slopes. In the southwestern atolls (Aldabra and Providence-Farquhar groups, the presence of a long dry season of up to nine months and the total absence of permanent natural freshwater prevents the breeding of anophelines and their successful colonization. The Seychelles does not have any native land mammals and like in other parts of the world (Antarctica, Iceland, New Caledonia, Central Pacific islands their absence is associated with the lack of anophelines. This suggests an obligatory relationship for anophelines to feed on terrestrial mammals, without alternative for blood-feeding sources, such as bats, birds and reptiles.

  17. Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae).

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    Callahan, Melissa S; McPeek, Mark A

    2016-01-01

    Reconstructing evolutionary patterns of species and populations provides a framework for asking questions about the impacts of climate change. Here we use a multilocus dataset to estimate gene trees under maximum likelihood and Bayesian models to obtain a robust estimate of relationships for a genus of North American damselflies, Enallagma. Using a relaxed molecular clock, we estimate the divergence times for this group. Furthermore, to account for the fact that gene tree analyses can overestimate ages of population divergences, we use a multi-population coalescent model to gain a more accurate estimate of divergence times. We also infer diversification rates using a method that allows for variation in diversification rate through time and among lineages. Our results reveal a complex evolutionary history of Enallagma, in which divergence events both predate and occur during Pleistocene climate fluctuations. There is also evidence of diversification rate heterogeneity across the tree. These divergence time estimates provide a foundation for addressing the relative significance of historical climatic events in the diversification of this genus.

  18. Population divergence times and historical demography in red knots and dunlins

    NARCIS (Netherlands)

    Buehler, DM; Baker, AJ

    2005-01-01

    We employed Bayesian coalescent modeling of samples of mitochondrial control region sequences in two species of shorebird, Red Knots (Calidris canutus) and Durdins (Calidris alpina) to estimate evolutionary effective population size, population divergence times, and time to most recent common ancest

  19. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals

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    Foote, M.; Hunter, J. P.; Janis, C. M.; Sepkoski, J. J. Jr

    1999-01-01

    Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records.

  20. Impact of curvature divergences on physical observers in a wormhole space-time with horizons

    CERN Document Server

    Olmo, Gonzalo J; Sanchez-Puente, A

    2016-01-01

    The impact of curvature divergences on physical observers in a black hole space-time which, nonetheless, is geodesically complete is investigated. This space-time is an exact solution of certain extensions of General Relativity coupled to Maxwell's electrodynamics and, roughly speaking, consists on two Reissner-Nordstr\\"{o}m (or Schwarzschild or Minkowski) geometries connected by a spherical wormhole near the center. We find that, despite the existence of infinite tidal forces, causal contact is never lost among the elements making up the observer. This suggests that curvature divergences may not be as pathological as traditionally thought.

  1. Divergence time estimates and the evolution of major lineages in the florideophyte red algae.

    Science.gov (United States)

    Yang, Eun Chan; Boo, Sung Min; Bhattacharya, Debashish; Saunders, Gary W; Knoll, Andrew H; Fredericq, Suzanne; Graf, Louis; Yoon, Hwan Su

    2016-02-19

    The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.

  2. Caspar controls resistance to Plasmodium falciparum in diverse anopheline species.

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    Lindsey S Garver

    2009-03-01

    Full Text Available Immune responses mounted by the malaria vector Anopheles gambiae are largely regulated by the Toll and Imd (immune deficiency pathways via the NF-kappaB transcription factors Rel1 and Rel2, which are controlled by the negative regulators Cactus and Caspar, respectively. Rel1- and Rel2-dependent transcription in A. gambiae has been shown to be particularly critical to the mosquito's ability to manage infection with the rodent malaria parasite Plasmodium berghei. Using RNA interference to deplete the negative regulators of these pathways, we found that Rel2 controls resistance of A. gambiae to the human malaria parasite Plasmodium falciparum, whereas Rel 1 activation reduced infection levels. The universal relevance of this defense system across Anopheles species was established by showing that caspar silencing also prevents the development of P. falciparum in the major malaria vectors of Asia and South America, A. stephensi and A. albimanus, respectively. Parallel studies suggest that while Imd pathway activation is most effective against P. falciparum, the Toll pathway is most efficient against P. berghei, highlighting a significant discrepancy between the human pathogen and its rodent model. High throughput gene expression analyses identified a plethora of genes regulated by the activation of the two Rel factors and revealed that the Toll pathway played a more diverse role in mosquito biology than the Imd pathway, which was more immunity-specific. Further analyses of key anti-Plasmodium factors suggest they may be responsible for the Imd pathway-mediated resistance phenotype. Additionally, we found that the fitness cost caused by Rel2 activation through caspar gene silencing was undetectable in sugar-fed, blood-fed, and P. falciparum-infected female A. gambiae, while activation of the Toll pathway's Rel1 had a major impact. This study describes for the first time a single gene that influences an immune mechanism that is able to abort

  3. Caspar controls resistance to Plasmodium falciparum in diverse anopheline species.

    Science.gov (United States)

    Garver, Lindsey S; Dong, Yuemei; Dimopoulos, George

    2009-03-01

    Immune responses mounted by the malaria vector Anopheles gambiae are largely regulated by the Toll and Imd (immune deficiency) pathways via the NF-kappaB transcription factors Rel1 and Rel2, which are controlled by the negative regulators Cactus and Caspar, respectively. Rel1- and Rel2-dependent transcription in A. gambiae has been shown to be particularly critical to the mosquito's ability to manage infection with the rodent malaria parasite Plasmodium berghei. Using RNA interference to deplete the negative regulators of these pathways, we found that Rel2 controls resistance of A. gambiae to the human malaria parasite Plasmodium falciparum, whereas Rel 1 activation reduced infection levels. The universal relevance of this defense system across Anopheles species was established by showing that caspar silencing also prevents the development of P. falciparum in the major malaria vectors of Asia and South America, A. stephensi and A. albimanus, respectively. Parallel studies suggest that while Imd pathway activation is most effective against P. falciparum, the Toll pathway is most efficient against P. berghei, highlighting a significant discrepancy between the human pathogen and its rodent model. High throughput gene expression analyses identified a plethora of genes regulated by the activation of the two Rel factors and revealed that the Toll pathway played a more diverse role in mosquito biology than the Imd pathway, which was more immunity-specific. Further analyses of key anti-Plasmodium factors suggest they may be responsible for the Imd pathway-mediated resistance phenotype. Additionally, we found that the fitness cost caused by Rel2 activation through caspar gene silencing was undetectable in sugar-fed, blood-fed, and P. falciparum-infected female A. gambiae, while activation of the Toll pathway's Rel1 had a major impact. This study describes for the first time a single gene that influences an immune mechanism that is able to abort development of P. falciparum

  4. Divergent Production in Gifted Adolescents Using Timed vs. Untimed Stimuli with Creative Prompting.

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    Johns, Gregg A.; Morse, Linda W.; Morse, David T.

    2000-01-01

    Two studies examined the role of time press on fluency, flexibility, and ratio-type flexibility scores from different divergent production tasks for two samples (total N=42) of gifted adolescents. Both studies found that gifted adolescents' rates of creative production, as measured by fluency alone or fluency and flexibility, did not appreciably…

  5. Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes

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    Mitchell, Sara N.; Kakani, Evdoxia G.; South, Adam; Howell, Paul I.; Waterhouse, Robert M.; Catteruccia, Flaminia

    2015-01-01

    The availability of genome sequences from 16 anopheline species provides unprecedented opportunities to study the evolution of reproductive traits relevant for malaria transmission. In Anopheles gambiae, a likely candidate for sexual selection is male 20-hydroxyecdysone (20E). Sexual transfer of this steroid hormone as part of a mating plug dramatically changes female physiological processes intimately tied to vectorial capacity. By combining phenotypic studies with ancestral state reconstructions and phylogenetic analyses, we show that mating plug transfer and male 20E synthesis are both derived characters that have coevolved in anophelines, driving the adaptation of a female 20E-interacting protein that promotes oogenesis via mechanisms also favoring Plasmodium survival. Our data reveal coevolutionary dynamics of reproductive traits between the sexes likely to have shaped the ability of anophelines to transmit malaria. PMID:25722409

  6. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades.

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    Turner, Alan H; Pritchard, Adam C; Matzke, Nicholas J

    2017-01-01

    Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to

  7. Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

    Directory of Open Access Journals (Sweden)

    Liswi Saif W

    2009-05-01

    Full Text Available Abstract Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh, blue-sensitive (BRh, and long-wavelength sensitive (LWRh opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total. Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya, and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya. Our family-level results are congruent with

  8. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades

    Science.gov (United States)

    Turner, Alan H.; Pritchard, Adam C.; Matzke, Nicholas J.

    2017-01-01

    Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a ‘smoothed’ timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears

  9. Phylogenetic relationship and time of divergence of Mus terricolor with reference to other Mus species

    Indian Academy of Sciences (India)

    MAHUA RUDRA; BISHWANATH CHATTERJEE; MIN BAHADUR

    2016-06-01

    Mitochondrial DNA control region ofMus terricolor , three aboriginal speciesM. spretus ,M. macedonicus ,M. spicilegus ;the Asian lineageM. caroli ,M. cervicolor ,M. cookii ; and the two house mice,M. musculus domesticusandM. m. castaneuswere analysed to estimate the substitution rate, phylogenetic relationship and the probable time of divergence. Results showedthatM. spretus ,M. caroliandM. terricolorare highly diverged from each other (caroli /terricolor =0.146,caroli /spretus =0.147 andterricolor /spretus =0.122), whereasM. spretusshowed less divergence with two house mice species (0.070 and0.071). Sequence divergence betweenM. terricolorand the Palearctic group were found to be ranging from 0.121 to 0.134.Phylogenetic analysis by minimum evolution, neighbour-joining, unweighed pair group method with arithmetic mean andmaximum parsimony showed almost similar topology. Two major clusters were found, one included the Asian lineage,M.caroli ,M. cookiiandM. cervicolorand the other included the house miceM. m. domesticus ,M. m. castaneusand the aboriginalmiceM. macedonicusandM. spicilegusalong withM. spretus , forming the Palearctic clade.M. terricolorwas positionedbetween the Palearctic and Asian clades. Results showed that Palearctic -terricolorand the Asian lineages diverged 5.47million years ago (Mya), whileM. terricolorhad split around 4.63 Mya from their ancestor.M. cervicolor ,M. cookiiandM.carolidiverged between 4.70 and 3.36 Mya, which indicates thatM. terricolorand the Asian lineages evolved simultaneously.M. spretusis expected to have diverged nearly 2.9 Mya from their most recent common ancestor

  10. The colonization of land by animals: molecular phylogeny and divergence times among arthropods

    Directory of Open Access Journals (Sweden)

    Lyons-Weiler Maureen

    2004-01-01

    Full Text Available Abstract Background The earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma. However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses. Results Significant support was found for the unconventional pairing of myriapods (millipedes and centipedes with chelicerates (spiders, scorpions, horseshoe crabs, etc. using nuclear and mitochondrial genes. Our estimated time for the divergence of millipedes (Diplopoda and centipedes (Chilopoda was 442 ± 50 Ma, and the divergence of insects and crustaceans was estimated as 666 ± 58 Ma. Our results also agree with previous studies suggesting a deep divergence (~1100 – 900 Ma for arthropods and deuterostomes, considerably predating the Cambrian Explosion seen in the animal fossil record. Conclusions The consistent support for a close relationship between myriapods and chelicerates, using mitochondrial and nuclear genes and different methods of analysis, suggests that this unexpected result is not an artefact of analysis. We propose the name Myriochelata for this group of animals, which includes many that immobilize prey with venom. Our molecular clock

  11. Anomalous divergence of a relaxation time in discontinuous shear thickening suspensions

    CERN Document Server

    Maharjan, Rijan

    2016-01-01

    We investigated the transient relaxation of a Discontinuous Shear Thickening (DST) suspension of cornstarch in water. Starting from a steady shear in a parallel plate rheometer, we stopped the top plate rotation and measured the transient stress relaxation. We found that at low effective packing fraction $\\phi_{eff}$, the suspensions exhibited a relaxation behavior consistent with a rheometric fluid in which the relaxation is determined by the steady-state viscosity. However, for larger $\\phi_{eff}$, we find up to two exponential relaxation regimes, which both become distinct from the rheometric model. The discrepancy between the measured relaxation times and the rheometric prediction was found to be as large as 4 orders of magnitude and diverges in the limit as $\\phi_{eff} \\rightarrow \\phi_c$, corresponding to the liquid solid transition, as the measured relaxation times diverge to infinity while the rheometric prediction approaches 0. In this limit, the measured relaxation time scales are on the order of $\\...

  12. Strongly confined fluids: Diverging time scales and slowing down of equilibration

    Science.gov (United States)

    Schilling, Rolf

    2016-06-01

    The Newtonian dynamics of strongly confined fluids exhibits a rich behavior. Its confined and unconfined degrees of freedom decouple for confinement length L →0 . In that case and for a slit geometry the intermediate scattering functions Sμ ν(q ,t ) simplify, resulting for (μ ,ν )≠(0 ,0 ) in a Knudsen-gas-like behavior of the confined degrees of freedom, and otherwise in S∥(q ,t ) , describing the structural relaxation of the unconfined ones. Taking the coupling into account we prove that the energy fluctuations relax exponentially. For smooth potentials the relaxation times diverge as L-3 and L-4, respectively, for the confined and unconfined degrees of freedom. The strength of the L-3 divergence can be calculated analytically. It depends on the pair potential and the two-dimensional pair distribution function. Experimental setups are suggested to test these predictions.

  13. A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2011-05-01

    Full Text Available Abstract Background Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA vary approximately twofold, from ~1,100 million years ago (Mya to ~2,300 Mya. Results We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval. Conclusion The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of

  14. Non-divergence of stochastic discrete time algorithms for PCA neural networks.

    Science.gov (United States)

    Lv, Jian Cheng; Yi, Zhang; Li, Yunxia

    2015-02-01

    Learning algorithms play an important role in the practical application of neural networks based on principal component analysis, often determining the success, or otherwise, of these applications. These algorithms cannot be divergent, but it is very difficult to directly study their convergence properties, because they are described by stochastic discrete time (SDT) algorithms. This brief analyzes the original SDT algorithms directly, and derives some invariant sets that guarantee the nondivergence of these algorithms in a stochastic environment by selecting proper learning parameters. Our theoretical results are verified by a series of simulation examples.

  15. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

    Science.gov (United States)

    Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

    2015-03-01

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way

  16. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae

    Directory of Open Access Journals (Sweden)

    Ober Karen A

    2010-08-01

    Full Text Available Abstract Background Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. Results According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Conclusions Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  17. Development of environmental tools for anopheline larval control

    OpenAIRE

    Mweresa Collins K; Imbahale Susan S; Takken Willem; Mukabana Wolfgang R

    2011-01-01

    Abstract Background Malaria mosquitoes spend a considerable part of their life in the aquatic stage, rendering them vulnerable to interventions directed to aquatic habitats. Recent successes of mosquito larval control have been reported using environmental and biological tools. Here, we report the effects of shading by plants and biological control agents on the development and survival of anopheline and culicine mosquito larvae in man-made natural habitats in western Kenya. Trials consisted ...

  18. Phylogeny of anopheline (Diptera: Culicidae) species in southern Africa, based on nuclear and mitochondrial genes.

    Science.gov (United States)

    Norris, Laura C; Norris, Douglas E

    2015-06-01

    A phylogeny of anthropophilic and zoophilic anopheline mosquito species was constructed, using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The ITS2 alignment, typically difficult due to its noncoding nature and large size variations, was aided by using predicted secondary structure, making this phylogenetically useful gene more amenable to investigation. This phylogeny is unique in explicitly including zoophilic, non-vector anopheline species in order to illustrate their relationships to malaria vectors. Two new, cryptic species, Anopheles funestus-like and Anopheles rivulorum-like, were found to be present in Zambia for the first time. Sequences from the D3 region of the 28S rDNA suggest that the Zambian An. funestus-like may be a hybrid or geographical variant of An. funestus-like, previously reported in Malawi. This is the first report of An. rivulorum-like sympatric with An. rivulorum (Leeson), suggesting that these are separate species rather than geographic variants.

  19. Inhibition of Malaria Infection in Transgenic Anopheline Mosquitoes Lacking Salivary Gland Cells.

    Science.gov (United States)

    Yamamoto, Daisuke S; Sumitani, Megumi; Kasashima, Katsumi; Sezutsu, Hideki; Matsuoka, Hiroyuki

    2016-09-01

    Malaria is an important global public health challenge, and is transmitted by anopheline mosquitoes during blood feeding. Mosquito vector control is one of the most effective methods to control malaria, and population replacement with genetically engineered mosquitoes to block its transmission is expected to become a new vector control strategy. The salivary glands are an effective target tissue for the expression of molecules that kill or inactivate malaria parasites. Moreover, salivary gland cells express a large number of molecules that facilitate blood feeding and parasite transmission to hosts. In the present study, we adapted a functional deficiency system in specific tissues by inducing cell death using the mouse Bcl-2-associated X protein (Bax) to the Asian malaria vector mosquito, Anopheles stephensi. We applied this technique to salivary gland cells, and produced a transgenic strain containing extremely low amounts of saliva. Although probing times for feeding on mice were longer in transgenic mosquitoes than in wild-type mosquitoes, transgenic mosquitoes still successfully ingested blood. Transgenic mosquitoes also exhibited a significant reduction in oocyst formation in the midgut in a rodent malaria model. These results indicate that mosquito saliva plays an important role in malaria infection in the midgut of anopheline mosquitoes. The dysfunction in the salivary glands enabled the inhibition of malaria transmission from hosts to mosquito midguts. Therefore, salivary components have potential in the development of new drugs or genetically engineered mosquitoes for malaria control.

  20. Do missing data influence the accuracy of divergence-time estimation with BEAST?

    Science.gov (United States)

    Zheng, Yuchi; Wiens, John J

    2015-04-01

    Time-calibrated phylogenies have become essential to evolutionary biology. A recurrent and unresolved question for dating analyses is whether genes with missing data cells should be included or excluded. This issue is particularly unclear for the most widely used dating method, the uncorrelated lognormal approach implemented in BEAST. Here, we test the robustness of this method to missing data. We compare divergence-time estimates from a nearly complete dataset (20 nuclear genes for 32 species of squamate reptiles) to those from subsampled matrices, including those with 5 or 2 complete loci only and those with 5 or 8 incomplete loci added. In general, missing data had little impact on estimated dates (mean error of ∼5Myr per node or less, given an overall age of ∼220Myr in squamates), even when 80% of sampled genes had 75% missing data. Mean errors were somewhat higher when all genes were 75% incomplete (∼17Myr). However, errors increased dramatically when only 2 of 9 fossil calibration points were included (∼40Myr), regardless of missing data. Overall, missing data (and even numbers of genes sampled) may have only minor impacts on the accuracy of divergence dating with BEAST, relative to the dramatic effects of fossil calibrations.

  1. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus)

    Institute of Scientific and Technical Information of China (English)

    LI ZhiQiang; GUO BaoCheng; LI JunBing; HE ShunPing; CHEN YiYu

    2008-01-01

    The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.

  2. The right time to happen: play developmental divergence in the two Pan species.

    Directory of Open Access Journals (Sweden)

    Elisabetta Palagi

    Full Text Available Bonobos, compared to chimpanzees, are highly motivated to play as adults. Therefore, it is interesting to compare the two species at earlier developmental stages to determine how and when these differences arise. We measured and compared some play parameters between the two species including frequency, number of partners (solitary, dyadic, and polyadic play, session length, and escalation into overt aggression. Since solitary play has a role in developing cognitive and physical skills, it is not surprising that chimpanzees and bonobos share similar developmental trajectories in the motivation to engage in this activity. The striking divergence in play developmental pathways emerged for social play. Infants of the two species showed comparable social play levels, which began to diverge during the juvenile period, a 'timing hotspot' for play development. Compared to chimpanzees, social play sessions in juvenile bonobos escalated less frequently into overt aggression, lasted longer, and frequently involved more than two partners concurrently (polyadic play. In this view, play fighting in juvenile bonobos seems to maintain a cooperative mood, whereas in juvenile chimpanzees it acquires more competitive elements. The retention of juvenile traits into adulthood typical of bonobos can be due to a developmental delay in social inhibition. Our findings show that the divergence of play ontogenetic pathways between the two Pan species and the relative emergence of play neotenic traits in bonobos can be detected before individuals reach sexual maturity. The high play motivation showed by adult bonobos compared to chimpanzees is probably the result of a long developmental process, rooted in the delicate transitional phase, which leads subjects from infancy to juvenility.

  3. Finite Divergence

    DEFF Research Database (Denmark)

    Hansen, Michael Edberg; Pandya, P. K.; Chaochen, Zhou

    1995-01-01

    the framework of duration calculus. Axioms and proof rules are given. Patterns of occurrence of divergence are classified into dense divergence, accumulative divergence and discrete divergence by appropriate axioms. Induction rules are given for reasoning about discrete divergence...

  4. Assessing divergence time of Spirulida and Sepiida (Cephalopoda) based on hemocyanin sequences.

    Science.gov (United States)

    Warnke, Kerstin Martina; Meyer, Achim; Ebner, Bettina; Lieb, Bernhard

    2011-02-01

    The phylogenetic position of the mesopelagic decabrachian cephalopod Spirula is still a matter of debate. Since hemocyanin has successfully been used to calibrate a molecular clock for many molluscan species, a molecular clock was calculated based on this gene with special attention to the cephalopod genera Spirula and Sepia. The obtained partial sequence comprising ca., one third (3567 bp) of the complete gene is similar to that of Sepia officinalis. The molecular clock was calibrated using the splits of Gastropoda-Cephalopoda (ca. 550 ± 50 mya) and Heterobranchia-Vetigastropoda (ca. 380 ± 10 mya). The resulting hemocyanin-based molecular clock is stable, and the estimated divergence time of Spirulida and Sepiida, some 150 ± 30 million years ago, can be deemed reliable.

  5. Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes.

    Science.gov (United States)

    Lu, Ying; Ran, Jin-Hua; Guo, Dong-Mei; Yang, Zu-Yu; Wang, Xiao-Quan

    2014-01-01

    Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

  6. Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes.

    Directory of Open Access Journals (Sweden)

    Ying Lu

    Full Text Available Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

  7. Depth, ice thickness, and ice-out timing cause divergent hydrologic responses among Arctic lakes

    Science.gov (United States)

    Arp, Christopher D.; Jones, Benjamin M.; Liljedahl, Anna K.; Hinkel, Kenneth M.; Welker, Jeffery A.

    2015-01-01

    Lakes are prevalent in the Arctic and thus play a key role in regional hydrology. Since many Arctic lakes are shallow and ice grows thick (historically 2-m or greater), seasonal ice commonly freezes to the lake bed (bedfast ice) by winter's end. Bedfast ice fundamentally alters lake energy balance and melt-out processes compared to deeper lakes that exceed the maximum ice thickness (floating ice) and maintain perennial liquid water below floating ice. Our analysis of lakes in northern Alaska indicated that ice-out of bedfast ice lakes occurred on average 17 days earlier (22-June) than ice-out on adjacent floating ice lakes (9-July). Earlier ice-free conditions in bedfast ice lakes caused higher open-water evaporation, 28% on average, relative to floating ice lakes and this divergence increased in lakes closer to the coast and in cooler summers. Water isotopes (18O and 2H) indicated similar differences in evaporation between these lake types. Our analysis suggests that ice regimes created by the combination of lake depth relative to ice thickness and associated ice-out timing currently cause a strong hydrologic divergence among Arctic lakes. Thus understanding the distribution and dynamics of lakes by ice regime is essential for predicting regional hydrology. An observed regime shift in lakes to floating ice conditions due to thinner ice growth may initially offset lake drying because of lower evaporative loss from this lake type. This potential negative feedback caused by winter processes occurs in spite of an overall projected increase in evapotranspiration as the Arctic climate warms.

  8. An Analysis of Early vs. Later Responses on a Divergent Production Task across Three Time Press Conditions.

    Science.gov (United States)

    Johns, Gregg A.; Morse, Linda W.; Morse, David T.

    2001-01-01

    This study examined the effects of three time-press and three creative-prompt conditions on early vs. later trial originality scores for three divergent production stimuli with 91 undergraduate students. Findings indicated a higher frequency of originality scores for the latter portions of trials for all time-press and prompting conditions.…

  9. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

    Institute of Scientific and Technical Information of China (English)

    Konstantinos ANGELIS; Mario DOS REIS

    2015-01-01

    Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir-tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combi-nation of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sort-ing. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 (5): 874–885, 2015].

  10. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

    2011-01-01

    event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......ue to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination...

  11. Muscles innervated by a single motor neuron exhibit divergent synaptic properties on multiple time scales.

    Science.gov (United States)

    Blitz, Dawn M; Pritchard, Amy E; Latimer, John K; Wakefield, Andrew T

    2017-01-19

    Adaptive changes in the output of neural circuits underlying rhythmic behaviors are relayed to muscles via motor neuron activity. Pre- and postsynaptic properties of neuromuscular junctions can impact the transformation from motor neuron activity to muscle response. Further, synaptic plasticity occurring on the time scale of inter-spike intervals can differ between multiple muscles innervated by the same motor neuron. In rhythmic behaviors, motor neuron bursts can elicit additional synaptic plasticity. However, it is unknown if plasticity regulated by the longer time scale of inter-burst intervals also differs between synapses from the same neuron, and whether any such distinctions occur across a physiological activity range. To address these issues, we measured electrical responses in muscles innervated by a chewing circuit neuron, the lateral gastric (LG) motor neuron, in a well-characterized small motor system, the stomatogastric nervous system (STNS) of the Jonah crab, Cancer borealis In vitro and in vivo, sensory, hormonal and modulatory inputs elicit LG bursting consisting of inter-spike intervals of 50-250 ms and inter-burst intervals of 2-24 s. Muscles expressed similar facilitation measured with paired stimuli except at the shortest inter-spike interval. However distinct decay time constants resulted in differences in temporal summation. In response to bursting activity, augmentation occurred to different extents and saturated at different inter-burst intervals in the three muscles. Further, augmentation interacted with facilitation, resulting in distinct intra-burst facilitation between muscles. Thus, responses of multiple target muscles diverge across a physiological activity range due to distinct synaptic properties sensitive to multiple time scales.

  12. Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird.

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    Brian Tilston Smith

    Full Text Available Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (Ne has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species' ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis. Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large Ne and two island lineages comprised of much smaller populations (small Ne. We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.

  13. Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird.

    Science.gov (United States)

    Smith, Brian Tilston; Klicka, John

    2013-01-01

    Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (Ne) has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species' ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis). Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large Ne) and two island lineages comprised of much smaller populations (small Ne). We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.

  14. Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

    Institute of Scientific and Technical Information of China (English)

    LIU Nian; ZHU Yong; WEI ZongXian; CHEN Jie; WANG QingBiao; JIAN ShuGuang; ZHOU DangWei; SHI Jing; YANG Yong; ZHONG Yang

    2009-01-01

    Araucariaceae is one of the most primitive families of the living conifers,and its phylogenetic relationships and divergence times are critically important issues.The DNA sequences of 8 genes,i.e.,nuclear ribosomal 18S and 26S rRNA,chloroplast 16S rRNA,rbcL,mafK and rps4,and mitochondrial coxl and atp1,obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae,indicating that the phylogenetic relationships among the three genera of this family should be ((Wollemia,Agathis),Araucaria).On the basis of the fossil calibrations of Wollemia and the two tribes Araucaria and Eutacta of the genus Araucaria,the divergence time of Araucariaceae was estimated to be (308±53) million years ago,that is,the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view.With the same gene combination,the divergence times of the genera Araucaria and Agathis were (246 ±47) and (61±5) Ma,respectively.Statistical analyses on the phylogenetic trees generated by using different genes and comparisons of thedivergence times estimated by using those genes suggested that the chloroplast mafK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.

  15. Minority-spin dynamics in the nonhomogeneous Ising model: Diverging time scales and exponents

    Science.gov (United States)

    Mullick, Pratik; Sen, Parongama

    2016-05-01

    We investigate the dynamical behavior of the Ising model under a zero-temperature quench with the initial fraction of up spins 0 ≤x ≤1 . In one dimension, the known results for persistence probability are verified; it shows algebraic decay for both up and down spins asymptotically with different exponents. It is found that the conventional finite-size scaling is valid here. In two dimensions, however, the persistence probabilities are no longer algebraic; in particular for x ≤0.5 , persistence for the up (minority) spins shows the behavior Pmin(t ) ˜t-γexp[-(t/τ ) δ] with time t , while for the down (majority) spins, Pmaj(t ) approaches a finite value. We find that the timescale τ diverges as (xc-x ) -λ, where xc=0.5 and λ ≃2.31 . The exponent γ varies as θ2 d+c0(xc-x ) β where θ2 d≃0.215 is very close to the persistence exponent in two dimensions; β ≃1 . The results in two dimensions can be understood qualitatively by studying the exit probability, which for different system size is found to have the form E (x ) =f [(x/-xc xc) L1 /ν] , with ν ≈1.47 . This result suggests that τ ˜Lz ˜ , where z ˜=λ/ν =1.57 ±0.11 is an exponent not explored earlier.

  16. Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice.

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    Eri Ogiso-Tanaka

    Full Text Available In rice (Oryza sativa L., there is a diversity in flowering time that is strictly genetically regulated. Some indica cultivars show extremely late flowering under long-day conditions, but little is known about the gene(s involved. Here, we demonstrate that functional defects in the florigen gene RFT1 are the main cause of late flowering in an indica cultivar, Nona Bokra. Mapping and complementation studies revealed that sequence polymorphisms in the RFT1 regulatory and coding regions are likely to cause late flowering under long-day conditions. We detected polymorphisms in the promoter region that lead to reduced expression levels of RFT1. We also identified an amino acid substitution (E105K that leads to a functional defect in Nona Bokra RFT1. Sequencing of the RFT1 region in rice accessions from a global collection showed that the E105K mutation is found only in indica, and indicated a strong association between the RFT1 haplotype and extremely late flowering in a functional Hd1 background. Furthermore, SNPs in the regulatory region of RFT1 and the E105K substitution in 1,397 accessions show strong linkage disequilibrium with a flowering time-associated SNP. Although the defective E105K allele of RFT1 (but not of another florigen gene, Hd3a is found in many cultivars, relative rate tests revealed no evidence for differential rate of evolution of these genes. The ratios of nonsynonymous to synonymous substitutions suggest that the E105K mutation resulting in the defect in RFT1 occurred relatively recently. These findings indicate that natural mutations in RFT1 provide flowering time divergence under long-day conditions.

  17. Divergence history of the Carpathian and smooth newts modelled in space and time.

    Science.gov (United States)

    Zieliński, P; Nadachowska-Brzyska, K; Dudek, K; Babik, W

    2016-08-01

    Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.

  18. Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

    Science.gov (United States)

    2016-01-01

    Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data. PMID:28336787

  19. Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini, Primates: An Analysis of Fossil and Molecular Data.

    Directory of Open Access Journals (Sweden)

    S Ivan Perez

    Full Text Available The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27-31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21-29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time

  20. Estimation of divergence times in litostomatean ciliates (Ciliophora: Intramacronucleata), using Bayesian relaxed clock and 18S rRNA gene.

    Science.gov (United States)

    Vďačný, Peter

    2015-08-01

    The class Litostomatea comprises a diverse assemblage of free-living and endosymbiotic ciliates. To understand diversification dynamic of litostomateans, divergence times of their main groups were estimated with the Bayesian molecular dating, a technique allowing relaxation of molecular clock and incorporation of flexible calibration points. The class Litostomatea very likely emerged during the Cryogenian around 680 Mya. The origin of the subclass Rhynchostomatia is dated to about 415 Mya, while that of the subclass Haptoria to about 654 Mya. The order Pleurostomatida, emerging about 556 Mya, was recognized as the oldest group within the subclass Haptoria. The order Spathidiida appeared in the Paleozoic about 442 Mya. The three remaining haptorian orders evolved in the Paleozoic/Mesozoic periods: Didiniida about 419 Mya, Lacrymariida about 269 Mya, and Haptorida about 194 Mya. The subclass Trichostomatia originated from a spathidiid ancestor in the Mesozoic about 260 Mya. A further goal of this study was to investigate the impact of various settings on posterior divergence time estimates. The root placement and tree topology as well as the priors of the rate-drift model, birth-death process and nucleotide substitution rate, had no significant effect on calculation of posterior divergence time estimates. However, removal of calibration points could significantly change time estimates at some nodes.

  1. Phylogeny and divergence time estimation of cheilostome bryozoans based on mitochodrial 16S rRNA sequences

    Institute of Scientific and Technical Information of China (English)

    HAO Jiasheng; LI Chunxiang; SUN Xiaoyan; YANG Qun

    2005-01-01

    The mitochondrial 16S rDNA sequences of 40 species of cheilostome bryozoans including those of 24 species newly determined were used to reconstruct the phylogenetic tree using neighboring-joining and maximum-parsimony methods. By applying molecular clock technique on the basis of the appropriate phylogeny and the fossil record, the divergence times of the two main cheilostome groups, Anasca and Ascophora sensu stricto, were estimated. The results show that the molecular phylogeny of the higher taxonomic groups (superfamilies and higher taxa) of cheilostome bryozoans is mostly in conflict with the morphology-based phylogenetic trees; the divergence of the extant groups of Anasca and those of Ascophora sensu stricto is estimated to have happened about 263 Ma (Permian Guadalupian Epoch) and 183 Ma (Early Jurassic), respectively.

  2. Phylogenetics of neotropical Platymiscium (Leguminosae: Dalbergieae): systematics, divergence times, and biogeography inferred from nuclear ribosomal and plastid DNA sequence data.

    Science.gov (United States)

    Saslis-Lagoudakis, Charilaos; Chase, Mark W; Robinson, Daniel N; Russell, Stephen J; Klitgaard, Bente B

    2008-10-01

    Platymiscium is a neotropical legume genus of forest trees in the Pterocarpus clade of the pantropical "dalbergioid" clade. It comprises 19 species (29 taxa), distributed from Mexico to southern Brazil. This study presents a molecular phylogenetic analysis of Platymiscium and allies inferred from nuclear ribosomal (nrITS) and plastid (trnL, trnL-F and matK) DNA sequence data using parsimony and Bayesian methods. Divergence times are estimated using a Bayesian method assuming a relaxed molecular clock (multidivtime). Within the Pterocarpus clade, new sister relationships are recovered: Pterocarpus + Etaballia, Inocarpus + Tipuana and Paramachaerium + Maraniona. Our results support monophyly of Platymiscium, which is resolved into three major clades, each with distinct geographic ranges and ecological preferences. Diversification in Platymiscium has been driven by habitat fragmentation, invasion of novel geographic regions, and ecological diversification, revealing general patterns of diversification in the neotropics. We hypothesize that Platymiscium arose in dry habitats of South America and radiated northward. The Amazon basin was invaded twice both within the last 5.6 My and Central America twice before the closure of the Isthmus of Panama. Divergence times of the P. pubescens complex, restricted to seasonally dry tropical forests of South America, support pre-Pleistocene divergence in this biome.

  3. The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.

    Science.gov (United States)

    Inoue, Jun G; Miya, Masaki; Venkatesh, Byrappa; Nishida, Mutsumi

    2005-04-11

    We determined the whole mitochondrial genome sequence for Indonesian coelacanth Latimeria menadoensis. The genome content and organization were identical to that of typical vertebrates including Comoran coelacanth, Latimeria chalumnae. The overall nucleotide differences between the two species (excluding the control region) was 4.28%. The divergence time between the two species was estimated using whole mitochondrial genome data from the two coelacanths and 26 actinopterygians that represent major actinopterygian lineages plus an outgroup. Partitioned Bayesian analyses were conducted with the two data sets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding ND6 gene) and concatenated nucleotide sequences from 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The molecular clock analysis was also conducted with the concatenated amino acid sequences from the 12 protein-coding genes after removing faster or more slowly evolving sequences. Using the sarcopterygian-actinopterygian split as a calibration point (450 Mya), divergence time estimation between L. menadoensis and L. chalumnae fell in the range of 40-30 Mya, which is much older than those of the previous studies (coelacanth habitat disjunction that allowed populations on either side of India to diverge.

  4. Genetic divergence and evolutionary times: calibrating a protein clock for South-European Stenasellus species (Crustacea, Isopoda

    Directory of Open Access Journals (Sweden)

    Valerio Ketmaier

    1997-01-01

    Full Text Available We studied genetic divergence in a group of exclusively stygobiont isopods of the family Stenasellidae. In particular, we assessed evolutionary relationships among several populations of Stenasellus racovitzai and Stenasellus virei. To place this study in a phylogenetic context. we used another species of Stenasellus, S. assorgiai, as an outgroup. S. racovitzai occurs in Corsica, Sardinia and in the fossil islands of the Tuscan Archipelago, while S. virei is a polytypic species widely distributed in the central France and Pyrenean area. This vicariant distribution is believed to be the result of the disjunction of the Sardinia-Corsica microplate from the Pyrenean region and its subsequent rotation. Since geological data provide time estimates for these events, we can use the genetic distance data to calibrate a molecular clock for this group of stygobiont isopods. The calibration of the molecular clock reveals a roughly linear relationship (r = 0.753 between the genetic distances and absolute divergence times, with a mean divergence rate (19.269 Myr/DNei, different from those previously reported in the literature and provides an opportunity to shed some light on the evolutionary scenarios of other Stenasellus species.

  5. Evolutionary relationships and divergence times among the native rats of Australia

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    Matisoo-Smith Elizabeth

    2010-12-01

    Full Text Available Abstract Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya. Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long, Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea

  6. Development of environmental tools for anopheline larval control

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    Mweresa Collins K

    2011-07-01

    Full Text Available Abstract Background Malaria mosquitoes spend a considerable part of their life in the aquatic stage, rendering them vulnerable to interventions directed to aquatic habitats. Recent successes of mosquito larval control have been reported using environmental and biological tools. Here, we report the effects of shading by plants and biological control agents on the development and survival of anopheline and culicine mosquito larvae in man-made natural habitats in western Kenya. Trials consisted of environmental manipulation using locally available plants, the introduction of predatory fish and/or the use of Bacillus thuringiensis var. israelensis (Bti in various combinations. Results Man-made habitats provided with shade from different crop species produced significantly fewer larvae than those without shade especially for the malaria vector Anopheles gambiae. Larval control of the African malaria mosquito An. gambiae and other mosquito species was effective in habitats where both predatory fish and Bti were applied, than where the two biological control agents were administered independently. Conclusion We conclude that integration of environmental management techniques using shade-providing plants and predatory fish and/or Bti are effective and sustainable tools for the control of malaria and other mosquito-borne disease vectors.

  7. Dusk to dawn activity patterns of anopheline mosquitoes in West Timor and Java, Indonesia.

    Science.gov (United States)

    Ndoen, Ermi; Wild, Clyde; Dale, Pat; Sipe, Neil; Dale, Mike

    2011-05-01

    Malaria is a serious health issue in Indonesia. We investigated the dusk to dawn anopheline mosquito activity patterns, host-seeking and resting locations in coastal plain, hilly and highland areas in West Timor and Java. Adult mosquitoes were captured landing on humans or resting in houses or animal barns. Data analyzed were: mosquito night-time activities; period of peak activity; night-time activity in specific periods of time and for mosquito resting locations. Eleven species were recorded; data were sparse for some species therefore detailed analyses were performed for four species only. In Java Anopheles vagus was common, with a bimodal pattern of high activity. In West Timor, its activity peaked around midnight. Other species with peak activity around the middle of the night were An. barbirostris and An. subpictus. Most species showed no biting and resting preference for indoors or outdoors, although An. barbirostris preferred indoors in West Timor, but outdoors in Java. An. aconitus and An. annularis preferred resting in human dwellings; An. subpictus and An. vagus preferred resting in animal barns. An. barbirostris preferred resting in human dwellings in West Timor and in animal barns in Java. The information is useful for planning the mosquito control aspect of malaria management. For example, where mosquito species have peak activity at night indoors, bednets and indoor residual spraying should reduce malaria risk, but where mosquitoes are most active outdoors, other options may be more effective.

  8. Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera based on multiple genes.

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    Min Li

    Full Text Available Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA. Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP, maximum likelihood (ML and Bayesian inference (BI with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s and Bayesian (BEAST molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.

  9. Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments.

    Science.gov (United States)

    Guo, Xianguang; Dai, Xin; Chen, Dali; Papenfuss, Theodore J; Ananjeva, Natalia B; Melnikov, Daniel A; Wang, Yuezhao

    2011-11-01

    Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.

  10. Adult anopheline ecology and malaria transmission in irrigated areas of South Punjab, Pakistan

    DEFF Research Database (Denmark)

    Herrel, N; Amerasinghe, F P; Ensink, J

    2004-01-01

    . Anopheles stephensi, An. culicifacies and An. subpictus populations peaked in August, September and October, respectively. High temperatures and low rainfall negatively affected seasonal abundance in our area. There were interesting differences in anopheline fauna between villages, with An. culicifacies......: Culicidae) could be related to malaria transmission in rural areas with intensive irrigation and a history of malaria epidemics. In this paper we present our observations from three villages located along an irrigation canal in South Punjab. The study was carried out from 1 April 1999 to 31 March 2000....... pulcherrimus Theobald (1.0%) and An. peditaeniatus Leicester (0.1%). Most mosquitoes (98.8%) were collected from indoor resting-sites whereas collections from potential resting-sites outdoors accounted for only 1.2% of total anopheline densities, confirming the endophilic behaviour of anophelines in Pakistan...

  11. The remarkable journey of adaptation of the Plasmodium falciparum malaria parasite to New World anopheline mosquitoes.

    Science.gov (United States)

    Molina-Cruz, Alvaro; Barillas-Mury, Carolina

    2014-08-01

    Plasmodium falciparum originated in Africa, dispersed around the world as a result of human migration and had to adapt to several different indigenous anopheline mosquitoes. Anophelines from the New World are evolutionary distant form African ones and this probably resulted in a more stringent selection of Plasmodium as it adapted to these vectors. It is thought that Plasmodium has been genetically selected by some anopheline species through unknown mechanisms. The mosquito immune system can greatly limit infection and P. falciparum evolved a strategy to evade these responses, at least in part mediated by Pfs47, a highly polymorphic gene. We propose that adaptation of P. falciparum to new vectors may require evasion of their immune system. Parasites with a Pfs47 haplotype compatible with the indigenous mosquito vector would be able to survive and be transmitted. The mosquito antiplasmodial response could be an important determinant of P. falciparum population structure and could affect malaria transmission in the Americas.

  12. The remarkable journey of adaptation of the Plasmodium falciparum malaria parasite to New World anopheline mosquitoes

    Directory of Open Access Journals (Sweden)

    Alvaro Molina-Cruz

    2014-08-01

    Full Text Available Plasmodium falciparum originated in Africa, dispersed around the world as a result of human migration and had to adapt to several different indigenous anopheline mosquitoes. Anophelines from the New World are evolutionary distant form African ones and this probably resulted in a more stringent selection of Plasmodium as it adapted to these vectors. It is thought that Plasmodium has been genetically selected by some anopheline species through unknown mechanisms. The mosquito immune system can greatly limit infection and P. falciparum evolved a strategy to evade these responses, at least in part mediated by Pfs47, a highly polymorphic gene. We propose that adaptation of P. falciparum to new vectors may require evasion of their immune system. Parasites with a Pfs47 haplotype compatible with the indigenous mosquito vector would be able to survive and be transmitted. The mosquito antiplasmodial response could be an important determinant of P. falciparum population structure and could affect malaria transmission in the Americas.

  13. Diverging sensitivity of soil water stress to changing snowmelt timing in the Western U.S.

    Science.gov (United States)

    Harpold, Adrian A.

    2016-06-01

    Altered snowpack regimes from regional warming threaten mountain ecosystems with greater water stress and increased likelihood of vegetation disturbance. The sensitivity of vegetation to changing snowpack conditions is strongly mediated by soil water storage, yet a framework to identify areas sensitive to changing snowpack regimes is lacking. In this study we ask two questions: (1) How will changing snowmelt alter the duration of soil water stress and length of the soil-mediated growing season (shortened to water stress and growing season, respectively)? and (2) What site characteristics increase the sensitivity of water stress and growing season duration to changes in snowmelt? We compiled soil moisture at 5, 20 and 50 cm depths from 62 SNOTEL sites with > 5 years of records and detailed soil properties. Soil water stress was estimated based on measured wilting point water content. The day of snow disappearance consistently explained the greatest variability in water stress across all site-years and within individual sites, while summer precipitation explained the most variability in growing season length. On average, a one day earlier snow disappearance resulted in 0.62 days greater water stress and 36 of 62 sites had significant relationships between snow disappearance and water stress. Despite earlier snow disappearance leading to greater water stress at nearly all sites, earlier snow disappearance led to both significant increases (4 of 62) and decreases (5 of 62) in growing season length. Satellite derived vegetation greenness confirmed site-dependent changes could both increase and reduce maximum annual vegetation greenness with earlier snow disappearance. A simple soil moisture model demonstrated the potential for diverging growing season length with earlier snow disappearance was more likely in areas with finer soil texture, greater rooting depth, greater potential evapotranspiration, and greater precipitation. More work is needed to understand the role of

  14. The impact of divergence time on the nature of population structure: an example from Iceland.

    Directory of Open Access Journals (Sweden)

    Alkes L Price

    2009-06-01

    Full Text Available The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs. We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.

  15. Malaria Situation and Anopheline Mosquitoes in Qom Province, Central Iran

    Directory of Open Access Journals (Sweden)

    MR Abai

    2010-12-01

    Full Text Available "nAbstract "nBackground: The aims of this study was to analysis the current situation of malaria and to find the distribution of anopheline mosquitoes, as probable vectors of the disease, in Qom Province, central Iran. "nMethods: This study was carried out in two parts. First stage was data collection about malaria cases using recorded documents of patients in the Province health center, during 2001–2008. The second stage was entomological survey conducted by mosquito larval collection method in 4 villages with different geographical positions in 2008. Data were analyzed using Excel software. "nResults: Of 4456 blood slides, 10.9% out were positive. Most of cases were imported from other countries (90.4%, mainly from Afghanistan (56.5% and Pakistan (16.3%. Slide positive rate showed a maximum of 16.9% and a minimum of 2.9% in 2008 and 2007, respectively. Plasmodium vivax was causative agent of 93.75% of cases, fol­lowed by P. falciparum (6.25%. More than 15 years old age group contained the most malaria reported cases (66.7%. Two Anopheles species, An. superpictus and An. claviger were collected and identified. This is the first report of Anopheles claviger in Qom Province. "nConclusion: Malaria is in the control stage in Qom Province. The rate of local transmission is very low (only 1 case, shows Anopheles superpictus, as the main malaria vector of central part of Iran, can play its role in malaria transmission in the area. "n  "nKeywords: Malaria, Iran, Epidemiology

  16. Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).

    Science.gov (United States)

    Dornburg, Alex; Brandley, Matthew C; McGowen, Michael R; Near, Thomas J

    2012-02-01

    Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.

  17. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families

    Directory of Open Access Journals (Sweden)

    Marcel eVan Tuinen

    2015-06-01

    Full Text Available Uncertainty in divergence time estimation is rarely studied from the perspective of phylogenetic node age. If available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10MY nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire

  18. Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

    Science.gov (United States)

    DeGiorgio, Michael; Degnan, James H

    2014-01-01

    To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches-MP-EST, STAR, STEAC, STELLS, and STEM-for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that topology-based methods often performed better using ML gene trees and methods employing coalescent times typically performed better using Bayesian gene trees, with MP-EST, STAR, STEAC, and STELLS outperforming STEM under most conditions. We examine why the STEM tree (also called GLASS or Maximum Tree) is less accurate on estimated gene trees by comparing estimated and true coalescence times, performing species tree inference using simulations, and analyzing a great ape data set keeping track of false positive and false negative rates for inferred clades. We find that although true coalescence times are more ancient than speciation times under the multispecies coalescent model, estimated coalescence times are often more recent than speciation times. This underestimation can lead to increased bias and lack of resolution with increased sampling (either alleles or loci) when gene trees are estimated with ML. The problem appears to be less severe using Bayesian gene-tree estimates.

  19. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates.

    Science.gov (United States)

    Charruau, P; Fernandes, C; Orozco-Terwengel, P; Peters, J; Hunter, L; Ziaie, H; Jourabchian, A; Jowkar, H; Schaller, G; Ostrowski, S; Vercammen, P; Grange, T; Schlötterer, C; Kotze, A; Geigl, E-M; Walzer, C; Burger, P A

    2011-02-01

    The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000-12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000-67 000 ya using an average mammalian microsatellite mutation rate and at 4700-44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70-110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

  20. Landscape determinants and remote sensing of anopheline mosquito larval habitats in the western Kenya highlands

    Directory of Open Access Journals (Sweden)

    Beck Louisa

    2006-02-01

    Full Text Available Abstract Background In the past two decades the east African highlands have experienced several major malaria epidemics. Currently there is a renewed interest in exploring the possibility of anopheline larval control through environmental management or larvicide as an additional means of reducing malaria transmission in Africa. This study examined the landscape determinants of anopheline mosquito larval habitats and usefulness of remote sensing in identifying these habitats in western Kenya highlands. Methods Panchromatic aerial photos, Ikonos and Landsat Thematic Mapper 7 satellite images were acquired for a study area in Kakamega, western Kenya. Supervised classification of land-use and land-cover and visual identification of aquatic habitats were conducted. Ground survey of all aquatic habitats was conducted in the dry and rainy seasons in 2003. All habitats positive for anopheline larvae were identified. The retrieved data from the remote sensors were compared to the ground results on aquatic habitats and land-use. The probability of finding aquatic habitats and habitats with Anopheles larvae were modelled based on the digital elevation model and land-use types. Results The misclassification rate of land-cover types was 10.8% based on Ikonos imagery, 22.6% for panchromatic aerial photos and 39.2% for Landsat TM 7 imagery. The Ikonos image identified 40.6% of aquatic habitats, aerial photos identified 10.6%, and Landsate TM 7 image identified 0%. Computer models based on topographic features and land-cover information obtained from the Ikonos image yielded a misclassification rate of 20.3–22.7% for aquatic habitats, and 18.1–25.1% for anopheline-positive larval habitats. Conclusion One-metre spatial resolution Ikonos images combined with computer modelling based on topographic land-cover features are useful tools for identification of anopheline larval habitats, and they can be used to assist to malaria vector control in western Kenya

  1. Diverging Cohesion?

    DEFF Research Database (Denmark)

    Charron, Nicholas

    2016-01-01

    Why do increases in globalisation in the face of European expansion lead to sharp levels of regional divergences in wealth in some countries but not in others? The central crux of this paper is that convergence/divergence trends in European states are conditioned by ‘state capacity’. State capaci...

  2. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families.

    Science.gov (United States)

    van Tuinen, Marcel; Torres, Christopher R

    2015-01-01

    Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree

  3. Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts.

    Science.gov (United States)

    Vea, Isabelle M; Grimaldi, David A

    2016-03-22

    The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228-273], and of the neococcoids 60 million years later [210-165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous.

  4. Impact of dams and irrigation schemes in Anopheline (Diptera: Culicidae) bionomics and malaria epidemiology

    OpenAIRE

    Jordi Sanchez-Ribas; Gabriel Parra-Henao; Anthony Érico Guimarães

    2012-01-01

    Irrigation schemes and dams have posed a great concern on public health systems of several countries, mainly in the tropics. The focus of the present review is to elucidate the different ways how these human interventions may have an effect on population dynamics of anopheline mosquitoes and hence, how local malaria transmission patterns may be changed. We discuss different studies within the three main tropical and sub-tropical regions (namely Africa, Asia and the Pacific and the Americas). ...

  5. Characterization of larval habitats for anopheline mosquitoes in a malarious area under elimination program in the southeast of Iran

    Institute of Scientific and Technical Information of China (English)

    Moussa Soleimani-Ahmadi; Hassan Vatandoost; Mehdi Zare

    2014-01-01

    Objective: To determine the effects of environmental characteristics of larval habitats on distribution and abundance of anopheline mosquitoes in Bashagard county, a malarious area in southeast of Iran. Methods: Larvae were collected monthly using the standard dipping method and identified using a morphological-based key. Environmental characteristics of the larval habitats were recorded. Water samples were taken from habitats during larval collection for physico-chemical characterization. Statistical analyses were performed. Results: In total 5150 anopheline larvae from 36 larval habitats were collected and identified. They comprised of six species: Anopheles culicifacies (29.36%), Anopheles moghulensis (25.20%),Anopheles dthali stephensi (5.01%). (18.02%), Anopheles superpictus (17.24%), Anopheles turkhudi (5.17%) and Anopheles The most common larval habitats were natural and clear water bodies such as riverbeds with sandy substrates and still water. Furthermore, the anopheline larvae were abundant in permanent and full sunlight habitats without vegetation and algae. Larval density was positively correlated with water temperature. Chemical characteristics including conductivity, total alkalinity, sulphate and chloride had significant effects on distribution and abundance of anopheline species.Conclusions:The result of this study indicates a correlation between some environmental characteristics and anopheline larvae abundance which can be considered for effective planning and implementing malaria elimination program in Iran.

  6. Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations.

    Science.gov (United States)

    Kittel, Rebecca N; Austin, Andrew D; Klopfstein, Seraina

    2016-08-01

    Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov

  7. [Molecular phylogeny and the time of divergence of minges (Chironomidae, Nematocera, Diptera) inferred from a partial nucleotide sequence of the cytochrome oxidase I gene (COI)].

    Science.gov (United States)

    Demin, A G; Polukonova, N V; Miuge, N S

    2011-10-01

    This is the first study to infer the phylogenetic structure of minges of the subfamily Chironominae from the amino acid sequence of cytochrome oxidase I (COI). The subdivision of Chironominae into two tribes, Chironomini and Tanytarsini, has been confirmed. The segregation of the genera Pseudochironomus and Riethia into a separate tribe has not been confirmed. Stenochironomus gibbus forms a branch considerably deviating from the subfamily Chironominae. The genus Micropsectra is formed by a large polyphyletic cluster that also includes the genera Virgotanytharsus, Reotanytharsus, Kenopsectra, and Parapsectra. Tanytarsus is the basal genus of the tribe Tanytarsini. The times of divergence of the main taxa of Chironominae have been estimated. The calculated time of divergence of the genus Chironomus disproves the assumption that it is phylogenetically old.

  8. Ecology of Anopheline (Diptera, Culicidae, malaria vectors around the Serra da Mesa Reservoir, State of Goiás, Brazil: 1 - Frequency and climatic factors

    Directory of Open Access Journals (Sweden)

    Anthony Érico Guimarães

    Full Text Available The ecology of anopheline species (Diptera, Culicidae was studied in the vicinity of the Serra da Mesa Reservoir, State of Goiás, Brazil. Climatic factors and frequency of anopheline populations were analyzed. Bimonthly human-bait and Shannon trap captures were conducted for 36 consecutive months (January 1997 through December 1999. A total of 5,205 adult anophelines belonging to five species were collected. Anopheles darlingi was the most frequently collected anopheline (61.4%, followed by An. albitarsis s.l. (35.4%, An. triannulatus. (2.5%, An. oswaldoi (0.4%, and An. evansae (0.2%. The water level and vegetation along the banks of the reservoir were crucial to the frequency of the various anopheline species. Climatic factors had a secondary influence. The reservoir's water-level stability, increased frequency of An. darlingi, and the arrival of gold prospectors were responsible for the increase in malaria cases.

  9. Larvivorous potential of the guppy, Poecilia reticulata, in anopheline mosquito control in riverbed pools below the Kotmale dam, Sri Lanka.

    Science.gov (United States)

    Kusumawathie, P H D; Wickremasinghe, A R; Karunaweera, N D; Wijeyaratne, M J S

    2008-01-01

    The larvivorous potential of Poecilia reticulata was studied in the laboratory and in the field. In the laboratory, the number of anopheline larvae consumed per fish per day and the number of larvae in fecal matter per fish were determined. In the field study, 29 of 60 selected riverbed pools in Kotmale oya, below the Kotmale dam, were stocked with P reticulata, whereas the rest served as controls. Anopheline larval surveys were carried out starting from 1 day prior to stocking of fish and on selected days subsequently. P. reticulata consumed an average of 117 +/- 32.33 larvae per fish per day. Fecal matter of P. reticulata contained an average of 2.7 +/- 2.68 larvae per fish . There was a significant reduction in the number of pools positive for anopheline larvae (P < .001) after stocking fish and the number of larvae per pool (P < .001) and per 100 dips (P < .001) as compared with controls.

  10. Survival of anopheline eggs and their susceptibility to infection with Metarhizium anisopliae and Beauveria bassiana under laboratory conditions.

    Science.gov (United States)

    Luz, Christian; Mnyone, Ladslaus L; Russell, Tanya L

    2011-09-01

    The viability of Anopheles gambiae sensu stricto and Anopheles arabiensis (Diptera: Culicidae) eggs over time and the ovicidal activity of Beauveria bassiana (Ascomycota: Cordycipitaceae) and Metarhizium anisopliae (Ascomycota: Clavicipitaceae) were investigated. Eggs were incubated in soil or leaf litter for up to 12 weeks at 26°C and 75%, 86% or >98% relative humidity (RH). Eggs were treated topically with M. anisopliae ICIPE-30 or B. bassiana I93-825 conidia in either water or oil-in-water formulations. Survival of eggs whether treated or not with fungus was similar, and untreated eggs generally did not survive longer than 2 weeks regardless of the substrate or humidity tested. After a minimal 5-day exposure, M. anisopliae at 5 × 10(6) conidia/cm(2) clearly reduced the number of larvae. The efficacy of the fungus increased when it was oil-in-water formulated, and eclosion was completely prevented regardless of the conidial concentration (10(5)-10(7) conidia/cm(2)) after a 10-day exposure in soils at >98% RH. Treatment of eggs with B. bassiana, however, failed to reduce the number of eclosing larvae. This is the first demonstration of the ovicidal activity by M. anisopliae against either A. gambiae s. s. or A. arabiensis and the results underline the potential of this fungus against anopheline mosquitoes.

  11. Bionomics of Anopheline species and malaria transmission dynamics along an altitudinal transect in Western Cameroon

    Directory of Open Access Journals (Sweden)

    Toto Jean-Claude

    2010-05-01

    Full Text Available Abstract Background Highland areas of Africa are mostly malaria hypoendemic, due to climate which is not appropriate for anophelines development and their reproductive fitness. In view of designing a malaria control strategy in Western Cameroon highlands, baseline data on anopheline species bionomics were collected. Methods Longitudinal entomological surveys were conducted in three localities at different altitudinal levels. Mosquitoes were captured when landing on human volunteers and by pyrethrum spray catches. Sampled Anopheles were tested for the presence of Plasmodium circumsporozoite proteins and their blood meal origin with ELISA. Entomological parameters of malaria epidemiology were assessed using Mac Donald's formula. Results Anopheline species diversity and density decreased globally from lowland to highland. The most aggressive species along the altitudinal transect was Anopheles gambiae s.s. of S molecular form, followed in the lowland and on the plateau by An. funestus, but uphill by An. hancocki. An. gambiae and An. ziemanni exhibited similar seasonal biting patterns at the different levels, whereas different features were observed for An. funestus. Only indoor resting species could be captured uphill; it is therefore likely that endophilic behaviour is necessary for anophelines to climb above a certain threshold. Of the ten species collected along the transect, only An. gambiae and An. funestus were responsible for malaria transmission, with entomological inoculation rates (EIR of 90.5, 62.8 and zero infective bites/human/year in the lowland, on the plateau and uphill respectively. The duration of gonotrophic cycle was consistently one day shorter for An. gambiae as compared to An. funestus at equal altitude. Altitudinal climate variations had no effect on the survivorship and the subsequent life expectancy of the adult stage of these malaria vectors, but most probably on aquatic stages. On the contrary increasing altitude

  12. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

    DEFF Research Database (Denmark)

    Jacobsen, Magnus W.; Hansen, Michael Møller; Orlando, Ludovic;

    2012-01-01

    the evolutionary history of the endangered Danish North Sea houting (NSH) and other closely related Danish and Baltic European lake whitefish (ELW). Two well-supported clades were found within both ELW and NSH, probably reflecting historical introgression via Baltic migrants. Although ELW and NSH...... colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long-term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence...

  13. Anopheline (Diptera:Culicidae) breeding in a traditional tank-based village ecosystem in north central Sri Lanka

    DEFF Research Database (Denmark)

    Amerasinghe, F P; Konradsen, F; Fonseka, K T;

    1997-01-01

    A 13-mo survey of immature anopheline mosquitoes breeding in surface water habitats was done at Mahameegaswewa village within the Huruluwewa watershed in north central Sri Lanka as part of a multidisciplinary study on malaria epidemiology. The watershed is representative of the ancient small tank...

  14. Environmental characteristics of anopheline mosquito larval habitats in a malaria endemic area in Iran

    Institute of Scientific and Technical Information of China (English)

    Moussa Soleimani-Ahmadi; Hassan Vatandoost; Ahmad-Ali Hanafi-Bojd; Mehdi Zare; Reza Safari; Abdolrasul Mojahedi; Fatemeh Poorahmad-Garbandi

    2013-01-01

    Objective: To determine the effects of environmental parameters of larval habitats on distribution and abundance of anopheline mosquitoes in Rudan county of Iran. Methods: This cross-sectional study was conducted during the mosquito breeding season from February 2010 to October 2011. The anopheline larvae were collected using the standard dipping method. The specimens were identified using a morphological-based key. Simultaneously with larval collection, environmental parameters of the larval habitats including water current and turbidity, sunlight situation, and substrate type of habitats were recorded. Water samples were taken from breeding sites during larval collection. Before collection of samples, the water temperature was measured. The water samples were analysed for turbidity, conductivity, total alkalinity, total dissolved solid, pH and ions including chloride, sulphate, calcium, and magnesium. Statistical correlation analysis and ANOVA test were used to analyze the association between environmental parameters and larval mosquito abundance. Results: In total 2 973 larvae of the genus Anopheles were collected from 25 larval habitats and identified using morphological characters. They comprised of six species:An. dthali turkhudi (3.30%), and An. apoci (1.14%). The most abundant species was An. dthali which were collected from all of the study areas. Larvae of two malaria vectors, An. dthali and An. stephensi, co-existed and collected in a wide range of habitats with different physico-chemical parameters. The most common larval habitats were man-made sites such as sand mining pools with clean and still water. The anopheline mosquitoes also preferred permanent habitats in sunlight with sandy substrates. The results indicated that there was a significant relationship between mean physico-chemical parameters such as water temperature, conductivity, total alkalinity, sulphate, chloride, and mosquito distribution and abundance. Conclusions: The results of this

  15. Impact of dams and irrigation schemes in Anopheline (Diptera: Culicidae bionomics and malaria epidemiology

    Directory of Open Access Journals (Sweden)

    Jordi Sanchez-Ribas

    2012-08-01

    Full Text Available Irrigation schemes and dams have posed a great concern on public health systems of several countries, mainly in the tropics. The focus of the present review is to elucidate the different ways how these human interventions may have an effect on population dynamics of anopheline mosquitoes and hence, how local malaria transmission patterns may be changed. We discuss different studies within the three main tropical and sub-tropical regions (namely Africa, Asia and the Pacific and the Americas. Factors such as pre-human impact malaria epidemiological patterns, control measures, demographic movements, human behaviour and local Anopheles bionomics would determine if the implementation of an irrigation scheme or a dam will have negative effects on human health. Some examples of successful implementation of control measures in such settings are presented. The use of Geographic Information System as a powerful tool to assist on the study and control of malaria in these scenarios is also highlighted.

  16. The ecology and larval habitats characteristics of anopheline mosquitoes (Diptera:Culicidae) in Aligudarz County (Luristan province, western Iran)

    Institute of Scientific and Technical Information of China (English)

    Hamid Amani; Mohammad Reza Yaghoobi-Ershadi; Hamid Kassiri

    2014-01-01

    Objective: To determine ecology and characteristics of the larval habitats of the genus Anopheles (Dipetra: Culicidae) in Aligudarz County, western Iran.Methods:larvae ecology in seven rural districts, Aligudarz County, from late April to late November 1997. Larvae were captured using the dipping method. Larval breeding places characteristics were noted according to water situation (turbid or clean, stagnant or running), substrate type, site type (man-made or natural), sunlight situation, site situation (transient or permanent, with or without vegetation). This descriptive cross-sectional research was carried out to study the anopheline Results: A total of 9 620 3rd and 4th instar larvae of Anopheles from 115 breeding places in 22 villages were captured, which belonged to the following species: Anopheles stephensi, Anopheles d’thali, Anopheles apoci, Anopheles superpictus (forms A and B), Anopheles marterii sogdianus, Anopheles turkhodi, Anopheles maculipennis S.L and Anopheles claviger. Anopheles stephensi,Anopheles maculipennis Anopheles superpictus (93.18%) was the most prevailed one and dispersed over the entire region. Larval habitats consisted of nine natural and three artificial larval habitats. The most important larval habitats were river edges (54.8%), rice fields (12.2%), and grassland (8.7%) with permanent or transient, stagnant or running and clean water, with or without vegetation, sand or mud substrate in full sunlight area.Conclusions:Regarding this research, river edges and rice fields are the most important S.L and Anopheles apoci were collected for the first time in this county. breeding places of malaria vectors in Aligudarz County. It is worthy of note in larvicidal programs.

  17. Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.

    Science.gov (United States)

    Campbell, Matthew A; López, J Andrés; Sado, Tetsuya; Miya, Masaki

    2013-11-01

    The increasing number of taxa and loci in molecular phylogenetic studies of basal euteleosts has brought stability in a controversial area. A key emerging aspect to these studies is a sister Esociformes (pike) and Salmoniformes (salmon) relationship. We evaluate mitochondrial genome support for a sister Esociformes and Salmoniformes hypothesis by surveying many potential outgroups for these taxa, employing multiple phylogenetic approaches, and utilizing a thorough sampling scheme. Secondly, we conduct a simultaneous divergence time estimation and phylogenetic inference in a Bayesian framework with fossil calibrations focusing on relationships within Esociformes+Salmoniformes. Our dataset supports a sister relationship between Esociformes and Salmoniformes; however the nearest relatives of Esociformes+Salmoniformes are inconsistent among analyses. Within the order Esociformes, we advocate for a single family, Esocidae. Subfamily relationships within Salmonidae are poorly supported as Salmoninae sister to Thymallinae+Coregoninae.

  18. Anopheline Diversity: Morphological and Molecular Variation of An. subpictus in Rural and Urban Areas of West Bengal

    Directory of Open Access Journals (Sweden)

    Satarupa Paul

    2013-04-01

    Full Text Available A systematic survey (March 2012- Feb 2013of Anopheline population in rural(Mogra and urban(Dumdum areas of West Bengal has been conducted to know the present population load of Anopheles subpictus. A reliminary attempt has been made to assess the potential morphological (wing as well as molecular variation of Anopheles subpictus by using ITS-2 sequence primer. A considerable sequence variation is observed between the rural and urban population of West Bengal.

  19. Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures.

    Science.gov (United States)

    Männistö, Minna K; Kurhela, Emilia; Tiirola, Marja; Häggblom, Max M

    2013-04-01

    The timing and extent of snow cover is a major controller of soil temperature and hence winter-time microbial activity and plant diversity in Arctic tundra ecosystems. To understand how snow dynamics shape the bacterial communities, we analyzed the bacterial community composition of windswept and snow-accumulating shrub-dominated tundra heaths of northern Finland using DNA- and RNA-based 16S rRNA gene community fingerprinting (terminal restriction fragment polymorphism) and clone library analysis. Members of the Acidobacteria and Proteobacteria dominated the bacterial communities of both windswept and snow-accumulating habitats with the most abundant phylotypes corresponding to subdivision (SD) 1 and 2 Acidobacteria in both the DNA- and RNA-derived community profiles. However, different phylotypes within Acidobacteria were found to dominate at different sampling dates and in the DNA- vs. RNA-based community profiles. The results suggest that different species within SD1 and SD2 Acidobacteria respond to environmental conditions differently and highlight the wide functional diversity of these organisms even within the SD level. The acidic tundra soils dominated by ericoid shrubs appear to select for diverse stress-tolerant Acidobacteria that are able to compete in the nutrient poor, phenolic-rich soils. Overall, these communities seem stable and relatively insensitive to the predicted changes in the winter-time snow cover.

  20. Anopheline larval habitats seasonality and species distribution: a prerequisite for effective targeted larval habitats control programmes.

    Directory of Open Access Journals (Sweden)

    Eliningaya J Kweka

    Full Text Available BACKGROUND: Larval control is of paramount importance in the reduction of malaria vector abundance and subsequent disease transmission reduction. Understanding larval habitat succession and its ecology in different land use managements and cropping systems can give an insight for effective larval source management practices. This study investigated larval habitat succession and ecological parameters which influence larval abundance in malaria epidemic prone areas of western Kenya. METHODS AND FINDINGS: A total of 51 aquatic habitats positive for anopheline larvae were surveyed and visited once a week for a period of 85 weeks in succession. Habitats were selected and identified. Mosquito larval species, physico-chemical parameters, habitat size, grass cover, crop cycle and distance to nearest house were recorded. Polymerase chain reaction revealed that An. gambiae s.l was the most dominant vector species comprised of An.gambiae s.s (77.60% and An.arabiensis (18.34%, the remaining 4.06% had no amplification by polymerase chain reaction. Physico-chemical parameters and habitat size significantly influenced abundance of An. gambiae s.s (P = 0.024 and An. arabiensis (P = 0.002 larvae. Further, larval species abundance was influenced by crop cycle (P≤0.001, grass cover (P≤0.001, while distance to nearest houses significantly influenced the abundance of mosquito species larvae (r = 0.920;P≤0.001. The number of predator species influenced mosquito larval abundance in different habitat types. Crop weeding significantly influenced with the abundance of An.gambiae s.l (P≤0.001 when preceded with fertilizer application. Significantly higher anopheline larval abundance was recorded in habitats in pasture compared to farmland (P = 0.002. When habitat stability and habitat types were considered, hoof print were the most productive followed by disused goldmines. CONCLUSION: These findings suggest that implementation of effective larval

  1. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

    Science.gov (United States)

    Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

    2016-10-01

    Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East.

  2. Interactions of grazing history, cattle removal and time since rain drive divergent short-term responses by desert biota.

    Directory of Open Access Journals (Sweden)

    Anke S K Frank

    Full Text Available Arid grasslands are used worldwide for grazing by domestic livestock, generating debate about how this pastoral enterprise may influence native desert biota. One approach to resolving this question is to experimentally reduce livestock numbers and measure the effects. However, a key challenge in doing this is that historical grazing impacts are likely to be cumulative and may therefore confound comparisons of the short-term responses of desert biota to changes in stocking levels. Arid areas are also subject to infrequent flooding rainfalls that drive productivity and dramatically alter abundances of flora and fauna. We took advantage of an opportunity to study the recent effects of a property-scale cattle removal on two properties with similarly varied grazing histories in central Australia. Following the removal of cattle in 2006 and before and after a significant rainfall event at the beginning of 2007, we sampled vegetation and small vertebrates on eight occasions until October 2008. Our results revealed significant interactions of time of survey with both grazing history and grazing removal for vascular plants, small mammals and reptiles. The mammals exhibited a three-way interaction of time, grazing history and grazing removal, thus highlighting the importance of careful sampling designs and timing for future monitoring. The strongest response to the cessation of grazing after two years was depressed reproductive output of plants in areas where cattle continued to graze. Our results confirm that neither vegetation nor small vertebrates necessarily respond immediately to the removal of livestock, but that rainfall events and cumulative grazing history are key determinants of floral and faunal performance in grassland landscapes with low and variable rainfall. We suggest that improved assessments could be made of the health of arid grazing environments if long-term monitoring were implemented to track the complex interactions that influence

  3. Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population.

    Science.gov (United States)

    Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E; Lummaa, Virpi

    2013-12-07

    The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.

  4. Multiple insecticide resistance mechanisms involving metabolic changes and insensitive target sites selected in anopheline vectors of malaria in Sri Lanka

    Directory of Open Access Journals (Sweden)

    Karunaratne SHP Parakrama

    2008-08-01

    Full Text Available Abstract Background The current status of insecticide resistance and the underlying resistance mechanisms were studied in the major vector of malaria, Anopheles culicifacies, and the secondary vector, Anopheles subpictus in five districts (Anuradhapura, Kurunegala, Moneragala, Puttalam and Trincomalee of Sri Lanka. Eight other anophelines, Anopheles annularis, Anopheles barbirostris, Anopheles jamesii, Anopheles nigerrimus, Anopheles peditaeniatus, Anopheles tessellatus, Anopheles vagus and Anopheles varuna from Anuradhapura district were also tested. Methods Adult females were exposed to the WHO discriminating dosages of DDT, malathion, fenitrothion, propoxur, λ-cyhalothrin, cyfluthrin, cypermethrin, deltamethrin, permethrin and etofenprox. The presence of metabolic resistance by esterase, glutathione S-transferase (GST and monooxygenase-based mechanisms, and the sensitivity of the acetylcholinesterase target site were assessed using synergists, and biochemical, and metabolic techniques. Results All the anopheline species had high DDT resistance. All An. culicifacies and An. subpictus populations were resistant to malathion, except An. culicifacies from Kurunegala, where there was no malathion carboxylesterase activity. Kurunegala and Puttalam populations of An. culicifacies were susceptible to fenitrothion. All the An. culicifacies populations were susceptible to carbamates. Both species were susceptible to the discriminating dosages of cypermethrin and cyfluthrin, but had different levels of resistance to other pyrethroids. Of the 8 other anophelines, only An. nigerrimus and An. peditaeniatus were resistant to all the insecticides tested, probably due to their high exposure to the insecticides used in agriculture. An. vagus showed some resistance to permethrin. Esterases, GSTs and monooxygenases were elevated in both An. culicifacies and An. subpictus. AChE was most sensitive to insecticides in Kurunegala and Trincomalee An. culicifacies

  5. Anofelinos de Santa Catarina (Diptera: Culicidae, Brasil Anophelines of Santa Catarina (Diptera: Culicidae, Brazil

    Directory of Open Access Journals (Sweden)

    Maria da Graça Teixeira Portes

    2010-04-01

    likelihood of reintroduction of the disease. METHODS: The following data were used: the database of the Entomology Group of the National Health Foundation, Santa Catarina (ACCES, 1997-2000; the epidemiological surveillance information system of the Health Surveillance Department (Malaria/SC; and the notifiable disease information system (SINAN/SC. These data were transferred to and analyzed in the Microsoft Office Excel 2007 software. RESULTS: Collections were carried out in 48 municipalities and 159 localities, and 12,310 culicids, 11,546 anophelines (93.7% and 764 others (6.2% were identified. Three subgenera and 13 species of anophelines were identified. CONCLUSIONS: Given that in the municipalities investigated, important vectors such as Anopheles cruzii and Anopheles albitasis were found to be present, with movements of infected individuals from endemic areas, these areas can be considered to be receptive and vulnerable to malaria. These species are suspected of being responsible for malaria transmission in this region, especially in the municipalities of Gaspar, Indaial and Rodeio.

  6. Quantum skew divergence

    Energy Technology Data Exchange (ETDEWEB)

    Audenaert, Koenraad M. R., E-mail: koenraad.audenaert@rhul.ac.uk [Department of Mathematics, Royal Holloway University of London, Egham TW20 0EX, United Kingdom and Department of Physics and Astronomy, University of Ghent, S9, Krijgslaan 281, B-9000 Ghent (Belgium)

    2014-11-15

    In this paper, we study the quantum generalisation of the skew divergence, which is a dissimilarity measure between distributions introduced by Lee in the context of natural language processing. We provide an in-depth study of the quantum skew divergence, including its relation to other state distinguishability measures. Finally, we present a number of important applications: new continuity inequalities for the quantum Jensen-Shannon divergence and the Holevo information, and a new and short proof of Bravyi's Small Incremental Mixing conjecture.

  7. Seasonal population changes and malaria transmission potential of Anopheles pharoensis and the minor anophelines in Mwea Irrigation Scheme, Kenya.

    Science.gov (United States)

    Mukiama, T K; Mwangi, R W

    1989-05-01

    A study in 1984 and 1985 showed that Anopheles gambiae s.l. and An. pharoensis were the major anophelines in Mwea Irrigation Scheme, Kenya, constituting 83.86% and 15.69% of the catch respectively. Four minor species made up the remaining 0.45%. The irrigation phase of the rice cultivation cycle in August, which linked the flooding effects of the two rainy seasons, resulted in major population increases of An. pharoensis and enabled continuous breeding for up to 9 months per year. The average of mean monthly proportions of unfed, bloodfed, and gravid females was 26.6, 58.8, and 14.6% respectively. The Plasmodium falciparum sporozoite rates for An. pharoensis were 1.3% by ELISA and 0.68% by dissection, while those for An. funestus were 1.7% by ELISA and 1.25% by dissection. An. pharoensis can contribute to the epidemiology of Malaria in the Mwea area.

  8. Unphysical divergences in response theory

    Science.gov (United States)

    Parker, Shane M.; Roy, Saswata; Furche, Filipp

    2016-10-01

    Transition densities between excited states are key for nonlinear theoretical spectroscopy and multi-state non-adiabatic molecular dynamics (NAMD) simulations. In the framework of response theory, these transition densities are accessible from poles of the quadratic response function. It was shown recently that the thus obtained transition densities within time-dependent Hartree-Fock (TDHF) and adiabatic time-dependent density functional theory (TDDFT) exhibit unphysical divergences when the difference in excitation energy of the two states of interest matches another excitation energy. This unphysical behavior is a consequence of spurious poles in the quadratic response function. We show that the incorrect pole structure of the quadratic response is not limited to TDHF and adiabatic TDDFT, but is also present in many other approximate many-electron response functions, including those from coupled cluster and multiconfigurational self-consistent field response theory. The divergences appear in regions of the potential energy surface where the ground state is perfectly well behaved, and they are frequently encountered in NAMD simulations of photochemical reactions. The origin of the divergences is traced to an incorrect instantaneous time-dependence of the effective Hamiltonian. The implications for computations of frequency-dependent response properties are considerable and call into question the validity of conventional approximate many-electron response theories beyond linear response.

  9. Zero modes and divergence of entanglement entropy

    CERN Document Server

    Mallayya, Krishnanand; Shankaranarayanan, S; Padmanabhan, T

    2014-01-01

    We investigate the cause of the divergence of the entanglement entropy for the free scalar fields in $(1+1)$ and $(D + 1)$ dimensional space-times. In a canonically equivalent set of variables, we show explicitly that the divergence in the entanglement entropy in $(1 + 1)-$ dimensions is due to the accumulation of large number of near-zero frequency modes as opposed to the commonly held view of divergence having UV origin. The feature revealing the divergence in zero modes is related to the observation that the entropy is invariant under a hidden scaling transformation even when the Hamiltonian is not. We discuss the role of dispersion relations and the dimensionality of the space-time on the behavior of entanglement entropy.

  10. Abundance, biting behaviour and parous rate of anopheline mosquito species in relation to malaria incidence in gold-mining areas of southern Venezuela.

    Science.gov (United States)

    Moreno, J E; Rubio-Palis, Y; Páez, E; Pérez, E; Sánchez, V

    2007-12-01

    A longitudinal entomological and epidemiological study was conducted in five localities of southern Venezuela between January 1999 and April 2000 to determine the abundance, biting behaviour and parity of anopheline mosquitoes (Diptera: Culicidae) in relation to climate variables and malaria incidence. A total of 3685 female anopheline mosquitoes, representing six species, were collected. The most abundant species were Anopheles marajoara Galvão & Damasceno (60.7%) and Anopheles darlingi Root (35.1%), which together represented 95.8% of the total anophelines collected. Abundance and species distribution varied by locality. Malaria prevalence varied from 12.5 to 21.4 cases per 1000 population. Transmission occurred throughout the year; the annual parasite index (API) for the study period was 813.0 cases per 1000 population, with a range of 71.6-2492 per 1000 population, depending on locality. Plasmodium vivax (Grassi & Feletti) (Coccidia: Plasmodiidae) accounted for 78.6% of cases, Plasmodium falciparum (Welch) for 21.4% and mixed infections (Pv+Pf) for 0.05) between mosquito abundance and rainfall. Correlations between malaria incidence by parasite species and mosquito abundance were not significant (P > 0.05). Monthly parous rates were similar for An. marajoara and An. darlingi throughout the year, with two peaks that coincided with the dry-rainy transition period and the period of less rain. Peaks in the incidence of malaria cases were observed 1 month after major peaks in biting rates of parous anophelines. Anopheles darlingi engages in biting activity throughout the night, with two minor peaks at 23.00-00.00 hours and 03.00-04.00 hours. Anopheles marajoara has a different pattern, with a biting peak at 19.00-21.00 hours and 76.6% of biting occurring before midnight. Although both vectors bite indoors and outdoors, they showed a highly significant (P Venezuela and to provide relevant information to be considered when planning and implementing vector control

  11. Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa.

    Science.gov (United States)

    Villegas, Luis Martínez; Pimenta, Paulo Filemon Paolucci

    2014-08-01

    Anophelines harbour a diverse microbial consortium that may represent an extended gene pool for the host. The proposed effects of the insect microbiota span physiological, metabolic and immune processes. Here we synthesise how current metagenomic tools combined with classical culture-dependent techniques provide new insights in the elucidation of the role of the Anopheles-associated microbiota. Many proposed malaria control strategies have been based upon the immunomodulating effects that the bacterial components of the microbiota appear to exert and their ability to express anti-Plasmodium peptides. The number of identified bacterial taxa has increased in the current "omics" era and the available data are mostly scattered or in "tables" that are difficult to exploit. Published microbiota reports for multiple anopheline species were compiled in an Excel® spreadsheet. We then filtered the microbiota data using a continent-oriented criterion and generated a visual correlation showing the exclusive and shared bacterial genera among four continents. The data suggested the existence of a core group of bacteria associated in a stable manner with their anopheline hosts. However, the lack of data from Neotropical vectors may reduce the possibility of defining the core microbiota and understanding the mosquito-bacteria interactive consortium.

  12. Biting Indices, Host-seeking Activity and Natural Infection Rates of Anopheline Species in Boa Vista, Roraima, Brazil from 1996 to 1998

    Directory of Open Access Journals (Sweden)

    Silva-Vasconcelos Adenildo da

    2002-01-01

    Full Text Available The epidemiology of the transmission of malaria parasites varies ecologically. To observe some entomological aspects of the malaria transmission in an urban environment, a longitudinal survey of anopheline fauna was performed in Boa Vista, Roraima, Brazil. A total of 7,263 anophelines was collected in human bait at 13 de Setembro and Caranã districts: Anopheles albitarsis sensu lato (82.8%, An. darlingi (10.3%, An. braziliensis (5.5%, An. peryassui (0.9% and An. nuneztovari (0.5%. Nightly 12 h collections showed that An. albitarsis was actively biting throughout the night with peak activities at sunset and at midnight. An. darlingi bit during all night and did not demonstrate a defined biting peak. Highest biting indices, entomological inoculation rates and malaria cases were observed seasonally during the rainy season (April-November. Hourly collections showed host seek activity for all mosquitoes peaked during the first hour after sunset. An. darlingi showed the highest plasmodial malaria infection rate followed by An. albitarsis, An. braziliensis and An. nuneztovari (8.5%, 4.6%, 3% and 2.6%, respectively. An. albitarsis was the most frequently collected anopheline, presented the highest biting index and it was the second most frequently collected infected species infected with malaria parasites. An. albitarsis and An. darlingi respectively, are the primary vectors of malaria throughout Boa Vista.

  13. Diversity of anopheline mosquitoes (Diptera: Culicidae) and classification based on the characteristics of the habitats where they were collected in Puerto Iguazú, Misiones, Argentina.

    Science.gov (United States)

    Ramirez, P G; Stein, M; Etchepare, E G; Almiron, W R

    2016-12-01

    In order to extend the knowledge of anopheline diversity and their habitats in three environments with different degrees of anthropic intervention in Puerto Iguazú, Misiones, anopheline larvae were collected and classified on the basis of similarities of their habitats. Spatio-temporal abundance was determined and larval diversity and complementarity index were calculated. Rank-abundance curves were performed to compare the composition, abundance, and species evenness among environments. A total of 783 larvae, belonging to six species: Anopheles argyritarsis, An. fluminensis, An. mediopunctatus, An. punctimacula, An. strodei s.l., and An. triannulatus s.l., were collected. A cluster analysis and a principal component analysis detected two groups; exposure to sunlight and type of habitat were the characteristics that explained the grouping of species. Higher abundances of anopheline larvae were observed during autumn and spring. The greatest richness was recorded in wild and peri-urban environments and the effective number of species was greater in the wild. Anopheles punctimacula and An. triannulatus s.l. are secondary vectors of malaria in other South American countries and both species were found in the three environments, so that deforestation poses a potential risk for malaria transmission as it contributes to the proliferation of larval habitats for these mosquitoes.

  14. Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa

    Directory of Open Access Journals (Sweden)

    Luis Martínez Villegas

    2014-08-01

    Full Text Available Anophelines harbour a diverse microbial consortium that may represent an extended gene pool for the host. The proposed effects of the insect microbiota span physiological, metabolic and immune processes. Here we synthesise how current metagenomic tools combined with classical culture-dependent techniques provide new insights in the elucidation of the role of the Anopheles-associated microbiota. Many proposed malaria control strategies have been based upon the immunomodulating effects that the bacterial components of the microbiota appear to exert and their ability to express anti-Plasmodium peptides. The number of identified bacterial taxa has increased in the current “omics” era and the available data are mostly scattered or in “tables” that are difficult to exploit. Published microbiota reports for multiple anopheline species were compiled in an Excel® spreadsheet. We then filtered the microbiota data using a continent-oriented criterion and generated a visual correlation showing the exclusive and shared bacterial genera among four continents. The data suggested the existence of a core group of bacteria associated in a stable manner with their anopheline hosts. However, the lack of data from Neotropical vectors may reduce the possibility of defining the core microbiota and understanding the mosquito-bacteria interactive consortium.

  15. Decoherence and infrared divergence

    Indian Academy of Sciences (India)

    J Kupsch

    2002-08-01

    The dynamics of a particle which is linearly coupled to a boson field is investigated. The boson field induces superselection rules for the momentum of the particle, if the field is infrared divergent. Thereby the Hamiltonian of the total system remains bounded from below.

  16. Divergence Time Estimation of Fishes in Leuciscinae in Xinjiang%新疆雅罗鱼亚科鱼类分化时间的估计

    Institute of Scientific and Technical Information of China (English)

    海萨; 蔡林钢; 孟玮; 杨天燕; 马徐发

    2014-01-01

    FishesinLeuciscinaewereoriginatedearlierinCyprinidae,andhavesignificantdifferencesinmorphology.Sofar,thephy-logeneticrelationshipswithinthesubfamilyLeuciscinaehavestillbeenverycontroversial.ThephylogeneticrelationshipswithinLeu-ciscinae w ere reconstructed in six species in Leuciscinae distributed in X injiang by cytb sequences and bayesian m ixed m odels analy-sis.T he divergence tim e of genera w ithin L euciscinae w ere estim ated using relaxed m olecular clock m ethod.G enus Tinca w as found at the base ofthe phylogentic tree;and genera Tinca and Phoxinus w ere originated atO ligocene,w hile genera Abramis, Rutilus and Leu-ciscus w ere found to be originated atM iocene.%在鲤科鱼类中雅罗鱼亚科鱼类起源较早,形态差异显著。迄今为止,有关雅罗鱼亚科的系统发育关系还存在很大的争议。本文以新疆分布的雅罗鱼亚科鱼类为对象,采用线粒体DNA中的cyt b基因序列,用贝叶斯联合模型分析数据,重建了雅罗鱼亚科的系统发育关系;结合鲤亚科和裂腹鱼亚科,用松散分子钟估算了雅罗鱼亚科属间的分歧时间。结果显示:丁鱥属(Tinca)处于系统发育树的基部,新疆雅罗鱼亚科鱼类中丁鱥属(36Ma)和鱥属(Phoxinus)(29Ma)的起源于渐新世,而欧鳊属(Abramis)(20Ma)、拟鲤属(Rutilus)(18Ma)、雅罗鱼属(Leuciscus)(13Ma)起源于中新世。

  17. Resolving Metazoan phyla divergence times during cambrian explosion by COX I protein molecules%COXI蛋白质分子确定“寒武纪生物大爆发”时期物种分歧时间

    Institute of Scientific and Technical Information of China (English)

    李可群

    2016-01-01

    By using the equation for calculating absolute evolutionary rates of biological molecules presented by the author and classic"molecular clock"Cytochrome oxidase subunit I ( COX I ) protein molecules , the metazoan phyla divergence times during Cambrian explosion were obtained .These results show that Protostomia and Deuterostomia separated at560 million years( myrs ) ago.The phyla divergence times of four major deuterstomia:Cephalochordata , Urochordata, Hemichordata and Echinodermata are 536 myrs ago, 540 myrs ago, 548 myrs ago and 545 myrs ago, respectively.These divergence times agree well with their fossil records , and are obviously better than those obtained by other current molecular clock methods .Our method may provide a new way to understand origins and evo-lution of creatures .%使用经典分子钟分子COX I蛋白质和作者提出的同源生物分子绝对进化速率计算公式,对“寒武纪生物大爆发”期间的一些主要动物门类分歧时间进行了计算。结果表明:原口动物和后口动物分歧时间为5.60亿年前,后口动物中的头索动物、尾索动物、半索动物和棘皮动物的分歧时间分别为5.36亿年前、5.40亿年前、5.48亿年前和5.45亿年前。这些结果与化石记录基本符合,明显好于现有分子钟理论得到的结果。为研究生物起源和演化提供了一种的新的思路和方法。

  18. Do Time Press, Stimulus, and Creative Prompt Influence the Divergent Production of Undergraduate Students? Yes, Yes, and No, Not Very Much.

    Science.gov (United States)

    Morse, David T.; Morse, Linda W.; Johns, Gregg A.

    2001-01-01

    This study examined the influence of time press, specific stimulus, and type of creativity prompt on fluency and flexibility scores of 75 undergraduates. Results suggest that time press has a strong, and typically linear influence on both fluency and flexibility scores. A significant difference across stimuli was observed for flexibility, but not…

  19. Environmental factors associated with larval habitats of anopheline mosquitoes (Diptera: Culicidae in irrigation and major drainage areas in the middle course of the Rift Valley, central Ethiopia

    Directory of Open Access Journals (Sweden)

    Oljira Kenea, Meshesha Balkew & Teshome Gebre-Michael

    2011-06-01

    Full Text Available Background & objectives: Larval control is an integral part of malaria vector management in Ethiopia andelsewhere. For effective larval control, a sound understanding of the factors responsible for spatio-temporalvariation in larval production is essential. A study was thus conducted to characterize larval habitats of anophelinemosquitoes in irrigation and major drainage areas between Adami Tulu and Meki towns, in the middle course ofthe Ethiopian Rift Valley.Methods: Aquatic habitats were sampled for anopheline larvae and the associated environmental variables(water temperature, turbidity, water current, water pH and other variables were measured, characterized andanalyzed.Results: Microscopic identification of the late instars (III and IV of anopheline larvae collected throughout thestudy period yielded nearly 47.6% Anopheles pharoensis, 32.1% An. arabiensis, 17.1% An. squamosus and only3.2% of other species (An. coustani and An. cinereus. Larvae of the local malaria vectors, An. arabiensis andAn. pharoensis were most abundantly sampled from sand pools and natural swamps, respectively. Logisticregression analysis detected four best predictor variables associated with larval abundance of malaria vectorspecies. Thus, relative abundance of An. arabiensis larvae was significantly and inversely associated with aquaticvegetation and water current, whereas the relative abundance of An. pharoensis larvae was significantly andpositively associated with water temperature and the presence of algae in the water bodies.Conclusion: Dry season anopheline larval habitats such as riverine sand pools that are created and maintainedby perennial water bodies and their associated water development projects need to be considered in vectorcontrol operations.

  20. Salivary gland proteome analysis reveals modulation of anopheline unique proteins in insensitive acetylcholinesterase resistant Anopheles gambiae mosquitoes.

    Directory of Open Access Journals (Sweden)

    Sylvie Cornelie

    Full Text Available Insensitive acetylcholinesterase resistance due to a mutation in the acetylcholinesterase (ace encoding ace-1 gene confers cross-resistance to organophosphate and carbamate insecticides in Anopheles gambiae populations from Central and West Africa. This mutation is associated with a strong genetic cost revealed through alterations of some life history traits but little is known about the physiological and behavioural changes in insects bearing the ace-1(R allele. Comparative analysis of the salivary gland contents between An. gambiae susceptible and ace-1(R resistant strains was carried out to charaterize factors that could be involved in modifications of blood meal process, trophic behaviour or pathogen interaction in the insecticide-resistant mosquitoes. Differential analysis of the salivary gland protein profiles revealed differences in abundance for several proteins, two of them showing major differences between the two strains. These two proteins identified as saglin and TRIO are salivary gland-1 related proteins, a family unique to anopheline mosquitoes, one of them playing a crucial role in salivary gland invasion by Plasmodium falciparum sporozoites. Differential expression of two other proteins previously identified in the Anopheles sialome was also observed. The differentially regulated proteins are involved in pathogen invasion, blood feeding process, and protection against oxidation, relevant steps in the outcome of malaria infection. Further functional studies and insect behaviour experiments would confirm the impact of the modification of the sialome composition on blood feeding and pathogen transmission abilities of the resistant mosquitoes. The data supports the hypothesis of alterations linked to insecticide resistance in the biology of the primary vector of human malaria in Africa.

  1. Anopheline species, some of their habits and relation to malaria in endemic areas of Rondônia State, Amazon region of Brazil.

    Science.gov (United States)

    Lourenço-de-Oliveira, R; Guimarães, A E; Arlé, M; da Silva, T F; Castro, M G; Motta, M A; Deane, L M

    1989-01-01

    In view of recent studies incriminating several species of anophelines, besides Anopheles darlingi, as malaria vectors in the Brazilian Amazon, we performed an anopheline survey in four localities--Ariquemes, Cujubim, Machadinho and Itapoã do Oeste--in Rondônia, the most malarious State in the Country. Twenty species were found. An. darlingi was, by far, the dominant species and the only one whose density coincided with that of malaria. On human baits it was more numerous in the immediate vicinity of houses than indoors where, however, it was almost the only species encountered. On both situations it fed mostly at sunset and during the first half of the night. It was less numerous far from houses and scarce inside the forest. Other species (An. triannulatus, An. evansae, An. albitarsis, An. strodei) appeared in appreciable numbers only in Ariquemes, both in areas with and without malaria. The remaining species were scanty. An. darlingi was confirmed as the primary local vector.

  2. BIOLOGICAL AND MORPHOLOGICAL EFFECTS OF CHITINSYNTHESIS INHIBITOR (TRIFLUMURON ON ANOPHELINE LARVAE

    Directory of Open Access Journals (Sweden)

    E. Farashiani

    1999-12-01

    Full Text Available Triflumuron (Bay sir 8514 is one of many benzoylated ureas, which inhibit chitin synthesis during insect molting and are commonly referred to as insect growth regulators or I. G. Rs. The post emergence efficacy of triflumuron (SC 48% was evaluated against larvae of Anopheles stephensi. The first instar larvae were exposed to tirflumuron at LC50 level (0.0001 mg/l in a continues exposure time. Among 1000 larvae listed 570 were passed to pupal stage (43% morality at the larvae of stage. The dead larvae generally showed different abnormalities, i.e. cuticle of these larvae was dark and thorax of them was inflated. 271 adults, off the pupae, emerged incompletely. At last, only 138 pupae developed completely to adults. It was noted that certain morphological abnormalities became evident in emerged adults. In the emerged adults, generally there were different abnormalities in wing or tarsus. They also showed some difficulties in mating or feeding behaviour in breeding cages. In the end of experiment, 3 out of 13 adults were oviposited. The effect of triflumuron on egg laying of adults was studied and the larvicid did not show any effect on egg laying of adults.

  3. The fauna, monthly activity and species composition of anophelines mosquito larva in breeding places, Qom province

    Directory of Open Access Journals (Sweden)

    Abedin Saghafipour

    2013-09-01

    Full Text Available Background: There is need to develop updated database related to malaria mosquito, because there is back prevalence of malaria in the past two decades in some areas of north and northwest of Iran categorized as epidemiologically clean areas previously. Vectors control is one of the main strategies in controlling the epidemics. In this study, species composition and monthly activity of anopheles mosquito larva in different breeding places in Qom province was assessed. Material and Methods: The present study was a cross-sectional one. It was carried out in all 5 parts of geographical areas of Qom province. Samples were collected every 15 days from the natural and artificial breeding places from April to October 2010, using dipping standard method of WHO. Mosquito larvae conserved in lactophenol medium. In the laboratory, the specimens were mounted in likidophor medium and microscopic slides were prepared from larvae, and identified using illustrated keys for Iranian mosquitoes. Results: A total of 298 larvae samples were collected and identified from different breeding places in various areas of Qom province. This larvae belonged to two subgenus of Anopheles and Cellia and including four species of An.(Ano.marteri, An.(Ano.claviger, An.(Cel.superpictus, and An.(Cel.turkhudi. An.(Ano. claviger, An.(Ano.marteri, and An.(Cel.turkhudi are reported for the first time in this province. An.(Ano.claviger was dominant species of larvae in the breeding places in Qom province and found in different larva habitats. The peak of activity of recent species is in late July and early August and its seasonal activity is in late April to late October. Conclusion: An.(Cel.superpictus which is Malaria vector in different parts of the world and Iran is the dominant species of the area had the second frequency. Having high potential for transmission and possibility of establishing a transmission cycle with low abundance is the characteristics of first species. Anopheles

  4. Behavioral patterns, parity rate and natural infection analysis in anopheline species involved in the transmission of malaria in the northeastern Brazilian Amazon region.

    Science.gov (United States)

    Barbosa, Ledayane Mayana Costa; Souto, Raimundo Nonato Picanço; Dos Anjos Ferreira, Ricardo Marcelo; Scarpassa, Vera Margarete

    2016-12-01

    The characterization of behavioral patterns allows a better understanding of the transmission dynamics and the design of more effective malaria vector control strategies. This study analyzed the behavioral patterns of the Anopheles species of the Coração district situated in the northeast of the Brazilian Amazon region. The behavioral patterns of the anopheline species were measured based on the 36 collection sites of this district from December 2010 to November 2011. Collections of four hours for three consecutive nights each month and four 12-h collections, comprising two in the rainy season and two in the dry season, were performed. Furthermore, to infer the anthropophily and zoophily indexes, four additional four-hour collections were performed. The samples were also evaluated for parity rate and natural infectivity for Plasmodium spp. A total of 1689 anophelines were captured, comprising of nine species and two subgenera (Nyssorhynchus - six species, and Anopheles - three species). Anopheles darlingi was the most abundant and widely distributed species in the area, followed by A. braziliensis and A.marajoara. Anopheles darlingi and A. marajoara were the only species present in the four collections of 12-h, but only A. darlingi showed activity throughout night. Anopheles darlingi was the most anthropophilic species (AI=0.40), but the zoophily index was higher (ZI=0.60), revealing an eclectic and opportunistic behavior. Of the six most frequent species, A. nuneztovari s.l. was the most zoophilic species (ZI=1.00). All captured species showed predominance towards biting in outdoor environments. Anopheles darlingi and A. braziliensis showed multimodal biting peaks, whereas A. marajoara revealed a stable pattern, with the biting peak after sunset. Using the PCR technique, no anopheline was found infected with the malaria parasite. Since A. darlingi and A. marajoara are recognized as important vectors in this region, the district of Coração may be considered as

  5. The effects of medieval dams on genetic divergence and demographic history in brown trout populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Limborg, Morten; Ferchaud, A.-L.;

    2014-01-01

    genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results: Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence...

  6. Malaria outside the Amazon region: natural Plasmodium infection in anophelines collected near an indigenous village in the Vale do Rio Branco, Itanhaém, SP, Brazil.

    Science.gov (United States)

    Neves, Amanda; Urbinatti, Paulo Roberto; Malafronte, Rosely dos Santos; Fernandes, Aristides; Paganini, Wanderley da Silva; Natal, Delsio

    2013-01-01

    A few cases of Plasmodium vivax malaria in which anophelines of subgenus Kerteszia were incriminated as vectors have been reported outside the Amazon region, in the Atlantic Forest. This study was carried out near an indigenous Guarani village in the Curucutu reserve, an environmental protection area in the municipality of Itanhaém in the state of São Paulo, Brazil, on November 30, 2009, February 18, 2010, April 29, 2010 and May 26, 2010. Mosquitoes were collected along the route to the Guarani village where the edge of the Branco river floodplain meets the forests on the mountain slopes. Adult forms were collected with CO(2)-baited CDC traps and Shannon traps from twilight to 10:00 P.M. Anopheles cruzii predominated in both traps. The other species collected in the CDC traps were An. pseudomaculipes/maculipes, An. fluminensis and An. mediopunctatus/forattinii/costai. In addition to the latter three species, An. apicimacula/intermedius and An. strodei were also found in the Shannon traps. All but An. cruzii and An. strodei belong to subgenus Anopheles. A total of 506 mosquitoes were assayed by PCR to detect natural infection by Plasmodium species. In the CDC traps, An. fluminensis and An. pseudomaculipes/maculipes were positive for Plasmodium malariae, while in the Shannon traps An. pseudomaculipes/maculipes was positive for Plasmodium vivax and Plasmodium malariae and An. cruzii was positive for P. malariae, resulting in a minimum infection rate of 0.24%. Our findings suggest that An. cruzii may be incriminated in the transmission of malaria between monkeys and humans, as this species was found to be infected by P. malariae. They also highlight the need for an understanding of the role of anophelines from outside subgenus Kerteszia in the transmission of malaria in the Atlantic Forest, as these were also found to be naturally infected by P. vivax and P. malariae.

  7. Hyperbolic Divergence Cleaning for SPH

    CERN Document Server

    Tricco, Terrence S

    2012-01-01

    We present SPH formulations of Dedner et al's hyperbolic/parabolic divergence cleaning scheme for magnetic and velocity fields. Our implementation preserves the conservation properties of SPH which is important for stability. This is achieved by deriving an energy term for the Psi field, and imposing energy conservation on the cleaning subsystem of equations. This necessitates use of conjugate operators for divB and gradPsi in the numerical equations. For both the magnetic and velocity fields, the average divergence error in the system is reduced by an order of magnitude with our cleaning algorithm. Divergence errors in SPMHD are maintained to < 1%, even for realistic 3D applications with a corresponding gain in numerical stability. Density errors for an oscillating elliptic water drop using weakly compressible SPH are reduced by a factor of two.

  8. Systematic variations in divergence angle

    CERN Document Server

    Okabe, Takuya

    2012-01-01

    Practical methods for quantitative analysis of radial and angular coordinates of leafy organs of vascular plants are presented and applied to published phyllotactic patterns of various real systems from young leaves on a shoot tip to florets on a flower head. The constancy of divergence angle is borne out with accuracy of less than a degree. It is shown that apparent fluctuations in divergence angle are in large part systematic variations caused by the invalid assumption of a fixed center and/or by secondary deformations, while random fluctuations are of minor importance.

  9. Mechanisms of protein sequence divergence and incompatibility.

    Directory of Open Access Journals (Sweden)

    Alon Wellner

    Full Text Available Alignments of orthologous protein sequences convey a complex picture. Some positions are utterly conserved whilst others have diverged to variable degrees. Amongst the latter, many are non-exchangeable between extant sequences. How do functionally critical and highly conserved residues diverge? Why and how did these exchanges become incompatible within contemporary sequences? Our model is phosphoglycerate kinase (PGK, where lysine 219 is an essential active-site residue completely conserved throughout Eukaryota and Bacteria, and serine is found only in archaeal PGKs. Contemporary sequences tested exhibited complete loss of function upon exchanges at 219. However, a directed evolution experiment revealed that two mutations were sufficient for human PGK to become functional with serine at position 219. These two mutations made position 219 permissive not only for serine and lysine, but also to a range of other amino acids seen in archaeal PGKs. The identified trajectories that enabled exchanges at 219 show marked sign epistasis - a relatively small loss of function with respect to one amino acid (lysine versus a large gain with another (serine, and other amino acids. Our findings support the view that, as theoretically described, the trajectories underlining the divergence of critical positions are dominated by sign epistatic interactions. Such trajectories are an outcome of rare mutational combinations. Nonetheless, as suggested by the laboratory enabled K219S exchange, given enough time and variability in selection levels, even utterly conserved and functionally essential residues may change.

  10. "Divergent" Ramanujan-type supercongruences

    CERN Document Server

    Guillera, Jesús

    2010-01-01

    "Divergent" Ramanujan-type series for $1/\\pi$ and $1/\\pi^2$ provide us with new nice examples of supercongruences of the same kind as those related to the convergent cases. In this paper we manage to prove three of the supercongruences by means of the Wilf--Zeilberger algorithmic technique.

  11. History repeats itself: genomic divergence in copepods.

    Science.gov (United States)

    Renaut, Sébastien; Dion-Côté, Anne-Marie

    2016-04-01

    Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the tape would lead evolution down a pathway radically different from the road actually taken (Gould 1989). This thought experiment has puzzled evolutionary biologists for a long time: how repeatable are evolutionary events? And if history does indeed repeat itself, what are the factors that may help us predict the path taken? A powerful means to address these questions at a small evolutionary scale is to study closely related populations that have evolved independently, under similar environmental conditions. This is precisely what Pereira et al. (2016) set out to do using marine copepods Tigriopus californicus, and present their results in this issue of Molecular Ecology. They show that evolution can be repeatable and even partly predictable, at least at the molecular level. As expected from theory, patterns of divergence were shaped by natural selection. At the same time, strong genetic drift due to small population sizes also constrained evolution down a similar evolutionary road, and probably contributed to repeatable patterns of genomic divergence.

  12. More on divergences in brane world models

    CERN Document Server

    Smolyakov, Mikhail N

    2013-01-01

    In this note a model in a space-time with compact extra dimension, describing five-dimensional fermion fields interacting with electromagnetic field localized on a brane, is presented. This model can be considered as a toy model for examining possible consequences of localization of gauge fields on a brane. It is shown that in the limit of infinite extra dimension the lowest order amplitudes of some processes in the resulting four-dimensional effective theory are divergent. Such a "localization catastrophe" can be inherent to more realistic bane world models with infinite extra dimension.

  13. Creative Cognition in Secondary Science: An exploration of divergent thinking in science among adolescents

    Science.gov (United States)

    Antink-Meyer, Allison; Lederman, Norman G.

    2015-07-01

    The divergent thinking skills in science of 282 US high school students were investigated across 16 weeks of instruction in order to determine whether typical academic time periods can significantly influence changes in thinking skills. Students' from 6 high school science classrooms completed the Scientific Structures Creativity Measure (SSCM) before and after a semester of instruction. Even the short time frame of a typical academic term was found to be sufficient to promote both improvements in divergent thinking skills as well as declining divergent thinking. Declining divergent thinking skills were more common in this time frame than were improvements. The nature of student performance on the SSCM and implications are discussed.

  14. Eliminating the "divergence problem" at Alaska's northern treeline

    Science.gov (United States)

    Wilmking, M.; Singh, J.

    2008-06-01

    Recently, an increasing off-set between tree-ring based temperature reconstructions and measured temperatures at high latitudes has been reported, the so called "divergence problem" (here "divergence effect"). This "divergence effect" seriously questions the validity of tree-ring based climate reconstructions, since it seems to violate the assumption of a stable response of trees to changing climate over time. In this study we eliminated the "divergence effect" in northern Alaska by careful selection of individual trees with consistently significant positive relationships with climate (17% of sample) and successfully attempted a divergence-free climate reconstruction using this sub-set. However, the majority of trees (83%) did not adhere to the uniformitarian principle as usually applied in dendroclimatology. Our results thus support the notion, that factors acting on an individual tree basis are the primary causes for the "divergence effect" (at least in northern Alaska). Neither different detrending methods nor factors acting on larger scales such as global dimming or an increase in UV-B radiation could explain our results. Our results also highlight the necessity to adapt the methods of paleoreconstruction using tree rings to account for non-stable climate growth relationships as these are found in the vast majority of sampled trees and seem to be the norm rather than the exception.

  15. Inference by Minimizing Size, Divergence, or their Sum

    CERN Document Server

    Riedel, Sebastian; McCallum, Andrew

    2012-01-01

    We speed up marginal inference by ignoring factors that do not significantly contribute to overall accuracy. In order to pick a suitable subset of factors to ignore, we propose three schemes: minimizing the number of model factors under a bound on the KL divergence between pruned and full models; minimizing the KL divergence under a bound on factor count; and minimizing the weighted sum of KL divergence and factor count. All three problems are solved using an approximation of the KL divergence than can be calculated in terms of marginals computed on a simple seed graph. Applied to synthetic image denoising and to three different types of NLP parsing models, this technique performs marginal inference up to 11 times faster than loopy BP, with graph sizes reduced up to 98%-at comparable error in marginals and parsing accuracy. We also show that minimizing the weighted sum of divergence and size is substantially faster than minimizing either of the other objectives based on the approximation to divergence present...

  16. Divergences in spinfoam quantum gravity

    CERN Document Server

    Smerlak, Matteo

    2012-01-01

    In this thesis we study the flat model, the main buidling block for the spinfoam approach to quantum gravity, with an emphasis on its divergences. Besides a personal introduction to the problem of quantum gravity, the manuscript consists in two part. In the first one, we establish an exact powercounting formula for the bubble divergences of the flat model, using tools from discrete gauge theory and twisted cohomology. In the second one, we address the issue of spinfoam continuum limit, both from the lattice field theory and the group field theory perspectives. In particular, we put forward a new proof of the Borel summability of the Boulatov-Freidel-Louapre model, with an improved control over the large-spin scaling behaviour. We conclude with an outlook of the renormalization program in spinfoam quantum gravity.

  17. Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

    Directory of Open Access Journals (Sweden)

    Miya Masaki

    2008-07-01

    Full Text Available Abstract Background Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. Bayesian estimations of divergence times that do not assume the molecular clock use time constraints at multiple nodes, usually based on the fossil records, as major boundary conditions. However, the fossil records of bony fishes may not adequately provide effective time constraints at multiple nodes. We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei. Results We added new mitogenomic sequence data from six cichlid species and conducted phylogenetic analyses using a large mitogenomic data set. We found a reciprocal monophyly of African and Neotropical cichlids and their sister group relationship to some Malagasy taxa (Ptychochrominae sensu Sparks and Smith. All of these taxa clustered with a Malagasy + Indo/Sri Lankan clade (Etroplinae sensu Sparks and Smith. The results of the phylogenetic analyses and divergence time estimations between continental cichlid clades were much more congruent with Gondwanaland origin and Cretaceous vicariant divergences than with Cenozoic transmarine dispersal between major continents. Conclusion We propose to add the biogeographic assumption of cichlid divergences by continental fragmentation as effective time constraints in dating teleostean divergence times. We conducted divergence time estimations among teleosts by incorporating these additional time constraints and achieved a considerable reduction in credibility intervals in the estimated divergence times.

  18. Boiling flow through diverging microchannel

    Indian Academy of Sciences (India)

    V S Duryodhan; S G Singh; Amit Agrawal

    2013-12-01

    An experimental study of flow boiling through diverging microchannel has been carried out in this work, with the aim of understanding boiling in nonuniform cross-section microchannel. Diverging microchannel of 4° of divergence angle and 146 m hydraulic diameter (calculated at mid-length) has been employed for the present study with deionised water as working fluid. Effect of mass flux (118–1182 kg/m2-s) and heat flux (1.6–19.2 W/cm2) on single and two-phase pressure drop and average heat transfer coefficient has been studied. Concurrently, flow visualization is carried out to document the various flow regimes and to correlate the pressure drop and average heat transfer coefficient to the underlying flow regime. Four flow regimes have been identified from the measurements: bubbly, slug, slug–annular and periodic dry-out/rewetting. Variation of pressure drop with heat flux shows one maxima which corresponds to transition from bubbly to slug flow. It is shown that significantly large heat transfer coefficient (up to 107 kW/m2-K) can be attained for such systems, for small pressure drop penalty and with good flow stability.

  19. Genetic divergence of tomato subsamples

    Directory of Open Access Journals (Sweden)

    André Pugnal Mattedi

    2014-02-01

    Full Text Available Understanding the genetic variability of a species is crucial for the progress of a genetic breeding program and requires characterization and evaluation of germplasm. This study aimed to characterize and evaluate 101 tomato subsamples of the Salad group (fresh market and two commercial controls, one of the Salad group (cv. Fanny and another of the Santa Cruz group (cv. Santa Clara. Four experiments were conducted in a randomized block design with three replications and five plants per plot. The joint analysis of variance was performed and characteristics with significant complex interaction between control and experiment were excluded. Subsequently, the multicollinearity diagnostic test was carried out and characteristics that contributed to severe multicollinearity were excluded. The relative importance of each characteristics for genetic divergence was calculated by the Singh's method (Singh, 1981, and the less important ones were excluded according to Garcia (1998. Results showed large genetic divergence among the subsamples for morphological, agronomic and organoleptic characteristics, indicating potential for genetic improvement. The characteristics total soluble solids, mean number of good fruits per plant, endocarp thickness, mean mass of marketable fruit per plant, total acidity, mean number of unmarketable fruit per plant, internode diameter, internode length, main stem thickness and leaf width contributed little to the genetic divergence between the subsamples and may be excluded in future studies.

  20. Ultraviolet and Infrared Divergences in Superstring Theory

    CERN Document Server

    Sen, Ashoke

    2015-01-01

    Superstring theory is known to be free from ultraviolet divergences but suffers from the usual infrared divergences that occur in quantum field theories. After briefly reviewing the origin of ultraviolet finiteness of superstring theory we describe recent progress towards the understanding of infrared divergences in superstring theory.

  1. New classification of natural breeding habitats for Neotropical anophelines in the Yanomami Indian Reserve, Amazon Region, Brazil and a new larval sampling methodology.

    Science.gov (United States)

    Sánchez-Ribas, Jordi; Oliveira-Ferreira, Joseli; Rosa-Freitas, Maria Goreti; Trilla, Lluís; Silva-do-Nascimento, Teresa Fernandes

    2015-09-01

    Here we present the first in a series of articles about the ecology of immature stages of anophelines in the Brazilian Yanomami area. We propose a new larval habitat classification and a new larval sampling methodology. We also report some preliminary results illustrating the applicability of the methodology based on data collected in the Brazilian Amazon rainforest in a longitudinal study of two remote Yanomami communities, Parafuri and Toototobi. In these areas, we mapped and classified 112 natural breeding habitats located in low-order river systems based on their association with river flood pulses, seasonality and exposure to sun. Our classification rendered seven types of larval habitats: lakes associated with the river, which are subdivided into oxbow lakes and nonoxbow lakes, flooded areas associated with the river, flooded areas not associated with the river, rainfall pools, small forest streams, medium forest streams and rivers. The methodology for larval sampling was based on the accurate quantification of the effective breeding area, taking into account the area of the perimeter and subtypes of microenvironments present per larval habitat type using a laser range finder and a small portable inflatable boat. The new classification and new sampling methodology proposed herein may be useful in vector control programs.

  2. New classification of natural breeding habitats for Neotropical anophelines in the Yanomami Indian Reserve, Amazon Region, Brazil and a new larval sampling methodology

    Directory of Open Access Journals (Sweden)

    Jordi Sánchez-Ribas

    2015-09-01

    Full Text Available Here we present the first in a series of articles about the ecology of immature stages of anophelines in the Brazilian Yanomami area. We propose a new larval habitat classification and a new larval sampling methodology. We also report some preliminary results illustrating the applicability of the methodology based on data collected in the Brazilian Amazon rainforest in a longitudinal study of two remote Yanomami communities, Parafuri and Toototobi. In these areas, we mapped and classified 112 natural breeding habitats located in low-order river systems based on their association with river flood pulses, seasonality and exposure to sun. Our classification rendered seven types of larval habitats: lakes associated with the river, which are subdivided into oxbow lakes and nonoxbow lakes, flooded areas associated with the river, flooded areas not associated with the river, rainfall pools, small forest streams, medium forest streams and rivers. The methodology for larval sampling was based on the accurate quantification of the effective breeding area, taking into account the area of the perimeter and subtypes of microenvironments present per larval habitat type using a laser range finder and a small portable inflatable boat. The new classification and new sampling methodology proposed herein may be useful in vector control programs.

  3. Statistical inference based on divergence measures

    CERN Document Server

    Pardo, Leandro

    2005-01-01

    The idea of using functionals of Information Theory, such as entropies or divergences, in statistical inference is not new. However, in spite of the fact that divergence statistics have become a very good alternative to the classical likelihood ratio test and the Pearson-type statistic in discrete models, many statisticians remain unaware of this powerful approach.Statistical Inference Based on Divergence Measures explores classical problems of statistical inference, such as estimation and hypothesis testing, on the basis of measures of entropy and divergence. The first two chapters form an overview, from a statistical perspective, of the most important measures of entropy and divergence and study their properties. The author then examines the statistical analysis of discrete multivariate data with emphasis is on problems in contingency tables and loglinear models using phi-divergence test statistics as well as minimum phi-divergence estimators. The final chapter looks at testing in general populations, prese...

  4. Log-Determinant Divergences Revisited: Alpha-Beta and Gamma Log-Det Divergences

    Directory of Open Access Journals (Sweden)

    Andrzej Cichocki

    2015-05-01

    Full Text Available This work reviews and extends a family of log-determinant (log-det divergences for symmetric positive definite (SPD matrices and discusses their fundamental properties. We show how to use parameterized Alpha-Beta (AB and Gamma log-det divergences to generate many well-known divergences; in particular, we consider the Stein’s loss, the S-divergence, also called Jensen-Bregman LogDet (JBLD divergence, Logdet Zero (Bhattacharyya divergence, Affine Invariant Riemannian Metric (AIRM, and other divergences. Moreover, we establish links and correspondences between log-det divergences and visualise them on an alpha-beta plane for various sets of parameters. We use this unifying framework to interpret and extend existing similarity measures for semidefinite covariance matrices in finite-dimensional Reproducing Kernel Hilbert Spaces (RKHS. This paper also shows how the Alpha-Beta family of log-det divergences relates to the divergences of multivariate and multilinear normal distributions. Closed form formulas are derived for Gamma divergences of two multivariate Gaussian densities; the special cases of the Kullback-Leibler, Bhattacharyya, Rényi, and Cauchy-Schwartz divergences are discussed. Symmetrized versions of log-det divergences are also considered and briefly reviewed. Finally, a class of divergences is extended to multiway divergences for separable covariance (or precision matrices.

  5. World health inequality: convergence, divergence, and development.

    Science.gov (United States)

    Clark, Rob

    2011-02-01

    Recent studies characterize the last half of the twentieth century as an era of cross-national health convergence, with some attributing welfare gains in the developing world to economic growth. In this study, I examine the extent to which welfare outcomes have actually converged and the extent to which economic development is responsible for the observed trends. Drawing from estimates covering 195 nations during the 1955-2005 period, I find that life expectancy averages converged during this time, but that infant mortality rates continuously diverged. I develop a narrative that implicates economic development in these contrasting trends, suggesting that health outcomes follow a "welfare Kuznets curve." Among poor countries, economic development improves life expectancy more than it reduces infant mortality, whereas the situation is reversed among wealthier nations. In this way, development has contributed to both convergence in life expectancy and divergence in infant mortality. Drawing from 674 observations across 163 countries during the 1980-2005 period, I find that the positive effect of GDP PC on life expectancy attenuates at higher levels of development, while the negative effect of GDP PC on infant mortality grows stronger.

  6. Molecular evolution and sequence divergence of plant chalcone synthase and chalcone synthase-Like genes.

    Science.gov (United States)

    Han, Yingying; Zhao, Wenwen; Wang, Zhicui; Zhu, Jingying; Liu, Qisong

    2014-06-01

    Plant chalcone synthase (CHS) and CHS-Like (CHSL) proteins are polyketide synthases. In this study, we evaluated the molecular evolution of this gene family using representative types of CHSL genes, including stilbene synthase (STS), 2-pyrone synthase (2-PS), bibenzyl synthase (BBS), acridone synthase (ACS), biphenyl synthase (BIS), benzalacetone synthase, coumaroyl triacetic acid synthase (CTAS), and benzophenone synthase (BPS), along with their CHS homologs from the same species of both angiosperms and gymnosperms. A cDNA-based phylogeny indicated that CHSLs had diverse evolutionary patterns. STS, ACS, and 2-PS clustered with CHSs from the same species (late diverged pattern), while CTAS, BBS, BPS, and BIS were distant from their CHS homologs (early diverged pattern). The amino-acid phylogeny suggested that CHS and CHSL proteins formed clades according to enzyme function. The CHSs and CHSLs from Polygonaceae and Arachis had unique evolutionary histories. Synonymous mutation rates were lower in late diverged CHSLs than in early diverged ones, indicating that gene duplications occurred more recently in late diverged CHSLs than in early diverged ones. Relative rate tests proved that late diverged CHSLs had unequal rates to CHSs from the same species when using fatty acid synthase, which evolved from the common ancestor with the CHS superfamily, as the outgroup, while the early diverged lineages had equal rates. This indicated that late diverged CHSLs experienced more frequent mutation than early diverged CHSLs after gene duplication, allowing obtaining new functions in relatively short period of time.

  7. A practical divergence measure for survival distributions that can be estimated from Kaplan-Meier curves.

    Science.gov (United States)

    Cox, Trevor F; Czanner, Gabriela

    2016-06-30

    This paper introduces a new simple divergence measure between two survival distributions. For two groups of patients, the divergence measure between their associated survival distributions is based on the integral of the absolute difference in probabilities that a patient from one group dies at time t and a patient from the other group survives beyond time t and vice versa. In the case of non-crossing hazard functions, the divergence measure is closely linked to the Harrell concordance index, C, the Mann-Whitney test statistic and the area under a receiver operating characteristic curve. The measure can be used in a dynamic way where the divergence between two survival distributions from time zero up to time t is calculated enabling real-time monitoring of treatment differences. The divergence can be found for theoretical survival distributions or can be estimated non-parametrically from survival data using Kaplan-Meier estimates of the survivor functions. The estimator of the divergence is shown to be generally unbiased and approximately normally distributed. For the case of proportional hazards, the constituent parts of the divergence measure can be used to assess the proportional hazards assumption. The use of the divergence measure is illustrated on the survival of pancreatic cancer patients. Copyright © 2016 John Wiley & Sons, Ltd.

  8. DISSIPATIVE DIVERGENCE OF RESONANT ORBITS

    Energy Technology Data Exchange (ETDEWEB)

    Batygin, Konstantin [Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 (United States); Morbidelli, Alessandro, E-mail: kbatygin@gps.caltech.edu [Departement Cassiopee, Universite de Nice-Sophia Antipolis, Observatoire de la Cote d' Azur, F-06304 Nice (France)

    2013-01-01

    A considerable fraction of multi-planet systems discovered by the observational surveys of extrasolar planets reside in mild proximity to first-order mean-motion resonances. However, the relative remoteness of such systems from nominal resonant period ratios (e.g., 2:1, 3:2, and 4:3) has been interpreted as evidence for lack of resonant interactions. Here, we show that a slow divergence away from exact commensurability is a natural outcome of dissipative evolution and demonstrate that libration of critical angles can be maintained tens of percent away from nominal resonance. We construct an analytical theory for the long-term dynamical evolution of dissipated resonant planetary pairs and confirm our calculations numerically. Collectively, our results suggest that a significant fraction of the near-commensurate extrasolar planets are in fact resonant and have undergone significant dissipative evolution.

  9. Dissipative Divergence of Resonant Orbits

    CERN Document Server

    Batygin, Konstantin

    2012-01-01

    A considerable fraction of multi-planet systems discovered by the observational surveys of extrasolar planets reside in mild proximity to first-order mean motion resonances. However, the relative remoteness of such systems from nominal resonant period ratios (e.g. 2:1, 3:2, 4:3) has been interpreted as evidence for lack of resonant interactions. Here we show that a slow divergence away from exact commensurability is a natural outcome of dissipative evolution and demonstrate that libration of critical angles can be maintained tens of percent away from nominal resonance. We construct an analytical theory for the long-term dynamical evolution of dissipated resonant planetary pairs and confirm our calculations numerically. Collectively, our results suggest that a significant fraction of the near-commensurate extrasolar planets are in fact resonant and have undergone significant dissipative evolution.

  10. Divergence operator and related inequalities

    CERN Document Server

    Acosta, Gabriel

    2017-01-01

    This Brief is mainly devoted to two classical and related results: the existence of a right inverse of the divergence operator and the so-called Korn Inequalities. It is well known that both results are fundamental tools in the analysis of some classic differential equations, particularly in those arising in fluid dynamics and elasticity. Several connections between these two topics and improved Poincaré inequalities are extensively treated. From simple key ideas the book is growing smoothly in complexity. Beginning with the study of these problems on star-shaped domains the arguments are extended first to John domains and then to Hölder α domains where the need of weighted spaces arises naturally. In this fashion, the authors succeed in presenting in an unified and concise way several classic and recent developments in the field. These features certainly makes this Brief useful for students, post-graduate students, and researchers as well.

  11. Divergence of optical vortex beams

    CERN Document Server

    Reddy, Salla Gangi; Prabhakar, Shashi; Anwar, Ali; Banerji, J; Singh, R P

    2015-01-01

    We show, both theoretically and experimentally, that the propagation of optical vortices in free space can be analysed by using the width ($w(z)$) of the host Gaussian beam and the inner and outer radii of the vortex beam at the source plane ($z=0$) as defined in \\textit{Optics Letters \\textbf{39,} 4364-4367 (2014)}. We also studied the divergence of vortex beams, considered as the rate of change of inner or outer radius with the propagation distance, and found that it varies with the order in the same way as that of the inner and outer radii at zero propagation distance. These results may be useful in designing optical fibers for orbital angular momentum modes that play a crucial role in quantum communication.

  12. Guises and disguises of quadratic divergences

    Energy Technology Data Exchange (ETDEWEB)

    Cherchiglia, A.L., E-mail: adriano@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Vieira, A.R., E-mail: arvieira@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Hiller, Brigitte, E-mail: brigitte@teor.fis.uc.pt [Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra (Portugal); Baêta Scarpelli, A.P., E-mail: scarpelli.apbs@dpf.gov.br [Setor Técnico-Científico, Departamento de Polícia Federal, Rua Hugo D’Antola, 95 - Lapa, São Paulo (Brazil); Sampaio, Marcos, E-mail: marcos.sampaio@durham.ac.uk [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Centre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road Durham DH1 3LE (United Kingdom)

    2014-12-15

    In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.

  13. Linkographic Evidence for Concurrent Divergent and Convergent Thinking in Creative Design

    Science.gov (United States)

    Goldschmidt, Gabriela

    2016-01-01

    For a long time, the creativity literature has stressed the role of divergent thinking in creative endeavor. More recently, it has been recognized that convergent thinking also has a role in creativity, and the design literature, which sees design as a creative activity a priori, has largely adopted this view: Divergent and convergent thinking are…

  14. Domestication of maize, sorghum, and sugarcane did not drive the divergence of their smut pathogens.

    Science.gov (United States)

    Munkacsi, Andrew B; Stoxen, Sam; May, Georgiana

    2007-02-01

    We investigated two alternative hypotheses for the origin of crop pathogen species: that human-mediated agricultural practices drove the divergence of many crop plant pathogen species or that coevolutionary processes in natural populations of the crops' ancestors drove divergence of pathogen species. We distinguished between these two hypotheses by constructing a robust multigene phylogeny and estimating the dates of divergence among four, monophyletic species of smut fungi (Ustilago maydis, U. scitaminea, Sporisorium reilianum, S. sorghi) known to specifically infect maize, sorghum, sugarcane, and their wild ancestors. Without a fossil record for smut fungi, we calibrated the pathogen species' divergence times to their plant host divergence times. Specifically, a calibration date of 10,000 years was employed to test the hypothesis that the fungal species originated at the time of domestication of their current hosts and a calibration date of 50 million years was employed to test the hypothesis that the fungal species originated on wild ancestors of their domesticated hosts. Substitution rates at five protein coding genes were calculated and rates obtained for the 10,000 year calibration date were orders of magnitude faster than those commonly reported for eukaryotes, thus rejecting the hypothesis that these smut pathogen species diverged at the time of domestication. In contrast, substitution rates obtained for the 50 million year calibration were comparable to eukaryotic substitution rates. We used the 50 million year calibration to estimate divergence times of taxa in two datasets, one comprised solely the focal species and one comprised the focal species and additional related taxa. Both datasets indicate that all taxa diverged millions of years ago, strongly supporting the hypothesis that smut species diverged before the time of domestication and modern agriculture. Thus, smut species diverged in the ecological context of natural host plant and fungal

  15. Survival of anopheline eggs and their susceptibility to infection with Metarhizium anisopliae and Beauveria bassiana under laboratory conditions

    NARCIS (Netherlands)

    Luz, C.; Mnyone, L.L.; Russell, T.L.

    2011-01-01

    The viability of Anopheles gambiae sensu stricto and Anopheles arabiensis (Diptera: Culicidae) eggs over time and the ovicidal activity of Beauveria bassiana (Ascomycota: Cordycipitaceae) and Metarhizium anisopliae (Ascomycota: Clavicipitaceae) were investigated. Eggs were incubated in soil or leaf

  16. Inequalities among New Non-Symmetric Divergence and Chi-Square Divergence Measure

    Directory of Open Access Journals (Sweden)

    Ram Naresh Saraswat

    2015-12-01

    Full Text Available Information divergence measures and their bounds are well known in the literature of Information Theory. In this research paper, we shall consider a new non-symmetric information divergence measure. Upper and lower bounds of new non-symmetric divergence measure are also considered.

  17. Inequalities among New Non-Symmetric Divergence and Chi-Square Divergence Measure

    OpenAIRE

    Ram Naresh Saraswat

    2015-01-01

    Information divergence measures and their bounds are well known in the literature of Information Theory. In this research paper, we shall consider a new non-symmetric information divergence measure. Upper and lower bounds of new non-symmetric divergence measure are also considered.

  18. Gauge-Invariance and Infrared Divergences in the Luminosity Distance

    CERN Document Server

    Biern, Sang Gyu

    2016-01-01

    Measurements of the luminosity distance have played a key role in discovering the late-time cosmic accel- eration. However, when accounting for inhomogeneities in the Universe, its interpretation has been plagued with infrared divergences in its theoretical predictions, which are in some cases used to explain the cosmic ac- celeration without dark energy. The divergences in most calculations are artificially removed by imposing an infrared cut-off scale. For the first time, we show that a gauge-invariant calculation of the luminosity distance is devoid of such divergences and consistent with the equivalence principle, eliminating the need to impose a cut-off scale. We present proper numerical calculations of the luminosity distance using the gauge-invariant expression and demonstrate that the numerical results with an ad hoc cut-off scale in previous calculations have negligible systematic errors as long as the cut-off scale is larger than the horizon scale. We discuss the origin of infrared divergences and t...

  19. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    performance. We explore the proposed impact of diverging relationship norms on relationship expectations using data from an ongoing field study of Danish buyers and Chinese suppliers. We link these diverging expectations to the business practices of Danish buyers and Chinese and their institutional contexts...... performance. An important reason for this is the diverging beliefs and expectations held by both parties in the buyer-seller dyad. The purpose of this contribution is to develop a framework for understanding the divergences in expectations and relationship norms in cross-cultural business relationships among...... SMEs. We discuss four relational expectations derived from the B2B literature on relational norms for addressing these divergences: Quality, frequency and scope of communication, role specifications and coordination of work nature of planning horizons, and trustworthiness and link these to relationship...

  20. Duality of Maximum Entropy and Minimum Divergence

    Directory of Open Access Journals (Sweden)

    Shinto Eguchi

    2014-06-01

    Full Text Available We discuss a special class of generalized divergence measures by the use of generator functions. Any divergence measure in the class is separated into the difference between cross and diagonal entropy. The diagonal entropy measure in the class associates with a model of maximum entropy distributions; the divergence measure leads to statistical estimation via minimization, for arbitrarily giving a statistical model. The dualistic relationship between the maximum entropy model and the minimum divergence estimation is explored in the framework of information geometry. The model of maximum entropy distributions is characterized to be totally geodesic with respect to the linear connection associated with the divergence. A natural extension for the classical theory for the maximum likelihood method under the maximum entropy model in terms of the Boltzmann-Gibbs-Shannon entropy is given. We discuss the duality in detail for Tsallis entropy as a typical example.

  1. Collinearity, convergence and cancelling infrared divergences

    CERN Document Server

    Lavelle, M; Lavelle, Martin; Mullan, David Mc

    2006-01-01

    The Lee-Nauenberg theorem is a fundamental quantum mechanical result which provides the standard theoretical response to the problem of collinear and infrared divergences. Its argument, that the divergences due to massless charged particles can be removed by summing over degenerate states, has been successfully applied to systems with final state degeneracies such as LEP processes. If there are massless particles in both the initial and final states, as will be the case at the LHC, the theorem requires the incorporation of disconnected diagrams which produce connected interference effects at the level of the cross-section. However, this aspect of the theory has never been fully tested in the calculation of a cross-section. We show through explicit examples that in such cases the theorem introduces a divergent series of diagrams and hence fails to cancel the infrared divergences. It is also demonstrated that the widespread practice of treating soft infrared divergences by the Bloch-Nordsieck method and handlin...

  2. Divergent thermopower without a quantum phase transition.

    Science.gov (United States)

    Limtragool, Kridsanaphong; Phillips, Philip W

    2014-08-22

    A general principle of modern statistical physics is that divergences of either thermodynamic or transport properties are only possible if the correlation length diverges. We show by explicit calculation that the thermopower in the quantum XY model d = 1 + 1 and the Kitaev model in d = 2 + 1 can (i) diverge even when the correlation length is finite and (ii) remain finite even when the correlation length diverges, thereby providing a counterexample to the standard paradigm. Two conditions are necessary: (i) the sign of the charge carriers and that of the group velocity must be uncorrelated and (ii) the current operator defined formally as the derivative of the Hamiltonian with respect to the gauge field does not describe a set of excitations that have a particle interpretation, as in strongly correlated electron matter. Recent experimental and theoretical findings on the divergent thermopower of a 2D electron gas are discussed in this context.

  3. Convergences and divergences in mortality

    Directory of Open Access Journals (Sweden)

    2004-04-01

    Full Text Available Abdel Omran's 1971 theory of "Epidemiologic Transition" was the first attempt to account for the extraordinary advances in health care made in industrialized countries since the 18th century. In the framework of the Demographic Transition, it implied a general convergence of life expectancies toward a limit imposed by the new epidemiological features of modern societies. However, important failures, occurred in the past decades (mainly the health crisis in Eastern Europe and AIDS in Africa, seem to have stopped that process of convergence. In fact such failures do not really contradict the theory. The latter is much more ruined by the unexpected dramatic improvement in the field of cardiovascular disease experienced since the seventies, which results in a new step of a more general process. On the basis of the broader concept of "Health Transition" initiated by Julio Frenk et al., the present paper tries to rethink the full process in term of divergence/convergence sequences inferred by successive major changes in health technologies and strategies.

  4. Mass generation and the problem of seagull divergences

    CERN Document Server

    Figueiredo, C T

    2016-01-01

    The gluon mass generation is a purely non-perturbative effect, and the natural framework to study it in the continuum are the Schwinger-Dyson equations (SDEs) of the theory. At the level of the SDEs the generation of such a mass is associated with the existence of infrared finite solutions for the gluon propagator. From the theoretical point of view, the dynamical gluon mass generation has been traditionally plagued with seagull divergences. In this work, we will review how such divergences can be eliminated completely by virtue of a characteristic identity, valid in dimensional regularization. As a pedagogical example, we will first discuss in the context of scalar QED how it is possible to eliminate all seagull divergences, by triggering the aforementioned special identity, which enforces the masslessness of the photon. Then, we will discuss what happens in QCD and present an Ansatz for the three gluon vertex, which completely eliminates all seagull divergences and at same time allows for the possibility of...

  5. One-Loop Divergences in 6D Conformal Gravity

    CERN Document Server

    Pang, Yi

    2012-01-01

    Using Exact Renormalization Group Equation approach and background field method, we investigate the one-loop problem in a six-dimensional conformal gravity theory whose Lagrangian takes the same form as holographic Weyl anomaly of multiple coincident M5-branes. We choose the backgrounds to be the symmetric Einstein spaces including S6, CP3, S2 \\times S4, S2 \\times CP2, S3 \\times S3 and S2 \\times S2 \\times S2. Evaluating the functional sums gives power-law and logarithmic divergences. We extract from the specific values of logarithmic divergence on above backgrounds, the coefficient in front of Euler density and two linear equations constraining the coefficients in front of three type-B conformal invariants. As a test of the effectiveness of Exact Renormalization Group Equation approach to quantum conformal gravity, we reexaminethe one-loop problem in four-dimensional conformal gravity and confirm the logarithmic divergence derived from generalized Schwinger-DeWitt method.

  6. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    A challenge in evolutionary computation is to create representations as evolvable as those in natural evolution. This paper hypothesizes that extinction events, i.e. mass extinctions, can significantly increase evolvability, but only when combined with a divergent search algorithm, i.e. a search...... for the capacity to evolve. This hypothesis is tested through experiments in two evolutionary robotics domains. The results show that combining extinction events with divergent search increases evolvability, while combining them with convergent search offers no similar benefit. The conclusion is that extinction...... events may provide a simple and effective mechanism to enhance performance of divergent search algorithms....

  7. A New Study of Two Divergence Metrics for Change Detection in Data Streams

    KAUST Repository

    Qahtan, Abdulhakim Ali Ali

    2014-08-01

    Streaming data are dynamic in nature with frequent changes. To detect such changes, most methods measure the difference between the data distributions in a current time window and a reference window. Divergence metrics and density estimation are required to measure the difference between the data distributions. Our study shows that the Kullback-Leibler (KL) divergence, the most popular metric for comparing distributions, fails to detect certain changes due to its asymmetric property and its dependence on the variance of the data. We thus consider two metrics for detecting changes in univariate data streams: a symmetric KL-divergence and a divergence metric measuring the intersection area of two distributions. The experimental results show that these two metrics lead to more accurate results in change detection than baseline methods such as Change Finder and using conventional KL-divergence.

  8. Creativity and Memory: Effects of an Episodic Specificity Induction on Divergent Thinking

    Science.gov (United States)

    Madore, Kevin P.; Addis, Donna Rose; Schacter, Daniel L.

    2015-01-01

    After receiving an episodic specificity induction - brief training in recollecting details of a recent event - people produce more episodic details when imagining future events and solving means-end problems than after receiving a control induction not focused on episodic retrieval. Here we show for the first time that an episodic specificity induction also enhances divergent creative thinking. In Experiment 1, participants exhibited a selective boost on a divergent thinking task that involves generating unusual uses of common objects after a specificity induction compared with a control induction; by contrast, performance was similar on an object association task thought to involve little divergent thinking. In Experiment 2, we replicated the specificity induction effect on divergent thinking using a different control induction, and also found that participants performed similarly on a convergent thinking task following both inductions. These experiments provide novel evidence that episodic memory is involved in divergent creative thinking. PMID:26205963

  9. Creativity and Memory: Effects of an Episodic-Specificity Induction on Divergent Thinking.

    Science.gov (United States)

    Madore, Kevin P; Addis, Donna Rose; Schacter, Daniel L

    2015-09-01

    People produce more episodic details when imagining future events and solving means-end problems after receiving an episodic-specificity induction-brief training in recollecting details of a recent event-than after receiving a control induction not focused on episodic retrieval. Here we show for the first time that an episodic-specificity induction also enhances divergent creative thinking. In Experiment 1, participants exhibited a selective boost on a divergent-thinking task (generating unusual uses of common objects) after a specificity induction compared with a control induction; by contrast, performance following the two inductions was similar on an object association task thought to involve little divergent thinking. In Experiment 2, we replicated the specificity-induction effect on divergent thinking using a different control induction, and also found that participants performed similarly on a convergent-thinking task following the two inductions. These experiments provide novel evidence that episodic memory is involved in divergent creative thinking.

  10. Stora's fine notion of divergent amplitudes

    CERN Document Server

    Várilly, Joseph C

    2016-01-01

    Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  11. Anopheline ecology and malaria transmission during the construction of an irrigation canal in an endemic district of Odisha, India

    Directory of Open Access Journals (Sweden)

    B. K. Panigrahi

    2013-12-01

    Full Text Available Background & objectives: A new irrigation canal system is under construction in Dhenkanal district of Odisha, to increase the production of rice crop and thereby improve the living standard of farmers in the project area. Construction of canal may increase the transmission of malaria by creating vector breeding habitats. Knowledge about bionomics of vectors will support authorities for appropriate management of the disease in a changing ecological set up. The aim of this study was to assess the malaria transmission in the bank of the canal area under construction. Methods: The entomological survey was carried out in three seasons, winter, summer and rainy during the period November 2008-October 2010 in the study area. Adult mosquitoes were collected by using suction tubes and flash lights. Mosquito species identification was done by using standard keys, separated according to abdominal conditions and were kept in an isopropanol for further molecular analysis of sibling species, presence of sporozoites and human blood meal. Larvae were collected by dippers and reared in the laboratory, and the emerged adults were identified to species. The epidemiology of malaria was evaluated from the data collected by the State Health Department. Insecticide succeptibility test was done by WHO method. Results: The adult mosquito collection from the study area showed the prevalence of 14 species belonging to three genera, i.e. Anopheles, Culex and Aedes. The per man hour densities (PMHD of An. culicifacies were 3.8, 1.4, 4.8; that of An. annularis were 2.1, 1, 2.1; and that of An. fluviatilis were 1.4, 0.3, 0.6 during winter, summer and rainy seasons respectively. Sibling species identified were: An. culicifacies A, B, C and D, An. annularis A and An. fluviatilis S. Sporozoite rates of An. culicifacies A and C were 1.1 and 0.5% respectively and that of An. annularis A was 2% (reported for the first time in the state. Both the vectors (An. culicifacies and An

  12. Effects of natural and sexual selection on adaptive population divergence and premating isolation in a damselfly.

    Science.gov (United States)

    Svensson, Erik I; Eroukhmanoff, Fabrice; Friberg, Magne

    2006-06-01

    The relative strength of different types of directional selection has seldom been compared directly in natural populations. A recent meta-analysis of phenotypic selection studies in natural populations suggested that directional sexual selection may be stronger in magnitude than directional natural selection, although this pattern may have partly been confounded by the different time scales over which selection was estimated. Knowledge about the strength of different types of selection is of general interest for understanding how selective forces affect adaptive population divergence and how they may influence speciation. We studied divergent selection on morphology in parapatric, natural damselfly (Calopteryx splendens) populations. Sexual selection was stronger than natural selection measured on the same traits, irrespective of the time scale over which sexual selection was measured. Visualization of the fitness surfaces indicated that population divergence in overall morphology is more strongly influenced by divergent sexual selection rather than natural selection. Courtship success of experimental immigrant males was lower than that of resident males, indicating incipient sexual isolation between these populations. We conclude that current and strong sexual selection promotes adaptive population divergence in this species and that premating sexual isolation may have arisen as a correlated response to divergent sexual selection. Our results highlight the importance of sexual selection, rather than natural selection in the adaptive radiation of odonates, and supports previous suggestions that divergent sexual selection promotes speciation in this group.

  13. A divergence-cleaning scheme for cosmological SPMHD simulations

    CERN Document Server

    Stasyszyn, F A; Beck, A M

    2012-01-01

    In magnetohydrodynamics (MHD), the magnetic field is evolved by the induction equation and coupled to the gas dynamics by the Lorentz force. We perform numerical smoothed particle magnetohydrodynamics (Spmhd) simulations and study the influence of a numerical magnetic divergence. For instabilities arising from divergence B related errors, we find the hyperbolic/parabolic cleaning scheme suggested by Dedner et al. 2002 to give good results and prevent numerical artifacts from growing. Additionally, we demonstrate that certain current Spmhd implementations of magnetic field regularizations give rise to unphysical instabilities in long-time simulations. We also find this effect when employing Euler potentials (divergenceless by definition), which are not able to follow the winding-up process of magnetic field lines properly. Furthermore, we present cosmological simulations of galaxy cluster formation at extremely high resolution including the evolution of magnetic fields. We show synthetic Faraday rotation maps ...

  14. Adaptation to divergent larval diets in the medfly, Ceratitis capitata.

    Science.gov (United States)

    Leftwich, Philip T; Nash, William J; Friend, Lucy A; Chapman, Tracey

    2017-02-01

    Variation in diet can influence the timing of major life-history events and can drive population diversification and ultimately speciation. Proximate responses of life histories to diet have been well studied. However, there are scant experimental data on how organisms adapt to divergent diets over the longer term. We focused on this omission by testing the responses of a global pest, the Mediterranean fruitfly, to divergent selection on larval diets of different nutritional profiles. Tests conducted before and after 30 generations of nutritional selection revealed a complex interplay between the effects of novel larval dietary conditions on both plastic and evolved responses. There were proximate-only responses to the larval diet in adult male courtship and the frequency of copulation. Males on higher calorie larval diets consistently engaged in more bouts of energetic courtship. In contrast, following selection, larval development time, and egg to adult survival showed evidence of evolved divergence between diet regimes. Adult body size showed evidence for adaptation, with flies being significantly heavier when reared on their "own" diet. The results show the multifaceted responses of individuals to dietary selection and are important in understanding the extreme generalism exhibited by the medfly.

  15. The Divergence of Neandertal and Modern Human Y Chromosomes

    Science.gov (United States)

    Mendez, Fernando L.; Poznik, G. David; Castellano, Sergi; Bustamante, Carlos D.

    2016-01-01

    Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups. PMID:27058445

  16. The Divergence of Neandertal and Modern Human Y Chromosomes.

    Science.gov (United States)

    Mendez, Fernando L; Poznik, G David; Castellano, Sergi; Bustamante, Carlos D

    2016-04-07

    Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes-including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447-806 kya). This is ∼2.1 (95% CI: 1.7-2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

  17. Vibhakti Divergence between Sanskrit and Hindi

    Science.gov (United States)

    Shukla, Preeti; Shukl, Devanand; Kulkarni, Amba

    Translation divergence at various levels between languages arises due to the different conventions followed by different languages for coding the information of grammatical relations. Though Sanskrit and Hindi belong to the same Indo-Aryan family and structurally as well as lexically Hindi inherits a lot from Sanskrit, yet divergences are observed at the level of function words such as vibhaktis. Pāṇini in his Aṣṭādhyāyī has assigned a default vibhakti to kārakas alongwith many scopes for exceptions. He handles these exceptions either by imposing a new kāraka role or by assigning a special vibhakti. However, these methods are not acceptable in Hindi in toto. Based on the nature of deviation, we propose seven cases of divergences in this paper.

  18. Application of Coherent State Approach for the cancellation of Infrared divergences to all orders in LFQED

    CERN Document Server

    More, Jai

    2015-01-01

    We sketch an all order proof of cancellation of infrared (IR) divergences in Light Front Quantum Electrodynamics (LFQED) using a coherent state formalism. In this talk, it has been shown that the true IR divergences in fermion self energy are eliminated to all orders in a light-front time-ordered perturbative calculation if one uses coherent state basis instead of the usual Fock basis to calculate the Hamiltonian matrix elements.

  19. 一个适于最大似然法估计物种分化年代的进化速率平滑近似方法%A heuristic rate smoothing procedure for maximum likelihood estmation of species divergence times

    Institute of Scientific and Technical Information of China (English)

    Ziheng YANG

    2004-01-01

    众所周知,物种分化年代的估计对分子钟(进化速率恒定)假定很敏感.另一方面,在远缘物种(例如哺乳纲不同目的动物)的比较中,分子钟几乎总是不成立的.这样在估计分化时间时考虑不同进化区系的速率差异至为重要.最大似然法可以很自然地考虑这种速率差异,并且可以同时分析多个基因位点的资料以及同时利用多重化石校正数据.以前提出的似然法需要研究者将进化树的树枝按速率分组,本文提出一个近似方法以使这个过程自动化.本方法综合了以前的似然法、贝斯法及近似速率平滑法的一些特征.此外,还对算法加以改进,以适应综合数据分析时某些基因在某些物种中缺乏资料的情形.应用新提出的方法来分析马达加斯加的倭狐猴的分化年代,并与以前的似然法及贝斯法的分析进行了比较[动物学报50(4):645-656,2004].%Estimation of species divergence times is well-known to be sensitive to violation of the molecular clock assumption (rate constancy over time). However, the molecular clock is almost always violated in comparisons of distantly related species, such as different orders of mammals. Thus it is important to take into account different rates among lineages when divergence times are estimated. The maximum likelihood method provides a framework for accommodating rate variation and can naturally accommodate heterogeneous datasets from multiple loci and fossil calibrations at multiple nodes.Previous implementations of the likelihood method require the researcher to assign branches to different rate classes. In this paper, I implement a heuristic rate-smoothing algorithm (the AHRS algorithm) to automate the assignment of branches to rate groups. The method combines features of previous likelihood, Bayesian and rate-smoothing methods. The likelihood algorithm is also improved to accommodate missing sequences at some loci in the combined analysis. The new

  20. Temporary divergence paralysis in viral meningitis.

    Science.gov (United States)

    Bakker, Stef L M; Gan, Ivan M

    2008-06-01

    A 43-year-old woman who reported diplopia and headache was found to have comitant esotropia at distance fixation and normal alignment at reading distance (divergence paralysis). Eye movement, including abduction, was normal as was the rest of the neurologic examination. Brain MRI was normal. Lumbar puncture showed an elevated opening pressure and a cerebrospinal fluid formula consistent with viral meningitis. The patient was treated with intravenous fluids and analgesics and with a temporary prism to alleviate diplopia. Within 3 weeks, she had fully recovered. This is the first report of divergence palsy in viral meningitis.

  1. Diverging Fluctuations of the Lyapunov Exponents.

    Science.gov (United States)

    Pazó, Diego; López, Juan M; Politi, Antonio

    2016-07-15

    We show that in generic one-dimensional Hamiltonian lattices the diffusion coefficient of the maximum Lyapunov exponent diverges in the thermodynamic limit. We trace this back to the long-range correlations associated with the evolution of the hydrodynamic modes. In the case of normal heat transport, the divergence is even stronger, leading to the breakdown of the usual single-function Family-Vicsek scaling ansatz. A similar scenario is expected to arise in the evolution of rough interfaces in the presence of suitably correlated background noise.

  2. Three dimensional simulations of viscous folding in diverging microchannels

    CERN Document Server

    Xu, Bingrui; Shin, Seungwon; Juric, Damir

    2016-01-01

    Three dimensional simulations on the viscous folding in diverging microchannels reported by Cubaud and Mason are performed using the parallel code BLUE for multi-phase flows. The more viscous liquid L_1 is injected into the channel from the center inlet, and the less viscous liquid L_2 from two side inlets. Liquid L_1 takes the form of a thin filament due to hydrodynamic focusing in the long channel that leads to the diverging region. The thread then becomes unstable to a folding instability, due to the longitudinal compressive stress applied to it by the diverging flow of liquid L_2. Given the long computation time, we were limited to a parameter study comprising five simulations in which the flow rate ratio, the viscosity ratio, the Reynolds number, and the shape of the channel were varied relative to a reference model. In our simulations, the cross section of the thread produced by focusing is elliptical rather than circular. The initial folding axis can be either parallel or perpendicular to the narrow di...

  3. Taming Infrared Divergences in the Effective Potential

    CERN Document Server

    Elias-Miro, J; Konstandin, T

    2014-01-01

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective ...

  4. Stora's fine notion of divergent amplitudes

    Directory of Open Access Journals (Sweden)

    Joseph C. Várilly

    2016-11-01

    Full Text Available Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  5. A problem with the correlation coefficient as a measure of gene expression divergence.

    Science.gov (United States)

    Pereira, Vini; Waxman, David; Eyre-Walker, Adam

    2009-12-01

    The correlation coefficient is commonly used as a measure of the divergence of gene expression profiles between different species. Here we point out a potential problem with this statistic: if measurement error is large relative to the differences in expression, the correlation coefficient will tend to show high divergence for genes that have relatively uniform levels of expression across tissues or time points. We show that genes with a conserved uniform pattern of expression have significantly higher levels of expression divergence, when measured using the correlation coefficient, than other genes, in a data set from mouse, rat, and human. We also show that the Euclidean distance yields low estimates of expression divergence for genes with a conserved uniform pattern of expression.

  6. Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

    Directory of Open Access Journals (Sweden)

    Quentin Rougemont

    2016-04-01

    Full Text Available Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis and brook lamprey (L. planeri show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC and Isolation with Migration (IM models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

  7. An investigation of merging and diverging cars on a multi-lane road using a cellular automation model

    Science.gov (United States)

    Jetto, K.; Ez-Zahraouy, H.; Benyoussef, A.

    2012-11-01

    In this paper, we have investigated two observed situations in a multi-lane road. The first one concerns a fast merging vehicle. The second situation is related to the case of a fast vehicle leaving the fastest lane back into the slowest lane and targeting a specific way out. We are interested in the relaxation time τ, i.e., which is the time that the merging (diverging) vehicle spends before reaching the desired lane. Using analytical treatment and numerical simulations for the NaSch model, we have found two states, namely, the free state in which the merging (diverging) vehicle reaches the desired lane, and the trapped state in which τ diverges. We have established phase diagrams for several values of the braking probability. In the second situation, we have shown that diverging from the fast lane targeting a specific way out is not a simple task. Even if the diverging vehicle is in the free phase, two different states can be distinguished. One is the critical state, in which the diverging car can probably reach the desired way out. The other is the safe state, in which the diverging car can surely reach the desired way out. In order to be in the safe state, we have found that the driver of the diverging car must know the critical distance (below which the way out will be out of his reach) in each lane. Furthermore, this critical distance depends on the density of cars, and it follows an exponential law.

  8. Investigation on Anopheline species in Chayu County, Linzhi Prefecture of Tibet Autonomous Region%西藏林芝地区察隅县按蚊种群调查

    Institute of Scientific and Technical Information of China (English)

    王洪举; 胡松林; 李松凌; 顾政诚; 陈建设; 朱国鼎; 黄芳

    2012-01-01

    目的 确定西藏林芝地区察隅县主要按蚊蚊种.方法 2010年7-8月在察隅县选择4个自然村,采用通宵/半通宵室内、外人饵帐诱捕法和通宵诱蚊灯诱捕法捕蚊,对捕获的按蚊进行形态学鉴定.结果 共捕获按蚊2 991只,其中带足按蚊2 284只(占76.36%),多斑按蚊种团667只(占22.30%),其他按蚊40只(占1.34%);带足按蚊室内、外半通宵平均密度分别为56.2只/夜和4只/夜,多斑按蚊种团室内、外半通宵平均密度分别为17.8只/夜和17.9只/夜;带足按蚊室内、外全通宵室内叮人率分别为28.1只/(人·夜)和2只/(人·夜),多斑按蚊种团全通宵室内、外叮人率均为8.9只/(人·夜).结论 带足按蚊和多斑按蚊为察隅县优势蚊种,是可能的疟疾传播媒介.%Objective To investigate Anopheline species in Chayu County of Linzhi Prefecture, Tibet Methods Four natural villages in Chayu County were selected in this study in 2010. The methods of overnighl/semi-overaight trapping indoor and outdoor human-bait, and overnight trapping with light traps were used, and all the Anopheline mosquitoes were confirmed by morphological characteristics. Results Totally 2 991 Anopheline mosquitoes were captured, with 76.36% (2 284/2 291) of An, peditae-niatus, 22.30% (667/2 291) of An. maculates group. The average densities of An. peditaeniatus by semi-overnight trapping were 56.2/per person indoor and 4/per person outdoor respectively, and the average densities of An. maculatus group by semi-overnight trapping were 17.8/per person indoor and 17.9/per person outdoor respectively. The man-biting rates of An. peditaeniatus by overnight trapping were 28.I/per person indoor and 2/per person outdoor respectively, and were both 8.9/per person to An. maculatus group. Conclusion An. peditaeniatus and An. maculatus group are the possible transmission vectors of malaria in Chayu County.

  9. Ecological divergence combined with ancient allopatry in lizard populations from a small volcanic island.

    Science.gov (United States)

    Suárez, N M; Pestano, J; Brown, R P

    2014-10-01

    Population divergence and speciation are often explained by geographical isolation, but may also be possible under high gene flow due to strong ecology-related differences in selection pressures. This study combines coalescent analyses of genetic data (11 microsatellite loci and 1 Kbp of mtDNA) and ecological modelling to examine the relative contributions of isolation and ecology to incipient speciation in the scincid lizard Chalcides sexlineatus within the volcanic island of Gran Canaria. Bayesian multispecies coalescent dating of within-island genetic divergence of northern and southern populations showed correspondence with the timing of volcanic activity in the north of the island 1.5-3.0 Ma ago. Coalescent estimates of demographic changes reveal historical size increases in northern populations, consistent with expansions from a volcanic refuge. Nevertheless, ecological divergence is also supported. First, the two morphs showed non-equivalence of ecological niches and species distribution modelling associated the northern morph with mesic habitat types and the southern morph with xeric habitat types. It seems likely that the colour morphs are associated with different antipredator strategies in the different habitats. Second, coalescent estimation of gene copy migration (based on microsatellites and mtDNA) suggest high rates from northern to southern morphs demonstrating the strength of ecology-mediated selection pressures that maintain the divergent southern morph. Together, these findings underline the complexity of the speciation process by providing evidence for the combined effects of ecological divergence and ancient divergence in allopatry.

  10. Eliminating the "divergence problem" at Alaska's northern treeline

    Directory of Open Access Journals (Sweden)

    M. Wilmking

    2008-06-01

    Full Text Available Recently, an increasing off-set between tree-ring based temperature reconstructions and measured temperatures at high latitudes has been reported, the so called "divergence problem" (here "divergence effect". This "divergence effect" seriously questions the validity of tree-ring based climate reconstructions, since it seems to violate the assumption of a stable response of trees to changing climate over time. In this study we eliminated the "divergence effect" in northern Alaska by careful selection of individual trees with consistently significant positive relationships with climate (17% of sample and successfully attempted a divergence-free climate reconstruction using this sub-set. However, the majority of trees (83% did not adhere to the uniformitarian principle as usually applied in dendroclimatology. Our results thus support the notion, that factors acting on an individual tree basis are the primary causes for the "divergence effect" (at least in northern Alaska. Neither different detrending methods nor factors acting on larger scales such as global dimming or an increase in UV-B radiation could explain our results. Our results also highlight the necessity to adapt the methods of paleoreconstruction using tree rings to account for non-stable climate growth relationships as these are found in the vast majority of sampled trees and seem to be the norm rather than the exception.

  11. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

    Science.gov (United States)

    Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

    2014-10-01

    Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

  12. PUBLIC INTEGRITY AND THE DIVERGENCE FROM IT

    Directory of Open Access Journals (Sweden)

    Simona‐Roxana ULMAN

    2013-12-01

    Full Text Available Public Integrity is one of the public sector’s essential objectives to attain. In contradiction, as a divergence from it, corruption is one of the persistent problems of the societies over years and it affects the credibility of public institutions and its ambassadors in front of the citizens and of the other related countries. All nations complain of corruption and, as it is observed in the Corruption Perception Index 2012, no country has a maximum score which shows that a country is totally clean. In this context, the study of the most important elements of the public integrity concept, the identification of what causes the divergence from it and the solutions detection become a relevant option for economic literature. In this context, the main objective of this paper is to emphasize the public integrity concept and its main aspects and to make a comparison between countries to achieve a large perspective of the world’s public integrity juncture.

  13. Rousseau and Marx: Convergence or divergence?

    Directory of Open Access Journals (Sweden)

    Lošonc Alpar

    2012-01-01

    Full Text Available Rousseau and Marx represent two paradigmatic variants of a radical opposition to the world. Without a doubt, there are significant moments of convergence between these thinkers, for instance in terms of division of labour, or in respect to the self-commandment. However, it is our contention that despite certain currents in literature, the tendencies of divergence are stronger than convergence, therefore, we argue that these thinkers signify two different variants of radical thought. We base these differences in a reading of Rousseau that focuses on collective authenticity, justice, self-presentation of people and protest against envy. Marx cannot be read from the perspective of the intensified crisis of non-authenticity, in fact, his critique of political economy generates a reflexive field (overcoming of the wage labour, etc., which is deeply divergent compared to Rousseau.

  14. Higgsed Stueckelberg vector and Higgs quadratic divergence

    Directory of Open Access Journals (Sweden)

    Durmuş Ali Demir

    2015-01-01

    Full Text Available Here we show that, a hidden vector field whose gauge invariance is ensured by a Stueckelberg scalar and whose mass is spontaneously generated by the Standard Model Higgs field contributes to quadratic divergences in the Higgs boson mass squared, and even leads to its cancellation at one-loop when Higgs coupling to gauge field is fine-tuned. In contrast to mechanisms based on hidden scalars where a complete cancellation cannot be achieved, stabilization here is complete in that the hidden vector and the accompanying Stueckelberg scalar are both free from quadratic divergences at one-loop. This stability, deriving from hidden exact gauge invariance, can have important implications for modeling dark phenomena like dark matter, dark energy, dark photon and neutrino masses. The hidden fields can be produced at the LHC.

  15. Multiple Source Adaptation and the Renyi Divergence

    CERN Document Server

    Mansour, Yishay; Rostamizadeh, Afshin

    2012-01-01

    This paper presents a novel theoretical study of the general problem of multiple source adaptation using the notion of Renyi divergence. Our results build on our previous work [12], but significantly broaden the scope of that work in several directions. We extend previous multiple source loss guarantees based on distribution weighted combinations to arbitrary target distributions P, not necessarily mixtures of the source distributions, analyze both known and unknown target distribution cases, and prove a lower bound. We further extend our bounds to deal with the case where the learner receives an approximate distribution for each source instead of the exact one, and show that similar loss guarantees can be achieved depending on the divergence between the approximate and true distributions. We also analyze the case where the labeling functions of the source domains are somewhat different. Finally, we report the results of experiments with both an artificial data set and a sentiment analysis task, showing the p...

  16. Adaptive Mixture Methods Based on Bregman Divergences

    CERN Document Server

    Donmez, Mehmet A; Kozat, Suleyman S

    2012-01-01

    We investigate adaptive mixture methods that linearly combine outputs of $m$ constituent filters running in parallel to model a desired signal. We use "Bregman divergences" and obtain certain multiplicative updates to train the linear combination weights under an affine constraint or without any constraints. We use unnormalized relative entropy and relative entropy to define two different Bregman divergences that produce an unnormalized exponentiated gradient update and a normalized exponentiated gradient update on the mixture weights, respectively. We then carry out the mean and the mean-square transient analysis of these adaptive algorithms when they are used to combine outputs of $m$ constituent filters. We illustrate the accuracy of our results and demonstrate the effectiveness of these updates for sparse mixture systems.

  17. The Validity of Divergent Grounded Theory Method

    Directory of Open Access Journals (Sweden)

    Martin Nils Amsteus PhD

    2014-02-01

    Full Text Available The purpose of this article is to assess whether divergence of grounded theory method may be considered valid. A review of literature provides a basis for understanding and evaluating grounded theory. The principles and nature of grounded theory are synthesized along with theoretical and practical implications. It is deduced that for a theory to be truly grounded in empirical data, the method resulting in the theory should be the equivalent of pure induction. Therefore, detailed, specified, stepwise a priori procedures may be seen as unbidden or arbitrary. It is concluded that divergent grounded theory can be considered valid. The author argues that securing methodological transparency through the description of the actual principles and procedures employed, as well as tailoring them to the particular circumstances, is more important than adhering to predetermined stepwise procedures. A theoretical foundation is provided from which diverse theoretical developments and methodological procedures may be developed, judged, and refined based on their own merits.

  18. Flow over convergent and divergent wall riblets

    Energy Technology Data Exchange (ETDEWEB)

    Koeltzsch, K.; Dinkelacker, A.; Grundmann, R. [Institut fuer Luft- und Raumfahrttechnik, Technische Universitaet Dresden, 36460 Merkers (Germany)

    2002-08-01

    Fast swimming sharks have small riblets on their skin, which are assumed to improve the swimming performance of the fish. Fluid dynamic experiments in water as well as in air confirm this assumption. With riblet surfaces as compared to smooth surfaces, drag reductions up to about 10% were measured. The overall riblet pattern on sharks shows parallel riblets directed from head to tail, but besides this overall pattern fast swimming sharks have also small areas with converging riblets and others with diverging riblets. In the present study the velocity field over convergent and divergent riblet patterns is investigated by hot-wire measurements in turbulent pipe flow. Significant changes in the near wall velocity field were found. (orig.)

  19. Black hole entropy divergence and the uncertainty principle

    CERN Document Server

    Brustein, Ram

    2011-01-01

    Black hole entropy has been shown by 't Hooft to diverge at the horizon. The region near the horizon is in a thermal state, so entropy is linear to energy which consequently also diverges. We find a similar divergence for the energy of the reduced density matrix of relativistic and non-relativistic field theories, extending previous results in quantum mechanics. This divergence is due to an infinitely sharp boundary, and it stems from the position/momentum uncertainty relation in the same way that the momentum fluctuations of a precisely localized quantum particle diverge. We show that when the boundary is smoothed the divergence is tamed. We argue that the divergence of black hole entropy can also be interpreted as a consequence of position/momentum uncertainty, and that 't Hooft's brick wall tames the divergence in the same way, by smoothing the boundary.

  20. 14 CFR 29.629 - Flutter and divergence.

    Science.gov (United States)

    2010-01-01

    ... AIRWORTHINESS STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Design and Construction General § 29.629 Flutter and divergence. Each aerodynamic surface of the rotorcraft must be free from flutter and divergence under...

  1. Automated leukocyte recognition using fuzzy divergence.

    Science.gov (United States)

    Ghosh, Madhumala; Das, Devkumar; Chakraborty, Chandan; Ray, Ajoy K

    2010-10-01

    This paper aims at introducing an automated approach to leukocyte recognition using fuzzy divergence and modified thresholding techniques. The recognition is done through the segmentation of nuclei where Gamma, Gaussian and Cauchy type of fuzzy membership functions are studied for the image pixels. It is in fact found that Cauchy leads better segmentation as compared to others. In addition, image thresholding is modified for better recognition. Results are studied and discussed.

  2. COMPARATIVE FINANCIAL STATEMENTS. CONVERGENCE VERSUS DIVERGENCE

    Directory of Open Access Journals (Sweden)

    Nicolae ECOBICI

    2010-09-01

    Full Text Available In this paper I compared the Romanian financial statements with the US GAAP financial statements in terms of two criteria: first the reference period and secondly the shape, structure and content of financial statements. Nowadays the two accounting systems, the French and Anglo-Saxon, tend to harmonize. I will present the convergences and the divergences between the financial statements of Romania, subject to OMFP 3055/2009, in parallel with the Anglo-Saxon accounting system.

  3. Phenotypic plasticity and divergence in gene expression.

    Science.gov (United States)

    Healy, Timothy M; Schulte, Patricia M

    2015-07-01

    The extent to which phenotypic plasticity, or the ability of a single genotype to produce different phenotypes in different environments, impedes or promotes genetic divergence has been a matter of debate within evolutionary biology for many decades (see, for example, Ghalambor et al. ; Pfennig et al. ). Similarly, the role of evolution in shaping phenotypic plasticity remains poorly understood (Pigliucci ). In this issue of Molecular Ecology, Dayan et al. () provide empirical data relevant to these questions by assessing the extent of plasticity and divergence in the expression levels of 2272 genes in muscle tissue from killifish (genus Fundulus) exposed to different temperatures. F. heteroclitus (Fig. A) and F. grandis are minnows that inhabit estuarine marshes (Fig. B) along the coasts of the Atlantic Ocean and Gulf of Mexico in North America. These habitats undergo large variations in temperature both daily and seasonally, and these fish are known to demonstrate substantial phenotypic plasticity in response to temperature change (e.g. Fangue et al. ). Furthermore, the range of F. heteroclitus spans a large latitudinal gradient of temperatures, such that northern populations experience temperatures that are on average ~10°C colder than do southern populations (Schulte ). By comparing gene expression patterns between populations of these fish from different thermal habitats held in the laboratory at three different temperatures, Dayan et al. () address two important questions regarding the interacting effects of plasticity and evolution: (i) How does phenotypic plasticity affect adaptive divergence? and (ii) How does adaptive divergence affect plasticity?

  4. An Exponential Regulator for Rapidity Divergences

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ye [Fermilab; Neill, Duff [MIT, Cambridge, CTP; Zhu, Hua Xing [MIT, Cambridge, CTP

    2016-04-01

    Finding an efficient and compelling regularization of soft and collinear degrees of freedom at the same invariant mass scale, but separated in rapidity is a persistent problem in high-energy factorization. In the course of a calculation, one encounters divergences unregulated by dimensional regularization, often called rapidity divergences. Once regulated, a general framework exists for their renormalization, the rapidity renormalization group (RRG), leading to fully resummed calculations of transverse momentum (to the jet axis) sensitive quantities. We examine how this regularization can be implemented via a multi-differential factorization of the soft-collinear phase-space, leading to an (in principle) alternative non-perturbative regularization of rapidity divergences. As an example, we examine the fully-differential factorization of a color singlet's momentum spectrum in a hadron-hadron collision at threshold. We show how this factorization acts as a mother theory to both traditional threshold and transverse momentum resummation, recovering the classical results for both resummations. Examining the refactorization of the transverse momentum beam functions in the threshold region, we show that one can directly calculate the rapidity renormalized function, while shedding light on the structure of joint resummation. Finally, we show how using modern bootstrap techniques, the transverse momentum spectrum is determined by an expansion about the threshold factorization, leading to a viable higher loop scheme for calculating the relevant anomalous dimensions for the transverse momentum spectrum.

  5. Genetic divergence predicts reproductive isolation in damselflies.

    Science.gov (United States)

    Sánchez-Guillén, R A; Córdoba-Aguilar, A; Cordero-Rivera, A; Wellenreuther, M

    2014-01-01

    Reproductive isolation is the defining characteristic of a biological species, and a common, but often untested prediction is a positive correlation between reproductive isolation and genetic divergence. Here, we test for this correlation in odonates, an order characterized by strong sexual selection. First, we measure reproductive isolation and genetic divergence in eight damselfly genera (30 species pairs) and test for a positive correlation. Second, we estimate the genetic threshold preventing hybrid formation and empirically test this threshold using wild populations of species within the Ischnura genus. Our results indicate a positive and strong correlation between reproductive isolation and genetic distance using both mitochondrial and nuclear genes cytochrome oxidase II (COII: r = 0.781 and 18S-28S: r = 0.658). Hybridization thresholds range from -0.43 to 1.78% for COII and -0.052-0.71% for 18S-28S, and both F1 -hybrids and backcrosses were detected in wild populations of two pairs of Ischnura species with overlapping thresholds. Our study suggests that threshold values are suitable to identify species prone to hybridization and that positive isolation-divergence relationships are taxonomically widespread.

  6. The direct Flow parametric Proof of Gauss' Divergence Theorem revisited

    DEFF Research Database (Denmark)

    Markvorsen, Steen

    The standard proof of the divergence theorem in undergraduate calculus courses covers the theorem for static domains between two graph surfaces. We show that within first year undergraduate curriculum, the flow proof of the dynamic version of the divergence theorem - which is usually considered o...... we apply the key instrumental concepts and verify the various steps towards this alternative proof of the divergence theorem....

  7. Spontaneous eye blinks during creative task correlate with divergent processing.

    Science.gov (United States)

    Ueda, Yoshiyuki; Tominaga, Atsuko; Kajimura, Shogo; Nomura, Michio

    2016-07-01

    Creativity consists of divergent and convergent thinking, with both related to individual eye blinks at rest. To assess underlying mechanisms between eye blinks and traditional creativity tasks, we investigated the relationship between creativity performance and eye blinks at rest and during tasks. Participants performed an alternative uses and remote association task while eye blinks were recorded. Results showed that the relationship between eye blinks at rest and creativity performance was compatible with those of previous research. Interestingly, we found that the generation of ideas increased as a function of eye blink number during the alternative uses task. On the other hand, during the remote association task, accuracy was independent of eye blink number during the task, but response time increased with it. Moreover, eye blink changes in participants who responded quickly during the remote association task were different depending on their resting state eye blinks; that is, participants with many eye blinks during rest showed little increasing eye blinks and achieved solutions quickly. Positive correlations between eye blinks during creative tasks and yielding ideas on the alternative uses task and response time on the remote association task suggest that eye blinks during creativity tasks relate to divergent thinking processes such as conceptual reorganization.

  8. Measuring grade inflation and grade divergence accounting for student quality

    Directory of Open Access Journals (Sweden)

    Horacio Matos-Díaz

    2014-12-01

    Full Text Available This study uses a rich longitudinal data-set of 13,202 full-time students belonging to 11 cohorts over 22 consecutive semesters (Fall 1995 to Spring 2006 to model the determinants of the grade inflation rates prevailing at the University of Puerto Rico at Bayamón. The following new interesting findings are reported: (1 Estimated rates vary significantly among and within the academic programs, implying grade divergence, depending on the time reference used: cohort time dummies or semesters since admission to the institution. (2 The rates are significantly related to the proportions of female students, students who switch from their original academic programs, and students from private schools. (3 Results suggest that, under determinate circumstances, average- and low-quality students consider higher grades as normal goods; conversely, high-quality students consider higher grades as inferior goods.

  9. An Analysis on Phylogenetic Relationship and Divergence Time of Yunnan Guangye Sang and Qinzhou Changguo Sang in Morus Genus Based on ITS Sequence%基于ITS分析云南光叶桑和钦州长果桑在桑属中的亲缘关系及分化时间

    Institute of Scientific and Technical Information of China (English)

    陈仁芳; 陈祥平; 范小敏; 陈家元; 刘泽听; 虞志伟

    2012-01-01

    content in Qinzhou Changguo Sang is 59. 72% with A at nucleotide 45 and with substitution of T by G at nucleotide 560. It has close phylogenetic relationship with Yunnan Hua Sang (Morus cathayana),both of which belong to group II in the constructed phylogenetic tree. Estimation by loose molecular clock method showed that the divergence time of Yingjing Chuan Sang, Ya'an Hua Sang, and Yunnan Changsui Sang is 8. 23 Ma, and that of Qinzhou Changguo Sang and Yunnan Hua Sang is 9. 67 Ma. The geologic age of their origination was the transient time between the Miocene epoch and the Pliocene epoch in Neogene Period. They are the species evolved in the migration towards southern and hilly areas to resist cold and arid environment of the earth.

  10. Constrained hyperbolic divergence cleaning in smoothed particle magnetohydrodynamics with variable cleaning speeds

    CERN Document Server

    Tricco, Terrence S; Bate, Matthew R

    2016-01-01

    We present an updated constrained hyperbolic/parabolic divergence cleaning algorithm for smoothed particle magnetohydrodynamics (SPMHD) that remains conservative with wave cleaning speeds which vary in space and time. This is accomplished by evolving the quantity $\\psi / c_h$ instead of $\\psi$. Doing so allows each particle to carry an individual wave cleaning speed, $c_h$, that can evolve in time without needing an explicit prescription for how it should evolve, preventing circumstances which we demonstrate could lead to runaway energy growth related to variable wave cleaning speeds. This modification requires only a minor adjustment to the cleaning equations and is trivial to adopt in existing codes. Finally, we demonstrate that our constrained hyperbolic/parabolic divergence cleaning algorithm, run for a large number of iterations, can reduce the divergence of the field to an arbitrarily small value, achieving $\

  11. Constrained hyperbolic divergence cleaning in smoothed particle magnetohydrodynamics with variable cleaning speeds

    Science.gov (United States)

    Tricco, Terrence S.; Price, Daniel J.; Bate, Matthew R.

    2016-10-01

    We present an updated constrained hyperbolic/parabolic divergence cleaning algorithm for smoothed particle magnetohydrodynamics (SPMHD) that remains conservative with wave cleaning speeds which vary in space and time. This is accomplished by evolving the quantity ψ /ch instead of ψ. Doing so allows each particle to carry an individual wave cleaning speed, ch, that can evolve in time without needing an explicit prescription for how it should evolve, preventing circumstances which we demonstrate could lead to runaway energy growth related to variable wave cleaning speeds. This modification requires only a minor adjustment to the cleaning equations and is trivial to adopt in existing codes. Finally, we demonstrate that our constrained hyperbolic/parabolic divergence cleaning algorithm, run for a large number of iterations, can reduce the divergence of the magnetic field to an arbitrarily small value, achieving ∇ ṡ B = 0 to machine precision.

  12. Bounding the bias of contrastive divergence learning

    DEFF Research Database (Denmark)

    Fischer, Anja; Igel, Christian

    2011-01-01

    Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k......, the number of variables in the RBM, and the maximum change in energy that can be produced by changing a single variable. The last reflects the dependence on the absolute values of the RBM parameters. The magnitude of the bias is also affected by the distance in variation between the modeled distribution...

  13. Convergent and Divergent Adaptations of Subterranean Rodents

    DEFF Research Database (Denmark)

    Fang, Xiaodong

    ) have evolved convergent and divergent traits in many of their morphological, physiological, and/or behavioral characteristics, which facilitate their adaptions to a similar underground burrowing life style. For example, all these three rodents show degenerate visual acuity and advanced sensory systems...... in the dark; they display remarkable tolerance to a living environment with an excess of carbon dioxide and ammonia, but lack of oxygen; they exhibit extraordinarily long lives, and keep a fantastic resistance to cancer and other aging-associated diseases. In this study, we reported the genomic...

  14. Projection Pursuit Through ϕ-Divergence Minimisation

    Directory of Open Access Journals (Sweden)

    Jacques Touboul

    2010-06-01

    Full Text Available In his 1985 article (“Projection pursuit”, Huber demonstrates the interest of his method to estimate a density from a data set in a simple given case. He considers the factorization of density through a Gaussian component and some residual density. Huber’s work is based on maximizing Kullback–Leibler divergence. Our proposal leads to a new algorithm. Furthermore, we will also consider the case when the density to be factorized is estimated from an i.i.d. sample. We will then propose a test for the factorization of the estimated density. Applications include a new test of fit pertaining to the elliptical copulas.

  15. The Eurozone Dynamic Cohesion: Convergence or Divergence

    Directory of Open Access Journals (Sweden)

    Antonin Rusek

    2013-08-01

    Full Text Available The long term economic dynamics of the Eurozone’s original 12 countries (Greece, Italy, Spain, Portugal, Ireland, Germany, Netherlands, Luxembourg, Belgium, Austria, Finland, France is analyzed and compared. It is today increasingly recognized that the diverging competitiveness between the Eurozone members is at the root of the current crisis. But the competitiveness dynamics and its impact on the crucial fiscal and financial variables during the common currency existence is seldom analyzed and compared, especially as far as the different groups of countries (and/or different areas within the Eurozone are concerned.

  16. Lindstedt series, ultraviolet divergences and Moser's theorem

    CERN Document Server

    Bonetto, F; Gentile, G; Mastropietro, V

    1995-01-01

    Moser's invariant tori for a class of nonanalytic quasi integrable even hamiltonian systems are shown to be analytic in the perturbation parameter. We do so by exhibiting a summation rule for the divergent series (``Lindstedt series") that formally define them. We find additional cancellations taking place in the formal series, besides the ones already known and necessary in the analytic case (\\ie to prove convergence of Lindtsedt algorithm for Kolmogorov's invariant tori). The method is interpreted in terms of a non renormalizable quantum field theory, considerably more singular than the one we pointed out in the analytic case.

  17. Genetic diversity, recombination, and divergence in animal associated Penicillium dipodomyis.

    Directory of Open Access Journals (Sweden)

    Daniel A Henk

    Full Text Available Penicillium dipodomyis is thought to be an exclusively asexual fungus associated with Kangaroo Rats, Dipodomys species, and is unique among Penicillium species in growing at 37°C but producing no known toxins. Lack of recombination within P. dipodomyis would result in limited adaptive flexibility but possibly enhance local adaptation and host selection via maintenance of favourable genotypes. Here, analysis of DNA sequence data from five protein-coding genes shows that recombination occurs within P. dipodomyis on a small spatial scale. Furthermore, detection of mating-type alleles supports outcrossing and a sexual cycle in P. dipodomyis. P. dipodomyis was a weaker competitor in in vitro assays with other Penicillium species found in association with Kanagaroo rats. Bayesian species level analysis suggests that the P. dipodomyis lineage diverged from closely related species also found in cheek pouches of Kangaroo Rats and their stored seeds about 11 million years ago, a similar divergence time as Dipodomys from its sister rodent taxa.

  18. Dynamical renormalization group resummation of finite temperature infrared divergences

    CERN Document Server

    Boyanovsky, D; Holman, R; Simionato, M

    1999-01-01

    We introduce the method of dynamical renormalization group to study relaxation and damping out of equilibrium directly in real time and applied it to the study of infrared divergences in scalar QED. This method allows a consistent resummation of infrared effects associated with the exchange of quasistatic transverse photons and leads to anomalous logarithmic relaxation of the form $e^{-\\alpha T t \\ln[t/t_0]}$ which prevents a quasiparticle interpretation of charged collective excitations at finite temperature. The hard thermal loop resummation program is incorporated consistently into the dynamical renormalization group yielding a picture of relaxation and damping phenomena in a plasma in real time that trascends the conceptual limitations of the quasiparticle picture and other type of resummation schemes. We derive a simple criterion for establishing the validity of the quasiparticle picture to lowest order.

  19. Angular-divergence calculation for Experimental Advanced Superconducting Tokamak neutral beam injection ion source based on spectroscopic measurements

    Energy Technology Data Exchange (ETDEWEB)

    Chi, Yuan, E-mail: jtext@hust.edu.cn [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Hu, Chundong [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Zhuang, Ge [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2014-02-15

    Calorimetric method has been primarily applied for several experimental campaigns to determine the angular divergence of high-current ion source for the neutral beam injection system on the Experimental Advanced Superconducting Tokamak (EAST). A Doppler shift spectroscopy has been developed to provide the secondary measurement of the angular divergence to improve the divergence measurement accuracy and for real-time and non-perturbing measurement. The modified calculation model based on the W7AS neutral beam injectors is adopted to accommodate the slot-type accelerating grids used in the EAST's ion source. Preliminary spectroscopic experimental results are presented comparable to the calorimetrically determined value of theoretical calculation.

  20. Convergence and divergence are mostly reciprocated properties of the connections in the network of cortical areas.

    Science.gov (United States)

    Négyessy, László; Nepusz, Tamás; Zalányi, László; Bazsó, Fülöp

    2008-10-22

    Cognition is based on the integrated functioning of hierarchically organized cortical processing streams in a manner yet to be clarified. Because integration fundamentally depends on convergence and the complementary notion of divergence of the neuronal connections, we analysed integration by measuring the degree of convergence/divergence through the connections in the network of cortical areas. By introducing a new index, we explored the complementary convergent and divergent nature of connectional reciprocity and delineated the backward and forward cortical sub-networks for the first time. Integrative properties of the areas defined by the degree of convergence/divergence through their afferents and efferents exhibited distinctive characteristics at different levels of the cortical hierarchy. Areas previously identified as hubs exhibit information bottleneck properties. Cortical networks largely deviate from random graphs where convergence and divergence are balanced at low reciprocity level. In the cortex, which is dominated by reciprocal connections, balance appears only by further increasing the number of reciprocal connections. The results point to the decisive role of the optimal number and placement of reciprocal connections in large-scale cortical integration. Our findings also facilitate understanding of the functional interactions between the cortical areas and the information flow or its equivalents in highly recurrent natural and artificial networks.

  1. Divergent pointing with the Cherenkov Telescope Array for surveys and beyond

    CERN Document Server

    ,

    2015-01-01

    The galactic and extragalactic surveys are two of the main proposed legacy projects of the Cherenkov Telescope Array (CTA), providing an unbiased view of the Universe at energies above tens of GeV. Considering Cherenkov telescopes' limited field of view ($<10^\\circ$), the time needed for those projects is large. The many telescopes of CTA will allow taking full advantage of new pointing modes in which telescopes point slightly offset from one another. This divergent pointing mode leads to an increase of the array field of view ($\\sim 14^\\circ$ or larger) with competitive performance compared to normal pointing. We present here a study of the performance of the divergent pointing for different array configurations and number of telescopes. We briefly discuss the prospect of using divergent pointing for surveys.

  2. Regulation of cell-to-cell variability in divergent gene expression

    Science.gov (United States)

    Yan, Chao; Wu, Shuyang; Pocetti, Christopher; Bai, Lu

    2016-03-01

    Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically `leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs.

  3. Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

    DEFF Research Database (Denmark)

    Alquezar Planas, David Eugenio; Mourier, Tobias; Bruhn, Christian Anders Wathne;

    2013-01-01

    . The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT) sequencing. Subsequent "primer walking" combined with Sanger sequencing...

  4. The Relation between Gray Matter Morphology and Divergent Thinking in Adolescents and Young Adults

    NARCIS (Netherlands)

    Cousijn, Janna; Koolschijn, P Cédric M P; Zanolie, Kiki; Kleibeuker, Sietske W; Crone, Eveline A

    2014-01-01

    Adolescence and early adulthood are developmental time periods during which creative cognition is highly important for adapting to environmental changes. Divergent thinking, which refers to generating novel and useful solutions to open-ended problems, has often been used as a measure of creative cog

  5. Creative Cognition in Secondary Science: An Exploration of Divergent Thinking in Science among Adolescents

    Science.gov (United States)

    Antink-Meyer, Allison; Lederman, Norman G.

    2015-01-01

    The divergent thinking skills in science of 282 US high school students were investigated across 16 weeks of instruction in order to determine whether typical academic time periods can significantly influence changes in thinking skills. Students' from 6 high school science classrooms completed the Scientific Structures Creativity Measure (SSCM)…

  6. Seven Means, Generalized Triangular Discrimination, and Generating Divergence Measures

    Directory of Open Access Journals (Sweden)

    Inder Jeet Taneja

    2013-04-01

    Full Text Available Jensen-Shannon, J-divergence and Arithmetic-Geometric mean divergences are three classical divergence measures known in the information theory and statistics literature. These three divergence measures bear interesting inequality among the three non-logarithmic measures known as triangular discrimination, Hellingar’s divergence and symmetric chi-square divergence. However, in 2003, Eve studied seven means from a geometrical point of view, which are Harmonic, Geometric, Arithmetic, Heronian, Contra-harmonic, Root-mean square and Centroidal. In this paper, we have obtained new inequalities among non-negative differences arising from these seven means. Correlations with generalized triangular discrimination and some new generating measures with their exponential representations are also presented.

  7. DIVERGENCE - FREE WAVELET SOLUTION TO THE STOKES PROBLEM

    Institute of Scientific and Technical Information of China (English)

    Yingchun Jiang

    2007-01-01

    In this paper, we use divergence-free wavelets to give an adaptive solution to the velocity field of the Stokes problem. We first use divergence-free wavelets to discretize the divergence-free weak formulation of the Stokes problem and obtain a discrete positive definite linear system of equations whose coefficient matrix is quasi-sparse; Secondly, an adaptive scheme is used to solve the discrete linear system of equations and the error estimation and complexity analysis are given.

  8. Some Divergence Properties of Asset Price Models

    Directory of Open Access Journals (Sweden)

    Wolfgang Stummer

    2001-12-01

    Full Text Available Abstract: We consider asset price processes Xt which are weak solutions of one-dimensional stochastic differential equations of the form (equation (2 Such price models can be interpreted as non-lognormally-distributed generalizations of the geometric Brownian motion. We study properties of the Iα-divergence between the law of the solution Xt and the corresponding drift-less measure (the special case α=1 is the relative entropy. This will be applied to some context in statistical information theory as well as to arbitrage theory and contingent claim valuation. For instance, the seminal option pricing theorems of Black-Scholes and Merton appear as a special case.

  9. Reliability and Security - Convergence or Divergence

    Directory of Open Access Journals (Sweden)

    Emil BURTESCU

    2010-01-01

    Full Text Available Reliability, as every technical field, must adapt to the new demands imposed by reality. Started initially as a field designed to control and ensure the smooth functionality of an element or technical system, reliability has reached the stage where the discussion is about the reliability management, similar to the other top-level fields. Security has its own contribution to the reliability of a system; a reliable system is a system with reliable security. In order for a system to be reliable, that means clear and safe, all its components must be reliable. In the following pages we will talk about the two main facts - reliability and security - to determine both the convergence and the divergence points.

  10. Suppression effects of Weibel instability for fast electron divergence

    Directory of Open Access Journals (Sweden)

    Sakagami H.

    2013-11-01

    Full Text Available Quasi-static magnetic fields, which are induced by the Weibel instability and grow to more than hundred Megagauss, lead to large divergence angle of fast electrons, hence lower energy coupling. To suppress the divergence, two different structures, namely density trough and punched out holes, are introduced to targets. In the density trough target, the Weibel instability is enhanced and the divergence is getting worse. On the other hand, the divergence angle is improved but the number of electrons is degraded for fast electrons (<3 MeV in the punched out target.

  11. Convergence Insufficiency/Divergence Insufficiency Convergence Excess/Divergence Excess: Some Facts and Fictions.

    Science.gov (United States)

    Khawam, Edward; Abiad, Bachir; Boughannam, Alaa; Saade, Joanna; Alameddine, Ramzi

    2015-01-01

    Great discrepancies are often encountered between the distance fixation and the near-fixation esodeviations and exodeviations. They are all attributed to either anomalies of the AC/A ratio or anomalies of the fusional convergence or divergence amplitudes. We report a case with pseudoconvergence insufficiency and another one with pseudoaccommodative convergence excess. In both cases, conv./div. excess and insufficiency were erroneously attributed to anomalies of the AC/A ratio or to anomalies of the fusional amplitudes. Our purpose is to show that numerous factors, other than anomalies in the AC/A ratio or anomalies in the fusional conv. or divergence amplitudes, can contaminate either the distance or the near deviations. This results in significant discrepancies between the distance and the near deviations despite a normal AC/A ratio and normal fusional amplitudes, leading to erroneous diagnoses and inappropriate treatment models.

  12. Convergence Insufficiency/Divergence Insufficiency Convergence Excess/Divergence Excess: Some Facts and Fictions

    Directory of Open Access Journals (Sweden)

    Edward Khawam

    2015-01-01

    Full Text Available Great discrepancies are often encountered between the distance fixation and the near-fixation esodeviations and exodeviations. They are all attributed to either anomalies of the AC/A ratio or anomalies of the fusional convergence or divergence amplitudes. We report a case with pseudoconvergence insufficiency and another one with pseudoaccommodative convergence excess. In both cases, conv./div. excess and insufficiency were erroneously attributed to anomalies of the AC/A ratio or to anomalies of the fusional amplitudes. Our purpose is to show that numerous factors, other than anomalies in the AC/A ratio or anomalies in the fusional conv. or divergence amplitudes, can contaminate either the distance or the near deviations. This results in significant discrepancies between the distance and the near deviations despite a normal AC/A ratio and normal fusional amplitudes, leading to erroneous diagnoses and inappropriate treatment models.

  13. Convergence Insufficiency/Divergence Insufficiency Convergence Excess/Divergence Excess: Some Facts and Fictions

    OpenAIRE

    Edward Khawam; Bachir Abiad; Alaa Boughannam; Joanna Saade; Ramzi Alameddine

    2015-01-01

    Great discrepancies are often encountered between the distance fixation and the near-fixation esodeviations and exodeviations. They are all attributed to either anomalies of the AC/A ratio or anomalies of the fusional convergence or divergence amplitudes. We report a case with pseudoconvergence insufficiency and another one with pseudoaccommodative convergence excess. In both cases, conv./div. excess and insufficiency were erroneously attributed to anomalies of the AC/A ratio or to anomalies ...

  14. Divergence in function and expression of the NOD26-like intrinsic proteins in plants

    Directory of Open Access Journals (Sweden)

    Feng Ying

    2009-07-01

    Full Text Available Abstract Background NOD26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out. Results The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss P. patens. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that NIPs should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct NIP groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of cis-acting regulatory elements in the promoter regions may partially explain their distinction in expression. Conclusion A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have

  15. Rapid ecological isolation and intermediate genetic divergence in lacustrine cyclic parthenogens

    Directory of Open Access Journals (Sweden)

    Costanzo Katie S

    2010-06-01

    Full Text Available Abstract Background Ecological shifts can promote rapid divergence and speciation. However, the role of ecological speciation in animals that reproduce predominantly asexually with periodic sex and strong dispersal, such as lacustrine cladocerans, is poorly understood. These life history traits may slow or prevent ecological lineage formation among populations. Proponents of the postglacial ecological isolation hypothesis for Daphnia suggest that some species have formed postglacially in adjacent, but ecologically different habitats. We tested this hypothesis with ecological, morphological, and multilocus coalescence analyses in the putative lacustrine sister species, Daphnia parvula and Daphnia retrocurva. Results Daphnia parvula and D. retrocurva showed strong habitat separation with rare co-occurrence. Lakes inhabited by D. parvula were smaller in size and contained lower densities of invertebrate predators compared to lakes containing D. retrocurva. In the laboratory, D. retrocurva was less vulnerable to invertebrate predation, whereas D. parvula was less vulnerable to vertebrate predation and was smaller and more transparent than D. retrocurva. The species are significantly differentiated at mitochondrial and nuclear loci and form an intermediate genetic divergence pattern between panmixia and reciprocal monophyly. Coalescence and population genetic modelling indicate a Late or Post Glacial time of divergence with a demographic expansion. Conclusions Despite their young age and mixed breeding system, D. parvula and D. retrocurva exhibit significant ecological and genetic divergence that is coincident with the formation of deep temperate glacial lakes. We propose that predation may have facilitated the rapid divergence between D. parvula and D. retrocurva and that intermediate divergence of aquatic cyclic parthenogens is likely more common than previously thought.

  16. Comparative phylogeography of two marine species of crustacean: Recent divergence and expansion due to environmental changes.

    Science.gov (United States)

    Zhang, Daizhen; Ding, Ge; Ge, Baoming; Zhang, Huabin; Tang, Boping; Yang, Guang

    2014-10-15

    Environmental changes, such as changes in the coastal topography due to Eurasian plate movements, climate oscillation during the Pleistocene, and alteration of ocean currents, have complicated the geographical structure of marine species and deepened their divergence between populations. As two widely distributed species of crustacean (Oratosquilla oratoria and Eriocheir japonica), weak differences were expected due to their high dispersal potential of planktonic larvae with ocean currents. However, results showed a significant genetic divergence between north of China and south of China in the study. In addition, the estimated north-south divergence time (27-30.5 Myr) of mantis shrimp was near the time of the Himalayan movement, and the China-Japan clade divergence time (10.5-11.9 Myr) of mitten crabs was also coincident with the time of the opening of the Sea of Japan. Thus, we hypothesized that environmental changes in the coastal topography contributed to the marine species divergence. Furthermore, based on phylogenetic analysis, network analysis and haplotype distribution, we surmised that mitten crabs originated from a population with the oldest haplotype (H6) and then divided into the north and south populations due to the recent Eurasian plate movements and ocean currents. And lineage of Japan originated from the north population for the opening of the Sea of Japan. While O. oratoria was guessed to originate from two separate populations in the China Sea. The results of "star-like" network, negative values in neutral test, and Tajima's D statistics of two marine species supported a recent rapid population expansion event after the Pleistocene glaciations.

  17. Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes.

    Science.gov (United States)

    Narang, Pooja; Wilson Sayres, Melissa A

    2016-12-31

    Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias.

  18. A phylogenomic approach to resolve the basal pterygote divergence.

    Science.gov (United States)

    Simon, Sabrina; Strauss, Sascha; von Haeseler, Arndt; Hadrys, Heike

    2009-12-01

    One of the most fascinating Bauplan transitions in the animal kingdom was the invention of insect wings, a change that also contributed to the success and enormous diversity of this animal group. However, the origin of insect flight and the relationships of basal winged insect orders are still controversial. Three hypotheses have been proposed to explain the phylogeny of winged insects: 1) the traditional Palaeoptera hypothesis (Ephemeroptera + Odonata, Neoptera), 2) the Metapterygota hypothesis (Ephemeroptera, Odonata + Neoptera), and 3) the Chiastomyaria hypothesis (Odonata, Ephemeroptera + Neoptera). Neither phylogenetic analyses of single genes nor even multiple marker systems (e.g., molecular markers + morphological characters) have yet been able to conclusively resolve basal pterygote divergences. A possible explanation for the lack of resolution is that the divergences took place in the mid-Devonian within a short period of time and attempts to solve this problem have been confounded by the major challenge of finding molecular markers to accurately track these short ancient internodes. Although phylogenomic data are available for Neoptera and some wingless (apterygote) orders, they are lacking for the crucial Odonata and Ephemeroptera orders. We adopt a multigene approach including data from two new expressed sequence tag projects-from the orders Ephemeroptera (Baetis sp.) and Odonata (Ischnura elegans)-to evaluate the potential of phylogenomic analyses in clarifying this unresolved issue. We analyzed two data sets that differed in represented taxa, genes, and overall sequence lengths: maxspe (15 taxa, 125 genes, and 31,643 amino acid positions) and maxgen (8 taxa, 150 genes, and 42,541 amino acid positions). Maximum likelihood and Bayesian inference analyses both place the Odonata at the base of the winged insects. Furthermore, statistical hypotheses testing rejected both the Palaeoptera and the Metapterygota hypotheses. The comprehensive molecular data set

  19. A bioenergetic basis for membrane divergence in archaea and bacteria.

    Science.gov (United States)

    Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

    2014-08-01

    Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet

  20. Understanding Spatiotemporal Patterns of Human Convergence and Divergence Using Mobile Phone Location Data

    Directory of Open Access Journals (Sweden)

    Xiping Yang

    2016-09-01

    Full Text Available Investigating human mobility patterns can help researchers and agencies understand the driving forces of human movement, with potential benefits for urban planning and traffic management. Recent advances in location-aware technologies have provided many new data sources (e.g., mobile phone and social media data for studying human space-time behavioral regularity. Although existing studies have utilized these new datasets to characterize human mobility patterns from various aspects, such as predicting human mobility and monitoring urban dynamics, few studies have focused on human convergence and divergence patterns within a city. This study aims to explore human spatial convergence and divergence and their evolutions over time using large-scale mobile phone location data. Using a dataset from Shenzhen, China, we developed a method to identify spatiotemporal patterns of human convergence and divergence. Eight distinct patterns were extracted, and the spatial distributions of these patterns are discussed in the context of urban functional regions. Thus, this study investigates urban human convergence and divergence patterns and their relationships with the urban functional environment, which is helpful for urban policy development, urban planning and traffic management.

  1. The Relationship Between Lateral Dominance and Divergent Cognitive Thought.

    Science.gov (United States)

    Williams, Barbara B.

    This study was designed to explore the relationship of lateral dominance to divergent cognitive thought. According to the screening results of the Harris Tests of Lateral Dominance, 36 subjects ranging from 9-12 years were divided equally into three groups of left, right, and mixed lateral dominance. In order to measure divergent cognitive…

  2. Transcriptome-wide patterns of divergence during allopatric evolution.

    Science.gov (United States)

    Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

    2016-04-01

    Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level.

  3. Some Effects of Testing Procedure on Divergent Thinking

    Science.gov (United States)

    Nicholls, John G.

    1971-01-01

    Game-like and test-like methods of divergent thinking assessment were compared with 10-year olds. Effects of method on score correlates were sufficient to allow the possibility that method may be implicated in outcomes of many studies of divergent thinking. (Author)

  4. The Mathematics of Divergence Based Online Learning in Vector Quantization

    NARCIS (Netherlands)

    Villmann, Thomas; Haase, Sven; Schleif, Frank-Michael; Hammer, Barbara; Biehl, Michael

    2010-01-01

    We propose the utilization of divergences in gradient descent learning of supervised and unsupervised vector quantization as an alternative for the squared Euclidean distance. The approach is based on the determination of the Fréchet-derivatives for the divergences, wich can be immediately plugged i

  5. Parametric R-norm directed-divergence convex function

    Science.gov (United States)

    Garg, Dhanesh; Kumar, Satish

    2016-06-01

    In this paper, we define parametric R-norm directed-divergence convex function and discuss their special cases and prove some properties similar to Kullback-Leibler information measure. From R-norm divergence measure new information measures have also been derived and their relations with different measures of entropy have been obtained and give its application in industrial engineering.

  6. On bounds of some dynamic information divergence measures

    OpenAIRE

    S. M. Sunoj; Linu, M.N.

    2013-01-01

    In this paper, we obtain certain bounds for some dynamic information divergences measures viz. Renyi’s divergence of order α and Kerridge’s inaccuracy, using likelihood ratio ordering. The results are also extended to weighted models and theoretical examples are given to supplement the results.

  7. On bounds of some dynamic information divergence measures

    Directory of Open Access Journals (Sweden)

    S. M. Sunoj

    2013-05-01

    Full Text Available In this paper, we obtain certain bounds for some dynamic information divergences measures viz. Renyi’s divergence of order α and Kerridge’s inaccuracy, using likelihood ratio ordering. The results are also extended to weighted models and theoretical examples are given to supplement the results.

  8. Mass divergence power counting for QCD in the Feynman gauge

    Energy Technology Data Exchange (ETDEWEB)

    Tucci, R.

    1986-03-01

    We present a mass divergence power counting technique for QCD in the Feyman gauge. For the process ..gamma..sup(*)->qanti q, we find the leading regions of integration and show that single diagrams are at worst logarithmically divergent. Using the Weyl representation facilitates the ..gamma.. matrix manipulations necessary for power counting and adds much physical insight. (orig.).

  9. An investigation of merging and diverging cars on a multi-lane road using a cellular automation model

    Institute of Scientific and Technical Information of China (English)

    K.Jetto; H.Ez-Zahraouy; A.Benyoussef

    2012-01-01

    In this paper,we have investigated two observed situations in a multi-lane road.The first one concerns a fast merging vehicle.The second situation is related to the case of a fast vehicle leaving the fastest lane back into the slowest lane and targeting a specific way out.We are interested in the relaxation time τ,i.e.,which is the time that the merging (diverging) vehicle spends before reaching the desired lane.Using analytical treatment and numerical simulations for the NaSch model,we have found two states,namely,the free state in which the merging (diverging) vehicle reaches the desired lane,and the trapped state in which τ diverges.We have established phase diagrams for several values of the braking probability.In the second situation,we have shown that diverging from the fast lane targeting a specific way out is not a simple task.Even if the diverging vehicle is in the free phase,two different states can be distinguished.One is the critical state,in which the diverging car can probably reach the desired way out.The other is the safe state,in which the diverging car can surely reach the desired way out.In order to be in the safe state,we have found that the driver of the diverging car must know the critical distance (below which the way out will be out of his reach) in each lane.Furthermore,this critical distance depends on the density of cars,and it follows an exponential law.

  10. Relations between dissipated work in non-equilibrium process and the family of Rényi divergences

    Science.gov (United States)

    Wei, Bo-Bo; Plenio, M. B.

    2017-02-01

    In this paper, we establish a general relation which directly links the dissipated work done on a system driven arbitrarily far from equilibrium, a fundamental quantity in thermodynamics, and the family of Rényi divergences between two states along the forward and reversed dynamics, a fundamental concept in information theory. Specifically, we find that the generating function of the dissipated work under an arbitrary time-dependent driving is related to the family of Rényi divergences between a non-equilibrium state along the forward process and a non-equilibrium state along its time-reversed process. This relation is a consequence of the principle of conservation of information and time reversal symmetry and is universally applicable to both finite classical system and finite quantum system under arbitrary driving process. The significance of the relation between the generating function of dissipated work and the family of Rényi divergences are two fold. On the one hand, the relation establishes that the macroscopic entropy production and its fluctuations are determined by the family of Rényi divergences, a measure of distinguishability of two states, between a microscopic process and its time reversal. On the other hand, this relation tells us that we can extract the family of Renyi divergences from the work measurement in a microscopic process. For classical systems the work measurement is straightforward, from which the family of Rényi divergences can be obtained; for quantum systems under time-dependent driving the characteristic function of work distributions can be measured from Ramsey interferences of a single spin, then we can extract the family of Renyi divergences from Ramsey interferences of a single spin.

  11. Exceptional giftedness in early adolescence and intrafamilial divergent thinking.

    Science.gov (United States)

    Runco, M A; Albert, R S

    1986-08-01

    Two groups of boys and their parents (N=54) were given five divergent thinking tests as one part of a longitudinal investigation on exceptional giftedness in early adolescence. One groups of adolescents was selected because their IQs were above 150, and the other group, was selected because of their outstanding math-science abilities. Canonical and bivariate analyses indicated that there was a strong correlation between the adolescents' divergent thinking test scores and their parents' divergent thinking test scores (Rc=.55). Additionally, there was some indication that these correlations differed in the two exceptionally gifted groups, with the high-IQ group having divergent thinking test scores related to those of both parents, and the math-science group having divergent thinking test scores related only to those of their mothers. These findings are very consistent with earlier investigations on exceptionally gifted adolescents.

  12. Analysis of kinematic waves arising in diverging traffic flow models

    CERN Document Server

    Jin, Wen-Long

    2010-01-01

    Diverging junctions are important network bottlenecks, and a better understanding of diverging traffic dynamics has both theoretical and practical implications. In this paper, we first introduce a continuous multi-commodity kinematic wave model of diverging traffic and then present a new framework for constructing kinematic wave solutions to its Riemann problem with jump initial conditions. In supply-demand space, the solutions on a link consist of an interior state and a stationary state, subject to admissible conditions such that there are no positive and negative kinematic waves on the upstream and downstream links respectively. In addition, the solutions have to satisfy entropy conditions consistent with various discrete diverge models. In the proposed analytical framework, kinematic waves on each link can be uniquely determined by the stationary and initial conditions, and we prove that the stationary states and boundary fluxes exist and are unique for the Riemann problem of diverge models when all or pa...

  13. Divergence-free Hardy space on

    Institute of Scientific and Technical Information of China (English)

    LOU; Zengjian

    2004-01-01

    [1]Gilbert, J. E., Hogan, J. A., Lakey, J. D., Atomic decomposition of divergence-free Hardy spaces, Mathematica Moraviza, 1997, Special Volume, Proc. IWAA: 33-52.[2]Chang, D. C., Krantz, S. G., Stein, E. M., HP theory on a smooth domain in RN and elliptic boundary value problems, J. Funct. Anal., 1993, 114: 286-347.[3]Schwarz, G., Hodge Decomposition-A method for solving boundary value problems, Lecture Notes in Mathematics, Vol. 1607, Berlin Heidelberg: Springer-Verlag, 1995.[4]Girault, V., Raviart, P. A., Finite Element Methods for Navier-Stokes Equations, Theory and Algorithms, Berlin Heidelberg: Springer-Verlag, 1986.[5]Stein, E. M., Singular Integrals and Differentiability Properties of Functions, Princeton: Princeton Univ. Press,1970.[6]Davies, B., Heat Kernels and Spectral Theory, Cambridge: Cambridge University Press, 1989.[7]Geymonat, G., Miller, S., Triantafylidis, N., Homogenization of nonlinear elastic materials, microscopic bifurcation and microscopic loss of rank-one convexity, Arch. Rational Mech. Anal., 1993, 122: 231-290.[8]Ball, J., Convexity conditions and existence theorems in nonlinear elasticity, Arch. Rational Mech. Anal., 1977,63: 337-403.[9]Zhang, K., On the coercivity of elliptic systems in two dimensional spaces, Bull. Austral. Math. Soc., 1996, 54:423-430.

  14. Divergent clonal selection dominates medulloblastoma at recurrence

    Science.gov (United States)

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  15. Diversity and Divergence of Dinoflagellate Histone Proteins.

    Science.gov (United States)

    Marinov, Georgi K; Lynch, Michael

    2015-12-08

    Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed.

  16. The Diverge of Liquidity and Inflation in the After-Crisis Time--Based on the Trend of Inflation Over Time%后危机时代流动性过剩与通货膨胀的偏离--基于长期通货膨胀趋势的解释视角

    Institute of Scientific and Technical Information of China (English)

    栗亮

    2014-01-01

    The paper argues the reason why the liquidity excess did not lead to the acceleration of inflation in the present time is because that inflation rate will drop over time. However, the asset price plays some roles in short term. We try to explain that why the liquidity excess did not raise the inflation, and we think the most mainly reasons are inflation targeting, the independence of central bank and the globalization.%本文认为此轮流动性过剩没有导致通货膨胀率明显上升的主要原因在长期来看应该是通货膨胀率不断降低的一般规律,在短期来看,资产价格起到了一定作用。本文试图从目标通货膨胀制、央行独立性和全球化的角度解释尽管目前全球出现普遍性的流动性过剩,但是通货膨胀却保持在相对平稳水平的原因。

  17. Creativity and sensory gating indexed by the P50: selective versus leaky sensory gating in divergent thinkers and creative achievers.

    Science.gov (United States)

    Zabelina, Darya L; O'Leary, Daniel; Pornpattananangkul, Narun; Nusslock, Robin; Beeman, Mark

    2015-03-01

    Creativity has previously been linked with atypical attention, but it is not clear what aspects of attention, or what types of creativity are associated. Here we investigated specific neural markers of a very early form of attention, namely sensory gating, indexed by the P50 ERP, and how it relates to two measures of creativity: divergent thinking and real-world creative achievement. Data from 84 participants revealed that divergent thinking (assessed with the Torrance Test of Creative Thinking) was associated with selective sensory gating, whereas real-world creative achievement was associated with "leaky" sensory gating, both in zero-order correlations and when controlling for academic test scores in a regression. Thus both creativity measures related to sensory gating, but in opposite directions. Additionally, divergent thinking and real-world creative achievement did not interact in predicting P50 sensory gating, suggesting that these two creativity measures orthogonally relate to P50 sensory gating. Finally, the ERP effect was specific to the P50 - neither divergent thinking nor creative achievement were related to later components, such as the N100 and P200. Overall results suggest that leaky sensory gating may help people integrate ideas that are outside of focus of attention, leading to creativity in the real world; whereas divergent thinking, measured by divergent thinking tests which emphasize numerous responses within a limited time, may require selective sensory processing more than previously thought.

  18. Optical studies of the flow start-up processes in four convergent-divergent nozzles

    Science.gov (United States)

    Opalka, Klaus O.

    1991-03-01

    In the context of design studies for the U.S. Large Blast/Thermal Simulator, BRL has sponsored optical studies of the flow start-up in convergent-divergent nozzles which have the flow-initiating diaphragm located in the nozzle throat. The experiments were performed in the 200 mm shock tube at the Ernst-Mach Institute in Freiburg (Breisgau), West-Germany. The scope of the studies included divergent nozzles with half cone angles of 6, 16, 45 and 90 deg tested at seven diaphragm pressure ratios ranging from 4 to 188 and resulting in shock strengths ranging from 1.4 to 4.4. Results were summarized in graphs of significant parameters, e.g., shock formation time, flow start-up period, flow expansion angle, and shock strength versus the driver pressure ratio and further compared with numerical results obtained with the BRL-Q1D hydrocode. The numerical-experimental comparison shows qualitative agreement. The flow phenomena are generally reproduced by the computations as long as they are not strongly dependent on viscous effects. The study shows that a pressure loss of 10 percent is connected to the presence of a large area discontinuity at the exit plane of the nozzle throat when no divergent nozzle is attached. Results suggest that a 45 deg divergent nozzle may present an acceptable compromise for minimizing these pressure losses by reducing the associated area discontinuities.

  19. Ecological divergence and speciation between lemur (Eulemur) sister species in Madagascar.

    Science.gov (United States)

    Blair, M E; Sterling, E J; Dusch, M; Raxworthy, C J; Pearson, R G

    2013-08-01

    Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate-based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Madagascar. We produced ENMs for eight species, all of which had significant validation support. Among the four sister species pairs, we found nonequivalent niches between sisters, varying degrees of niche overlap in ecological and geographic space, and support for multiple divergence processes. Specifically, three sister-pair comparisons supported the null model that niches are no more divergent than the available background region. These findings are consistent with an allopatric speciation model, and for two sister pairs (E. collaris-E. cinereiceps and E. rufus-E. rufifrons), a riverine barrier has been previously proposed for driving allopatric speciation. However, for the fourth sister pair E. flavifrons-E. macaco, we found support for significant niche divergence, and consistent with their parapatric distribution on an ecotone and the lack of obvious geographic barriers, these findings most strongly support a parapatric model of speciation. These analyses thus suggest that various speciation processes have led to diversification among closely related Eulemur species.

  20. Developmental rate: A unifying mechanism for sympatric divergence in postglacial fishes?

    Directory of Open Access Journals (Sweden)

    Megan V. MCPHEE, David L. G. NOAKES, Fred W. ALLENDORF

    2012-02-01

    Full Text Available Morphologically divergent ecotypes arise in fish populations on postglacial time scales, and resource polymorphisms are often invoked to explain their origin. However, genetic recombination can constrain the ability of divergent selection to produce reproductive isolation in sympatry. Recombination breaks up favorable combinations of traits (”adaptive suites” if indivi- dual traits are affected by different loci. Recombination also breaks up any association between traits under divergent selection and traits contributing to reproductive isolation. Thus, ecological speciation in the absence of preexisting barriers to gene flow is more likely when pleiotropy minimizes the number of loci involved. Here, we revisit research conducted by Carl Hubbs in the early 1900s on the effects of developmental rate on morphological traits in fishes. Hubbs’ work provides a mechanism to explain how sympatric divergence by trophic polymorphism can occur despite the challenges of recombination. We consider the implications of Hubbs’ observations for ecological speciation with gene flow in fishes, as well as rapid evolution in captive fish populations [Current Zoology 58 (1: 21–34, 2012].

  1. Phenotypic divergence during speciation is inversely associated with differences in seasonal migration.

    Science.gov (United States)

    Delmore, Kira E; Kenyon, Haley L; Germain, Ryan R; Irwin, Darren E

    2015-11-22

    Differences in seasonal migration might promote reproductive isolation and differentiation by causing populations in migratory divides to arrive on the breeding grounds at different times and/or produce hybrids that take inferior migratory routes. We examined this question by quantifying divergence in song, colour, and morphology between sister pairs of North American migratory birds. We predicted that apparent rates of phenotypic differentiation would differ between pairs that do and do not form migratory divides. Consistent with this prediction, results from mixed effects models and Ornstein-Uhlenbeck models of evolution showed different rates of divergence between these groups; surprisingly, differentiation was greater among non-divide pairs. We interpret this finding as a result of variable rates of population blending and fusion between partially diverged forms. Ancient pairs of populations that subsequently fused are now observed as a single form, whereas those that did not fuse are observable as pairs and included in our study. We propose that fusion of two populations is more likely to occur when they have similar migratory routes and little other phenotypic differentiation that would cause reproductive isolation. By contrast, pairs with migratory divides are more likely to remain reproductively isolated, even when differing little in other phenotypic traits. These findings suggest that migratory differences may be one among several isolating barriers that prevent divergent populations from fusing and thereby increase the likelihood that they will continue differentiating as distinct species.

  2. Developmental rate: A unifying mechanism for sympatric divergence in postglacial fishes?

    Institute of Scientific and Technical Information of China (English)

    Megan V. MCPHEE; David L. G. NOAKES; Fred W. ALLENDORF

    2012-01-01

    Morphologically divergent ecotypes arise in fish populations on postglacial time scales,and resource polymorphisms are often invoked to explain their origin.However,genetic recombination can constrain the ability of divergent selection to produce reproductive isolation in sympatry.Recombination breaks up favorable combinations of traits (”adaptive suites”) if individual traits are affected by different loci.Recombination also breaks up any association between traits under divergent selection and traits contributing to reproductive isolation.Thus,ecological speciation in the absence of preexisting barriers to gene flow is more likely when pleiotropy minimizes the number of loci involved.Here,we revisit research conducted by Carl Hubbs in the early 1900s on the effects of developmental rate on morphological traits in fishes.Hubbs' work provides a mechanism to explain how sympatric divergence by trophic polymorphism can occur despite the challenges of recombination.We consider the implications of Hubbs' observations for ecological speciation with gene flow in fishes,as well as rapid evolution in captive fish populations [Current Zoology 58 (1):21-34,2012].

  3. Fauna anofélica da cidade de Belém, Pará, Brasil: dados atuais e retrospectivos Anophelines in Belém, Pará, Brazil: current and retrospective data

    Directory of Open Access Journals (Sweden)

    Ana de Nazaré Martins da Silva

    2006-08-01

    Full Text Available Relato de coletas de anofelinos realizadas em Belém, Pará, Brasil, de 1995 a 2004, comparando os dados obtidos com os de levantamentos anteriores, feitos a partir da década de 1930. Nesses, vinte espécies haviam sido identificadas: Anopheles albitarsis s.l., An. aquasalis, An. argyritarsis, An. braziliensis, An. darlingi, An. eiseni, An. evansae, An. galvaoi, An. intermedius, An. kompi, An. mediopunctatus, An. nimbus, An. nuneztovari, An. oswaldoi, An. peryassui, An. punctimacula, An. shannoni, An. strodei, An. thomasi e An. triannulatus. Sete (An. argyritarsis, An. eiseni, An. galvaoi, An. kompi, An. nimbus, An. punctimacula e An. thomasi não são agora registradas. A permanência de tantas outras espécies provavelmente decorre da preservação de áreas de mata no âmbito urbano. Duas delas são consideradas de importância vetorial (An. darlingi e An. aquasalis. Esta última continua sendo a de maior densidade nas coletas (46,26% dos adultos e 99,21% das larvas e é a única registrada em todos os distritos administrativos. Existe, portanto, risco potencial de transmissão de malária em todo o município.We present the results of anopheline captures in Belém, Pará, Brazil, from 1995-2004, and a comparison with captures from 1930-1999. In the earlier period, 20 species were identified: Anopheles albitarsis s.l., An. aquasalis, An. argyritarsis, An. braziliensis, An. darlingi, An. eiseni, An. evansae, An. galvaoi, An. intermedius, An. kompi, An. mediopunctatus, An. nimbus, An. nuneztovari, An. oswaldoi, An. peryassui, An. punctimacula, An. shannoni, An. strodei, An. thomasi, and An. triannulatus. Seven of these species were not found in 1995-2004 (An. argyritarsis, An. eiseni, An. galvaoi, An. kompi, An. nimbus, An. punctimacula, and An. thomasi. The persistence of so many species is probably due to the local preservation of forest areas. Two species are of vectorial importance (An. darlingi and An. aquasalis. An. aquasalis is still

  4. Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae).

    Science.gov (United States)

    Jackson, Jennifer A; Steel, Debbie J; Beerli, P; Congdon, Bradley C; Olavarría, Carlos; Leslie, Matthew S; Pomilla, Cristina; Rosenbaum, Howard; Baker, C Scott

    2014-07-07

    Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies.

  5. Event-Driven Contrastive Divergence for Spiking Neuromorphic Systems

    Directory of Open Access Journals (Sweden)

    Emre eNeftci

    2014-01-01

    Full Text Available Restricted Boltzmann Machines (RBMs and Deep Belief Networks have been demonstrated to perform efficiently in variety of applications, such as dimensionality reduction, feature learning, and classification. Their implementation on neuromorphic hardware platforms emulating large-scale networks of spiking neurons can have significant advantages from the perspectives of scalability, power dissipation and real-time interfacing with the environment. However the traditional RBM architecture and the commonly used training algorithm known as Contrastive Divergence (CD are based on discrete updates and exact arithmetics which do not directly map onto a dynamical neural substrate. Here, we present an event-driven variation of CD to train a RBM constructed with Integrate & Fire (I&F neurons, that is constrained by the limitations of existing and near future neuromorphic hardware platforms. Our strategy is based on neural sampling, which allows us to synthesize a spiking neural network that samples from a target Boltzmann distribution. The reverberating activity of the network replaces the discrete steps of the CD algorithm, while Spike Time Dependent Plasticity (STDP carries out the weight updates in an online, asynchronous fashion.We demonstrate our approach by training an RBM composed of leaky I&F neurons with STDP synapses to learn a generative model of the MNIST hand-written digit dataset, and by testing it in recognition, generation and cue integration tasks. Our results contribute to a machine learning-driven approach for synthesizing networks of spiking neurons capable of carrying out practical, high-level functionality.

  6. Divergence compensation for hardware-in-the-loop simulation of stiffness-varying discrete contact in space

    Science.gov (United States)

    Qi, Chenkun; Zhao, Xianchao; Gao, Feng; Ren, Anye; Hu, Yan

    2016-11-01

    The hardware-in-the-loop (HIL) contact simulation for flying objects in space is challenging due to the divergence caused by the time delay. In this study, a divergence compensation approach is proposed for the stiffness-varying discrete contact. The dynamic response delay of the motion simulator and the force measurement delay are considered. For the force measurement delay, a phase lead based force compensation approach is used. For the dynamic response delay of the motion simulator, a response error based force compensation approach is used, where the compensation force is obtained from the real-time identified contact stiffness and real-time measured position response error. The dynamic response model of the motion simulator is not required. The simulations and experiments show that the simulation divergence can be compensated effectively and satisfactorily by using the proposed approach.

  7. Metric Divergence Measures and Information Value in Credit Scoring

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    Guoping Zeng

    2013-01-01

    Full Text Available Recently, a series of divergence measures have emerged from information theory and statistics and numerous inequalities have been established among them. However, none of them are a metric in topology. In this paper, we propose a class of metric divergence measures, namely, , and study their mathematical properties. We then study an important divergence measure widely used in credit scoring, called information value. In particular, we explore the mathematical reasoning of weight of evidence and suggest a better alternative to weight of evidence. Finally, we propose using as alternatives to information value to overcome its disadvantages.

  8. Human exposure to anopheline mosquitoes occurs primarily indoors, even for users of insecticide-treated nets in Luangwa Valley, South-east Zambia

    Directory of Open Access Journals (Sweden)

    Seyoum Aklilu

    2012-05-01

    Full Text Available Abstract Background Current front line malaria vector control methods such as indoor residual spraying (IRS and long-lasting insecticidal nets (LLINs, rely upon the preference of many primary vectors to feed and/or rest inside human habitations where they can be targeted with domestically-applied insecticidal products. We studied the human biting behaviour of the malaria vector Anopheles funestus Giles and the potential malaria vector Anopheles quadriannulatus Theobald in Luangwa valley, south-east Zambia. Methods Mosquitoes were collected by human landing catch in blocks of houses with either combined use of deltamethrin-based IRS and LLINs or LLINs alone. Human behaviour data were collected to estimate how much exposure to mosquito bites indoors and outdoors occurred at various times of the night for LLIN users and non-users. Results Anopheles funestus and An. quadriannulatus did not show preference to bite either indoors or outdoors: the proportions [95% confidence interval] caught indoors were 0.586 [0.303, 0.821] and 0.624 [0.324, 0.852], respectively. However, the overwhelming majority of both species were caught at times when most people are indoors. The proportion of mosquitoes caught at a time when most people are indoors were 0.981 [0.881, 0.997] and 0.897 [0.731, 0.965], respectively, so the proportion of human exposure to both species occuring indoors was high for individuals lacking LLINs (An. funestus: 0.983 and An. quadriannulatus: 0.970, respectively. While LLIN users were better protected, more than half of their exposure was nevertheless estimated to occur indoors (An. funestus: 0.570 and An. quadriannulatus: 0.584. Conclusions The proportion of human exposure to both An. funestus and An. quadriannulatus occuring indoors was high in the area and hence both species might be responsive to further peri-domestic measures if these mosquitoes are susceptible to insecticidal products.

  9. Orbital Divergence and Relaxation in the Gravitational N-Body Problem

    CERN Document Server

    Hut, P

    2001-01-01

    One of the fundamental aspects of statistical behaviour in many-body systems is exponential divergence of neighbouring orbits, which is often discussed in terms of Liapounov exponents. Here we study this topic for the classical gravitational N-body problem. The application we have in mind is to old stellar systems such as globular star clusters, where N~10^6, and so we concentrate on spherical, centrally concentrated systems with total energy E<0. Hitherto no connection has been made between the time scale for divergence (denoted here by t_e) and the two-body relaxation time scale (t_r), even though both may be calculated by consideration of two-body encounters. In this paper we give a simplified model showing that divergence in phase space is initially roughly exponential, on a timescale proportional to the crossing time (defined as a mean time for a star to cross from one side of the system to another). In this phase t_e is much less than t_r, if N is not too small (i.e. N is much more than about 30). Af...

  10. Statistical properties of the maximum Lyapunov exponent calculated via the divergence rate method.

    Science.gov (United States)

    Franchi, Matteo; Ricci, Leonardo

    2014-12-01

    The embedding of a time series provides a basic tool to analyze dynamical properties of the underlying chaotic system. To this purpose, the choice of the embedding dimension and lag is crucial. Although several methods have been devised to tackle the issue of the optimal setting of these parameters, a conclusive criterion to make the most appropriate choice is still lacking. An accepted procedure to rank different embedding methods relies on the evaluation of the maximum Lyapunov exponent (MLE) out of embedded time series that are generated by chaotic systems with explicit analytic representation. The MLE is evaluated as the local divergence rate of nearby trajectories. Given a system, embedding methods are ranked according to how close such MLE values are to the true MLE. This is provided by the so-called standard method in a way that exploits the mathematical description of the system and does not require embedding. In this paper we study the dependence of the finite-time MLE evaluated via the divergence rate method on the embedding dimension and lag in the case of time series generated by four systems that are widely used as references in the scientific literature. We develop a completely automatic algorithm that provides the divergence rate and its statistical uncertainty. We show that the uncertainty can provide useful information about the optimal choice of the embedding parameters. In addition, our approach allows us to find which systems provide suitable benchmarks for the comparison and ranking of different embedding methods.

  11. Divergence of East Asians and Europeans estimated using male- and female-specific genetic markers.

    Science.gov (United States)

    Tateno, Yoshio; Komiyama, Tomoyoshi; Katoh, Toru; Munkhbat, Batmunkh; Oka, Akira; Haida, Yuko; Kobayashi, Hiroyuki; Tamiya, Gen; Inoko, Hidetoshi

    2014-03-01

    To study the male and female lineages of East Asian and European humans, we have sequenced 25 short tandem repeat markers on 453 Y-chromosomes and collected sequences of 72 complete mitochondrial genomes to construct independent phylogenetic trees for male and female lineages. The results indicate that East Asian individuals fall into two clades, one that includes East Asian individuals only and a second that contains East Asian and European individuals. Surprisingly, the European individuals did not form an independent clade, but branched within in the East Asians. We then estimated the divergence time of the root of the European clade as ∼ 41,000 years ago. These data indicate that, contrary to traditional views, Europeans diverged from East Asians around that time. We also address the origin of the Ainu lineage in northern Japan.

  12. Species divergence and phylogenetic variation of ecophysiological traits in lianas and trees.

    Directory of Open Access Journals (Sweden)

    Rodrigo S Rios

    Full Text Available The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [A(max], dark respiration rate [R(d], and specific leaf area [SLA] are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that R(d evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species, and trees were more related than expected by chance (phylogenetic clustering across 71 species. Lianas showed evenness for R(d, while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. R(d followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for A(max. R(d may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades.

  13. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

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    Logue Kyle

    2013-02-01

    Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

  14. Attack Vulnerability of Network with Duplication-Divergence Mechanism

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We study the attack vulnerability of network with duplication-divergence mechanism. Numerical results have shown that the duplication-divergence network with larger retention probability a is more robust against target attack relatively. Furthermore, duplication-divergence network is broken down more quickly than its counterpart BA network under target attack. Such result is consistent with the fact of WWW and Internet networks under target attack. So duplication-divergence model is a more realistic one for us to investigate the characteristics of the world wide web in future. We also observe that the exponent 7 of degree distribution and average degree are important parameters of networks, reflecting the performance of networks under target attack. Our results are helpful to the research on the security of network.

  15. Multiple solutions for possibly degenerate equations in divergence form

    Directory of Open Access Journals (Sweden)

    Andrea Pinamonti

    2016-08-01

    Full Text Available Via variational methods, we establish the existence of at least two distinct weak solutions for the Dirichlet problem associated to a possibly degenerate equation in divergence form.

  16. Role of mantle flow in Nubia-Somalia plate divergence

    Science.gov (United States)

    Stamps, D. S.; Iaffaldano, G.; Calais, E.

    2015-01-01

    Present-day continental extension along the East African Rift System (EARS) has often been attributed to diverging sublithospheric mantle flow associated with the African Superplume. This implies a degree of viscous coupling between mantle and lithosphere that remains poorly constrained. Recent advances in estimating present-day opening rates along the EARS from geodesy offer an opportunity to address this issue with geodynamic modeling of the mantle-lithosphere system. Here we use numerical models of the global mantle-plates coupled system to test the role of present-day mantle flow in Nubia-Somalia plate divergence across the EARS. The scenario yielding the best fit to geodetic observations is one where torques associated with gradients of gravitational potential energy stored in the African highlands are resisted by weak continental faults and mantle basal drag. These results suggest that shear tractions from diverging mantle flow play a minor role in present-day Nubia-Somalia divergence.

  17. Scalar Field Quantization Without Divergences In All Spacetime Dimensions

    CERN Document Server

    Klauder, John R

    2011-01-01

    Covariant, self-interacting scalar quantum field theories admit solutions for low enough spacetime dimensions, but when additional divergences appear in higher dimensions, the traditional approach leads to results, such as triviality, that are less than satisfactory. Guided by idealized but soluble nonrenormalizable models, a nontraditional proposal for the quantization of covariant scalar field theories is advanced, which achieves a term-by-term, divergence-free, perturbation analysis of interacting models expanded about a suitable pseudofree theory, which differs from a free theory by an O(\\hbar^2) counterterm. These positive features are secured within a functional integral formulation by a local, nonclassical, counterterm that effectively transforms parameter changes in the action from generating mutually singular measures, which are the basis for divergences, to equivalent measures, thereby removing all divergences. The use of an alternative model about which to perturb is already supported by properties...

  18. Acoustic propagation in partially choked converging-diverging ducts

    Science.gov (United States)

    Kelly, J. J.; Nayfeh, A. H.; Watson, L. T.

    1982-01-01

    A computer model based on the wave-envelope technique is used to study acoustic propagation in converging-diverging hard walled and lined circular ducts carrying near sonic mean flows. The influences of the liner admittance, boundary layer thickness, spinning mode number, and mean Mach number are considered. The numerical results indicate that the diverging portion of the duct can have a strong reflective effect for partially choked flows.

  19. Numerical Optimization of converging diverging miniature cavitating nozzles

    Science.gov (United States)

    Chavan, Kanchan; Bhingole, B.; Raut, J.; Pandit, A. B.

    2015-12-01

    The work focuses on the numerical optimization of converging diverging cavitating nozzles through nozzle dimensions and wall shape. The objective is to develop design rules for the geometry of cavitating nozzles for desired end-use. Two main aspects of nozzle design which affects the cavitation have been studied i.e. end dimensions of the geometry (i.e. angle and/or curvature of the inlet, outlet and the throat and the lengths of the converging and diverging sections) and wall curvatures(concave or convex). Angle of convergence at the inlet was found to control the cavity growth whereas angle of divergence of the exit controls the collapse of cavity. CFD simulations were carried out for the straight line converging and diverging sections by varying converging and diverging angles to study its effect on the collapse pressure generated by the cavity. Optimized geometry configurations were obtained on the basis of maximum Cavitational Efficacy Ratio (CER)i.e. cavity collapse pressure generated for a given permanent pressure drop across the system. With increasing capabilities in machining and fabrication, it is possible to exploit the effect of wall curvature to create nozzles with further increase in the CER. Effect of wall curvature has been studied for the straight, concave and convex shapes. Curvature has been varied and effect of concave and convex wall curvatures vis-à-vis straight walls studied for fixed converging and diverging angles.It is concluded that concave converging-diverging nozzles with converging angle of 20° and diverging angle of 5° with the radius of curvature 0.03 m and 0.1530 m respectively gives maximum CER. Preliminary experiments using optimized geometry are indicating similar trends and are currently being carried out. Refinements of the CFD technique using two phase flow simulations are planned.

  20. THE DIVERGENCE OF LAGRANGE INTERPOLATION IN EQUIDISTANT NODES

    Institute of Scientific and Technical Information of China (English)

    Lu Zhikang; Xia Mao

    2003-01-01

    It is a classical result of Bernstein that the sequence of Lagrange interpolation polynomials to | x | at equally spaced nodes in [- 1,1] diverges everywhere, except at zero and the end-points. In this paper we show that the sequence of Lagrange interpolation polynomials corresponding to the functions which possess better smoothness on equidistant nodes in [-1,1] still diverges every where in the interval except at zero and the end-points.

  1. Multimodal registration of remotely sensed images based on Jeffrey's divergence

    Science.gov (United States)

    Xu, Xiaocong; Li, Xia; Liu, Xiaoping; Shen, Huanfeng; Shi, Qian

    2016-12-01

    Entropy-based measures (e.g., mutual information, also known as Kullback-Leiber divergence), which quantify the similarity between two signals, are widely used as similarity measures for image registration. Although they are proven superior to many classical statistical measures, entropy-based measures, such as mutual information, may fail to yield the optimum registration if the multimodal image pair has insufficient scene overlap region. To overcome this challenge, we proposed using the symmetric form of Kullback-Leiber divergence, namely Jeffrey's divergence, as the similarity measure in practical multimodal image registration tasks. Mathematical analysis was performed to investigate the causes accounting for the limitation of mutual information when dealing with insufficient scene overlap image pairs. Experimental registrations of SPOT image, Landsat TM image, ALOS PalSAR image, and DEM data were carried out to compare the performance of Jeffrey's divergence and mutual information. Results indicate that Jeffrey's divergence is capable of providing larger feasible search space, which is favorable for exploring optimum transformation parameters in a larger range. This superiority of Jeffrey's divergence was further confirmed by a series of paradigms. Thus, the proposed model is more applicable for registering image pairs that are greatly misaligned or have an insufficient scene overlap region.

  2. MHC adaptive divergence between closely related and sympatric African cichlids.

    Directory of Open Access Journals (Sweden)

    Jonatan Blais

    Full Text Available BACKGROUND: The haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa. METHODOLOGY/PRINCIPAL FINDINGS: Divergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites. CONCLUSIONS/SIGNIFICANCE: We propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.

  3. Epigenetic divergence as a potential first step in darter speciation.

    Science.gov (United States)

    Smith, Tracy A; Martin, Michael D; Nguyen, Michael; Mendelson, Tamra C

    2016-04-01

    Recent studies show that epigenetic variation in the form of DNA methylation may serve as a substrate for selection. Theory suggests that heritable epigenetic marks that increase fitness should increase in frequency in a population, and these changes may result in novel morphology, behaviour, or physiology, and ultimately reproductive isolation. Therefore, epigenetic variation might provide the first substrate for selection during the course of evolutionary divergence. This hypothesis predicts that populations in the earliest stages of divergence will differentiate in their methylome prior to any genetic differentiation. While several studies have investigated natural epigenetic variation, empirical studies that test predictions about its role in speciation are surprisingly scarce. Here, we investigate DNA methylation variation using an isoschizomeric digest method, Methyl-Sensitive Amplified Polymorphism, across multiple stages of evolutionary divergence in natural populations of North American stream fishes. We show that epigenetic differentiation between methylomes is greater than genetic divergence among closely related populations across two river drainages. Additionally, we demonstrate that epigenetic divergence is a stronger predictor of the strength of behavioural reproductive isolation and suggest that changes in the methylome could influence the evolution of reproductive isolation between species. Our findings suggest a role for epigenetics not only in the initiation of divergence, but also in the maintenance of species boundaries over greater evolutionary timescales.

  4. The impact of pyrethroid resistance on the efficacy of insecticide-treated bed nets against African anopheline mosquitoes: systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Clare Strode

    2014-03-01

    Full Text Available Pyrethroid insecticide-treated bed nets (ITNs help contribute to reducing malaria deaths in Africa, but their efficacy is threatened by insecticide resistance in some malaria mosquito vectors. We therefore assessed the evidence that resistance is attenuating the effect of ITNs on entomological outcomes.We included laboratory and field studies of African malaria vectors that measured resistance at the time of the study and used World Health Organization-recommended impregnation regimens. We reported mosquito mortality, blood feeding, induced exophily (premature exit of mosquitoes from the hut, deterrence, time to 50% or 95% knock-down, and percentage knock-down at 60 min. Publications were searched from 1 January 1980 to 31 December 2013 using MEDLINE, Cochrane Central Register of Controlled Trials, Science Citation Index Expanded, Social Sciences Citation Index, African Index Medicus, and CAB Abstracts. We stratified studies into three levels of insecticide resistance, and ITNs were compared with untreated bed nets (UTNs using the risk difference (RD. Heterogeneity was explored visually and statistically. Included were 36 laboratory and 24 field studies, reported in 25 records. Studies tested and reported resistance inconsistently. Based on the meta-analytic results, the difference in mosquito mortality risk for ITNs compared to UTNs was lower in higher resistance categories. However, mortality risk was significantly higher for ITNs compared to UTNs regardless of resistance. For cone tests: low resistance, risk difference (RD 0.86 (95% CI 0.72 to 1.01; moderate resistance, RD 0.71 (95% CI 0.53 to 0.88; high resistance, RD 0.56 (95% CI 0.17 to 0.95. For tunnel tests: low resistance, RD 0.74 (95% CI 0.61 to 0.87; moderate resistance, RD 0.50 (95% CI 0.40 to 0.60; high resistance, RD 0.39 (95% CI 0.24 to 0.54. For hut studies: low resistance, RD 0.56 (95% CI 0.43 to 0.68; moderate resistance, RD 0.39 (95% CI 0.16 to 0.61; high resistance, RD 0

  5. Reticulation, divergence, and the phylogeography-phylogenetics continuum.

    Science.gov (United States)

    Edwards, Scott V; Potter, Sally; Schmitt, C Jonathan; Bragg, Jason G; Moritz, Craig

    2016-07-19

    Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.

  6. The Kalash genetic isolate: ancient divergence, drift, and selection.

    Science.gov (United States)

    Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

    2015-05-01

    The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319-2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600-12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.

  7. A Robust volume conservative divergence-free ISPH framework for free-surface flow problems

    Science.gov (United States)

    Pahar, Gourabananda; Dhar, Anirban

    2016-10-01

    This study presents a Volume Conservative approach for resolving volume conservation issue in divergence-free incompressible Smoothed Particle Hydrodynamics (ISPH). Irregular free surface deformation may introduce error in volume computation, which has a cascading effect over time. Proposed correction decreases this numerical compressibility to a minimal value. The correction is obtained directly by solving Navier-Stokes momentum equation. Consequently, the framework does not require any parametric study for mixed source/sink term or iterative solution of pressure Poisson equations. The correction is implemented on four different types of flow: (a) pressurized flow in a closed box, (b) dambreak flow, (c) flow through porous block, (d) lock-exchange flow of immiscible fluids (both free-surface and pressurized flow). All four scenarios are shown to have minimal error compared to pure divergence-free ISPH.

  8. Divergent and dynamic activity of endogenous retroviruses in burn patients and their inflammatory potential.

    Science.gov (United States)

    Lee, Kang-Hoon; Rah, HyungChul; Green, Tajia; Lee, Young-Kwan; Lim, Debora; Nemzek, Jean; Wahl, Wendy; Greenhalgh, David; Cho, Kiho

    2014-04-01

    Genes constitute ~3% of the human genome, whereas human endogenous retroviruses (HERVs) represent ~8%. We examined post-burn HERV expression in patients' blood cells, and the inflammatory potentials of the burn-associated HERVs were evaluated. Buffy coat cells, collected at various time points from 11 patients, were screened for the expression of eight HERV families, and we identified their divergent expression profiles depending on patient, HERV, and time point. The population of expressed HERV sequences was patient-specific, suggesting HERVs' inherent genomic polymorphisms and/or differential expression potentials depending on characteristics of patients and courses of injury response. Some HERVs were shared among the patients, while the others were divergent. Interestingly, one burn-associated HERV gag gene from a patient's genome induced IL-6, IL-1β, Ptgs-2, and iNOS. These findings demonstrate that injury stressors initiate divergent HERV responses depending on patient, HERV, and disease course and implicate HERVs as genetic elements contributing to polymorphic injury pathophysiology.

  9. Concrete ensemble Kalman filters with rigorous catastrophic filter divergence.

    Science.gov (United States)

    Kelly, David; Majda, Andrew J; Tong, Xin T

    2015-08-25

    The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature.

  10. Expression Divergence of Tandemly Arrayed Genes in Human and Mouse

    Directory of Open Access Journals (Sweden)

    Valia Shoja

    2007-01-01

    Full Text Available Tandemly arrayed genes (TAGs account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.

  11. Sandwiched Rényi divergence satisfies data processing inequality

    Energy Technology Data Exchange (ETDEWEB)

    Beigi, Salman [School of Mathematics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5746, Tehran (Iran, Islamic Republic of)

    2013-12-15

    Sandwiched (quantum) α-Rényi divergence has been recently defined in the independent works of Wilde et al. [“Strong converse for the classical capacity of entanglement-breaking channels,” preprint http://arxiv.org/abs/arXiv:1306.1586 (2013)] and Müller-Lennert et al. [“On quantum Rényi entropies: a new definition, some properties and several conjectures,” preprint http://arxiv.org/abs/arXiv:1306.3142v1 (2013)]. This new quantum divergence has already found applications in quantum information theory. Here we further investigate properties of this new quantum divergence. In particular, we show that sandwiched α-Rényi divergence satisfies the data processing inequality for all values of α > 1. Moreover we prove that α-Holevo information, a variant of Holevo information defined in terms of sandwiched α-Rényi divergence, is super-additive. Our results are based on Hölder's inequality, the Riesz-Thorin theorem and ideas from the theory of complex interpolation. We also employ Sion's minimax theorem.

  12. Scalar field quantization without divergences in all spacetime dimensions

    Science.gov (United States)

    Klauder, John R.

    2011-07-01

    Covariant, self-interacting scalar quantum field theories admit solutions for low enough spacetime dimensions, but when additional divergences appear in higher dimensions, the traditional approach leads to results, such as triviality, that are less than satisfactory. Guided by idealized but soluble nonrenormalizable models, a nontraditional proposal for the quantization of covariant scalar field theories is advanced, which achieves a term-by-term, divergence-free, perturbation analysis of interacting models expanded about a suitable pseudofree theory, which differs from a free theory by an O(planck2) counterterm. These positive features are realized within a functional integral formulation by a local, nonclassical, counterterm that effectively transforms parameter changes in the action from generating mutually singular measures, which are the basis for divergences, to equivalent measures, thereby removing all divergences. The use of an alternative model about which to perturb is already supported by properties of the classical theory and is allowed by the inherent ambiguity in the quantization process itself. This procedure not only provides acceptable solutions for models for which no acceptable, faithful solution currently exists, e.g. phiv4n, for spacetime dimensions n >= 4, but offers a new, divergence-free solution for less-singular models as well, e.g. phiv4n, for n = 2, 3. Our analysis implies similar properties for multicomponent scalar models, such as those associated with the Higgs model.

  13. Rotational and divergent kinetic energy in the mesoscale model ALADIN

    Directory of Open Access Journals (Sweden)

    V. Blažica

    2013-03-01

    Full Text Available Kinetic energy spectra from the mesoscale numerical weather prediction (NWP model ALADIN with horizontal resolution 4.4 km are split into divergent and rotational components which are then compared at horizontal scales below 300 km and various vertical levels. It is shown that about 50% of kinetic energy in the free troposphere in ALADIN is divergent energy. The percentage increases towards 70% near the surface and in the upper troposphere towards 100 hPa. The maximal percentage of divergent energy is found at stratospheric levels around 100 hPa and at scales below 100 km which are not represented by the global models. At all levels, the divergent energy spectra are characterised by shallower slopes than the rotational energy spectra, and the difference increases as horizontal scales become larger. A very similar vertical distribution of divergent energy is obtained by using the standard ALADIN approach for the computation of spectra based on the extension zone and by applying detrending approach commonly used in mesoscale NWP community.

  14. Concrete ensemble Kalman filters with rigorous catastrophic filter divergence

    Science.gov (United States)

    Kelly, David; Majda, Andrew J.; Tong, Xin T.

    2015-01-01

    The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature. PMID:26261335

  15. A New Measure of Fuzzy Directed Divergence and Its Application in Image Segmentation

    Directory of Open Access Journals (Sweden)

    P.K Bhatia

    2013-03-01

    Full Text Available An approach to develop new measures of fuzzy directed divergence is proposed here. A new measure of fuzzy directed divergence is proposed, and some mathematical properties of this measure are proved. The application of fuzzy directed divergence in image segmentation is explained. The proposed technique minimizes the fuzzy divergence or the separation between the actual and ideal thresholded image.

  16. Individual Differences and Age-Related Changes in Divergent Thinking in Toddlers and Preschoolers

    Science.gov (United States)

    Bijvoet-van den Berg, Simone; Hoicka, Elena

    2014-01-01

    Divergent thinking shows the ability to search for new ideas, which is an important factor contributing to innovation and problem solving. Current divergent thinking tests allow researchers to study children's divergent thinking from the age of 3 years on. This article presents the first measure of divergent thinking that can be used with children…

  17. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings.

    Science.gov (United States)

    Carling, Matt D; Brumfield, Robb T

    2008-01-01

    Phylogenetic and population genetic analyses of DNA sequence data from 10 nuclear loci were used to test species divergence hypotheses within Passerina buntings, with special focus on a strongly supported, but controversial, sister relationship between Passerina amoena and P. caerulea inferred from a previous mitochondrial study. Here, a maximum-likelihood analysis of a concatenated 10-locus data set, as well as minimize-deep-coalescences and maximum-likelihood analyses of the locus-specific gene trees, recovered the traditional sister relationship between P. amoena and P. cyanea. In addition, a more recent divergence time estimate between P. amoena and P. cyanea than between P. amoena and P. caerulea provided evidence for the traditional sister relationship. These results provide a compelling example of how lineage sorting stochasticity can lead to incongruence between gene trees and species trees, and illustrate how phylogenetic and population genetic analyses can be integrated to investigate evolutionary relationships between recently diverged taxa.

  18. Effects of microchannel geometry on preconcentration intensity in microfluidic chips with straight or convergent-divergent microchannels.

    Science.gov (United States)

    Chen, Chia-Lin; Yang, Ruey-Jen

    2012-03-01

    Preconcentration microfluidic devices are fabricated incorporating straight or convergent-divergent microchannels and hydrogel or Nafion membranes. Sample preconcentration is achieved utilizing concentration-polarization effects. The effects of the microchannel geometry on the preconcentration intensity are systematically examined. It is shown that for the preconcentrator with the straight microchannel, the time required to achieve a satisfactory preconcentration intensity increases with an increasing channel depth. For the convergent-divergent microchannel, the preconcentration intensity increases with a reducing convergent channel width. Comparing the preconcentration performance of the two different microchannel configurations, it is found that for an equivalent width of the main microchannel, the concentration effect in the convergent-divergent microchannel is faster than that in the straight microchannel.

  19. Theoretical analysis of some problems in the measurement of beam divergence angle for EAST neutral beam injector

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Beam angular divergence is one of the indicators to evaluate the beam quality. Operating parameters of the beam extraction system could be adjusted to gain better beam quality following the measurement results, which will be helpful not only to study the transmission characteristics of the beam and the power distribution on the heat load components, but also to understand the real-time working condition of the ion source and beam extraction system. This study includes: (1) the theoretical analysis of beam extraction pulse duration for measurement of beam angular divergence; (2) the theoretical analysis of beam intensity distribution during beam transmission for Experimental Advanced Superconducting Tokomak (EAST) neutral beam injector. Those theoretical analyses could point the way to the measurement of beam divergence angle for EAST neutral beam injector.

  20. Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures

    NARCIS (Netherlands)

    Kusters, E.; Della Pina, S.; Castel, R.; Souer, E.; Koes, R.

    2015-01-01

    Higher plant species diverged extensively with regard to the moment (flowering time) and position (inflorescence architecture) at which flowers are formed. This seems largely caused by variation in the expression patterns of conserved genes that specify floral meristem identity (FMI), rather than ch

  1. A genomic island linked to ecotype divergence in Atlantic cod

    DEFF Research Database (Denmark)

    Hansen, Jakob Hemmer; Eg Nielsen, Einar; Therkildsen, Nina O.;

    2013-01-01

    gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two......The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced....... Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high...

  2. Android Malware Detection Using Kullback-Leibler Divergence

    Directory of Open Access Journals (Sweden)

    Vanessa N. COOPER

    2015-03-01

    Full Text Available Many recent reports suggest that mareware applications cause high billing to victims by sending and receiving hidden SMS messages. Given that, there is a need to develop necessary technique to identify malicious SMS operations as well as differentiate between good and bad SMS operations within applications.In this paper, we apply Kullback-Leibler Divergence (KLD as a distance metric to identify the difference between good and bad SMS operations. We develop a set of elements that represent sending or receiving of SMS messages, both legitimately and maliciously. Then, we compare the divergence of the trained set of elements. Our evaluation shows that the divergence between good and bad applications remains significantly high, whereas between two applications performing the same SMS operations remain low. We evaluate the proposed KLD-based concept for identifying a set of malware applications. The initial results show that our approach can identify all known malware and has less false positive warning.

  3. To be liked versus respected: Divergent goals in interracial interactions.

    Science.gov (United States)

    Bergsieker, Hilary B; Shelton, J Nicole; Richeson, Jennifer A

    2010-08-01

    Pervasive representations of Blacks and Latinos as unintelligent and of Whites as racist may give rise to divergent impression management goals in interracial interactions. We present studies showing that in interracial interactions racial minorities seek to be respected and seen as competent more than Whites do, whereas Whites seek to be liked and seen as moral more than racial minorities do. These divergent impression management goals are reflected in Whites' and racial minorities' self-report responses (Studies 1a, 1b, 2, and 4) and behaviors (Studies 3a and 3b). Divergent goals are observed in pre-existing relationships (Study 2), as well as in live interactions (Studies 3a, 3b, and 4), and are associated with higher levels of negative other-directed affect (Study 4). Implications of these goals for interracial communication and misunderstandings are discussed.

  4. Ice flux divergence anomalies on 79north Glacier, Greenland

    DEFF Research Database (Denmark)

    Seroussi, H.; Morlighem, M.; Rignot, E.;

    2011-01-01

    The ice flux divergence of a glacier is an important quantity to examine because it determines the rate of temporal change of its thickness. Here, we combine high-resolution ice surface velocity observations of Nioghalvfjerdsfjorden (79north) Glacier, a major outlet glacier in north Greenland......, with a dense grid of ice thickness data collected with an airborne radar sounder in 1998, to examine its ice flux divergence. We detect large variations, up to 100 m/yr, in flux divergence on grounded ice that are incompatible with what we know of the glacier surface mass balance, basal mass balance...... onto a regular grid using a scheme (here block kriging) that does not conserve mass or ice flux. This problem is not unique to 79north Glacier but is common to all conventional ice thickness surveys of glaciers and ice sheets; and fundamentally limits the application of ice thickness grids to high...

  5. Noise Characteristics of Overexpanded Jets from Convergent-Divergent Nozzles

    Science.gov (United States)

    Zaman, K. B. M. Q.

    2008-01-01

    A broadband noise component occurring in the overexpanded flow regime with convergent-divergent nozzles is identified. Relative to a convergent nozzle, at same pressure ratios, this excess noise can lead to a large increase in the overall sound pressure levels. Several features distinguish it from the more familiar broadband shock associated noise. Unlike the latter, it is observed even at shallow polar locations and there is no noticeable shift of the spectral content in frequency with observation angle. The amplitudes are found to be more pronounced with nozzles having larger half-angle of the divergent section. The noise apparently occurs when a shock resides within the divergent section of the nozzle and results from random unsteady motion of the shock.

  6. Summation of Divergent Power Series by Means of Factorial Series

    CERN Document Server

    Weniger, Ernst Joachim

    2010-01-01

    Factorial series played a major role in Stirling's classic book "Methodus Differentialis" (1730), but now only a few specialists still use them. This article wants to show that this neglect is unjustified, and that factorial series are useful numerical tools for the summation of divergent (inverse) power series. This is documented by summing the divergent asymptotic expansion for the exponential integral $E_{1} (z)$ and the factorially divergent Rayleigh-Schr\\"{o}dinger perturbation expansion for the quartic anharmonic oscillator. Stirling numbers play a key role since they occur as coefficients in expansions of an inverse power in terms of inverse Pochhammer symbols and vice versa. It is shown that the relationships involving Stirling numbers are special cases of more general orthogonal and triangular transformations.

  7. Divergent Effects of Dendritic Cells on Pancreatitis

    Science.gov (United States)

    2015-09-01

    cells, Gr1+ inflammatory monocytes and neutrophils, or TNF production were induced to develop chronic pancreatitis in the context of DC overexpansion...Z. Yao, W. Cao, and Y.J. Liu. 2005. TSLP-activated dendritic cells induce an inflammatory T helper type 2 cell response through OX40 ligand. J. Exp...Public reporting burden for this collection of information is estimated to average 1 hour per response , including the time for reviewing instructions

  8. Diverging responses of tropical Andean biomes under future climate conditions.

    Science.gov (United States)

    Tovar, Carolina; Arnillas, Carlos Alberto; Cuesta, Francisco; Buytaert, Wouter

    2013-01-01

    Observations and projections for mountain regions show a strong tendency towards upslope displacement of their biomes under future climate conditions. Because of their climatic and topographic heterogeneity, a more complex response is expected for biodiversity hotspots such as tropical mountain regions. This study analyzes potential changes in the distribution of biomes in the Tropical Andes and identifies target areas for conservation. Biome distribution models were developed using logistic regressions. These models were then coupled to an ensemble of 8 global climate models to project future distribution of the Andean biomes and their uncertainties. We analysed projected changes in extent and elevational range and identified regions most prone to change. Our results show a heterogeneous response to climate change. Although the wetter biomes exhibit an upslope displacement of both the upper and the lower boundaries as expected, most dry biomes tend to show downslope expansion. Despite important losses being projected for several biomes, projections suggest that between 74.8% and 83.1% of the current total Tropical Andes will remain stable, depending on the emission scenario and time horizon. Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure. For the remaining area (13.1%-17.4%), there is no agreement between model projections. These results challenge the common believe that climate change will lead to an upslope displacement of biome boundaries in mountain regions. Instead, our models project diverging responses, including downslope expansion and large areas projected to remain stable. Lastly, a significant part of the area expected to change is already affected by land use changes, which has important implications for management. This, and the inclusion of a comprehensive uncertainty analysis, will help to inform conservation strategies in the Tropical Andes, and to guide similar assessments for other

  9. Diverging Responses of Tropical Andean Biomes under Future Climate Conditions

    Science.gov (United States)

    Tovar, Carolina; Arnillas, Carlos Alberto; Cuesta, Francisco; Buytaert, Wouter

    2013-01-01

    Observations and projections for mountain regions show a strong tendency towards upslope displacement of their biomes under future climate conditions. Because of their climatic and topographic heterogeneity, a more complex response is expected for biodiversity hotspots such as tropical mountain regions. This study analyzes potential changes in the distribution of biomes in the Tropical Andes and identifies target areas for conservation. Biome distribution models were developed using logistic regressions. These models were then coupled to an ensemble of 8 global climate models to project future distribution of the Andean biomes and their uncertainties. We analysed projected changes in extent and elevational range and identified regions most prone to change. Our results show a heterogeneous response to climate change. Although the wetter biomes exhibit an upslope displacement of both the upper and the lower boundaries as expected, most dry biomes tend to show downslope expansion. Despite important losses being projected for several biomes, projections suggest that between 74.8% and 83.1% of the current total Tropical Andes will remain stable, depending on the emission scenario and time horizon. Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure. For the remaining area (13.1%–17.4%), there is no agreement between model projections. These results challenge the common believe that climate change will lead to an upslope displacement of biome boundaries in mountain regions. Instead, our models project diverging responses, including downslope expansion and large areas projected to remain stable. Lastly, a significant part of the area expected to change is already affected by land use changes, which has important implications for management. This, and the inclusion of a comprehensive uncertainty analysis, will help to inform conservation strategies in the Tropical Andes, and to guide similar assessments for

  10. Evolution of Weighted Networks by Duplication-Divergence Mechanism

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-Guo; YAN Jia-Ren; LIU Zi-Ran; WANG Li

    2006-01-01

    @@ The duplication and divergence process is ubiquitous in nature and man-made networks. Motivated by the duplication-divergence mechanism which depicts the growth of protein networks, we propose a weighted network model in which topological evolution is coupled with weight dynamics. Large scale numerical results indicate that our model can naturally generate networks with power-law-like distributions of degree, strength and weight.The degree-strength correlation is illustrated as well. These properties are in agreement well with empirical data observed in real-world systems. Furthermore, by altering the retention probability σ, weighted, structured exponential networks are realized.

  11. [A novel metabolomic data scaling method based on K-L divergence].

    Science.gov (United States)

    Deng, Ling-Li; Cheng, Kian-Kai; Shen, Gui-Ping; Zhou, Ling; Liu, Xin-Zhuo; Dong, Ji-Yang; Chen, Zhong

    2014-10-01

    A new scaling method in the current study based on Kullback-Leibler (K-L) divergence is proposed for NMR metabolomic data. The proposed method (called K-L scaling) is a supervised scaling method as group information is incorporated in the scaling procedure. Notably, K-L divergence measures the difference between two different datasets by their probability distributions, it can be used for the analysis of data that either follows Gaussian or non-Gaussian distributions. In K-L scaling, all variables were first standardized to unit variance, then their variance was adjusted using Kullback-Leibler divergence to highlight the significant variables. K-L scaling can tell effectively the difference in spectral data points between two experimental groups, and then enhances the weights of biological-relevant variables, and at the same time reduces the weight of noise and uninformative variables. The developed method was applied to a H-NMR metabolomic dataset acquired from human urine. Analysis results of the dataset showed that this new scaling method is efficient in suppressing the contribution of noise in the resulting multivariate model In addition, it can increase the weights of important variables, and improve the interpretability and predictability of subsequent principal component regression (PCR) and partial least squares discriminant analysis (PLS-DA). Furthermore, the scaling method facilitated the identification of metabolic signatures. The current result suggested that the developed K-L scaling method may become a useful alternative for the preprocessing of NMR-based metabolomic data.

  12. Extraordinarily rapid life-history divergence between Cryptasterina sea star species.

    Science.gov (United States)

    Puritz, Jonathan B; Keever, Carson C; Addison, Jason A; Byrne, Maria; Hart, Michael W; Grosberg, Richard K; Toonen, Robert J

    2012-10-07

    Life history plays a critical role in governing microevolutionary processes such as gene flow and adaptation, as well as macroevolutionary processes such speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life-history differences between sister species of sea stars. Cryptasterina hystera has evolved a suite of derived life-history traits (including internal self-fertilization and brood protection) that differ from its sister species Cryptasterina pentagona, a gonochoric broadcast spawner. We show that these species have only been reproductively isolated for approximately 6000 years (95% highest posterior density of 905-22 628), and that this life-history change may be responsible for dramatic genetic consequences, including low nucleotide diversity, zero heterozygosity and no gene flow. The rapid divergence of these species rules out some mechanisms of isolation such as adaptation to microhabitats in sympatry, or slow divergence by genetic drift during prolonged isolation. We hypothesize that the large phenotypic differences between species relative to the short divergence time suggests that the life-history differences observed may be direct responses to disruptive selection between populations. We speculate that local environmental or demographic differences at the southern range margin are possible mechanisms of selection driving one of the fastest known marine speciation events.

  13. Using convergent and divergent tasks to improve writing and language learning motivation

    Directory of Open Access Journals (Sweden)

    Hamid Marashi

    2015-01-01

    Full Text Available This study was an attempt to investigate the comparative impact of convergent and divergent condition tasks on EFL learners’ writing and motivation. Sixty female intermediate EFL learners were selected from among a total number of 90 through their performance on a sample piloted PET and further homogenized in terms of their writing and motivation. Based on the results, the students were randomly assigned to two experimental groups with 30 participants in each. Both groups underwent the same amount of teaching time during 18 sessions of treatment which included using divergent tasks for the first group and convergent tasks for the second. A posttest (the writing section of another sample PET and Gardener’s Attitude and Motivation Test Battery (used also earlier for the homogenization were administered at the end of the treatment to both groups and their mean scores on the test were compared through independent samples t-tests. The results led to the rejection of the first null hypothesis, thereby demonstrating that the learners in the convergent group benefited significantly more than those in the divergent group in terms of improving their writing. The second null hypothesis was not rejected, however, meaning that the two treatments were not significantly different in terms of improving the learners’ motivation.

  14. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina).

    Science.gov (United States)

    McCormack, J E; Peterson, A T; Bonaccorso, E; Smith, T B

    2008-05-01

    The pine-oak woodlands of the Mexican highlands harbour significant biological diversity, yet little is known about the evolutionary history of organisms inhabiting this region. We assessed genetic and phenotypic differentiation in 482 individuals representing 27 populations of the Mexican jay (Aphelocoma ultramarina) - a widespread bird species of the Mexican highlands - to test whether populations in the central and northern Mexican sierras display discrete breaks between groups, which would be consistent with a role for the different mountain chains in divergence and speciation. We found abrupt breaks in mitochondrial DNA (mtDNA; ND2 and control region) delineating four major genetic groups found in the Sierra Madre Occidental, Sierra Madre Oriental, southern Central Plateau (Bajio), and Transvolcanic Belt. These mtDNA groups were largely corroborated by data from nuclear microsatellites and phenotypic data, except that clades from the Central Plateau and Sierra Madre Oriental showed clinal change in these data sets. Uncertainty about the mutation rate for our mitochondrial markers warrants considerable caution with regard to estimating divergence times, but the major genetic groups appear to have split before the most extreme period of glacial cycling that marked the last 0.7 million years and after Mexico's period of major mountain formation. The fact that some genetic breaks do not coincide with well-known geographic barriers suggests a role for ecology in divergence and speciation, and we discuss implications for taxonomy and conservation.

  15. Combustion characteristics of low concentration coal mine methane in divergent porous media burner

    Institute of Scientific and Technical Information of China (English)

    Lin Baiquan; Dai Huaming⇑; Wang Chaoqun; Li Qingzhao; Wang Ke; Zheng Yuanzhen

    2014-01-01

    Low-concentration methane (LCM) has been one of the biggest difficulties in using coal mine methane. And previous studies found that premixed combustion in porous media is an effective method of low cal-orific gas utilization. This paper studied the combustion of LCM in a divergent porous medium burner (DPMB) by using computational fluid dynamics (CFD), and investigated the effect of gas initial tempera-ture on combustion characteristic, the distribution of temperature and pollutant at different equivalence ratios in detail. Besides, the comparison of divergent and cylindrical burners was also performed in this paper. The results show that:the peak temperature in DPMB increases as the increasing of equivalence ratio, which is also suitable for the outlet NO discharge;the linear correlation is also discovered between peak temperature and equivalence ratios;NO emission at the initial temperature of 525 K is 5.64 times, larger than NO emission at the initial temperature of 300 K. Thus, it is preferable to balance the effect of thermal efficiency and environment simultaneously when determining the optimal initial temperature range. The working parameter limits of divergent burner are wider than that of cylindrical one which contributes to reducing the influence of LCM concentration and volume fluctuation on combustion.

  16. Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus

    Directory of Open Access Journals (Sweden)

    Gissi Carmela

    2007-02-01

    Full Text Available Abstract Background Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. Results We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. Conclusion Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.

  17. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    KAUST Repository

    Kuo, Dwight

    2010-07-23

    Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

  18. [Comparative analysis of spatial EEG organization on models of non-verbal divergent and convergent thinking].

    Science.gov (United States)

    Sviderskaia, N E; Antonov, A G; Butneva, L S

    2007-01-01

    Features of neurophysiological organization of two main thinking types playing different roles in creative processes, i.e., divergent and convergent were studied with participation of 30 right-handed male subjects at the age from 30 to 50 years. Two tests were presented: (1) creation of many visual images on the basis of two simple geometrical figures (the model of divergent thinking) and (2) classification of a figure element with one of the offered standard samples (convergent thinking). The number of created images or correctly classified elements for five minutes served a criterion of performance productivity. It was found that performance of the divergent test with high productivity (as compared to low productivity) was characterized by a greater increase in non-linear interactions between the cortical potentials, especially in the axis right frontal--left occipital areas. At the same time, under conditions of high productivity, the number of active narrow-frequency spectral-coherent EEG bands increased. The data confirm the notion of neurophysiological organization of creative processes, according to which creative processes require the intensification of retrieval operations (both conscious and unconscious), based on extensive interhemispheric interaction and involvement of a system of EEG coherent structures oscillating with different frequencies.

  19. Divergence of flowering genes in soybean

    Indian Academy of Sciences (India)

    Moon Young Kim; Jin Hee Shin; Yang Jae Kang; Sang Rea Shim; Suk-Ha Lee

    2012-11-01

    Soybean genome sequences were blasted with Arabidopsis thaliana regulatory genes involved in photoperiod-dependent flowering. This approach enabled the identification of 118 genes involved in the flowering pathway. Two genome sequences of cultivated (Williams 82) and wild (IT182932) soybeans were employed to survey functional DNA variations in the flowering-related homologs. Forty genes exhibiting nonsynonymous substitutions between G. max and G. soja were catalogued. In addition, 22 genes were found to co-localize with QTLs for six traits including flowering time, first flower, pod maturity, beginning of pod, reproductive period, and seed filling period. Among the genes overlapping the QTL regions, two LHY/CCA1 genes, GI and SFR6 contained amino acid changes. The recently duplicated sequence regions of the soybean genome were used as additional criteria for the speculation of the putative function of the homologs. Two duplicated regions showed redundancy of both flowering-related genes and QTLs. ID 12398025, which contains the homeologous regions between chr 7 and chr 16, was redundant for the LHY/CCA1 and SPA1 homologs and the QTLs. Retaining of the CRY1 gene and the pod maturity QTLs were observed in the duplicated region of ID 23546507 on chr 4 and chr 6. Functional DNA variation of the LHY/CCA1 gene (Glyma07g05410) was present in a counterpart of the duplicated region on chr 7, while the gene (Glyma16g01980) present in the other portion of the duplicated region on chr 16 did not show a functional sequence change. The gene list catalogued in this study provides primary insight for understanding the regulation of flowering time and maturity in soybean.

  20. Parallel and Divergent Interpreting in an Elementary School Classroom

    Science.gov (United States)

    Wolbers, Kimberly A.; Dimling, Lisa M.; Lawson, Heather R.; Golos, Debbie B.

    2012-01-01

    The study examined the extent to which a highly qualified interpreter remained parallel with or diverged from the original classroom discourse in her interpreting for a 3rd-grade deaf student in science, social studies, and resource room. The interpreter's signed and verbalized expressions were compared to the class participants' expressions for…

  1. Three dimensional simulations of viscous folding in diverging microchannels

    Science.gov (United States)

    Xu, Bingrui; Chergui, Jalel; Shin, Seungwon; Juric, Damir

    2016-11-01

    Three dimensional simulations on the viscous folding in diverging microchannels reported by Cubaud and Mason are performed using the parallel code BLUE for multi-phase flows. The more viscous liquid L1 is injected into the channel from the center inlet, and the less viscous liquid L2 from two side inlets. Liquid L1 takes the form of a thin filament due to hydrodynamic focusing in the long channel that leads to the diverging region. The thread then becomes unstable to a folding instability, due to the longitudinal compressive stress applied to it by the diverging flow of liquid L2. We performed a parameter study in which the flow rate ratio, the viscosity ratio, the Reynolds number, and the shape of the channel were varied relative to a reference model. In our simulations, the cross section of the thread produced by focusing is elliptical rather than circular. The initial folding axis can be either parallel or perpendicular to the narrow dimension of the chamber. In the former case, the folding slowly transforms via twisting to perpendicular folding, or it may remain parallel. The direction of folding onset is determined by the velocity profile and the elliptical shape of the thread cross section in the channel that feeds the diverging part of the cell.

  2. Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae).

    Science.gov (United States)

    Bayly, Michael J; Ladiges, Pauline Y

    2007-07-01

    The presence of divergent paralogues of nuclear ribosomal DNA, from the 18S-5.8S-26S cistron, is reported in members of Eucalyptus subg. Eucalyptus. These paralogues, which include non-functional pseudogenes, probably diverged prior to the differentiation of species groups in subg. Eucalyptus. When compared with presumably functional sequences, the pseudogenes show greater sequence variation between species, particularly in the 5.8S gene. They are also characterised by reduced GC content, associated with a reduced number of CpG and CpNpG methylation sites, and an increase in the inferred number of methylation-induced substitutions. Some pseudogenes also lack motifs that are usually conserved in plants, both in ITS1 and the 5.8S gene. Two main lineages of pseudogenes are identified, one isolated from a group of western Australian species, one from a group of eastern Australian species. It is not clear whether these two lineages of pseudogenes are orthologous, or represent independent divergences from functional sequence types. The presence of divergent rDNA paralogues highlights the need for caution when interpreting eucalypt phylogenies based on ITS sequences.

  3. Convergent and Divergent Validity of the Devereux Student Strengths Assessment

    Science.gov (United States)

    Nickerson, Amanda B.; Fishman, Callen

    2009-01-01

    This study assessed the convergent and divergent validity of the Devereux Student Strengths Assessment (DESSA; LeBuffe, Shapiro, & Naglieri, 2008). A total of 227 (n = 94 teachers, n = 133 parents) raters completed the DESSA, in addition to the Behavioral and Emotional Rating Scales-2 (BERS-2; Epstein, 2004) and/or the Behavior Assessment…

  4. Navier–Stokes flow in converging–diverging distensible tubes

    Directory of Open Access Journals (Sweden)

    Taha Sochi

    2015-09-01

    Full Text Available We use a method based on the lubrication approximation in conjunction with a residual-based mass-continuity iterative solution scheme to compute the flow rate and pressure field in distensible converging–diverging tubes for Navier–Stokes fluids. We employ an analytical formula derived from a one-dimensional version of the Navier–Stokes equations to describe the underlying flow model that provides the residual function. This formula correlates the flow rate to the boundary pressures in straight cylindrical elastic tubes with constant-radius. We validate our findings by the convergence toward a final solution with fine discretization as well as by comparison to the Poiseuille-type flow in its convergence toward analytic solutions found earlier in rigid converging–diverging tubes. We also tested the method on limiting special cases of cylindrical elastic tubes with constant-radius where the numerical solutions converged to the expected analytical solutions. The distensible model has also been endorsed by its convergence toward the rigid Poiseuille-type model with increasing the tube wall stiffness. Lubrication-based one-dimensional finite element method was also used for verification. In this investigation five converging–diverging geometries are used for demonstration, validation and as prototypes for modeling converging–diverging geometries in general.

  5. Ground state energies from converging and diverging power series expansions

    Science.gov (United States)

    Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E.; Su, Q.; Grobe, R.

    2016-10-01

    It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh-Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state's spatial extension is comparable to L. Once the binding strength is so strong that the ground state's extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

  6. Diverging trends in female old-age mortality: A reappraisal

    Directory of Open Access Journals (Sweden)

    Laura Staetsky

    2009-12-01

    Full Text Available Over the second half of the 20th century a number of divergences and convergences of mortality schedules were observed across the world. Some of these developments remain incompletely understood. In recent overviews of old-age female mortality Mesle and Vallin (2006, Population and Development Review and Rau, Soroko, Jasilionis, and Vaupel (2008, Population and Development Review describe two contrasting patterns of mortality change between the mid-1980s and the end of the 20th century: a pattern of a large decrease in mortality exhibited by France and Japan and a pattern of a smaller decrease, stability or a certain increase in mortality shown by Denmark, the United States and the Netherlands. No satisfactory explanation of this phenomenon has been proposed so far. This paper shows that the divergence is, to a very significant extent, due to the differential impact of smoking related mortality on female populations of France and Japan versus Denmark, the United States and the Netherlands. The end to the diverging trends is demonstrated. Other lifestyle factors potentially implicated in the divergence are also discussed.

  7. Bubble divergences and gauge symmetries in spin foams

    CERN Document Server

    Bonzom, Valentin

    2013-01-01

    Spin foams are candidate state-sum models for transition amplitudes in quantum gravity. An active research subject is to identify the possible divergences of spin foam models, or alternatively to show that models are finite. We will discuss in detail the (non--occurrence of) divergences in the Barrett-Crane model, formulated as an integral of delta function weights only. We will furthermore present a simple method to estimate the divergence degree of the so-called bubbles for general spin foam models. Divergences in spin foams are expected to be related to the existence of gauge symmetries (diffeomorphisms). Thus we have to conclude that such gauge symmetries are not (fully) present in the model we consider. But we will identify a class of gauge symmetries which occur at special solutions of the equations imposed by the delta function weights. This situation is surprisingly similar to the case of broken diffeomorphism symmetries in discrete gravity, which are present around flat solutions. We introduce a meth...

  8. Constrained Transport vs. Divergence Cleanser Options in Astrophysical MHD Simulations

    Science.gov (United States)

    Lindner, Christopher C.; Fragile, P.

    2009-01-01

    In previous work, we presented results from global numerical simulations of the evolution of black hole accretion disks using the Cosmos++ GRMHD code. In those simulations we solved the magnetic induction equation using an advection-split form, which is known not to satisfy the divergence-free constraint. To minimize the build-up of divergence error, we used a hyperbolic cleanser function that simultaneously damped the error and propagated it off the grid. We have since found that this method produces qualitatively and quantitatively different behavior in high magnetic field regions than results published by other research groups, particularly in the evacuated funnels of black-hole accretion disks where Poynting-flux jets are reported to form. The main difference between our earlier work and that of our competitors is their use of constrained-transport schemes to preserve a divergence-free magnetic field. Therefore, to study these differences directly, we have implemented a constrained transport scheme into Cosmos++. Because Cosmos++ uses a zone-centered, finite-volume method, we can not use the traditional staggered-mesh constrained transport scheme of Evans & Hawley. Instead we must implement a more general scheme; we chose the Flux-CT scheme as described by Toth. Here we present comparisons of results using the divergence-cleanser and constrained transport options in Cosmos++.

  9. Divergent RNA transcription: a role in promoter unwinding?

    Science.gov (United States)

    Naughton, Catherine; Corless, Samuel; Gilbert, Nick

    2013-01-01

    New approaches using biotinylated-psoralen as a probe for investigating DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA transcription generates negative supercoiling at promoters facilitating initiation complex formation and subsequent promoter clearance.

  10. THE DIVERGENCE OF LAGRANGE INTERPOLATION FOR |x|α

    Institute of Scientific and Technical Information of China (English)

    Zhikang Lu; Xifang Ge

    2005-01-01

    This paper shows that the sequence of Lagrange interpolation polynomials corresponding to the function f(x) = |x|α(1 <α< 2) on [-1, 1] can diverge everywhere in the interval except at zero and the end-points.

  11. Micropolar Fluids Using B-spline Divergence Conforming Spaces

    KAUST Repository

    Sarmiento, Adel

    2014-06-06

    We discretized the two-dimensional linear momentum, microrotation, energy and mass conservation equations from micropolar fluids theory, with the finite element method, creating divergence conforming spaces based on B-spline basis functions to obtain pointwise divergence free solutions [8]. Weak boundary conditions were imposed using Nitsche\\'s method for tangential conditions, while normal conditions were imposed strongly. Once the exact mass conservation was provided by the divergence free formulation, we focused on evaluating the differences between micropolar fluids and conventional fluids, to show the advantages of using the micropolar fluid model to capture the features of complex fluids. A square and an arc heat driven cavities were solved as test cases. A variation of the parameters of the model, along with the variation of Rayleigh number were performed for a better understanding of the system. The divergence free formulation was used to guarantee an accurate solution of the flow. This formulation was implemented using the framework PetIGA as a basis, using its parallel stuctures to achieve high scalability. The results of the square heat driven cavity test case are in good agreement with those reported earlier.

  12. Play and Divergent Problem Solving: Evidence Supporting a Reciprocal Relationship.

    Science.gov (United States)

    Wyver, Shirley R.; Spence, Susan H.

    1999-01-01

    Three studies examined the relationship between specific forms of preschoolers' social and pretend play and divergent/convergent problem solving. Naturalistic and experimental designs were used to provide clearer account of relationship and to challenge assumption of single direction of influence. Results support complex reciprocal causality model…

  13. Divergence of Temperature and Wind Signals in Tree Rings at Port Angeles, WA

    Science.gov (United States)

    Hamilton, W. L.

    2007-12-01

    At Port Angeles, WA some divergence of tree response to temperature may be explained by previously reported response of trees to wind. Near a weather station there two intermixed populations of low elevation Douglas-fir were found, of which roughly half showed positive response of annual ring width eccentricity to integrated, instrumentally measured hourly wind velocity over the same time interval and in the same direction. The other half responded negatively to the same wind along the same measurement transect azimuth. A similar result was obtained for wind when using ring width data from the downwind sides of the trees, where much of the wind signal was retained by modulation of early wood growth. This is similar to the Wilmking et al. description of divergent temperature response of transect mean ring width in high elevation trees on the Alaska Brooks Range; where a third showed positive, a third showed negative and a third had insignificant correlation with temperature. Eccentricity in Port Angeles northeast-southwest and southeast-northwest transects shows significant divergence of both wind and wind-associated temperature response from 1997 to 2001. Alternating power and lag of wind and temperature correlations with eccentricity at certain azimuths suggests that wind and temperature may operate interdependently in affecting eccentric growth. Response power and sign were highly dependent on the tree, transect azimuth and lag. Trees responded with wind azimuth resolution close to 10°, suggesting that accuracy and precision of sampling azimuth are important. Response power on most transects in most trees was usually higher at zero response lag. Eccentricity response to temperature and wind was usually of opposite sign. Northeast and southeast transect mean width showed weak, temperature-driven divergence at one-year lag. Analysis is underway back to 1982. At Port Angeles warmer winds from the Strait of Juan de Fuca flowed from the northern sector. No clear time

  14. Mitochondrial divergence between slow- and fast-aging garter snakes.

    Science.gov (United States)

    Schwartz, Tonia S; Arendsee, Zebulun W; Bronikowski, Anne M

    2015-11-01

    Mitochondrial function has long been hypothesized to be intimately involved in aging processes--either directly through declining efficiency of mitochondrial respiration and ATP production with advancing age, or indirectly, e.g., through increased mitochondrial production of damaging free radicals with age. Yet we lack a comprehensive understanding of the evolution of mitochondrial genotypes and phenotypes across diverse animal models, particularly in species that have extremely labile physiology. Here, we measure mitochondrial genome-types and transcription in ecotypes of garter snakes (Thamnophis elegans) that are adapted to disparate habitats and have diverged in aging rates and lifespans despite residing in close proximity. Using two RNA-seq datasets, we (1) reconstruct the garter snake mitochondrial genome sequence and bioinformatically identify regulatory elements, (2) test for divergence of mitochondrial gene expression between the ecotypes and in response to heat stress, and (3) test for sequence divergence in mitochondrial protein-coding regions in these slow-aging (SA) and fast-aging (FA) naturally occurring ecotypes. At the nucleotide sequence level, we confirmed two (duplicated) mitochondrial control regions one of which contains a glucocorticoid response element (GRE). Gene expression of protein-coding genes was higher in FA snakes relative to SA snakes for most genes, but was neither affected by heat stress nor an interaction between heat stress and ecotype. SA and FA ecotypes had unique mitochondrial haplotypes with amino acid substitutions in both CYTB and ND5. The CYTB amino acid change (Isoleucine → Threonine) was highly segregated between ecotypes. This divergence of mitochondrial haplotypes between SA and FA snakes contrasts with nuclear gene-flow estimates, but correlates with previously reported divergence in mitochondrial function (mitochondrial oxygen consumption, ATP production, and reactive oxygen species consequences).

  15. Experimental demonstration of using divergence cost-function in SPGD algorithm for coherent beam combining with tip/tilt control.

    Science.gov (United States)

    Geng, Chao; Luo, Wen; Tan, Yi; Liu, Hongmei; Mu, Jinbo; Li, Xinyang

    2013-10-21

    A novel approach of tip/tilt control by using divergence cost function in stochastic parallel gradient descent (SPGD) algorithm for coherent beam combining (CBC) is proposed and demonstrated experimentally in a seven-channel 2-W fiber amplifier array with both phase-locking and tip/tilt control, for the first time to our best knowledge. Compared with the conventional power-in-the-bucket (PIB) cost function for SPGD optimization, the tip/tilt control using divergence cost function ensures wider correction range, automatic switching control of program, and freedom of camera's intensity-saturation. Homemade piezoelectric-ring phase-modulator (PZT PM) and adaptive fiber-optics collimator (AFOC) are developed to correct piston- and tip/tilt-type aberrations, respectively. The PIB cost function is employed for phase-locking via maximization of SPGD optimization, while the divergence cost function is used for tip/tilt control via minimization. An average of 432-μrad of divergence metrics in open loop has decreased to 89-μrad when tip/tilt control implemented. In CBC, the power in the full width at half maximum (FWHM) of the main lobe increases by 32 times, and the phase residual error is less than λ/15.

  16. Lithosphere continental rifting and necking in 3D analogue experiments: role of plate divergence rate.

    Science.gov (United States)

    Nestola, Y.; Storti, F.; Cavozzi, C.

    2014-12-01

    The evolution of lithosphere necking is a fundamental parameter controlling the structural architecture and thermal state of rifted margins. Despite a large number of analogue and numerical modelling studies on lithosphere extension are available in the literature, a quantitative experimental description of lithosphere necking evolution is still lacking. Extensional strain rate and thermal layering of the lithosphere exert a fundamental control on necking shape and evolution. We focused our experimental work on the former parameter and simulated the progression of lithosphere thinning and necking during asymmetric orthogonal rifting at different plate divergence rates. Our models involve a 4-layer mechanical continental lithosphere, which rests on a glucose syrup asthenosphere. Both the topography and the base of the lithosphere were monitored by time-lapse laser scanning. This technical approach allowed us to quantify the evolution in space and time of the thinning factors for the crust, mantle, and lithosphere as a whole. Laser-scanning monitoring provided also a detailed picture of the evolving neck shape, which shows a strong dependency on the strain-rate. At low strain-rates, necking is "boxed" with steep flanks and a flat-lying roof, and few deep basins develop at surface. At high strain-rates, more distributed thinning occurs and isolates portions of less deformed mantle. More distributed deformation affects the model topography. Despite large differences in shape, the aspect ratio (amplitude/wavelength) of the cross-sectional neck shapes converges towards very similar values at the end of the experiments.The significant differences and evolutionary pathways produced by the plate divergence rate on the lithosphere necking profile, suggest that this parameter exert a fundamental control on localization vs. distribution of deformation in the crust as in the whole mechanical lithosphere. Furthermore, it can exert a fundamental control on the time and space

  17. Bayesian molecular clock dating of species divergences in the genomics era.

    Science.gov (United States)

    dos Reis, Mario; Donoghue, Philip C J; Yang, Ziheng

    2016-02-01

    Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.

  18. Divergência genética em linhagens de melancia Genetic divergence in watermelon lines

    Directory of Open Access Journals (Sweden)

    Flávio de França Souza

    2005-06-01

    Full Text Available A divergência genética entre 31 genótipos de melancia foi avaliada por meio da análise de variáveis canônicas e de técnicas de agrupamento (Tocher e método hierárquico de Ward baseadas na distância generalizada de Mahalanobis (D²ii'. Trinta linhagens, obtidas a partir de acessos coletados no Nordeste brasileiro e a cultivar 'Crimson Sweet' foram avaliadas quanto ao número de dias para o aparecimento da primeira flor masculina e da primeira flor feminina (NDM e NDF; número do nó da primeira flor masculina e da primeira flor feminina (NGM e NGF; número de frutos por planta (NFP; comprimento de rama principal (CRP; peso médio de fruto (PMF; teor de sólidos solúveis (TSS; diâmetro transversal e longitudinal do fruto (DTF e DLF e espessura média de casca (EMC. O experimento foi realizado em delineamento de blocos ao acaso com três repetições, compostas por parcelas de sete plantas. As características que mais contribuíram para a divergência entre as linhagens foram número de frutos por planta, diâmetro longitudinal, teor de sólidos solúveis e peso médio de fruto. Foram formados três grupos por meio do método de otimização de Tocher, três por meio do método hierárquico de Ward e quatro grupos pela dispersão gráfica baseada nas duas primeiras variáveis canônicas. Neste caso, o grupo I compôs-se de sete linhagens de Pernambuco e uma da Bahia; o grupo II reuniu todas as 21 linhagens do Maranhão; os grupos III e IV foram compostos pela linhagem 97-0247.008 (Pernambuco e pela cultivar Crimson Sweet, respectivamente. As linhagens 87-019.021 e 87-019.022 foram as mais semelhantes, enquanto a linhagem 87-019.023 e 'Crimson Sweet' apresentaram maior dissimilaridade pela distância generalizada Mahalanobis (D²ii'. Os cruzamentos mais promissores serão aqueles realizados entre Crimson Sweet e as linhagens do grupo II. Cruzamentos entre Crimson Sweet e as linhagens do grupo I serão interessantes para a obtenção de

  19. Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

    Directory of Open Access Journals (Sweden)

    James A. Schulte

    2013-01-01

    Full Text Available Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1 whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2 using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

  20. An automated optimization tool for high-dose-rate (HDR) prostate brachytherapy with divergent needle pattern

    Science.gov (United States)

    Borot de Battisti, M.; Maenhout, M.; de Senneville, B. Denis; Hautvast, G.; Binnekamp, D.; Lagendijk, J. J. W.; van Vulpen, M.; Moerland, M. A.

    2015-10-01

    Focal high-dose-rate (HDR) for prostate cancer has gained increasing interest as an alternative to whole gland therapy as it may contribute to the reduction of treatment related toxicity. For focal treatment, optimal needle guidance and placement is warranted. This can be achieved under MR guidance. However, MR-guided needle placement is currently not possible due to space restrictions in the closed MR bore. To overcome this problem, a MR-compatible, single-divergent needle-implant robotic device is under development at the University Medical Centre, Utrecht: placed between the legs of the patient inside the MR bore, this robot will tap the needle in a divergent pattern from a single rotation point into the tissue. This rotation point is just beneath the perineal skin to have access to the focal prostate tumor lesion. Currently, there is no treatment planning system commercially available which allows optimization of the dose distribution with such needle arrangement. The aim of this work is to develop an automatic inverse dose planning optimization tool for focal HDR prostate brachytherapy with needle insertions in a divergent configuration. A complete optimizer workflow is proposed which includes the determination of (1) the position of the center of rotation, (2) the needle angulations and (3) the dwell times. Unlike most currently used optimizers, no prior selection or adjustment of input parameters such as minimum or maximum dose or weight coefficients for treatment region and organs at risk is required. To test this optimizer, a planning study was performed on ten patients (treatment volumes ranged from 8.5 cm3to 23.3 cm3) by using 2-14 needle insertions. The total computation time of the optimizer workflow was below 20 min and a clinically acceptable plan was reached on average using only four needle insertions.

  1. Pleistocene speciation in North American lichenized fungi and the impact of alternative species circumscriptions and rates of molecular evolution on divergence estimates.

    Directory of Open Access Journals (Sweden)

    Steven D Leavitt

    Full Text Available Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree framework.

  2. On the Benefits of Divergent Search for Evolved Representations

    DEFF Research Database (Denmark)

    Lehman, Joel; Risi, Sebastian; Stanley, Kenneth O

    2012-01-01

    eventually converge to a point in the search space that locally maximizes the fitness function. The problem is that individuals that maximize fitness do not need good representations because a representation’s future potential is not reflected by its current fitness. In contrast, search methods without...... novelty search, which explicitly rewards novelty, i.e. behaviors that diverge from previously encountered behaviors. In many experiments, novelty search demonstrates significant representational advantages over traditional fitness-based search, such as evolving more compact solutions, uncovering more...... evolvable representations, and more fully exploiting representational features. The conclusion is that divergent evolutionary algorithms like novelty search may exert selection pressure towards higher quality representations than traditional convergent approaches to search....

  3. Divergent series, summability and resurgence II simple and multiple summability

    CERN Document Server

    Loday-Richaud, Michèle

    2016-01-01

    Addressing the question how to “sum” a power series in one variable when it diverges, that is, how to attach to it analytic functions, the volume gives answers by presenting and comparing the various theories of k-summability and multisummability. These theories apply in particular to all solutions of ordinary differential equations. The volume includes applications, examples and revisits, from a cohomological point of view, the group of tangent-to-identity germs of diffeomorphisms of C studied in volume 1. With a view to applying the theories to solutions of differential equations, a detailed survey of linear ordinary differential equations is provided which includes Gevrey asymptotic expansions, Newton polygons, index theorems and Sibuya’s proof of the meromorphic classification theorem that characterizes the Stokes phenomenon for linear differential equations. This volume is the second of a series of three entitled Divergent Series, Summability and Resurgence. It is aimed at graduate students and res...

  4. Divergence-free MHD Simulations with the HERACLES Code

    Directory of Open Access Journals (Sweden)

    Vides J.

    2013-12-01

    Full Text Available Numerical simulations of the magnetohydrodynamics (MHD equations have played a significant role in plasma research over the years. The need of obtaining physical and stable solutions to these equations has led to the development of several schemes, all requiring to satisfy and preserve the divergence constraint of the magnetic field numerically. In this paper, we aim to show the importance of maintaining this constraint numerically. We investigate in particular the hyperbolic divergence cleaning technique applied to the ideal MHD equations on a collocated grid and compare it to the constrained transport technique that uses a staggered grid to maintain the property. The methods are implemented in the software HERACLES and several numerical tests are presented, where the robustness and accuracy of the different schemes can be directly compared.

  5. Compound liquid crystal microlens array with convergent and divergent functions.

    Science.gov (United States)

    Kang, Shengwu; Zhang, Xinyu

    2016-04-20

    Based on the common liquid crystal microlens, a new compound structure for a liquid crystal (LC) microlens array is proposed. The structure consists of two sub LC microlens arrays with properties of light divergence and convergence. The structure has two LC layers: one to form the positive sub lens, one for the negative. The patterned electrode and plane electrode are used in both sub microlens arrays. When two sub microlens arrays are electrically controlled separately, they can diverge or converge the incident light, respectively. As two sub microlens arrays are both applied on the voltage, the focal length of the compound LC microlens becomes larger than that of the LC microlens with a single LC layer. Another feature of a compound LC microlens array is that it can make the target contour become visible under intense light. The mechanisms are described in detail, and the experimental data are given.

  6. Perturbation Theory in Supersymmetric QED: Infrared Divergences and Gauge Invariance

    CERN Document Server

    Dine, Michael; Haber, Howard E; Haskins, Laurel Stephenson

    2016-01-01

    We study some aspects of perturbation theory in $N=1$ supersymmetric abelian gauge theories with massive charged matter. In general gauges, infrared (IR) divergences and nonlocal behavior arise in 1PI diagrams, associated with a $1/k^4$ term in the propagator for the vector superfield. We examine this structure in supersymmetric QED. The IR divergences are gauge-dependent and must cancel in physical quantities like the electron pole mass. We demonstrate that cancellation takes place in a nontrivial way, amounting to a reorganization of the perturbative series from powers of $e^2$ to powers of $e$. We also show how these complications are avoided in cases where a Wilsonian effective action can be defined.

  7. Climate change promotes hybridisation between deeply divergent species

    Science.gov (United States)

    Chiocchio, Andrea; Zampiglia, Mauro; Nascetti, Giuseppe

    2017-01-01

    Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridisations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufo and Bufotes viridis species groups). We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future. PMID:28348926

  8. Kullback-Leibler Divergence Approach to Partitioned Update Kalman Filter

    OpenAIRE

    Raitoharju, Matti; García-Fernández, Ángel F.; Piché, Robert

    2016-01-01

    Kalman filtering is a widely used framework for Bayesian estimation. The partitioned update Kalman filter applies a Kalman filter update in parts so that the most linear parts of measurements are applied first. In this paper, we generalize partitioned update Kalman filter, which requires the use oft the second order extended Kalman filter, so that it can be used with any Kalman filter extension. To do so, we use a Kullback-Leibler divergence approach to measure the nonlinearity of the measure...

  9. Instability of diverging and converging flows in an annulus

    CERN Document Server

    Ilin, Konstantin

    2012-01-01

    The stability of two-dimensional diverging and converging flows in an annulus between two permeable cylinders is examined. The basic flow is irrotational and has both the radial and azimuthal components. It is shown that for a wide range of the parameters of the problem, the basic flow is unstable to small two-dimensional perturbations. The instability is inviscid and oscillatory and persists if the viscosity of the fluid is taken into consideration.

  10. Infrared Divergences from Soft and Collinear Gauge Bosons

    CERN Document Server

    Jameson, Paul

    2007-01-01

    I review the Lee-Nauenberg thereom and discuss its inclusion of photons which are disconnected at the level of the S-matrix but connected at the level of the cross-section when there are initial and final state charged particles. I then expose a new set of soft collinear divergences in massless gauge theories which are omitted in the standard Lee-Nauenberg approach. It seems that highly questionable assumptions are needed to obtain finite cross-sections.

  11. Critical Initiation Conditions for Gaseous Diverging Spherical Detonations

    OpenAIRE

    Desbordes, D.

    1995-01-01

    The diverging spherical detonation wave in gaseous explosives is obtained either with a point source of explosion of energy E or through the transmission of a plane detonation from a cylindrical tube of diameter d into a large volume. The mechanism of detonation initiation in both cases is based on the shock to detonation transition. The experimental critical conditions lead to an initiation criterion for detonation resulting from the competition between the expansion behind the leading shock...

  12. On the Divergent American Reactions to Terrorism and Climate Change

    OpenAIRE

    Sunstein, Cass R.

    2006-01-01

    Two of the most important sources of catastrophic risk are terrorism and climate change. The United States has responded aggressively to the risk of terrorism while doing very little about the risk of climate change. For the United States alone, the cost of the Iraq war is now in excess of the anticipated cost of the Kyoto Protocol. The divergence presents a puzzle; it also raises more general questions about both risk perception and the public demand for legislation. The best explanation for...

  13. Divergence Measures Tool:An Introduction with Brief Tutorial

    Science.gov (United States)

    2014-03-01

    on tutorial are provided in this report. 15. SUBJECT TERMS Divergence measures, natural language processing, text corpus, text domain, text genre ...in detecting differences across a wide range of Arabic-language text files (they varied by genre , domain, spelling variation, size, etc.), our...screenshots are cropped down to that portion of screen layout most relevant to the accompanying description . Cropped screenshots in figures in sections

  14. Bregman divergence as general framework to estimate unnormalized statistical models

    CERN Document Server

    Gutmann, Michael

    2012-01-01

    We show that the Bregman divergence provides a rich framework to estimate unnormalized statistical models for continuous or discrete random variables, that is, models which do not integrate or sum to one, respectively. We prove that recent estimation methods such as noise-contrastive estimation, ratio matching, and score matching belong to the proposed framework, and explain their interconnection based on supervised learning. Further, we discuss the role of boosting in unsupervised learning.

  15. Beam divergence changing mechanism for short-range inter-unmanned aerial vehicle optical communications.

    Science.gov (United States)

    Heng, Kiang Huat; Zhong, Wen-De; Cheng, Tee Hiang; Liu, Ning; He, Yingjie

    2009-03-10

    The problems associated with using a single fixed beam divergence for short-range inter-unmanned aerial vehicle free-space optical communications are discussed. To overcome the problems, a beam divergence changing mechanism is proposed. Four different methods are then proposed to implement the beam divergence changing mechanism. The performance of these methods is evaluated in terms of transmission distance under adverse weather conditions. The results show that the performance is greatly improved when the beam divergence changing mechanism is used.

  16. Bayesian-Pearson Divergence Estimator Based on Grouped Data

    Institute of Scientific and Technical Information of China (English)

    BaoxueZhang; QingxunMeng

    2004-01-01

    A new method along with Bayesian approach for estimating the parameter in the distribution function F(x; θ) by using grouped data is developed in this paper. The support of F(x;θ) is divided into disjointed intervals as -∞ = x0 < x1 <… < xk-1 divergence D(p; q) is introduced to scale the distance between the probabilities pj(θ),j = 1,..., k and the samples from the posterior distribution (Dirichlet distribution) of the probabilities. Then by minimizing the Pearson divergence D(p;q), the ‘posterior' samples of the parameter θ can be obtained, through which statistical inference including Bayesian-Pearson Divergence Estimator of the parameter can be processed. Simulations and a numerical example emt:loying this method are presented.

  17. Automatic leukocyte nucleus segmentation by intuitionistic fuzzy divergence based thresholding.

    Science.gov (United States)

    Jati, Arindam; Singh, Garima; Mukherjee, Rashmi; Ghosh, Madhumala; Konar, Amit; Chakraborty, Chandan; Nagar, Atulya K

    2014-03-01

    The paper proposes a robust approach to automatic segmentation of leukocyte's nucleus from microscopic blood smear images under normal as well as noisy environment by employing a new exponential intuitionistic fuzzy divergence based thresholding technique. The algorithm minimizes the divergence between the actual image and the ideally thresholded image to search for the final threshold. A new divergence formula based on exponential intuitionistic fuzzy entropy has been proposed. Further, to increase its noise handling capacity, a neighborhood-based membership function for the image pixels has been designed. The proposed scheme has been applied on 110 normal and 54 leukemia (chronic myelogenous leukemia) affected blood samples. The nucleus segmentation results have been validated by three expert hematologists. The algorithm achieves an average segmentation accuracy of 98.52% in noise-free environment. It beats the competitor algorithms in terms of several other metrics. The proposed scheme with neighborhood based membership function outperforms the competitor algorithms in terms of segmentation accuracy under noisy environment. It achieves 93.90% and 94.93% accuracies for Speckle and Gaussian noises, respectively. The average area under the ROC curves comes out to be 0.9514 in noisy conditions, which proves the robustness of the proposed algorithm.

  18. A vadose zone water fluxmeter with divergence control

    Science.gov (United States)

    Gee, G. W.; Ward, A. L.; Caldwell, T. G.; Ritter, J. C.

    2002-08-01

    Unsaturated water flux densities are needed to quantify water and contaminant transfer within the vadose zone. However, water flux densities are seldom measured directly and often are predicted with uncertainties of an order or magnitude or more. A water fluxmeter was designed, constructed, and tested to directly measure drainage fluxes in field soils. The fluxmeter was designed to minimize divergence. It concentrates flow into a narrow sensing region filled with a fiberglass wick. The wick applies suction, proportional to its length, and passively drains the meter. The meter can be installed in an augured borehole at almost any depth below the root zone. Water flux through the meter is measured with a self-calibrating tipping bucket, with a sensitivity of ~4 mL tip-1. For our meter this is equivalent to detection limit of ~0.1 mm. Passive-wick devices previously have not properly corrected for flow divergence. Laboratory measurements supported predictions of a two-dimensional (2-D) numerical model, which showed that control of the collector height H and knowledge of soil hydraulic properties are required for improving divergence control, particularly at fluxes below 1000 mm yr-1. The water fluxmeter is simple in concept, is inexpensive, and has the capability of providing continuous and reliable monitoring of unsaturated water fluxes ranging from less than 1 mm yr-1 to more than 1000 mm yr-1.

  19. Peaches tree genetic divergence for brown rot reaction

    Directory of Open Access Journals (Sweden)

    Américo Wagner Júnior

    2011-10-01

    Full Text Available It was evaluated the genetic divergence in peach genotypes for brown rot reaction. It was evaluated 26 and 29 peach genotypes in the 2009/2010 and 2010/2011 production cycle, respectively. The experiment was carried out at the Laboratório de Fitossanidade, da UTFPR - Campus Dois Vizinhos. The experimental design was entirely randomized, considering each peach genotype a treatment, and it was use three replication of nine fruits. The treatment control use three replication of three peach. The fruit epidermis were inoculated individually with 0.15 mL of M. fructicola conidial suspension (1.0 x 10(5 spores mL-1. In the control treatment was sprayed with 0.15 mL of distilled water. The fruits were examined 72 and 120 hours after inoculation, and the incidence and severity disease were evaluated. These results allowed realized study for genetic divergence, used as dissimilarity measure the Generalized Mahalanobis distance. Cluster analysis using Tocher´s optimization method and distances in the plan were applied. There was smallest genetic divergence among peach trees evaluated for brown rot, what can difficult to obtain resistance in the genotypes.

  20. Dynamics of detonations with a constant mean flow divergence

    CERN Document Server

    Borzou, Bijan

    2016-01-01

    The present work addresses the question of whether mean field macroscopic models are suitable to describe the dynamics of real cellular detonations. This question is posed in the framework of detonations with stream-tube area divergence that is kept constant, as to generate attenuated detonations in quasi-steady state. An exponential horn geometry is used, in order to keep the source term due to geometrical divergence constant in the governing equations of mean flow, and hence permit to establish steady travelling waves with constant losses. The experiments were conducted in two mixtures 2C$_2$H$_2$+5O$_2$+21Ar, characterized by a relatively weak instability, and C$_3$H$_8$+5O$_2$, characterized by a much more unstable cellular structure. The experiments demonstrated that such quasi-steady state detonations can be realized. The experiments permitted a unique detonation speed - divergence scaling laws to be developed. Quantitative comparisons were made with steady wave predictions based on the underlying chemi...

  1. Torsional stiffness degradation and aerostatic divergence of suspension bridge decks

    Science.gov (United States)

    Zhang, Z. T.; Ge, Y. J.; Yang, Y. X.

    2013-07-01

    The mechanism of aerostatic torsional divergence (ATD) of long-span suspension bridges is investigated. A theoretical analysis on the basis of a generalized model is presented, showing that the vertical motion of a bridge deck is crucial to the torsional stiffness of the whole suspended system, and that the vertical motion of either cable with a magnitude beyond a certain threshold could result in a sudden degradation of the torsional stiffness of the system. This vertical motion-induced degradation of stiffness is recognized as the main reason for the ATD. Long-span suspension bridges are susceptible to such a type of divergence, especially when they are immersed in turbulent wind fields. The divergences that occur in turbulent wind fields differ significantly from those in smooth wind fields, and the difference is well explained by the generalized model that the loosening of any one cable could result in the vanishing of the part of stiffness provided by the whole cable system. The mechanism revealed in this paper leads to a definition of the critical wind speed of the ATD in a turbulent flow; that is, the one resulting in a vertical motion so large as to loosen either cable to a stressless state. Numerical results from the nonlinear finite-element (FE) analysis of the Xihoumen suspension bridge, in conjunction with observations from wind tunnel tests on an aero-elastic full bridge model, are in support of the viewpoint presented in this study.

  2. Beam divergence effects on high power optical parametric oscillation

    Institute of Scientific and Technical Information of China (English)

    Li Hui-Qing; Geng Ai-Cong; Bo Yong; Wu Ling-An; Cui Da-Fu; Xu Zu-Yan

    2005-01-01

    The beam divergence effects of the input pump laser on a high power nanosecond optical parametric oscillator (OPO) have been numerically simulated. The OPO conversion efficiency is affected due to the angular deviation of real laser beams from ideal phase matching conditions. Our theoretical model is based on the decomposition of the Gaussian beam and assumes each component has a single deviation angle and thus a Particular wave vector mismatch. We take into account the variable intensity profile in the spatial and temporal domains of the Gaussian beam, the pump depletion effects for large-signal processes as well as the oscillatory effects of the three waves. Two nonlinear crystals β-BaB2O4 (BBO) and LiB3O5 (LBO) have been investigated in detail. The results indicate that the degree of beam divergence strongly influences the maximum pump intensity, optimum crystal length and OPO conversion efficiency.The impact of beam divergence is much more severe in the case of critical phase-matching for BBO than in the case of non-critical phase-matching for LBO. The results provide a way to choose the optimum parameters for a high power ns OPO such as the nonlinear material, the crystal length and the pump intensity, etc. Good agreement is obtained with our experimental results.

  3. The impact of physical exercise on convergent and divergent thinking

    Directory of Open Access Journals (Sweden)

    Lorenza S Colzato

    2013-12-01

    Full Text Available Anecdotal literature suggests that creative people sometimes use bodily movement to help overcome mental blocks and lack of inspiration. Several studies have shown that physical exercise may sometimes enhance creative thinking, but the evidence is still inconclusive. In this study we investigated whether creativity in convergent- and divergent-thinking tasks is affected by acute moderate and intense physical exercise in athletes (n=48 and non-athletes (n=48. Exercise interfered with divergent thinking in both groups. The impact on convergent thinking, the task that presumably required more cognitive control, depended on the training level: while in non-athletes performance was significantly impaired by exercise, athletes showed a benefit that approached significance. The findings suggest that acute exercise may affect both, divergent and convergent thinking. In particular, it seems to affect control-hungry tasks through exercise-induced ego-depletion, which however is less pronounced in individuals with higher levels of physical fitness, presumably because of the automatization of movement control, fitness-related neuroenergetic benefits, or both.

  4. Hemispheric Connectivity and the Visual-Spatial Divergent-Thinking Component of Creativity

    Science.gov (United States)

    Moore, Dana W.; Bhadelia, Rafeeque A.; Billings, Rebecca L.; Fulwiler, Carl; Heilman, Kenneth M.; Rood, Kenneth M. J.; Gansler, David A.

    2009-01-01

    Background/hypothesis: Divergent thinking is an important measurable component of creativity. This study tested the postulate that divergent thinking depends on large distributed inter- and intra-hemispheric networks. Although preliminary evidence supports increased brain connectivity during divergent thinking, the neural correlates of this…

  5. Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing.

    Science.gov (United States)

    Alquezar-Planas, David E; Mourier, Tobias; Bruhn, Christian A W; Hansen, Anders J; Vitcetz, Sarah Nathalie; Mørk, Søren; Gorodkin, Jan; Nielsen, Hanne Abel; Guo, Yan; Sethuraman, Anand; Paxinos, Ellen E; Shan, Tongling; Delwart, Eric L; Nielsen, Lars P

    2013-01-01

    Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT) sequencing. Subsequent "primer walking" combined with Sanger sequencing validated the RS platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described.

  6. Niche Divergence versus Neutral Processes: Combined Environmental and Genetic Analyses Identify Contrasting Patterns of Differentiation in Recently Diverged Pine Species

    OpenAIRE

    Alejandra Moreno-Letelier; Alejandra Ortíz-Medrano; Daniel Piñero

    2013-01-01

    BACKGROUND AND AIMS: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental ...

  7. Divergência genética em genótipos de girassol Genetic divergence in sunflower genotypes

    Directory of Open Access Journals (Sweden)

    Edson Perito Amorim

    2007-12-01

    Full Text Available Uma investigação sobre a diversidade genética entre 15 genótipos de girassol, por meio de 12 características agronômicas, foi implementada no Instituto Agronômico, Campinas, Brasil. Análises de variância univariada e multivariada revelaram diferenças entre os genótipos. A distância generalizada de Mahalanobis indicou um alto grau de divergência genética. Os genótipos foram agrupados em três grupos. As características início do florescimento, 50% do florescimento, número de folhas e altura da inserção do capítulo contribuíram com grande parte da divergência genética observada. Por meio desses resultados, é possível identificar materiais divergentes e com características agronômicas complementares para o desenvolvimento de novos cultivares superiores.An investigation about the genetical diversity among fifteen sunflower genotypes using twelve agronomical characteristics was implanted at the Agronomic Institute, Campinas Brazil. Univariate and multivariate analyses of variance revealed the presence of differences among the genotypes. The generalized distance of Mahalanobis indicated the presence of genetic diversity. The genotypes were grouped into tree clusters. Among the investigated characteristics, the beginning of flowering, 50% flowering, leaf number and head height of chapter insertion exhibited high contribution towards genetic divergence. Through these studies it is possible to identify divergent material with further agronomical features for the development of new superior sunflower cultivars.

  8. Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species.

    Directory of Open Access Journals (Sweden)

    Alejandra Moreno-Letelier

    Full Text Available BACKGROUND AND AIMS: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. METHODS: Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. KEY RESULTS AND CONCLUSION: Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.

  9. AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

    to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer.

  10. Vector tomography for reconstructing electric fields with non-zero divergence in bounded domains

    Science.gov (United States)

    Koulouri, Alexandra; Brookes, Mike; Rimpiläinen, Ville

    2017-01-01

    In vector tomography (VT), the aim is to reconstruct an unknown multi-dimensional vector field using line integral data. In the case of a 2-dimensional VT, two types of line integral data are usually required. These data correspond to integration of the parallel and perpendicular projection of the vector field along the integration lines and are called the longitudinal and transverse measurements, respectively. In most cases, however, the transverse measurements cannot be physically acquired. Therefore, the VT methods are typically used to reconstruct divergence-free (or source-free) velocity and flow fields that can be reconstructed solely from the longitudinal measurements. In this paper, we show how vector fields with non-zero divergence in a bounded domain can also be reconstructed from the longitudinal measurements without the need of explicitly evaluating the transverse measurements. To the best of our knowledge, VT has not previously been used for this purpose. In particular, we study low-frequency, time-harmonic electric fields generated by dipole sources in convex bounded domains which arise, for example, in electroencephalography (EEG) source imaging. We explain in detail the theoretical background, the derivation of the electric field inverse problem and the numerical approximation of the line integrals. We show that fields with non-zero divergence can be reconstructed from the longitudinal measurements with the help of two sparsity constraints that are constructed from the transverse measurements and the vector Laplace operator. As a comparison to EEG source imaging, we note that VT does not require mathematical modeling of the sources. By numerical simulations, we show that the pattern of the electric field can be correctly estimated using VT and the location of the source activity can be determined accurately from the reconstructed magnitudes of the field.

  11. Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae).

    Science.gov (United States)

    Misiewicz, Tracy M; Fine, Paul V A

    2014-05-01

    Soil heterogeneity is an important driver of divergent natural selection in plants. Neotropical forests have the highest tree diversity on earth, and frequently, soil specialist congeners are distributed parapatrically. While the role of edaphic heterogeneity in the origin and maintenance of tropical tree diversity is unknown, it has been posited that natural selection across the patchwork of soils in the Amazon rainforest is important in driving and maintaining tree diversity. We examined genetic and morphological differentiation among populations of the tropical tree Protium subserratum growing parapatrically on the mosaic of white-sand, brown-sand and clay soils found throughout western Amazonia. Nuclear microsatellites and leaf morphology were used to (i) quantify the extent of phenotypic and genetic divergence across habitat types, (ii) assess the importance of natural selection vs. drift in population divergence, (iii) determine the extent of hybridization and introgression across habitat types, (iv) estimate migration rates among populations. We found significant morphological variation correlated with soil type. Higher levels of genetic differentiation and lower migration rates were observed between adjacent populations found on different soil types than between geographically distant populations on the same soil type. PST -FST comparisons indicate a role for natural selection in population divergence among soil types. A small number of hybrids were detected suggesting that gene flow among soil specialist populations may occur at low frequencies. Our results suggest that edaphic specialization has occurred multiple times in P. subserratum and that divergent natural selection across edaphic boundaries may be a general mechanism promoting and maintaining Amazonian tree diversity.

  12. Sequence of inequalities among fuzzy mean difference divergence measures and their applications.

    Science.gov (United States)

    Tomar, Vijay Prakash; Ohlan, Anshu

    2014-01-01

    This paper presents a sequence of fuzzy mean difference divergence measures. The validity of these fuzzy mean difference divergence measures is proved axiomatically. In addition, it introduces a sequence of inequalities among some of these fuzzy mean difference divergence measures. The applications of proposed fuzzy mean difference divergence measures in the context of pattern recognition have been presented using a numerical example. It is shown that the proposed fuzzy mean difference divergence measures are well suited to use with linguistic variables. Finally, on establishing inequalities, we find that our proposed measures are computationally much more efficient.

  13. Test technology on divergence angle of laser range finder based on CCD imaging fusion

    Science.gov (United States)

    Shi, Sheng-bing; Chen, Zhen-xing; Lv, Yao

    2016-09-01

    Laser range finder has been equipped with all kinds of weapons, such as tank, ship, plane and so on, is important component of fire control system. Divergence angle is important performance and incarnation of horizontal resolving power for laser range finder, is necessary appraised test item in appraisal test. In this paper, based on high accuracy test on divergence angle of laser range finder, divergence angle test system is designed based on CCD imaging, divergence angle of laser range finder is acquired through fusion technology for different attenuation imaging, problem that CCD characteristic influences divergence angle test is solved.

  14. Divergência genética em feijão-caupi Genetic divergence among cowpea

    Directory of Open Access Journals (Sweden)

    Adriana Rodrigues Passos

    2007-01-01

    Full Text Available Este trabalho objetivou avaliar a divergência genética entre genótipos de feijão-caupi, visando à seleção dos mais divergentes e de maior potencial produtivo para indicar como genitores em cruzamentos genéticos para futura recomendação de cultivares aos agricultores do Recôncavo Baiano. Os experimentos foram desenvolvidos na Escola de Agronomia da Universidade Federal da Bahia, Cruz das Almas (BA, utilizando-se 22 genótipos do tipo prostrado e 20 do tipo semi-ereto, dispostos em delineamento de blocos casualizados, com quatro repetições. Foram analisados os caracteres altura da planta, comprimento de vagem, massa de vagens, massa de grãos por vagem, número de grãos por vagem, massa de cem grãos, índice de grãos, produtividade de vagem e de grãos. A divergência genética foi obtida através da distância generalizada de Mahalanobis. Novas combinações gênicas promissoras podem surgir nos cruzamentos entre os genótipos TE97-309G-1, TE97-367G-3, TE97-367G-11 e TE97-430G-12 do tipo prostrado e TE97-321G-4 e TE97-404-1E-1 do tipo semi-ereto. A seleção dos genótipos TE93-244-23F-1, TE97-299G-10 e BR 17-Gurguéia tipo prostrado e os genótipos TE97-321G-4, TE97-406-2E, TE96-282-22G e EV x 91-2E-1 tipo semi-ereto demonstram superioridade para a produtividade de grãos. Os caracteres comprimento de vagem, massa de grãos por vagem e produtividade de vagens são os que mais contribuem para a divergência genética.This work aimed to evaluate the genetic divergence among cowpea genotypes, for selection of most divergent genotypes and of highest yield potential as parents in crossings as well as for future recommendation of cultivars in the reconcave region in Bahia, Brazil. The experiment was carried out Agronomy School of Universidade Federal da Bahia, Cruz das Almas, State of Bahia, using twenty two erect cowpea and twenty semi-erect cowpea genotypes, in a randomized design, with four replications. The following characters

  15. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates

    Directory of Open Access Journals (Sweden)

    Boore Jeffrey L

    2008-05-01

    Full Text Available Abstract Background Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications. Results The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR. Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony or as the sister to Pinus (the only conifer representative in a monophyletic gymnosperm clade (maximum likelihood, bayesian. Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants. Conclusion Although the basic organization of the Welwitschia plastome is typical, its

  16. Individual differences and age-related changes in divergent thinking in toddlers and preschoolers.

    Science.gov (United States)

    Bijvoet-van den Berg, Simone; Hoicka, Elena

    2014-06-01

    Divergent thinking shows the ability to search for new ideas, which is an important factor contributing to innovation and problem solving. Current divergent thinking tests allow researchers to study children's divergent thinking from the age of 3 years on. This article presents the first measure of divergent thinking that can be used with children as young as 2 years. The Unusual Box test is a nonverbal and nonimitative test in which children play individually with a novel toy and novel objects. Divergent thinking is scored as the number of different actions performed. Study 1 shows that the Unusual Box test is a valid measure of divergent thinking as it correlates with standard measures of divergent thinking in 3- and 4-year-olds. Study 2 indicates that the test can be used with 2-year-olds, as it shows high test-retest reliability, demonstrating that 2-year-olds can think divergently. Across both studies, individual differences and age-related changes were found, indicating that some children are better at divergent thinking than others and that children's divergent thinking increases with age. This test will allow researchers to gain insight into the early emergence of divergent thinking.

  17. An Intercomparison Between Divergence-Cleaning and Staggered Mesh Formulations for Numerical Magnetohydrodynamics

    CERN Document Server

    Balsara, D; Balsara, Dinshaw; Kim, Jongsoo

    2003-01-01

    In recent years, several different strategies have emerged for evolving the magnetic field in numerical MHD. Some of these methods can be classified as divergence-cleaning schemes, where one evolves the magnetic field components just like any other variable in a higher order Godunov scheme. The fact that the magnetic field is divergence-free is imposed post-facto via a divergence-cleaning step. Other schemes for evolving the magnetic field rely on a staggered mesh formulation which is inherently divergence-free. The claim has been made that the two approaches are equivalent. In this paper we cross-compare three divergence-cleaning schemes based on scalar and vector divergence-cleaning and a popular divergence-free scheme. All schemes are applied to the same stringent test problem. Several deficiencies in all the divergence-cleaning schemes become clearly apparent with the scalar divergence-cleaning schemes performing worse than the vector divergence-cleaning scheme. The vector divergence-cleaning scheme also ...

  18. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

    Directory of Open Access Journals (Sweden)

    Thomas Mailund

    Full Text Available We present a hidden Markov model (HMM for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a the bonobo and common chimpanzee, (b the eastern and western gorilla, and (c the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

  19. Chloroplast genome evolution in early diverged leptosporangiate ferns.

    Science.gov (United States)

    Kim, Hyoung Tae; Chung, Myong Gi; Kim, Ki-Joong

    2014-05-01

    In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnVGCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

  20. Rethinking conformity and imitation: divergence, convergence, and social understanding.

    Science.gov (United States)

    Hodges, Bert H

    2014-01-01

    Social and developmental psychologists have stressed the pervasiveness and strength of humans' tendencies to conform and to imitate, and social anthropologists have argued that these tendencies are crucial to the formation of cultures. Research from four domains is reviewed and elaborated to show that divergence is also pervasive and potent, and it is interwoven with convergence in a complex set of dynamics that is often unnoticed or minimized. First, classic research in social conformity is reinterpreted in terms of truth, trust, and social solidarity, revealing that dissent is its most salient feature. Second, recent studies of children's use of testimony to guide action reveal a surprisingly sophisticated balance of trust and prudence, and a concern for truth and charity. Third, new experiments indicate that people diverge from others even under conditions where conformity seems assured. Fourth, current studies of imitation provide strong evidence that children are both selective and faithful in who, what, and why they follow others. All of the evidence reviewed points toward children and adults as being engaged, embodied partners with others, motivated to learn and understand the world, others, and themselves in ways that go beyond goals and rules, prediction and control. Even young children act as if they are in a dialogical relationship with others and the world, rather than acting as if they are solo explorers or blind followers. Overall, the evidence supports the hypothesis that social understanding cannot be reduced to convergence or divergence, but includes ongoing activities that seek greater comprehensiveness and complexity in the ability to act and interact effectively, appropriately, and with integrity.

  1. Evolution of cichlid vision via trans-regulatory divergence

    Directory of Open Access Journals (Sweden)

    O’Quin Kelly E

    2012-12-01

    Full Text Available Abstract Background Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. Results We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73% occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Conclusions Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the

  2. One-loop divergences in massive gravity theory

    CERN Document Server

    Buchbinder, Ioseph L; Shapiro, Ilya L

    2012-01-01

    The one-loop divergences are calculated for the recently proposed ghost-free version of massive gravity, where the action depends on both metric and external tensor field f. The non-polynomial structure of the massive term is reduced to a more standard form by means of auxiliary tensor field, which is settled on-shell after quantum calculations are performed. As one should expect, the counterterms do not reproduce the form of the classical action. Moreover, the result has the form of the power series in f.

  3. One-loop divergences in massive gravity theory

    Science.gov (United States)

    Buchbinder, I. L.; Pereira, D. D.; Shapiro, I. L.

    2012-05-01

    The one-loop divergences are calculated for the recently proposed ghost-free massive gravity model, where the action depends on both metric and external tensor field f. The non-polynomial structure of the massive term is reduced to a more standard form by means of auxiliary tensor field, which is settled on-shell after quantum calculations are performed. As one should expect, the counter-terms do not reproduce the form of the classical action. Moreover, the result has the form of the power series in f.

  4. HYDROMAGNETIC DIVERGENT CHANNEL FLOW OF A VISCOELASTIC ELECTRICALLY CONDUCTING FLUID

    Directory of Open Access Journals (Sweden)

    RITA CHOUDHURY

    2011-10-01

    Full Text Available A theoretical study for the two-dimensional boundary layer flow through a divergent channel of a visco-elastic electrically conducting fluid in presence of transverse magnetic field has been considered. Similarity solutions are obtained by considering a special form of magnetic field. The analytical expressions for velocity and skin friction at the wall have been obtained and numerically worked out for different values of the flow parametersinvolved in the solution. The velocity and the skin friction coefficient have been presented graphically to observe the visco-elastic effects for various values of the flow parameters across the boundary layer.

  5. Logarithmic divergent thermal conductivity in two-dimensional nonlinear lattices.

    Science.gov (United States)

    Wang, Lei; Hu, Bambi; Li, Baowen

    2012-10-01

    Heat conduction in three two-dimensional (2D) momentum-conserving nonlinear lattices are numerically calculated via both nonequilibrium heat-bath and equilibrium Green-Kubo algorithms. It is expected by mainstream theories that heat conduction in such 2D lattices is divergent and the thermal conductivity κ increases with lattice length N logarithmically. Our simulations for the purely quartic lattice firmly confirm it. However, very robust finite-size effects are observed in the calculations for the other two lattices, which well explain some existing studies and imply the extreme difficulties in observing their true asymptotic behaviors with affordable computation resources.

  6. Porous waveguide facilitated low divergence quantum cascade laser*

    Institute of Scientific and Technical Information of China (English)

    Yin Wen; Lu Quanyong; Liu Wannfeng; Zhang Jinchuan; Wang Lijun; Liu Junqi; Li Lu; Liu Fengqi; Wang Zhanguo

    2011-01-01

    A quantum cscade laser with a porous waveguide structure emitting at 4.5 μm is reported. A branchlike porous structure filled with metal material was fabricated on both sides of the laser ridge by an electrochemical etching process. In contrast to the common ridge waveguide laser, devices with a porous structure give rather better beam quality. Utilizing this porous structure as a high-order mode absorber, the device exhibited fundamental transverse mode emission with a nearly diffraction limited far-field beam divergence angle of 4.9°.

  7. Landau-Squire jet in a radially diverging electrical current

    Energy Technology Data Exchange (ETDEWEB)

    Boyarevich, V.V.; Shilova, E.I.

    1977-07-01

    An examination is made of a precise solution to the classical Landau-Squire problem in a radially diverging electrical current. The formulated problem was shown to be described by two parameters one of which characterizes the electromagnetic effect, and the other - the hydrodynamic impulse. Determinations were made of the regions of permissible parameter values at which the solution remains limited. Flow pictures are presented in relation to the input ratio of electromagnetic forces and the hydrodynamic impulse. 10 references, 6 figures, 2 tables.

  8. A possible explanation for the divergent projection of ENSO amplitude change under global warming

    Science.gov (United States)

    Chen, Lin; Li, Tim; Yu, Yongqiang; Behera, Swadhin K.

    2017-02-01

    The El Niño-Southern Oscillation (ENSO) is the greatest climate variability on interannual time scale, yet what controls ENSO amplitude changes under global warming (GW) is uncertain. Here we show that the fundamental factor that controls the divergent projections of ENSO amplitude change within 20 coupled general circulation models that participated in the Coupled Model Intercomparison Project phase-5 is the change of climatologic mean Pacific subtropical cell (STC), whose strength determines the meridional structure of ENSO perturbations and thus the anomalous thermocline response to the wind forcing. The change of the thermocline response is a key factor regulating the strength of Bjerknes thermocline and zonal advective feedbacks, which ultimately lead to the divergent changes in ENSO amplitude. Furthermore, by forcing an ocean general circulation mode with the change of zonal mean zonal wind stress estimated by a simple theoretical model, a weakening of the STC in future is obtained. Such a change implies that ENSO variability might strengthen under GW, which could have a profound socio-economic consequence.

  9. Fabrication of Converging and Diverging Polymeric Microlens Arrays By A Thermocapillary Replication Technique

    Science.gov (United States)

    Lim, Soon Wei Daniel; Fiedler, Kevin R.; Troian, Sandra M.

    2016-11-01

    Thermocapillary forces offer a powerful method for sculpting air/liquid interfaces at microscale dimensions. Here we demonstrate how square arrays of slender chilled pins in close proximity to a molten nanofilm enforce periodic distributions of thermocapillary stresses suitable for fabricating microlens arrays with ultrasmooth surfaces and excellent focusing capability. We applied this technique to shape and then solidify polystyrene films on quartz to form converging and diverging microlens arrays. By adjusting the growth time, width of the chilled pins, and pin pitch, we created simple convex, simple concave, caldera-like and even hierarchical microarray components. The latter two tend to form when the pitch and pin width are comparable in size. The diverging arrays were incorporated into a Shack-Hartmann wavefront sensor for imaging spatial fluctuations in refractive index caused by bursts of cooled spray. The caldera-like arrays were used to collimate an incident beam into annuli. These demonstrations illustrate how spatiotemporal control over thermocapillary distributions can be used to fabricate a multiplicity of micro-optical components in a single, non-contact step. This work was supported by the Kiyo and Eiko Tomiyasu SURF scholarship (SWDL) and an NSTRF fellowship (KRF).

  10. Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus.

    Science.gov (United States)

    Fouquet, Antoine; Recoder, Renato; Teixeira, Mauro; Cassimiro, José; Amaro, Renata Cecília; Camacho, Agustín; Damasceno, Roberta; Carnaval, Ana Carolina; Moritz, Craig; Rodrigues, Miguel Trefaut

    2012-03-01

    Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups.

  11. Divergence date estimation and a comprehensive molecular tree of extant cetaceans.

    Science.gov (United States)

    McGowen, Michael R; Spaulding, Michelle; Gatesy, John

    2009-12-01

    Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene-Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning approximately 10 million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea.

  12. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence.

    Science.gov (United States)

    Org, Tõnis; Duan, Dan; Ferrari, Roberto; Montel-Hagen, Amelie; Van Handel, Ben; Kerényi, Marc A; Sasidharan, Rajkumar; Rubbi, Liudmilla; Fujiwara, Yuko; Pellegrini, Matteo; Orkin, Stuart H; Kurdistani, Siavash K; Mikkola, Hanna Ka

    2015-03-12

    Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic marks. Our data suggest that, rather than recruiting corepressors to enhancers, Scl prevents ectopic cardiogenesis by occupying enhancers that cardiac factors, such as Gata4 and Hand1, use for gene activation. Although hematopoietic Gata factors bind with Scl to both activated and repressed genes, they are dispensable for cardiac repression, but necessary for activating genes that enable hematopoietic stem/progenitor cell development. These results suggest that a unique subset of enhancers in lineage-specific genes that are accessible for regulators of opposing fates during the time of the fate decision provide a platform where the divergence of mutually exclusive fates is orchestrated.

  13. Gender-based screening for chlamydial infection and divergent infection trends in men and women.

    Directory of Open Access Journals (Sweden)

    Susan M Rogers

    Full Text Available OBJECTIVES: To assess the potential impact of chlamydial screening policy that recommends routine screening of women but not men. METHODS: Population surveys of probability samples of Baltimore adults aged 18 to 35 years in 1997-1998 and 2006-2009 collected biospecimens to estimate trends in undiagnosed chlamydial infection. Survey estimates are compared to surveillance data on diagnosed chlamydial infections reported to the Health Department. RESULTS: Prevalence of undiagnosed chlamydial infection among men increased from 1.6% to 4.0%, but it declined from 4.3% to 3.1% among women (p = 0.028 for test of interaction. The annual (average number of diagnosed infections was substantially higher among women than men in both time periods and increased among both men and women. Undiagnosed infection prevalence was substantially higher among black than non-black adults (4.0% vs 1.2%, p = 0.042 in 1997-98 and 5.5% vs 0.7%, p<0.001 in 2006-09. CONCLUSION: Divergent trends in undiagnosed chlamydial infection by gender parallel divergent screening recommendations that encourage chlamydial testing for women but not for men.

  14. PT-symmetry breaking with divergent potentials: lattice and continuum cases

    CERN Document Server

    Joglekar, Yogesh N; Saxena, Avadh

    2014-01-01

    We investigate the parity- and time-reversal ($\\mathcal{PT}$)-symmetry breaking in lattice models in the presence of long-ranged, non-hermitian, $\\mathcal{PT}$-symmetric potentials that remain finite or become divergent in the continuum limit. By scaling analysis of the fragile $\\mathcal{PT}$ threshold for an open finite lattice, we show that continuum loss-gain potentials $V_\\alpha(x)\\propto i |x|^\\alpha \\mathrm{sign}(x)$ have a positive $\\mathcal{PT}$-breaking threshold for $\\alpha>-2$, and a zero threshold for $\\alpha\\leq -2$. When $\\alpha<0$ localized states with complex (conjugate) energies in the continuum energy-band occur at higher loss-gain strengths. We investigate the signatures of $\\mathcal{PT}$-symmetry breaking in coupled waveguides, and show that the emergence of localized states dramatically shortens the relevant time-scale in the $\\mathcal{PT}$-symmetry broken region.

  15. Duplication and divergent evolution of the CHS and CHS-like genes in the chalcone synthase (CHS) superfamily

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The enzymes of the CHS-superfamily are responsible for biosynthesis of a wide range of natural products in plants. They are important for flower pigmentation, protection against UV light and defense against phytopathogens. Many plants were found to contain multiple copies of CHS genes. This review summarizes the recent progress in the studies of the CHS-superfamily, focusing on the duplication and divergent evolution of the CHS and CHS-like genes. Comparative analyses of gene structure, expression patterns and catalytic properties revealed extensive differentiation in both regulation and function among duplicate CHS genes. It is also proposed that the CHS-like enzymes in the CHS-superfamily evolved from CHS at different times in various organisms. The CHS-superfamily thus offers a valuable model to study the rates and patterns of sequence divergence between duplicate genes.

  16. On calculation of quasi-two-dimensional divergence-free projections for visualization of three-dimensional incompressible flows

    CERN Document Server

    Gelfgat, Alexander

    2015-01-01

    A visualization of three-dimensional incompressible flows by divergence-free quasi-two-dimensional projections of the velocity field on three coordinate planes was recently proposed. The projections were calculated using divergence-free Galerkin bases, which resulted in the whole procedure being complicated and CPU-time consuming. Here we propose an alternative way based on the Chorin projection combined with a SIMPLE-like iteration. The approach proposed is much easier in realization, allows for faster computations, and can be generalized for arbitrary curvilinear orthogonal coordinates. To illustrate the visualization method, examples of flow visualization in cylindrical and spherical coordinates, as well as post-processing of experimental 3D-PTV data are presented.

  17. Marker-aided genetic divergence analysis in Brassica

    Indian Academy of Sciences (India)

    V. Arunachalam; Shefali Verma; V. Sujata; K. V. Prabhu

    2005-08-01

    Genetic divergence was evaluated in 31 breeding lines from four Brassica species using Mahalanobis’ $D^{2}$. A new method of grouping using $D^{2}$ values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.

  18. Transcriptional divergence and conservation of human and mouse erythropoiesis.

    Science.gov (United States)

    Pishesha, Novalia; Thiru, Prathapan; Shi, Jiahai; Eng, Jennifer C; Sankaran, Vijay G; Lodish, Harvey F

    2014-03-18

    Mouse models have been used extensively for decades and have been instrumental in improving our understanding of mammalian erythropoiesis. Nonetheless, there are several examples of variation between human and mouse erythropoiesis. We performed a comparative global gene expression study using data from morphologically identical stage-matched sorted populations of human and mouse erythroid precursors from early to late erythroblasts. Induction and repression of major transcriptional regulators of erythropoiesis, as well as major erythroid-important proteins, are largely conserved between the species. In contrast, at a global level we identified a significant extent of divergence between the species, both at comparable stages and in the transitions between stages, especially for the 500 most highly expressed genes during development. This suggests that the response of multiple developmentally regulated genes to key erythroid transcriptional regulators represents an important modification that has occurred in the course of erythroid evolution. In developing a systematic framework to understand and study conservation and divergence between human and mouse erythropoiesis, we show how mouse models can fail to mimic specific human diseases and provide predictions for translating findings from mouse models to potential therapies for human disease.

  19. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Science.gov (United States)

    Sutphin, George L; Mahoney, J Matthew; Sheppard, Keith; Walton, David O; Korstanje, Ron

    2016-11-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  20. Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

    Directory of Open Access Journals (Sweden)

    Xiangyu Guan, Song Qin, Fangqing Zhao, Xiaowen Zhang, Xuexi Tang

    2007-01-01

    Full Text Available Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs, and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state. We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

  1. Spontaneous divergent elbow dislocation after Sauve-Kapandji procedure.

    Science.gov (United States)

    Moritomo, Hisao; Izawa, Kazutaka; Murase, Tsuyoshi; Hashimoto, Hideo; Goto, Akira; Masatomi, Takashi

    2003-01-01

    This is a report on an unusual complication of the Sauve-Kapandji procedure in patients with rheumatoid arthritis. Two women with rheumatoid arthritis who previously had an ipsilateral Sauve-Kapandji procedure experienced spontaneous transverse divergent elbow dislocations without evident trauma. Their radiographs showed medial dislocation of the proximal ulna, which was separated from the radial head. The radial head and distal end of the ulnar shaft showed remarkable instability by a pronation and supination motion without the radial and ulnar shafts being separated from each other. Stress radiographic examination showed significant loosening of all ligaments except the medial collateral ligament around the elbow and did not show disruption of the interosseous membrane. A unique chronic twist radioulnar dissociation which consists of gross instability of the radial head and the distal ulna without disruption of the interosseous membrane was considered to cause instability of the humeroulnar joint, which results in medial dislocation of the proximal ulna. This report suggests that there is a direct cause and effect relationship between the residual distal ulnar instability and the development of transverse divergent dislocation of the elbow in patients with rheumatoid arthritis after the Sauve-Kapandji procedure.

  2. A highly divergent Puumala virus lineage in southern Poland.

    Science.gov (United States)

    Rosenfeld, Ulrike M; Drewes, Stephan; Ali, Hanan Sheikh; Sadowska, Edyta T; Mikowska, Magdalena; Heckel, Gerald; Koteja, Paweł; Ulrich, Rainer G

    2017-01-16

    Puumala virus (PUUV) represents one of the most important hantaviruses in Central Europe. Phylogenetic analyses of PUUV strains indicate a strong genetic structuring of this hantavirus. Recently, PUUV sequences were identified in the natural reservoir, the bank vole (Myodes glareolus), collected in the northern part of Poland. The objective of this study was to evaluate the presence of PUUV in bank voles from southern Poland. A total of 72 bank voles were trapped in 2009 at six sites in this part of Poland. RT-PCR and IgG-ELISA analyses detected three PUUV positive voles at one trapping site. The PUUV-infected animals were identified by cytochrome b gene analysis to belong to the Carpathian and Eastern evolutionary lineages of bank vole. The novel PUUV S, M and L segment nucleotide sequences showed the closest similarity to sequences of the Russian PUUV lineage from Latvia, but were highly divergent to those previously found in northern Poland, Slovakia and Austria. In conclusion, the detection of a highly divergent PUUV lineage in southern Poland indicates the necessity of further bank vole monitoring in this region allowing rational public health measures to prevent human infections.

  3. Structures of pyruvate kinases display evolutionarily divergent allosteric strategies.

    Science.gov (United States)

    Morgan, Hugh P; Zhong, Wenhe; McNae, Iain W; Michels, Paul A M; Fothergill-Gilmore, Linda A; Walkinshaw, Malcolm D

    2014-09-01

    The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.

  4. Divergent models of diabetes among American Indian elders.

    Science.gov (United States)

    Henderson, Linda Carson

    2010-12-01

    The purpose of this study was to examine belief systems about diabetes in American Indian elders, and the effects of culture on care-seeking, adherence, and diabetes self-care. Health belief theory predicts that care-seeking and medical adherence are a function of culturally mediated beliefs that result in behaviors that effect health status. In order to elicit cultural meanings of diabetes, in-depth interviews were conducted with an intensity sample of 30 American Indian diabetic elders (55+). Two models of diabetes were identified, divergent in terms of 1) health behaviors, and 2) cultural identification. One model was characterized by delayed care-seeking, and a non-valuing of adherence to diabetes self-care. Non-adherence to medical recommendations was perceived as being socially desirable, because adherence placed the elder outside their peer group. The second model was characterized by early care-seeking and improved adherence to diabetes self-care. These divergent models of diabetes, in which care-seeking, diabetes self-care, and adherence vary as a function of cultural immersion, has implications for health education and disease management and may contribute substantially to health disparities.

  5. Rapid divergence of two classes of Haemophilus ducreyi.

    Science.gov (United States)

    Ricotta, Emily E; Wang, Nan; Cutler, Robin; Lawrence, Jeffrey G; Humphreys, Tricia L

    2011-06-01

    Haemophilus ducreyi, the etiologic agent of chancroid, expresses variants of several key virulence factors. While previous reports suggested that H. ducreyi strains formed two clonal populations, the differences between, and diversity within, these populations were unclear. To assess their variability, we examined sequence diversity at 11 H. ducreyi loci, including virulence and housekeeping genes, augmenting published data sets with PCR-amplified genes to acquire data for at least 10 strains at each locus. While sequences from all 11 loci place strains into two distinct groups, there was very little variation within each group. The difference between alleles of the two groups was variable and large at 3 loci encoding surface-exposed proteins (0.4 < K(S) < 1.3, where K(S) is divergence at synonymous sites) but consistently small at genes encoding cytoplasmic or periplasmic proteins (K(S) < 0.09). The data suggest that the two classes have recently diverged, that recombination has introduced variant alleles into at least 3 distinct loci, and that these alleles have been confined to one of the two classes. In addition, recombination is evident among alleles within, but not between, classes. Rather than clones of the same species, these properties indicate that the two classes may form distinct species.

  6. Gene duplication and divergence affecting drug content in Cannabis sativa.

    Science.gov (United States)

    Weiblen, George D; Wenger, Jonathan P; Craft, Kathleen J; ElSohly, Mahmoud A; Mehmedic, Zlatko; Treiber, Erin L; Marks, M David

    2015-12-01

    Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency.

  7. Effect of fringe divergence in fluid acceleration measurement using LDA

    Energy Technology Data Exchange (ETDEWEB)

    Chun, Se Jong; Sung, Hyung Jin [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of); Nobach, Holger; Tropea, Cam [Technische Universitat Darmstadt, Darmstadt (Germany)

    2004-07-01

    The laser Doppler technique is well-established as a velocity measurement technique of high precision for flow velocity. Recently, the laser Doppler technique has also been used to measure acceleration of fluid particles. Acceleration is interesting from a fluid mechanics point of view, since the Navier Stokes equations, specifically the left-hand-side, are formulated in terms of fluid acceleration. Further, there are several avenues to estimating the dissipation rate using the acceleration. However such measurements place additional demands on the design of the optical system; in particular fringe non-uniformity must be held below about 0.0001 to avoid systematic errors. Relations expressing fringe divergence as a function of the optical parameters of the system have been given in the literature; however, direct use of these formulae to minimize fringe divergence lead either to very large measurement volumes or to extremely high intersection angles. This dilemma can be resolved by using an off-axis receiving arrangement, in which the measurement volume is truncated by a pinhole in front of the detection plane. In the present study an optical design study is performed for optimizing laser Doppler systems for fluid acceleration measurements. This is followed by laboratory validation using a round free jet and a stagnation flow, two flows in which either fluid acceleration has been previously measured or in which the acceleration is known analytically. A 90 degree off-axis receiving angle is used with a pinhole or a slit.

  8. [Genetic divergence of mitochondrial DNA in white char Salvelinus albus and northern Dolly Varden char Salvelinus malma malma].

    Science.gov (United States)

    Oleĭnik, A G; Skurikhina, L A; Brykov, Vl A

    2010-03-01

    Comparative analysis of mitochondrial DNA variation was performed in white char Salvelinus albus and in its putative ancestor species, northern Dolly Varden char Salvelinus malma malma. Highly statistically significant differentiation of S. albus and S. m. malma in the areas of sympatric (Kamchatka River basin) and allopatric (Kronotskoe Lake and Kronotskaya River) residence was demonstrated. The mtDNA divergence between S. albus and S. m. malma did not exceed the range ofintraspecific variation in the populations of northern Dolly Varden char. At the same time, clusterization pattern of the Salvelinus chars provides hypothesis on the common origin of two allopatric populations of white char. Genealogical analysis of haplotypes indicates that S. albus and S. m. malma currently demonstrate incomplete radiation of mitochondrial lineages. The low nucleotide divergence estimates between S. albus and S. m. malma reflect the short time period since the beginning of the radiation of ancestral lineages. These estimates are determined by ancestral polymorphism and haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.

  9. Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs.

    Science.gov (United States)

    Roesti, Marius; Hendry, Andrew P; Salzburger, Walter; Berner, Daniel

    2012-06-01

    Evolutionary diversification is often initiated by adaptive divergence between populations occupying ecologically distinct environments while still exchanging genes. The genetic foundations of this divergence process are largely unknown and are here explored through genome scans in multiple independent lake-stream population pairs of threespine stickleback. We find that across the pairs, overall genomic divergence is associated with the magnitude of divergence in phenotypes known to be under divergent selection. Along this same axis of increasing diversification, genomic divergence becomes increasingly biased towards the centre of chromosomes as opposed to the peripheries. We explain this pattern by within-chromosome variation in the physical extent of hitchhiking, as recombination is greatly reduced in chromosome centres. Correcting for this effect suggests that a great number of genes distributed widely across the genome are involved in the divergence into lake vs. stream habitats. Analyzing additional allopatric population pairs, however, reveals that strong divergence in some genomic regions has been driven by selection unrelated to lake-stream ecology. Our study highlights a major contribution of large-scale variation in recombination rate to generating heterogeneous genomic divergence and indicates that elucidating the genetic basis of adaptive divergence might be more challenging than currently recognized.

  10. Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon.

    Science.gov (United States)

    Wessinger, Carolyn A; Hileman, Lena C; Rausher, Mark D

    2014-08-05

    Distinct floral pollination syndromes have emerged multiple times during the diversification of flowering plants. For example, in western North America, a hummingbird pollination syndrome has evolved more than 100 times, generally from within insect-pollinated lineages. The hummingbird syndrome is characterized by a suite of floral traits that attracts and facilitates pollen movement by hummingbirds, while at the same time discourages bee visitation. These floral traits generally include large nectar volume, red flower colour, elongated and narrow corolla tubes and reproductive organs that are exerted from the corolla. A handful of studies have examined the genetic architecture of hummingbird pollination syndrome evolution. These studies find that mutations of relatively large effect often explain increased nectar volume and transition to red flower colour. In addition, they suggest that adaptive suites of floral traits may often exhibit a high degree of genetic linkage, which could facilitate their fixation during pollination syndrome evolution. Here, we explore these emerging generalities by investigating the genetic basis of floral pollination syndrome divergence between two related Penstemon species with different pollination syndromes--bee-pollinated P. neomexicanus and closely related hummingbird-pollinated P. barbatus. In an F2 mapping population derived from a cross between these two species, we characterized the effect size of genetic loci underlying floral trait divergence associated with the transition to bird pollination, as well as correlation structure of floral trait variation. We find the effect sizes of quantitative trait loci for adaptive floral traits are in line with patterns observed in previous studies, and find strong evidence that suites of floral traits are genetically linked. This linkage may be due to genetic proximity or pleiotropic effects of single causative loci. Interestingly, our data suggest that the evolution of floral traits

  11. Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis

    Directory of Open Access Journals (Sweden)

    Ornelas Juan

    2011-02-01

    Full Text Available Abstract Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma, and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the

  12. Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka populations

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    Habicht Christopher

    2011-02-01

    Full Text Available Abstract Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance and ecology (spawning habitat and timing driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second

  13. Divergência genética entre cultivares de caupi Genetic divergence among cultivars of cowpea

    Directory of Open Access Journals (Sweden)

    Francisco José de Oliveira

    2003-05-01

    Full Text Available O objetivo deste trabalho foi quantificar a divergência genética de cultivares de caupi, agrupadas por análise multivariada visando à seleção de parentais superiores. Foram utilizadas 16 cultivares de caupi [Vigna unguiculata (L. Walp.] do banco de germoplasma do Centro de Ciências Agrárias da Universidade Federal do Ceará. As observações fenotípicas foram realizadas num ensaio com delineamento experimental em blocos completos casualizados, com seis blocos e 16 tratamentos, incluindo três testemunhas, com parcela experimental de 24 m² e área útil de 16 m², sendo quatro fileiras de plantas, com espaços de 1,0 x 0,5 m, contendo duas plantas por cova. Para mensurar os caracteres fenotípicos, cinco plantas competitivas, localizadas nas duas fileiras centrais da parcela, foram tomadas ao acaso. Os cruzamentos entre os grupos I [TVx-337-3F e Vita-4 (TVu 1977-OD] e II (Bengala e V-4 Alagoas podem resultar em produção de novas combinações gênicas, por serem divergentes e reunirem maior número de caracteres agronomicamente desejáveis. Os caracteres que mais contribuem para divergência genética são o comprimento da vagem (36,80% e o peso de 100 sementes (19,21%.This work aimed to determine the genetic divergence among cowpea cultivars [Vigna unguiculata (L. Walp.] when grouped in a multivariate analysis concerning to select superior parents. So 16 cowpea cultivars were used from the germplasm bank of the Centro de Ciências Agrárias of the Universidade Federal do Ceará, in Brazil. The data were accomplished in complete randomized blocks, with six blocks, 16 treatments and three cultivar checks. The total area of experimental plots was 24 m² and the net area was 16 m², displayed in four rows, plants were spaced about 1.0 x 0.5 m with two plants in each plot. The phenotypic data were estimated from five competitive plants as casual samples on two central rows of each replicate. Breeding among the groups I [TVx-337-3F and

  14. Genomic islands of divergence are not affected by geography of speciation in sunflowers.

    Science.gov (United States)

    Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

    2013-01-01

    Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

  15. Understanding creative cultural divergence: a Bakhtinian reflection from a culture-crossing scholar

    Science.gov (United States)

    Hsu, Pei-Ling

    2012-03-01

    I respond to Baron and Chen's article on creative cultural divergence, which they describe as the novel pedagogy of diverging from culturally generated educational expectations. Their article provides an analysis on how an experienced Taiwanese teacher drew on different forms of creative cultural divergence to facilitate students' critical thinking and science inquiry. To better understand the phenomenon of creative cultural divergence, I draw on Bakhtin's concepts of outsideness, novelization, and internally persuasive discourse to analyze how these divergences are produced. These concepts not only help us to understand the phenomenon of creative cultural divergence, they also help me to reflect on my own culture-crossing experience. The implications of these concepts for culture and education are further discussed.

  16. Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

    Directory of Open Access Journals (Sweden)

    Runemark Anna

    2010-09-01

    Full Text Available Abstract Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s ST for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that

  17. Divergence of gene body DNA methylation and evolution of plant duplicate genes.

    Directory of Open Access Journals (Sweden)

    Jun Wang

    Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

  18. Systematization of basic divergent integrals in perturbation theory and renormalization group functions

    Energy Technology Data Exchange (ETDEWEB)

    Brito, L.C.T. [Federal University of Minas Gerais, Physics Department, ICEx, PO Box 702, 30.161-970 Belo Horizonte, MG (Brazil)], E-mail: lctbrito@fisica.ufmg.br; Fargnoli, H.G. [Federal University of Minas Gerais, Physics Department, ICEx, PO Box 702, 30.161-970 Belo Horizonte, MG (Brazil)], E-mail: helvecio@fisica.ufmg.br; Baeta Scarpelli, A.P. [Centro Federal de Educacao Tecnologica, MG, Avenida Amazonas, 7675, 30510-000 Nova Gameleira, Belo Horizonte, MG (Brazil)], E-mail: scarp@fisica.ufmg.br; Sampaio, Marcos [Federal University of Minas Gerais, Physics Department, ICEx, PO Box 702, 30.161-970 Belo Horizonte, MG (Brazil)], E-mail: msampaio@fisica.ufmg.br; Nemes, M.C. [Federal University of Minas Gerais, Physics Department, ICEx, PO Box 702, 30.161-970 Belo Horizonte, MG (Brazil)], E-mail: carolina@fisica.ufmg.br

    2009-03-23

    We show that to n loop order the divergent content of a Feynman amplitude is spanned by a set of basic (logarithmically divergent) integrals I{sub log}{sup (i)}({lambda}{sup 2}), i=1,2,...,n, {lambda} being the renormalization group scale, which need not be evaluated. Only the coefficients of the basic divergent integrals are show to determine renormalization group functions. Relations between these coefficients of different loop orders are derived.

  19. [Complexity analysis of gait signal based on Jensen-Shannon divergence].

    Science.gov (United States)

    Wang, Peicun; Wang, Jun

    2014-06-01

    When people are walking, they will produce gait signals and different people will produce different gait signals. The research of the gait signal complexity is really of great significance for medicine. By calculating people's gait signal complexity, we can assess a person's health status and thus timely detect and diagnose diseases. In this study, the Jensen-Shannon divergence (JSD), the method of complexity analysis, was used to calculate the complexity of gait signal in the healthy elderly, healthy young people and patients with Parkinson's disease. Then we detected the experimental data by variance detection. The results showed that the difference among the complexity of the three gait signals was great. Through this research, we have got gait signal complexity range of patients with Parkinson's disease, the healthy elderly and healthy young people, respectively, which would provide an important basis for clinical diagnosis.

  20. Reduced description of nonequilibrium processes and correlation functions. Divergences and non-analyticity

    Directory of Open Access Journals (Sweden)

    A.I.Sokolovsky

    2006-01-01

    Full Text Available A complete theory for investigation of time correlation functions is developed on the basis of the Bogolyubov reduced description method proceeding from his functional hypothesis. The problem of convergence in the theory of nonequilibrium processes and its relation to the non-analytic dependence of basic values of the theory on a small parameter of the perturbation theory are discussed. A natural regularization of integral equations of the theory is proposed. In the framework of a model of slow variables (hydrodynamics of a fluid, kinetics of a gas a generalized perturbation theory without divergencies is constructed corresponding to a partial summation in a usual perturbation theory. Properties of Green functions are discussed on the basis of resolvent formalism for the Liouville operator. A generalized Ernst and Dorfman theory is elaborated allowing to study the peculiarities of correlation and Green functions and to solve the convergence problem in the reduced description method.

  1. A Divergence Statistics Extension to VTK for Performance Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Pebay, Philippe Pierre [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bennett, Janine Camille [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-02-01

    This report follows the series of previous documents ([PT08, BPRT09b, PT09, BPT09, PT10, PB13], where we presented the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k -means, order and auto-correlative statistics engines which we developed within the Visualization Tool Kit ( VTK ) as a scalable, parallel and versatile statistics package. We now report on a new engine which we developed for the calculation of divergence statistics, a concept which we hereafter explain and whose main goal is to quantify the discrepancy, in a stasticial manner akin to measuring a distance, between an observed empirical distribution and a theoretical, "ideal" one. The ease of use of the new diverence statistics engine is illustrated by the means of C++ code snippets. Although this new engine does not yet have a parallel implementation, it has already been applied to HPC performance analysis, of which we provide an example.

  2. Microfluidic converging/diverging channels optimised for homogeneous extensional deformation

    Science.gov (United States)

    Zografos, K.; Oliveira, M. S. N.

    2016-01-01

    In this work, we optimise microfluidic converging/diverging geometries in order to produce constant strain-rates along the centreline of the flow, for performing studies under homogeneous extension. The design is examined for both two-dimensional and three-dimensional flows where the effects of aspect ratio and dimensionless contraction length are investigated. Initially, pressure driven flows of Newtonian fluids under creeping flow conditions are considered, which is a reasonable approximation in microfluidics, and the limits of the applicability of the design in terms of Reynolds numbers are investigated. The optimised geometry is then used for studying the flow of viscoelastic fluids and the practical limitations in terms of Weissenberg number are reported. Furthermore, the optimisation strategy is also applied for electro-osmotic driven flows, where the development of a plug-like velocity profile allows for a wider region of homogeneous extensional deformation in the flow field. PMID:27478523

  3. Convergent and divergent mechanisms of sugar recognition across kingdoms.

    Science.gov (United States)

    Taylor, Maureen E; Drickamer, Kurt

    2014-10-01

    Protein modules that bind specific oligosaccharides are found across all kingdoms of life from single-celled organisms to man. Different, overlapping and evolving designations for sugar-binding domains in proteins can sometimes obscure common features that often reflect convergent solutions to the problem of distinguishing sugars with closely similar structures and binding them with sufficient affinity to achieve biologically meaningful results. Structural and functional analysis has revealed striking parallels between protein domains with widely different structures and evolutionary histories that employ common solutions to the sugar recognition problem. Recent studies also demonstrate that domains descended from common ancestors through divergent evolution appear more widely across the kingdoms of life than had previously been recognized.

  4. Summation of divergent series: Order-dependent mapping

    CERN Document Server

    Zinn-Justin, Jean

    2010-01-01

    Summation methods play a very important role in quantum field theory because all perturbation series are divergent and the expansion parameter is not always small. A number of methods have been tried in this context, most notably Pade approximants, Borel--Pade summation, Borel transformation with mapping, which we briefly describe and one on which we concentrate here, Order-Dependent Mapping (ODM). We recall the basis of the method, for a class of series we give intuitive arguments to explain its convergence and illustrate its properties by several simple examples. Since the method was proposed, some rigorous convergence proofs were given. The method has also found a number of applications and we shall list a few.

  5. Performance evaluation of advanced industrial SPECT system with diverging collimator.

    Science.gov (United States)

    Park, Jang Guen; Jung, Sung-Hee; Kim, Jong Bum; Moon, Jinho; Yeom, Yeon Soo; Kim, Chan Hyeong

    2014-12-01

    An advanced industrial SPECT system with 12-fold-array diverging collimator was developed for flow visualization in industrial reactors and was discussed in the previous study. The present paper describes performance evaluation of the SPECT system under both static- and dynamic- flow conditions. Under static conditions, the movement of radiotracer inside the test reactor was compared with that of color tracer (blue ink) captured with a high-speed camera. The comparison of the reconstructed images obtained with the radiotracer and the SPECT system showed fairly good agreement with video-frames of the color tracer obtained with the camera. Based on the results of the performance evaluation, it is concluded that the SPECT system is suitable for investigation and visualization of flows in industrial flow reactors.

  6. Kullback-Leibler divergence and the Pareto-Exponential approximation.

    Science.gov (United States)

    Weinberg, G V

    2016-01-01

    Recent radar research interests in the Pareto distribution as a model for X-band maritime surveillance radar clutter returns have resulted in analysis of the asymptotic behaviour of this clutter model. In particular, it is of interest to understand when the Pareto distribution is well approximated by an Exponential distribution. The justification for this is that under the latter clutter model assumption, simpler radar detection schemes can be applied. An information theory approach is introduced to investigate the Pareto-Exponential approximation. By analysing the Kullback-Leibler divergence between the two distributions it is possible to not only assess when the approximation is valid, but to determine, for a given Pareto model, the optimal Exponential approximation.

  7. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.

    Science.gov (United States)

    Gallone, Brigida; Steensels, Jan; Prahl, Troels; Soriaga, Leah; Saels, Veerle; Herrera-Malaver, Beatriz; Merlevede, Adriaan; Roncoroni, Miguel; Voordeckers, Karin; Miraglia, Loren; Teiling, Clotilde; Steffy, Brian; Taylor, Maryann; Schwartz, Ariel; Richardson, Toby; White, Christopher; Baele, Guy; Maere, Steven; Verstrepen, Kevin J

    2016-09-01

    Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP.

  8. Entangled inequalities, divergent struggles: migration and the Argentine textile industry

    Directory of Open Access Journals (Sweden)

    Sergio Caggiano

    2014-09-01

    Full Text Available Despite the economic recovery that followed the 2001-2002 crisis in Argentina, sectors that rely on a significant migrant worker presence, such as textiles, have maintained and consolidated previously-existing forms of exploitation and discrimination. In this context, trade unions and other civil society actors are fighting against the inequalities that affect Bolivian migrant workers in the textile industry in Buenos Aires and La Plata. This article seeks to understand some of the limitations of that struggle. Such limitations relate to the difficulty of acting on entangled inequalities, and respond to the seemingly irreconcilable forms of association in terms of class, nationality or ethnicity of these organisations, which generate divergent characterisations of the inequalities and of the actors involved.

  9. Research Performance Progress Report: Diverging Supernova Explosion Experiments on NIF

    Energy Technology Data Exchange (ETDEWEB)

    Plewa, Tomasz [Florida State Univ., Tallahassee, FL (United States)

    2016-10-25

    The aim of this project was to design a series of blast-wave driven Rayleigh-Taylor (RT) experiments on the National Ignition Facility (NIF). The experiments of this kind are relevant to mixing in core-collapse supernovae (ccSNe) and have the potential to address previously unanswered questions in high-energy density physics (HEDP) and astrophysics. The unmatched laser power of the NIF laser offers a unique chance to observe and study “new physics” like the mass extensions observed in HEDP RT experiments performed on the Omega laser [1], which might be linked to self-generated magnetic fields [2] and so far could not be reproduced by numerical simulations. Moreover, NIF is currently the only facility that offers the possibility to execute a diverging RT experiment, which would allow to observe processes such as inter-shell penetration via turbulent mixing and shock-proximity effects (distortion of the shock by RT spikes).

  10. A Divergence Statistics Extension to VTK for Performance Analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Pebay, Philippe Pierre; Bennett, Janine Camille

    2015-02-01

    This report follows the series of previous documents ([PT08, BPRT09b, PT09, BPT09, PT10, PB13], where we presented the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k -means, order and auto-correlative statistics engines which we developed within the Visualization Tool Kit ( VTK ) as a scalable, parallel and versatile statistics package. We now report on a new engine which we developed for the calculation of divergence statistics, a concept which we hereafter explain and whose main goal is to quantify the discrepancy, in a stasticial manner akin to measuring a distance, between an observed empirical distribution and a theoretical, "ideal" one. The ease of use of the new diverence statistics engine is illustrated by the means of C++ code snippets. Although this new engine does not yet have a parallel implementation, it has already been applied to HPC performance analysis, of which we provide an example.

  11. Global divergence of the human follicle mite Demodex folliculorum

    DEFF Research Database (Denmark)

    Palopoli, Michael F.; Fergus, Daniel J.; Minot, Samuel

    2015-01-01

    Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries...... American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years......, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model...

  12. Optimism in Reinforcement Learning Based on Kullback-Leibler Divergence

    CERN Document Server

    Filippi, Sarah; Garivier, Aurélien

    2010-01-01

    We consider model-based reinforcement learning in finite Markov Decision Processes (MDPs), focussing on so-called optimistic strategies. Optimism is usually implemented by carrying out extended value iterations, under a constraint of consistency with the estimated model transition probabilities. In this paper, we strongly argue in favor of using the Kullback-Leibler (KL) divergence for this purpose. By study- ing the linear maximization problem under KL constraints, we provide an efficient algorithm for solving KL-optimistic extended value iteration. When implemented within the structure of UCRL2, the near-optimal method introduced by [Auer et al, 2008], this algorithm also achieves bounded regrets in the undiscounted case. We however provide some geometric arguments as well as a concrete illustration on a simulated example to explain the observed improved practical behavior, particularly when the MDP has reduced connectivity. To analyze this new algorithm, termed KL-UCRL, we also rely on recent deviation bou...

  13. Agreements and Divergences in German Idealism: Regarding the Publication

    Directory of Open Access Journals (Sweden)

    Hugo Ochoa

    2011-12-01

    Full Text Available The history of German Idealism is marked by points of agreement and divergence among those who attempted to complete a task that might have remained unfinished in terms of its first formulations and that would lead to the definitive constitution of philosophy. In this sense, the correspondence among Kant, Fichte, Schelling, and Hegel makes it possible to unravel, to some extent, the non-explicitassumptions underlying the systems of these thinkers, since it reveals the questions,objectives, initial formulations, discussions, and differences that would later acquire a systematic structure. This article attempts to show how despite the intention of these philosophers to remain faithful to an original impulse, that allegedfidelity was based on essential misunderstandings.

  14. Divergent series, summability and resurgence I monodromy and resurgence

    CERN Document Server

    Mitschi, Claude

    2016-01-01

    Providing an elementary introduction to analytic continuation and monodromy, the first part of this volume applies these notions to the local and global study of complex linear differential equations, their formal solutions at singular points, their monodromy and their differential Galois groups. The Riemann-Hilbert problem is discussed from Bolibrukh’s point of view. The second part expounds 1-summability and Ecalle’s theory of resurgence under fairly general conditions. It contains numerous examples and presents an analysis of the singularities in the Borel plane via “alien calculus”, which provides a full description of the Stokes phenomenon for linear or non-linear differential or difference equations. The first of a series of three, entitled Divergent Series, Summability and Resurgence, this volume is aimed at graduate students, mathematicians and theoretical physicists interested in geometric, algebraic or local analytic properties of dynamical systems. It includes useful exercises with solution...

  15. Independence divergence-generated binary trees of amino acids.

    Science.gov (United States)

    Tusnády, G E; Tusnády, G; Simon, I

    1995-05-01

    The discovery of the relationship between amino acids is important in terms of the replacement ability, as used in protein engineering homology studies, and gaining a better understanding of the roles which various properties of the residues play in the creation of a unique, stable, 3-D protein structure. Amino acid sequences of proteins edited by evolution are anything but random. The measure of nonrandomness, i.e. the level of editing, can be characterized by an independence divergence value. This parameter is used to generate binary tree relationships between amino acids. The relationships of residues presented in this paper are based on protein building features and not on the physico-chemical characteristics of amino acids. This approach is not biased by the tautology present in all sequence similarity-based relationship studies. The roles which various physico-chemical characteristics play in the determination of the relationships between amino acids are also discussed.

  16. Divergence model for measurement of Goos-Hanchen shift

    Science.gov (United States)

    Gray, Jeffrey Frank

    In this effort a new measurement technique for the lateral Goos-Hanchen shift is developed, analyzed, and demonstrated. The new technique uses classical image formation methods fused with modern detection and analysis methods to achieve higher levels of sensitivity than obtained with prior practice. Central to the effort is a new mathematical model of the dispersion seen at a step shadow when the Goos-Hanchen effect occurs near critical angle for total internal reflection. Image processing techniques are applied to measure the intensity distribution transfer function of a new divergence model of the Goos-Hanchen phenomena providing verification of the model. This effort includes mathematical modeling techniques, analytical derivations of governing equations, numerical verification of models and sensitivities, optical design of apparatus, image processing. Keywords--Goos-Hanchen, total internal reflection, evanescent waves, image processing, Canny filters, sub-pixel, Superresolution.

  17. Highly divergent mussel lineages in isolated Indonesian marine lakes

    Directory of Open Access Journals (Sweden)

    Leontine E. Becking

    2016-10-01

    Full Text Available Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI, and two nuclear markers (18S and 28S. In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence, two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%, we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present. Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.

  18. Experimental Investigation of 'Transonic Resonance' with Convergent-Divergent Nozzles

    Science.gov (United States)

    Zaman, K. B. M. Q.; Dahl, M. D.; Bencic, T. J.; Zaman, Khairul (Technical Monitor)

    2001-01-01

    Convergent-divergent nozzles, when run at pressure ratios lower than the design value, often undergo a flow resonance accompanied by the emission of acoustic tones. The phenomenon, different in characteristics from conventional 'screech' tones, has been studied experimentally. Unlike screech, the frequency increases with increasing supply pressure. There is a 'staging' behavior; 'odd harmonic' stages resonate at lower pressures while the fundamental occurs in a range of higher pressures corresponding to a fully expanded Mach number (M(sub j)) around unity. The frequency (f(sub N)) variation with M(sub j) depends on the half angle-of-divergence (theta) of the nozzle. At smaller theta, the slope of f(sub N) versus M(sub j) curve becomes steeper. The resonance involves standing waves and is driven by unsteady shock/boundary layer interaction. The distance between the foot of the shock and the nozzle exit imposes the lengthscale (L'). The fundamental corresponds to a quarterwave resonance, the next stage at a lower supply pressure corresponds to a three-quarter-wave resonance, and so on. The principal trends in the frequency variation are explained simply from the characteristic variation of the length-scale L'. Based on the data, correlation equations are provided for the prediction of f(sub N). A striking feature is that tripping of the boundary layer near the nozzle's throat tends to suppress the resonance. In a practical nozzle a tendency for the occurrence of the phenomenon is thought to be a source of 'internal noise'; thus, there is a potential for noise benefit simply by appropriate boundary layer tripping near the nozzle's throat.

  19. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle.

    Directory of Open Access Journals (Sweden)

    Jared E Decker

    2014-03-01

    Full Text Available The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

  20. Highly divergent mussel lineages in isolated Indonesian marine lakes

    Science.gov (United States)

    de Leeuw, Christiaan A.; Knegt, Bram; Maas, Diede L.; de Voogd, Nicole J.; Abdunnur; Suyatna, Iwan; Peijnenburg, Katja T.C.A.

    2016-01-01

    Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago. PMID:27761314

  1. Fractional integration associated with second order divergence operators on Rn

    Institute of Scientific and Technical Information of China (English)

    DENG; Donggao(

    2003-01-01

    [1]McIntosh, A., Operators which have an H∞-calculus, Miniconference on Operator Theory and Partial Differential Equations (Proceedings of the Centre for Mathematical Analysis, ANU), 1986, 14: 210.[2]Stein, E. M., Singular Integral and Differentiability Properties of Functions, Princeton: Princeton Univ. Press,1970.[3]Auscher, P., Tchamitchian, P., Square Root Problem for Divergence Operators and Related Topics, Astérisque,vol. 249, 1998.[4]Auscher, P., Coulhon, T., Tchamitchian, P., Absence de principe du maximum pour certaines équations paraboliques complexes, Coll. Math., 1996, 171: 87.[5]Auscher, P., Hofmann, S., Lacey, M., The solution of Kato's conjectures, C. R. Acad. Sci. Paris Sr. I Math.,2001, 332: 601.[6]Davies, E. B., Uniformly elliptic operators with measurable coefficients, J. Funct. Anal., 1995, 132: 141.[7]Liskevich, V., Vogt, H., On Lp-spectrum and essential spectra of second order elliptic operators, Proc. London Math. Soc., 2000, 80: 590.[8]Duong, X. T., McIntosh, A., Singular integral operators with non-smooth kernels on irregular domains, Rev.Mat. Iberoamericana, 1999, 15: 233.[9]Lions, J. L., Espaces d'interpolation et domaines de puissances fractionnaires, J. Math. Soc. Japan, 1962, 14:233.[10]Auscher, P., McIntosh, A., Nahmod, A., The square root problem of Kato in one dimension, and first order elliptic systems, Indiana Univ. Math. J., 1997, 46: 659.[11]Deng, D. G., Hah, Y. S., Theory of Hp Spaces (in Chinese), Beijing: Peking Univ. Press, 1992.Vector subdivision schemes in (Lp(Rs))r(1 ≤ p ≤∞) spacesLI Song(李松)[12]Auscher,P.,Tchamitchian,P.,Square roots of elliptic second order divergence operators on strongly Lipschitz domain:L2 theory ,to appear in Journal d' Analyse Mathematique.

  2. Comparison of protein interaction networks reveals species conservation and divergence

    Directory of Open Access Journals (Sweden)

    Teng Maikun

    2006-10-01

    Full Text Available Abstract Background Recent progresses in high-throughput proteomics have provided us with a first chance to characterize protein interaction networks (PINs, but also raised new challenges in interpreting the accumulating data. Results Motivated by the need of analyzing and interpreting the fast-growing data in the field of proteomics, we propose a comparative strategy to carry out global analysis of PINs. We compare two PINs by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs. Using this approach we perform twenty-one pairwise comparisons among the seven recently available PINs of E.coli, H.pylori, S.cerevisiae, C.elegans, D.melanogaster, M.musculus and H.sapiens. In spite of the incompleteness of data, PIN comparison discloses species conservation at the network level and the identified CoNSs are also functionally conserved and involve in basic cellular functions. We investigate the yeast CoNSs and find that many of them correspond to known complexes. We also find that different species harbor many conserved interaction regions that are topologically identical and these regions can constitute larger interaction regions that are topologically different but similar in framework. Based on the species-to-species difference in CoNSs, we infer potential species divergence. It seems that different species organize orthologs in similar but not necessarily the same topology to achieve similar or the same function. This attributes much to duplication and divergence of genes and their associated interactions. Finally, as the application of CoNSs, we predict 101 protein-protein interactions (PPIs, annotate 339 new protein functions and deduce 170 pairs of orthologs. Conclusion Our result demonstrates that the cross-species comparison strategy we adopt is powerful for the exploration of biological problems from the perspective of networks.

  3. Divergent environmental filters drive functional segregation of European peatlands

    Science.gov (United States)

    Robroek, B.; Jassey, V.; Bragazza, L.; Buttler, A.

    2015-12-01

    Plant communities are largely shaped by prevailing climatic conditions. As a result, environmental change is expected to alter the (functional) composition in plant communities. Because plants, and particularly the composition of plant species, play an important role in driving ecosystem processes, it is crucial that we improve our understanding on which environmental factors are most important in shaping plant communities. Here we presnt the results for a cross-Eurpean study, were we assessed the role of environmnetal conditions on plant community composition in 56 peatlands. We show that plant species richness and diversity are relatively stable across the main environmental gradients. Nevertheless, we observe large changes in the plant community structure. In other words, species turnover increased with increasing differences in environmental viariables. Such turnover in the community composition is largely associated to gradients temperature and precipitation, whilst nutrients -often reported as major driver for changes in peatland ecosystems- were only important at the end of the gradient of current deposition levels in Europe. Using a combination of species distribution modelling and species co-occurence patterns, we identified two spatially non-exclusive groups of plant species. Species within a distinct group responded similarly to bioclimatic variables and nutrient deposition levels, whilst between group response was mirrored. These results suggest that these two groups of plants are subjected to divergent environmental filters. Additionally, European peatlands aggregate into two distinct clusters based on plant functional trait composition. Each cluster was dominated by plant species from either one of the two co-response groups. Overall, our results demonstrate that environmental change results in a gradual replacement of plant species from two divergent groups, consequently affecting the functional trait composition in peatlands.

  4. A Δ11 desaturase gene genealogy reveals two divergent allelic classes within the European corn borer (Ostrinia nubilalis

    Directory of Open Access Journals (Sweden)

    Harrison Richard G

    2010-04-01

    Full Text Available Abstract Background Moth pheromone mating systems have been characterized at the molecular level, allowing evolutionary biologists to study how changes in protein sequence or gene expression affect pheromone phenotype, patterns of mating, and ultimately, the formation of barriers to gene exchange. Recent studies of Ostrinia pheromones have focused on the diversity of sex pheromone desaturases and their role in the specificity of pheromone production. Here we produce a Δ11 desaturase genealogy within Ostrinia nubilalis. We ask what has been the history of this gene, and whether this history suggests that changes in Δ11 desaturase have been involved in the divergence of the E and Z O. nubilalis pheromone strains. Results The Δ11 desaturase gene genealogy does not differentiate O. nubilalis pheromone strains. However, we find two distinct clades, separated by 2.9% sequence divergence, that do not sort with pheromone strain, geographic origin, or emergence time. We demonstrate that these clades do not represent gene duplicates, but rather allelic variation at a single gene locus. Conclusions Analyses of patterns of variation at the Δ11 desaturase gene in ECB suggest that this enzyme does not contribute to reproductive isolation between pheromone strains (E and Z. However, our genealogy reveals two deeply divergent allelic classes. Standing variation at loci that contribute to mate choice phenotypes may permit novel pheromone mating systems to arise in the presence of strong stabilizing selection.

  5. Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards.

    Science.gov (United States)

    Lavretsky, Philip; Dacosta, Jeffrey M; Hernández-Baños, Blanca E; Engilis, Andrew; Sorenson, Michael D; Peters, Jeffrey L

    2015-11-01

    Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST  = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST  = 0.017) but comparable to mtDNA (ΦST  = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

  6. A scalable block-preconditioning strategy for divergence-conforming B-spline discretizations of the Stokes problem

    KAUST Repository

    Côrtes, A.M.A.

    2016-10-01

    The recently introduced divergence-conforming B-spline discretizations allow the construction of smooth discrete velocity-pressure pairs for viscous incompressible flows that are at the same time inf−supinf−sup stable and pointwise divergence-free. When applied to the discretized Stokes problem, these spaces generate a symmetric and indefinite saddle-point linear system. The iterative method of choice to solve such system is the Generalized Minimum Residual Method. This method lacks robustness, and one remedy is to use preconditioners. For linear systems of saddle-point type, a large family of preconditioners can be obtained by using a block factorization of the system. In this paper, we show how the nesting of “black-box” solvers and preconditioners can be put together in a block triangular strategy to build a scalable block preconditioner for the Stokes system discretized by divergence-conforming B-splines. Besides the known cavity flow problem, we used for benchmark flows defined on complex geometries: an eccentric annulus and hollow torus of an eccentric annular cross-section.

  7. Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures.

    Science.gov (United States)

    Kusters, Elske; Della Pina, Serena; Castel, Rob; Souer, Erik; Koes, Ronald

    2015-08-15

    Higher plant species diverged extensively with regard to the moment (flowering time) and position (inflorescence architecture) at which flowers are formed. This seems largely caused by variation in the expression patterns of conserved genes that specify floral meristem identity (FMI), rather than changes in the encoded proteins. Here, we report a functional comparison of the promoters of homologous FMI genes from Arabidopsis, petunia, tomato and Antirrhinum. Analysis of promoter-reporter constructs in petunia and Arabidopsis, as well as complementation experiments, showed that the divergent expression of leafy (LFY) and the petunia homolog aberrant leaf and flower (ALF) results from alterations in the upstream regulatory network rather than cis-regulatory changes. The divergent expression of unusual floral organs (UFO) from Arabidopsis, and the petunia homolog double top (DOT), however, is caused by the loss or gain of cis-regulatory promoter elements, which respond to trans-acting factors that are expressed in similar patterns in both species. Introduction of pUFO:UFO causes no obvious defects in Arabidopsis, but in petunia it causes the precocious and ectopic formation of flowers. This provides an example of how a change in a cis-regulatory region can account for a change in the plant body plan.

  8. Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity.

    Directory of Open Access Journals (Sweden)

    Manabu Sakamoto

    Full Text Available BACKGROUND: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. METHODOLOGY/PRINCIPAL FINDINGS: A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time. The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. CONCLUSIONS/SIGNIFICANCE: Ancestors of large cats in the 'Panthera' lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider

  9. Phenotypic divergence in reproductive traits of a moth population experiencing a phenological shift.

    Science.gov (United States)

    Santos, Helena M; Paiva, Maria-Rosa; Rocha, Susana; Kerdelhué, Carole; Branco, Manuela

    2013-12-01

    Allochrony that is reproductive isolation by time may further lead to divergence of reproductive adaptive traits in response to different environmental pressures over time. A unique "summer" population of the pine processionary moth Thaumetopoea pityocampa, reproductively isolated from the typical winter populations by allochronic differentiation, is here analyzed. This allochronically shifted population reproduces in the spring and develops in the summer, whereas "winter" populations reproduce in the late summer and have winter larval development. Both summer and winter populations coexist in the same pine stands, yet they face different climatic pressures as their active stages are present in different seasons. The occurrence of significant differences between the reproductive traits of the summer population and the typical winter populations (either sympatric or allopatric) is thus hypothesized. Female fecundity, egg size, egg covering, and egg parasitism were analyzed showing that the egg load was lower and that egg size was higher in the summer population than in all the studied winter populations. The scales that cover the egg batches of T. pityocampa differed significantly between populations in shape and color, resulting in a looser and darker covering in the summer population. The single specialist egg parasitoid species of this moth was almost missing in the summer population, and the overall parasitism rates were lower than in the winter population. Results suggest the occurrence of phenotypic differentiation between the summer population and the typical T. pityocampa winter populations for the life-history traits studied. This work provides an insight into how ecological divergence may follow the process of allochronic reproductive isolation.

  10. Why do lifespan variability trends for the young and old diverge? A perturbation analysis

    Directory of Open Access Journals (Sweden)

    Michal Engelman

    2014-05-01

    Full Text Available Background: Variation in lifespan has followed strikingly different trends for the young and old: while overall lifespan variability has decreased as life expectancy at birth has risen, the variability conditional on survival to older ages has increased. These diverging trends reflect changes in the underlying demographic parameters determining age-specific mortality. Objective: We ask why the variation in the adult ages at death has followed a different trend than the variation at younger ages, and aim to explain the diverging patterns in terms of historical changes in the age schedule of mortality. Methods: Using simulations, we show that the empirical trends in lifespan variation are well characterized using the Siler model, which describes the mortality hazard across the full lifespan using functions representing early-life, later-life, and background mortality. We then obtain maximum likelihood estimates of the Siler parameters over time. Finally, we express lifespan variation in terms of a Markov chain model, and apply matrix calculus perturbation analysis to compute the sensitivity of age-specific lifespan variance trends to the changing Siler model parameters. Results: Our analysis produces a detailed quantification of the impact of changing demographic parameters on the pattern of lifespan variability at all ages, highlighting the impact of declining childhood mortality on the reduction of lifespan variability and the impact of improved survival in adulthood on the rising variability of lifespans at older ages. Conclusions: These findings provide insight into the dynamic relationship between the age pattern of survival improvements and time trends in lifespan variability.

  11. Segmenting the human genome based on states of neutral genetic divergence.

    Science.gov (United States)

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-03

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  12. Divergent selection and the evolution of signal traits and mating preferences.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.

  13. Competitive Interactions upon Secondary Contact Drive Elevational Divergence in Tropical Birds.

    Science.gov (United States)

    Freeman, Benjamin G

    2015-10-01

    Tropical mountains harbor exceptionally high biodiversity, which is in part due to the marked elevational stratification of tropical biotas. However, the factors that influence the evolution of elevational distributions remain uncertain. I used a database of sister species of tropical montane birds from 41 families and three regions-the Neotropics, the Himalayas, and New Guinea-to test whether patterns of elevational divergence were consistent with (1) a stochastic process, (2) ecological sorting of elevational divergence that occurred in allopatry, or (3) elevational divergence driven by competitive interactions upon secondary contact. The stochastic and ecological sorting hypotheses predict that increased elevational divergence in sympatric sister species is explained by their greater evolutionary age, whereas the competitive interactions hypothesis predicts that elevational divergence is explained by geographical overlap. I found that genetic distances were unrelated to elevational divergence and that allopatric sister species occupied similar elevational distributions regardless of genetic distance in each region. Instead, sympatry was the only significant predictor of elevational divergence; regardless of evolutionary age, sympatric sister species had greater elevational divergence than allopatric sister species in each region, as predicted by the competitive interactions hypothesis. Importantly, this pattern occurred in all three geographic regions, which suggests that competition-driven elevational divergence upon secondary contact is a general process of community assembly in tropical montane avifaunas.

  14. Acidic ribosomal proteins and histone H3 from Leishmania present a high rate of divergence

    Directory of Open Access Journals (Sweden)

    Ysabel Montoya

    2000-08-01

    Full Text Available Another additional peculiarity in Leishmania will be discussed about of the amino acid divergence rate of three structural proteins: acidic ribosomal P1 and P2b proteins, and histone H3 by using multiple sequence alignment and dendrograms. These structural proteins present a high rate of divergence regarding to their homologous protein in Trypanosoma cruzi. At this regard, L. (V. peruviana P1 and T. cruzi P1 showed 57.4% of divergence rate. Likewise, L. (V. braziliensis histone H3 and acidic ribosomal P2 protein exhibited 31.8% and 41.7% respectively of rate of divergence in comparison with their homologous in T. cruzi.

  15. Divergence in timing of parental care and migration in barnacle geese

    NARCIS (Netherlands)

    Jonker, R.M.; Kuiper, M.W.; Snijders, L.; Wieren, van S.E.; Ydenberg, R.C.; Prins, H.H.T.

    2011-01-01

    In migratory geese, the extended association of parents and offspring is thought to play a crucial role in culturally transmitting the migration strategy to the next generation. Goslings migrate with their parents and associate closely with them almost until the next breeding season. Families do not

  16. Time-Synchronized CW-Laser Induced Fluorescence Velocity Measurements of a Diverging Cusped Field Thruster

    Science.gov (United States)

    2013-10-01

    signal is collected by a 100 mm diameter plano -convex lens with a focal length of 250 mm. This lens is oriented 30◦ from the exit plane, a distance of...the vacuum chamber and is focused into a 125 mm focal length monochromator with a photomultiplier tube (PMT) by a second 100 mm diameter plano -convex

  17. Conservation Policy in Time and Space: Lessons from Divergent Approaches to Salvage Logging on Public Lands

    Directory of Open Access Journals (Sweden)

    George Robinson

    1999-06-01

    Full Text Available A 50-yr precedent was reversed in 1995 when, following a powerful windstorm, salvage logging was disallowed in the protected Adirondack Park State Forest Preserve of New York, United States. Damage from a similar windstorm in 1950 had provoked massive salvage operations, approved by the New York State legislature on the grounds of fire prevention and resource conservation. Following the 1995 storm, state conservation officers and consulting ecologists were prepared with up-to-date assessment tools and a theoretical framework that treated large disturbances as normal ecosystem processes; the executive branch acted in accord with their recommendations to forgo salvage. Prior to these events in New York State, federal forest preserves in western states had recently been opened to salvage sales, following a widespread series of fires and insect outbreaks. In this latter case, under the rubric of "forest health," legislative amendments were added to unrelated bills and passed without open debate. This lack of public exposure may have denied opportunities for an ecological basis to a key policy decision that carries substantial ecological implications. On the one hand, Adirondack Park salvage policies have evolved to address large-scale forest disturbances as natural events rather than catastrophes that demand intervention. On the other hand, federal salvage policies have arisen in a different political and economic background, and have so far largely escaped scientific scrutiny.

  18. Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

    Directory of Open Access Journals (Sweden)

    Zhu Zhujun

    2010-11-01

    Full Text Available Abstract Background Nod26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III. In some grasses, the NIP III subgroup proteins (NIP2s were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s. Results The NIP III subgroup is more ancient with a divergence time that predates the monocot-dicot split. The proliferation of NIP2 genes in modern grass species is primarily attributed to whole genome and segmental chromosomal duplication events. The structure of NIP2 genes is relatively conserved, possessing five exons and four introns. All NIP2s possess an ar/R filter consisting of G, S, G, and R, except for the cucumber CsNIP2;2, where a small G in the H2 is substituted with the bulkier C residue. Our maximum likelihood analysis revealed that NIP2s, especially the loop A (LA region, have undergone strong selective pressure for adaptive evolution. The analysis at the amino acid level provided strong statistical evidences for the functional divergence between monocot and dicot NIP III subgroup proteins. In addition, several SDPs (Specificity Determining Positions responsible for functional specificity were predicted. Conclusions The present study provides the first evidences of functional divergence between dicot and monocot NIP2s, and suggests that positive selection, as well as a radical shift of evolutionary rate at some critical amino acid sites is the primary

  19. Geodetic observations in Iceland: divergent plate boundary influenced by a hotspot

    Science.gov (United States)

    Ofeigsson, Benedikt Gunnar; Hreinsdóttir, Sigrun; Sigmundsson, Freysteinn; Arnadottir, Thora; Vogfjord, Kristin; Geirsson, Halldor; Einarsson, Pall; Jonsson, Sigurjon; Villemin, Thierry; Fjalar Sigurdsson, Sigurdur; Roberts, Matthew; Sturkell, Erik; Lafemina, Peter C.; Bennett, Richard; Voelksen, Christof; Valsson, Gudmundur; Sigurdsson, Thorarinn

    2013-04-01

    The mid Atlantic ridge, separating the Eurasian and North American tectonic plates, is mostly buried below the Atlantic. There are, however, a few places where subaerial exposure of the mid-oceanic rift system allows geodetic observations of the deformation associated with the plate boundary. Iceland is the largest portion of the system emerged above sea level, a consequence of excessive volcanism caused by the interaction of a mantle plume with the mid-oceanic ridge. Iceland is therefore a unique site to study processes associated with divergent plate boundaries, and the effects of the plume-ridge interaction. A network of continuous GPS stations have been operating in Iceland since 1995 when the first station was installed in Reykjavik. Since then, stations have been added to the network at different points in time, with over 70 stations presently in operation. The network has been used e.g. for studies of deformation associated with the divergent plate boundary, micro-plate formation due to rift jumps, the plate-spreading deformation cycle associated with rifting episodes, strain rates and stress accumulation on transform zones connecting the ridge segments and deformation due to magmatic processes. In addition the GPS network is used in studies of the deformation associated with mass variations of Iceland's glaciers. The continuous GPS network serves as monitoring tool in Iceland, both for volcanic and seismic hazards but also as a research tool. In the recent Futurvolc project, which partly builds on EPOS, the data from the continuous GPS network along with data from the seismic network and InSAR observations, will serve as the main input in joint analyses of long and short term magma movements in volcanic regions. The establishment of the continuous GPS network in Iceland has provided an ideal tool to further increase our understanding of the geodynamic processes associated with divergent plate boundaries and plume-ridge interaction as well as establishing a

  20. Differential patterns of divergence in ocean drifters: Implications for larval flatfish advection and recruitment

    Science.gov (United States)

    Wilderbuer, Thomas; Duffy-Anderson, Janet T.; Stabeno, Phyllis; Hermann, Albert

    2016-05-01

    In an effort to better understand the physics of the eastern Bering Sea shelf current as it relates to flatfish advection to favorable near-shore areas, sets of multiple, satellite-tracked, oceanic drifters were released in 2010, 2012 and 2013. The release sites and dates were chosen to coincide with known spawning locations for northern rock sole (Lepidopsetta polyxystra) and known time of larval emergence. The drifters were drogued 5-each at 20 and 40 m in 2010 and 2012, and 4 at 40 m and 2 at 20 m in 2013. The locations of drifters were used to calculate divergence over a 90-day period that corresponds to the larval pelagic duration of Bering Sea shelf northern rock sole. Results indicate that there are alternating periods of positive and negative divergence with an overall trend toward drifter separation after 90 days, roughly the end of the rock sole planktonic larval period. Examination of the drifter behavior at the hourly scale indicates that semi-daily tidal forcing is the primary mechanism of drifter divergence and convergence. Field observations of early-stage northern rock sole larval distributions over the same period indicate that predominant oceanographic advection is northerly over the continental shelf among preflexion stages, though juveniles are predominantly found in nursery areas located ~ 400 km eastward and inshore. Evidence from drifter deployments suggests that behavioral movements during the postflexion and early juvenile larval phases that optimize eastward periodicity of tidal cycles is a viable mechanism to enhance eastward movement of northern rock sole larvae to favorable nursery grounds. A regional ocean modeling system (ROMS) was implemented to track the different rates of dispersion in simulations both with and without tidal forcing, and was used to estimate effective horizontal eddy diffusion in the case of both isobaric (fixed-depth) and Lagrangian (neutrally buoyant) particles. The addition of tidal forcing had a pronounced

  1. Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax.

    Science.gov (United States)

    Li, Kexin; Wang, Liuyang; Knisbacher, Binyamin A; Xu, Qinqin; Levanon, Erez Y; Wang, Huihua; Frenkel-Morgenstern, Milana; Tagore, Satabdi; Fang, Xiaodong; Bazak, Lily; Buchumenski, Ilana; Zhao, Yang; Lövy, Matěj; Li, Xiangfeng; Han, Lijuan; Frenkel, Zeev; Beiles, Avigdor; Cao, Yi Bin; Wang, Zhen Long; Nevo, Eviatar

    2016-07-05

    Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk-basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological-genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.

  2. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

    Directory of Open Access Journals (Sweden)

    Abiyad eBaig

    2015-11-01

    Full Text Available Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN and cpn60 did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70, of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.

  3. Environmental determinants of population divergence in life-history traits for an invasive species: climate, seasonality and natural enemies.

    Science.gov (United States)

    Seiter, S; Kingsolver, J

    2013-08-01

    Invasive species cope with novel environments through both phenotypic plasticity and evolutionary change. However, the environmental factors that cause evolutionary divergence in invasive species are poorly understood. We developed predictions for how different life-history traits, and plasticity in those traits, may respond to environmental gradients in seasonal temperatures, season length and natural enemies. We then tested these predictions in four geographic populations of the invasive cabbage white butterfly (Pieris rapae) from North America. We examined the influence of two rearing temperatures (20 and 26.7 °C) on pupal mass, pupal development time, immune function and fecundity. As predicted, development time was shorter and immune function was greater in populations adapted to longer season length. Also, phenotypic plasticity in development time was greater in regions with shorter growing seasons. Populations differed significantly in mean and plasticity of body mass and fecundity, but these differences were not associated with seasonal temperatures or season length. Our study shows that some life-history traits, such as development time and immune function, can evolve rapidly in response to latitudinal variation in season length and natural enemies, whereas others traits did not. Our results also indicate that phenotypic plasticity in development time can also diverge rapidly in response to environmental conditions for some traits.

  4. Neuroglobin of seals and whales: evidence for a divergent role in the diving brain.

    Science.gov (United States)

    Schneuer, M; Flachsbarth, S; Czech-Damal, N U; Folkow, L P; Siebert, U; Burmester, T

    2012-10-25

    Although many physiological adaptations of diving mammals have been reported, little is known about how their brains sustain the high demands for metabolic energy and thus O(2) when submerged. A recent study revealed in the deep-diving hooded seal (Cystophora cristata) a unique shift of the oxidative energy metabolism and neuroglobin, a respiratory protein that is involved in neuronal hypoxia tolerance, from neurons to astrocytes. Here we have investigated neuroglobin in another pinniped species, the harp seal (Pagophilus groenlandicus), and in two cetaceans, the harbor porpoise (Phocoena phocoena) and the minke whale (Balaenoptera acutorostrata). Neuroglobin sequences, expression levels and patterns were compared with those of terrestrial relatives, the ferret (Mustela putorius furo) and the cattle (Bos taurus), respectively. Neuroglobin sequences of whales and seals only differ in two or three amino acids from those of cattle and ferret, and are unlikely to confer functional differences, e.g. in O(2) affinity. Neuroglobin is expressed in the astrocytes also of P. groenlandicus, suggesting that the shift of neuroglobin and oxidative metabolism is a common adaptation in the brains of deep-diving phocid seals. In the cetacean brain neuroglobin resides in neurons, like in terrestrial mammals. However, neuroglobin mRNA expression levels were 4-15 times higher in the brains of harbor porpoises and minke whales than in terrestrial mammals or in seals. Thus neuroglobin appears to play a specific role in diving mammals, but seals and whales have evolved divergent strategies to cope with cerebral hypoxia. The specific function of neuroglobin that conveys hypoxia tolerance may either relate to oxygen supply or protection from reactive oxygen species. The different strategies in seals and whales resulted from a divergent evolution and an independent adaptation to diving.

  5. The geography and ecology of plant speciation: range overlap and niche divergence in sister species.

    Science.gov (United States)

    Anacker, Brian L; Strauss, Sharon Y

    2014-03-07

    A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under 'budding' speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister-non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.

  6. On the characteristics of sea ice divergence/convergence in the Southern Beaufort Sea

    Directory of Open Access Journals (Sweden)

    J. V. Lukovich

    2014-07-01

    Full Text Available An understanding of spatial gradients in sea ice motion, or deformation, is essential to understanding of ocean-sea-ice-atmosphere interactions and realistic representations of sea ice in models used for the purposes of prediction. This is particularly true for the southern Beaufort Sea, where significant offshore hydrocarbon resource development increases the risk of oil and other contaminants dispersing into the marginal ice zone. In this study, sea ice deformation is examined through evaluation of ice beacon triplets from September to November 2009 in the southern Beaufort Sea (SBS, defined according to distance from the coastline on deployment. Results from this analysis illustrate that ice beacon triplets in the SBS demonstrate spatiotemporal differences in their evolution at the periphery and interior of the ice pack. The time rate of change in triplet area highlights two intervals of enhanced divergence and convergence in fall, 2009. Investigation of sea ice and atmospheric conditions during these intervals shows that until mid-September, all triplets respond to northerly flow, while during the second interval of enhanced divergence/convergence in October only one triplet responds to persistent northeasterly flow due to its proximity to the ice edge, in contrast to triplets located at the interior of the pack. Differences in sea ice deformation and dispersion near the pack ice edge and interior are further demonstrated in the behavior of triplets B and C in late October/early November. The results from this analysis highlight differences in dispersion and deformation characteristics based on triplet proximity to the southernmost ice edge and coastline, with implications for modeling studies pertaining to sea ice dynamics and dispersion.

  7. Narrow endemics on coastal plains: Miocene divergence of the critically endangered genus Avellara (Compositae).

    Science.gov (United States)

    Fernández-Mazuecos, M; Jiménez-Mejías, P; Martín-Bravo, S; Buide, M L; Álvarez, I; Vargas, P

    2016-07-01

    Critically endangered species representing ancient, evolutionarily isolated lineages must be given priority when allocating resources for conservation projects. Sound phylogenetic analyses and divergence time estimations are required to detect them, and studies on their population genetics, ecological requirements and breeding system are needed to understand their evolutionary history and to design efficient conservation strategies. Here we present the paradigmatic case of Avellara, a critically endangered monotypic genus of Compositae inhabiting a few swamps in the west-southwest Iberian coastal plains. Our phylogenetic and dating analyses based on nuclear (ITS) and plastid (matK) DNA sequences support a Miocene (>8.6 Ma) divergence between Avellara and closely related genera, resulting in marked morphological and ecological differentiation. We found alarmingly low levels of genetic diversity, based on AFLPs and plastid DNA sequences, and confirmed the prevalence of clonal reproduction. Species distribution modelling suggested a large macroclimatically suitable area for Avellara in the western Iberian Peninsula, but its apparently narrow microecological requirements restrict its distribution to peatlands with low-mineralised waters. Although five populations have been recorded from Spain and Portugal in the past, its current distribution may be reduced to only one population, recurrently found in the last decade but threatened by herbivory and habitat degradation. All this confirms the consideration of Avellara as a threatened species with high phylogenetic singularity, and makes it a flagship species for plant conservation in both Spain and Portugal that should be given priority in the design of in situ and ex situ conservation programmes.

  8. Convergent and divergent processing of majority and minority arguments: effects on focal and related attitudes

    NARCIS (Netherlands)

    de Dreu, C.; de Vries, N.K.; Gordijn, E.H.; Schuurman, M.S.

    1999-01-01

    This research concerned attitude change towards a majority or minority position as a function of convergent and divergent message processing. Results of a 2 (majority/minority support for persuasive arguments)×3(convergent/divergent/no-processing instructions) experiment showed that recipients ident

  9. Convergent and divergent processing of majority and minority arguments : effects on focal and related attitudes

    NARCIS (Netherlands)

    De Dreu, CKW; De Vries, NK; Gordijn, EH; Schuurman, MS

    1999-01-01

    This research concerned attitude change towards a majority or minority position as a function of convergent and divergent message processing. Results of a 2 (majority/minority support for persuasive arguments) x 3 (convergent/divergent/no-processing instructions) experiment showed that recipients id

  10. Atmospheric radiative flux divergence from Clouds and Earth Radiant Energy System (CERES)

    Science.gov (United States)

    Smith, Louis G.; Charlock, Thomas P.; Crommelynk, D.; Rutan, David; Gupta, Shashi

    1990-01-01

    A major objective of the Clouds and Earth Radiant Energy System (CERES) is the computation of vertical profiles through the atmosphere of the divergence of radiation flux, with global coverage. This paper discusses the need for radiation divergence and presents some options for its inference from CERES measurements and other data from the Earth Observating System.

  11. Divergent Task Performance in Older Adults: Declarative Memory or Creative Potential?

    Science.gov (United States)

    Leon, Susan A.; Altmann, Lori J. P.; Abrams, Lise; Gonzalez Rothi, Leslie J.; Heilman, Kenneth M.

    2014-01-01

    Divergent thinking is a process or method used to generate creative ideas by exploring many possible solutions or responses, and is a critical element of creativity. Lesion and imaging studies have shown that the frontal lobes are important in mediating divergent thinking, and frontal lobe function is highly dependent on white matter connections…

  12. Estimates of radiative flux divergence in the atmosphere from satellite data

    Science.gov (United States)

    Smith, G. L.; Charlock, Thomas P.; Bess, T. D.; Gupta, Shashi; Rutan, David; Rose, Fred G.

    1990-01-01

    Several options for the inference of the atmospheric radiative flux divergence (ARD) on the basis of satellite data are discussed. Attention is given to the clear-sky case and the cloudy-sky case. LW ARD profiles for different climatological regimes are presented and the effect of cloud base height on LW ARD divergence at various heights is illustrated.

  13. Reproductive isolation related to mimetic divergence in the poison frog Ranitomeya imitator

    DEFF Research Database (Denmark)

    Twomey, Evan; Vestergaard, Jacob Schack; Summers, Kyle

    2014-01-01

    phenotypic transition zone, neutral genetic divergence and assortative mating, suggesting that divergent selection to resemble different model species has led to a breakdown in gene flow between these two populations. These results extend the effects of mimicry on speciation into a vertebrate system...

  14. Photoreactions with a Twist: Atropisomerism-Driven Divergent Reactivity of Enones with UV and Visible Light.

    Science.gov (United States)

    Vallavoju, Nandini; Sreenithya, Avadakkam; Ayitou, Anoklase J-L; Jockusch, Steffen; Sunoj, Raghavan B; Sivaguru, Jayaraman

    2016-08-01

    Light-induced transformation of atropisomeric and achiral enones displays divergent reactivity. Photocyclization leading to 3,4-dihydroquinolin-2-one was observed with achiral enone carboxamide, whereas the atropisomeric enone carboxamides underwent hydrogen abstraction leading to spiro-β-lactams. Detailed photochemical, photophysical, and theoretical investigations have provided insight into this divergent reactivity and selectivity.

  15. Regulatory divergence of X-linked genes and hybrid male sterility in mice.

    Science.gov (United States)

    Oka, Ayako; Shiroishi, Toshihiko

    2014-01-01

    Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

  16. Dike-induced contraction along oceanic and continental divergent plate boundaries

    KAUST Repository

    Trippanera, D.

    2014-10-28

    The axis of divergent plate boundaries shows extension fractures and normal faults at the surface. Here we present evidence of contraction along the axis of the oceanic ridge of Iceland and the continental Main Ethiopian Rift. Contraction is found at the base of the tilted hanging wall of dilational normal faults, balancing part of their extension. Our experiments suggest that these structures result from dike emplacement. Multiple dike injection induces subsidence above and uplift to the sides of the dikes; the transition in between is accommodated by reverse faults and subsequent peripheral inward dipping normal faults. Our results suggest that contraction is a direct product of magma emplacement along divergent plate boundaries, at various scales, marking a precise evolutionary stage and initiating part of the extensional structures (extension fractures and normal faults). Key Points Contraction along divergent plate boundaries results from dike emplacementContraction generates extensional structures along divergent plate boundariesSurface deformation along divergent plate boundaries may be magma induced

  17. Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene

    Directory of Open Access Journals (Sweden)

    Derek J. Taylor

    2014-09-01

    Full Text Available An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.

  18. On the small divergence of laser-driven ion beams from nanometer thick foils

    Energy Technology Data Exchange (ETDEWEB)

    Bin, J. H.; Ma, W. J.; Allinger, K.; Kiefer, D.; Khrennikov, K.; Karsch, S.; Krausz, F.; Habs, D.; Schreiber, J. [Fakultät für Physik, Ludwig-Maximilians-Universität München, D-85748 Garching (Germany); Max-Planck-Institut für Quantenoptik, D-85748 Garching (Germany); Wang, H. Y. [Max-Planck-Institut für Quantenoptik, D-85748 Garching (Germany); State Key Laboratory of Nuclear Physics and Technology, and Key Lab of High Energy Density Physics Simulation, CAPT, Peking University, Beijing 100871 (China); Reinhardt, S.; Hilz, P.; Tajima, T. [Fakultät für Physik, Ludwig-Maximilians-Universität München, D-85748 Garching (Germany); Yan, X. Q. [State Key Laboratory of Nuclear Physics and Technology, and Key Lab of High Energy Density Physics Simulation, CAPT, Peking University, Beijing 100871 (China)

    2013-07-15

    We report on experimental studies of divergence of proton beams from nanometer thick diamond-like carbon foils irradiated by a linearly polarized intense laser with high contrast. Proton beams with extremely small divergence (half angle) of 2° are observed in addition with a remarkably well-collimated feature over the whole energy range, showing one order of magnitude reduction of the divergence angle in comparison to the results from μm thick targets. Similar features are reproduced in two-dimensional particle-in-cell simulations with parameters representing our experiments, indicating a strong influence from the electron density distribution on the divergence of protons. Our comprehensive experimental study reveals grand opportunities for using nm foils in experiments that require high ion flux and small divergence.

  19. Divergence in olfactory host plant preference in D. mojavensis in response to cactus host use.

    Science.gov (United States)

    Date, Priya; Dweck, Hany K M; Stensmyr, Marcus C; Shann, Jodi; Hansson, Bill S; Rollmann, Stephanie M

    2013-01-01

    Divergence in host adaptive traits has been well studied from an ecological and evolutionary perspective, but identification of the proximate mechanisms underlying such divergence is less well understood. Behavioral preferences for host plants are often mediated by olfaction and shifts in preference may be accompanied by changes in the olfactory system. In this study, we examine the evolution of host plant preferences in cactophilic Drosophila mojavensis that feeds and breeds on different cacti throughout its range. We show divergence in electrophysiological responses and olfactory behavior among populations with host plant shifts. Specifically, significant divergence was observed in the Mojave Desert population that specializes on barrel cactus. Differences were observed in electrophysiological responses of the olfactory organs and in behavioral responses to barrel cactus volatiles. Together our results suggest that the peripheral nervous system has changed in response to different ecological environments and that these changes likely contribute to divergence among D. mojavensis populations.

  20. Testing founder effect speciation: Divergence population genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)

    Science.gov (United States)

    Yeung, Carol K.L.; Tsai, Pi-Wen; Chesser, R. Terry; Lin, Rong-Chien; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien

    2011-01-01

    Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10-8) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we

  1. Real and metaphorical hunger: the case of The Divergent Trilogy

    Directory of Open Access Journals (Sweden)

    Cristina Paravano

    2015-05-01

    Full Text Available The present contribution investigates how the issue of hunger becomes a means of expressing and communicating personal and social identity in Veronica Roth’s best seller trilogy Divergent (2011-13. Roth portrays a dystopian future developing a multifaceted concept of hunger, both real and figurative, and using food as a cultural metaphor. The trilogy is set in a post-apocalyptic Chicago, whose population is divided into five allegorical factions, according to a number of personal and social characteristics. The life of each faction seems to be based on a form of metaphorical hunger: those who pursue selflessness and altruism belong to Abnegation, peace and harmony to Amity, honesty and truth to Candor, danger and adventure to Dauntless, and knowledge and power to Erudite. Those people who are excluded become factionless: they are outcasts who live their life in extreme poverty and experience real physical hunger. On the other hand, I will show how the numerous references to food and eating pervading the novels help to map the characters’ personalities and identities as single individuals and as groups.

  2. Divergence among an international population of Trichophyton tonsurans isolates.

    Science.gov (United States)

    Abdel-Rahman, Susan M; Sugita, Takashi; González, Gloria M; Ellis, David; Arabatzis, Michalis; Vella-Zahra, Loranne; Viguié-Vallanet, Calude; Hiruma, Masataro; Leeder, J Steven; Preuett, Barry

    2010-01-01

    Trichophyton tonsurans is a widely distributed pathogen that demonstrates a significant degree of genetic and phenetic heterogeneity. To date, the degree of genetic relatedness among geographically segregated isolates has not been explored. This investigation evaluates the extent of genetic variation among an international population of T. tonsurans isolates and examines the relatedness of isolates within and between countries. Molecular strain typing was performed on 198 isolates obtained from 14 countries. A mixed-marker strategy utilizing 27 sequence variations in 13 gene loci was applied to all isolates and cluster analysis was performed to examine the relationship between strains. Phylogenetic analysis was used to corroborate the findings of the cluster analysis with T. equinum strains serving as an out-group. In total, 47 distinct strain types were identified represented by seven clusters and one singleton. There appeared to be a moderate degree of clustering among isolates obtained from North America, Asia and Australia, although European isolates were uniformly distributed among the majority of clusters. The degree of genetic variation observed in this study coupled with the geographic localization would support the argument for allopatric divergence within this species.

  3. Divergent signaling via SUMO modification: potential for CFTR modulation.

    Science.gov (United States)

    Ahner, Annette; Gong, Xiaoyan; Frizzell, Raymond A

    2016-02-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is generally responsible for the cAMP/PKA regulated anion conductance at the apical membranes of secretory epithelial cells. Mutations in CFTR underlie cystic fibrosis (CF), in which the most common variant, F508del, causes protein misfolding and its proteasome-mediated degradation. A new pathway that contributes to mutant CFTR degradation is mediated by the small heat shock protein, Hsp27, which cooperates with Ubc9, the E2 enzyme for SUMOylation, to selectively conjugate mutant CFTR with SUMO-2/3. This SUMO paralog can form polychains, which are recognized by the ubiquitin E3 enzyme, RNF4, leading to CFTR ubiquitylation and recognition by the proteasome. We found also that F508del CFTR could be modified by SUMO-1, a paralog that does not support SUMO polychain formation. The use of different SUMO paralogs to modify and target a single substrate for divergent purposes is not uncommon. In this short review we discuss the possibility that conjugation with SUMO-1 could protect mutant CFTR from disposal by RNF4 and similar ubiquitin ligases. We hypothesize that such a pathway could contribute to therapeutic efforts to stabilize immature mutant CFTR and thereby enhance the action of therapeutics that correct CFTR trafficking to the apical membranes.

  4. Novel divergent nidovirus in a python with pneumonia.

    Science.gov (United States)

    Bodewes, Rogier; Lempp, Charlotte; Schürch, Anita C; Habierski, Andre; Hahn, Kerstin; Lamers, Mart; von Dörnberg, Katja; Wohlsein, Peter; Drexler, Jan Felix; Haagmans, Bart L; Smits, Saskia L; Baumgärtner, Wolfgang; Osterhaus, Albert D M E

    2014-11-01

    The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales.

  5. Divergent hemispheric reasoning strategies: reducing uncertainty versus resolving inconsistency

    Science.gov (United States)

    Marinsek, Nicole; Turner, Benjamin O.; Gazzaniga, Michael; Miller, Michael B.

    2014-01-01

    Converging lines of evidence from diverse research domains suggest that the left and right hemispheres play distinct, yet complementary, roles in inferential reasoning. Here, we review research on split-brain patients, brain-damaged patients, delusional patients, and healthy individuals that suggests that the left hemisphere tends to create explanations, make inferences, and bridge gaps in information, while the right hemisphere tends to detect conflict, update beliefs, support mental set-shifts, and monitor and inhibit behavior. Based on this evidence, we propose that the left hemisphere specializes in creating hypotheses and representing causality, while the right hemisphere specializes in evaluating hypotheses, and rejecting those that are implausible or inconsistent with other evidence. In sum, we suggest that, in the domain of inferential reasoning, the left hemisphere strives to reduce uncertainty while the right hemisphere strives to resolve inconsistency. The hemispheres’ divergent inferential reasoning strategies may contribute to flexible, complex reasoning in the healthy brain, and disruption in these systems may explain reasoning deficits in the unhealthy brain. PMID:25374526

  6. Genome size increases in recently diverged hornwort clades.

    Science.gov (United States)

    Bainard, Jillian D; Villarreal, Juan Carlos

    2013-08-01

    As our knowledge of plant genome size estimates continues to grow, one group has continually been neglected: the hornworts. Hornworts (Anthocerotophyta) have been traditionally grouped with liverworts and mosses because they share a haploid dominant life cycle; however, recent molecular studies place hornworts as the sister lineage to extant tracheophytes. Given the scarcity of information regarding the DNA content of hornworts, our objective was to estimate the 1C-value for a range of hornwort species within a phylogenetic context. Using flow cytometry, we estimated genome size for 36 samples representing 24 species. This accounts for roughly 10% of known hornwort species. Haploid genome sizes (1C-value) ranged from 160 Mbp or 0.16 pg (Leiosporoceros dussii) to 719 Mbp or 0.73 pg (Nothoceros endiviifolius). The average 1C-value was 261 ± 104 Mbp (0.27 ± 0.11 pg). Ancestral reconstruction of genome size on a hornwort phylogeny suggests a small ancestral genome size and revealed increases in genome size in the most recently divergent clades. Much more work is needed to understand DNA content variation in this phylogenetically important group, but this work has significantly increased our knowledge of genome size variation in hornworts.

  7. Alberta's and Ontario's liquor boards: why such divergent outcomes?

    Science.gov (United States)

    Bird, Malcolm G

    2010-01-01

    The provinces of Alberta and Ontario have chosen very different methods to distribute alcoholic beverages: Alberta privatized the Alberta Liquor Control Board (ALCB) in 1993 and established a private market to sell beverage alcohol, while Ontario, in stark contrast, opted to retain and expand the Liquor Control Board of Ontario (LCBO). This article examines the reasons for the divergent policy choices made by Ralph Klein and Mike Harris' Conservative governments in each province. The article draws on John Kingdon's “multiple streams decision-making model,” to examine the mindsets of the key decision-makers, as well as “historical institutionalism,” to organize the pertinent structural, historical and institutional variables that shaped the milieu in which decision-makers acted. Unique, province-specific political cultures, histories, institutional configurations (including the relative influence of a number of powerful actors), as well as the fact that the two liquor control boards were on opposing trajectories towards their ultimate fates, help to explain the different decisions made by each government. Endogenous preference construction in this sector, furthermore, implies that each system is able to satisfy all relevant stakeholders, including consumers.

  8. Nonequilibrium Quantum Systems: Divergence between Global and Local Descriptions

    Directory of Open Access Journals (Sweden)

    Pedro D. Manrique

    2015-01-01

    Full Text Available Even photosynthesis—the most basic natural phenomenon underlying life on Earth—involves the nontrivial processing of excitations at the pico- and femtosecond scales during light-harvesting. The desire to understand such natural phenomena, as well as interpret the output from ultrafast experimental probes, creates an urgent need for accurate quantitative theories of open quantum systems. However it is unclear how best to generalize the well-established assumptions of an isolated system, particularly under nonequilibrium conditions. Here we compare two popular approaches: a description in terms of a direct product of the states of each individual system (i.e., a local approach versus the use of new states resulting from diagonalizing the whole Hamiltonian (i.e., a global approach. The main difference lies in finding suitable operators to derive the Lindbladian and hence the master equation. We show that their equivalence fails when the system is open, in particular under the experimentally ubiquitous condition of a temperature gradient. By solving for the steady state populations and calculating the heat flux as a test observable, we uncover stark differences between the formulations. This divergence highlights the need to establish rigorous ranges of applicability for such methods in modeling nanoscale transfer phenomena—including during the light-harvesting process in photosynthesis.

  9. When goals diverge: Staff consensus and the organizational climate.

    Science.gov (United States)

    Melnick, Gerald; Ulaszek, Wendy R; Lin, Hsiu-Ju; Wexler, Harry K

    2009-08-01

    A sample of correctional officers and prison substance abuse treatment staff collected by the National Criminal Justice Treatment Practices Survey is used to provide an exploratory study of an aspect of organizational culture consisting of consensus (agreement) among prison personnel regarding their beliefs about rehabilitation in the presence of conflicting organizational goals and aspects of the organizational climate important to change. Findings show that among those staff members responding to the survey, the belief in rehabilitation scale mean score was associated with higher levels of organizational commitment, and interdepartmental coordination. However, an hierarchical linear modeling (HLM) analysis that used an index score derived from the standard deviation for staff consensus regarding these same beliefs about rehabilitation produced a different pattern of results, showing that high levels of consensus were associated with job frustration, cynicism towards the ability of the institution to change, and lower levels of organizational commitment. The authors conclude that, although the sample may not express the beliefs of corrections officers or prison-based treatment staff at large, within the sample, consensus appeared to play a unique role in evaluating the effect of divergent goals on organizational climate as it relates to change, and warrants consideration when considering the effects of organizational climate.

  10. Genetic differentiation, niche divergence, and the origin and maintenance of the disjunct distribution in the Blossomcrown Anthocephala floriceps (Trochilidae).

    Science.gov (United States)

    Lozano-Jaramillo, María; Rico-Guevara, Alejandro; Cadena, Carlos Daniel

    2014-01-01

    Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7-2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.

  11. Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution

    Indian Academy of Sciences (India)

    Jan Janecka; Bhanu Chowdhary; William Murphy

    2012-11-01

    Sequence evolution behaves in a relatively consistent manner, leading to one of the fundamental paradigms in biology, the existence of a `molecular clock’. The molecular clock can be distilled to the concept of accumulation of substitutions, through time yielding a stable rate from which we can estimate lineage divergence. Over the last 50 years, evolutionary biologists have obtained an in-depth understanding of this clock’s nuances. It has been fine-tuned by taking into account the vast heterogeneity in rates across lineages and genes, leading to `relaxed’ molecular clock methods for timetree reconstruction. Sequence rate varies with life history traits including body size, generation time and metabolic rate, and we review recent studies on this topic. However, few studies have explicitly examined correlates between molecular evolution and morphological evolution. The patterns observed across diverse lineages suggest that rates of molecular and morphological evolution are largely decoupled. We discuss how identifying the molecular mechanisms behind rapid functional radiations are central to understanding evolution. The vast functional divergence within mammalian lineages that have relatively `slow’ sequence evolution refutes the hypotheses that pulses in diversification yielding major phenotypic change are the result of steady accumulation of substitutions. Patterns rather suggest phenotypic divergence is likely caused by regulatory alterations mediated through mechanisms such as insertions/deletions in functional regions. These can rapidly arise and sweep to fixation faster than predicted from a lineage’s sequence neutral substitution rate, enabling species to leapfrog between phenotypic `islands’. We suggest research directions that could illuminate mechanisms behind the functional diversity we see today.

  12. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones.

    Science.gov (United States)

    Harrison, Richard G; Larson, Erica L

    2016-06-01

    Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.

  13. Second language learners’ divergence from target language pragmatic norms

    Directory of Open Access Journals (Sweden)

    Maria Pia Gomez-Laich

    2016-06-01

    Full Text Available Pragmatic competence is an indispensable aspect of language ability in order for second and foreign language (L2/FL learners to understand and be understood in their interactions with both native and nonnative speakers of the target language. Without a proper understanding of the pragmatic rules in the target language, learners may run the risk of coming across as insensitive and rude. Several researchers (Bardovi-Harlig, 2001; Kasper & Rose, 2002 suggest that L2 pragmatics not only can be taught in the L2/FL classroom, but, more importantly, that explicit approaches that involve direct explanation of target pragmatic features are beneficial for learning pragmatics. Just as native speakers of a language acquire a “set of dispositions to act in certain ways, which generates cognitive and bodily practices in the individual” (Watts, 2003, p. 149, instructors can help learners to become aware of the pragmatic features that characterize the target language. Although the importance of explicit teaching of pragmatics is well recognized in the literature, learning norms and rules of pragmatics largely depends on learners’ subjectivity. Learners’ convergence or divergence from the L2 pragmatic norms, both consciously and out of awareness, sometimes depends on whether these norms fit their image of self and their L1 cultural identity. Since identity-related conflict can have significant consequences for the acquisition of second language pragmatics, failing to consider the centrality of learners’ identities will produce an inadequate understanding of SLA. This paper synthesizes studies that document the reasons why learners opt to remain foreign by resisting certain L2 practic-es. The following synthesis question was proposed: Why do language learners resist the pragmatic norms of the target language?

  14. Genomic divergence during speciation driven by adaptation to altitude.

    Science.gov (United States)

    Chapman, Mark A; Hiscock, Simon J; Filatov, Dmitry A

    2013-12-01

    Even though Darwin's "On the Origin of Species" implied selection being the main driver of species formation, the role of natural selection in speciation remains poorly understood. In particular, it remains unclear how selection at a few genes can lead to genomewide divergence and the formation of distinct species. We used a particularly attractive clear-cut case of recent plant ecological speciation to investigate the demography and genomic bases of species formation driven by adaptation to contrasting conditions. High-altitude Senecio aethnensis and low-altitude S. chrysanthemifolius live at the extremes of a mountain slope on Mt. Etna, Sicily, and form a hybrid zone at intermediate altitudes but remain morphologically distinct. Genetic differentiation of these species was analyzed at the DNA polymorphism and gene expression levels by high-throughput sequencing of transcriptomes from multiple individuals. Out of ≈ 18,000 genes analyzed, only a small number (90) displayed differential expression between the two species. These genes showed significantly elevated species differentiation (FST and Dxy), consistent with diversifying selection acting on these genes. Genomewide genetic differentiation of the species is surprisingly low (FST = 0.19), while ≈ 200 genes showed significantly higher (false discovery rate 0.6) interspecific differentiation and evidence for local adaptation. Diversifying selection at only a handful of loci may be enough for the formation and maintenance of taxonomically well-defined species, despite ongoing gene flow. This provides an explanation of why many closely related species (in plants, in particular) remain phenotypically and ecologically distinct despite ongoing hybridization, a question that has long puzzled naturalists and geneticists alike.

  15. Divergent creative thinking in young and older adults: Extending the effects of an episodic specificity induction.

    Science.gov (United States)

    Madore, Kevin P; Jing, Helen G; Schacter, Daniel L

    2016-08-01

    Recent research has suggested that an episodic specificity induction-brief training in recollecting the details of a past experience-enhances divergent creative thinking on the alternate uses task (AUT) in young adults, without affecting performance on tasks thought to involve little divergent thinking; however, the generalizability of these results to other populations and tasks is unknown. In the present experiments, we examined whether the effects of an episodic specificity induction would extend to older adults and a different index of divergent thinking, the consequences task. In Experiment 1, the specificity induction significantly enhanced divergent thinking on the AUT in both young and older adults, as compared with a control induction not requiring specific episodic retrieval; performance on a task involving little divergent thinking (generating associates for common objects) did not vary as a function of induction. No overall age-related differences were observed on either task. In Experiment 2, the specificity induction significantly enhanced divergent thinking (in terms of generating consequences of novel scenarios) in young adults, relative to another control induction not requiring episodic retrieval. To examine the types of creative ideas affected by the induction, the participants in both experiments also labeled each of their divergent-thinking responses as an "old idea" from memory or a "new idea" from imagination. New, and to some extent old, ideas were significantly boosted following the specificity induction relative to the control. These experiments provide novel evidence that an episodic specificity induction can boost divergent thinking in young and older adults, and indicate that episodic memory is involved in multiple divergent-thinking tasks.

  16. Divergent Arctic-Boreal Vegetation Changes between North America and Eurasia over the Past 30 Years

    Directory of Open Access Journals (Sweden)

    Arindam Samanta

    2013-05-01

    Full Text Available Arctic-Boreal region—mainly consisting of tundra, shrub lands, and boreal forests—has been experiencing an amplified warming over the past 30 years. As the main driving force of vegetation growth in the north, temperature exhibits tight coupling with the Normalized Difference Vegetation Index (NDVI—a proxy to photosynthetic activity. However, the comparison between North America (NA and northern Eurasia (EA shows a weakened spatial dependency of vegetation growth on temperature changes in NA during the past decade. If this relationship holds over time, it suggests a 2/3 decrease in vegetation growth under the same rate of warming in NA, while the vegetation response in EA stays the same. This divergence accompanies a circumpolar widespread greening trend, but 20 times more browning in the Boreal NA compared to EA, and comparative greening and browning trends in the Arctic. These observed spatial patterns of NDVI are consistent with the temperature record, except in the Arctic NA, where vegetation exhibits a similar long-term trend of greening to EA under less warming. This unusual growth pattern in Arctic NA could be due to a lack of precipitation velocity compared to the temperature velocity, when taking velocity as a measure of northward migration of climatic conditions.

  17. Synchrony and Divergence in Stream Metabolism across the Continental United States

    Science.gov (United States)

    Appling, A.; Read, J. S.; Hall, R. O., Jr.; Stets, E.; Stanley, E. H.; Bernhardt, E. S.; Heffernan, J. B.; Arroita, M.; Griffiths, N.; Harvey, J. W.; Lorenz, D. L.; Winslow, L.; Yackulic, C. B.

    2015-12-01

    River and stream ecosystems experience highly variable inputs of water, nutrients, organic matter, heat, and light over the scales of hours to storms to seasons. Despite the unstable physical and chemical environments of such ecosystems, benthic and pelagic communities persist and even thrive. Whole-stream metabolism estimates allow us to quantify the overall activity of these diverse and responsive communities. They also provide a holistic way to assess how the temporal patterns of that activity are structured by streams' dynamic hydrology and resource availability. We synthesized continental-scale datasets of high-frequency dissolved oxygen, discharge, water temperature, and light to estimate metabolism in over 200 streams to answer the question, "What are the drivers of synchrony and divergence in the temporal patterns of metabolism among streams of North America?" We find that short-term disturbances in the form of storms and cloudy days have strong proximate, dampening effects on whole-ecosystem metabolism; however, despite these strong proximate effects, streams with similar resource and discharge regimes are largely synchronous in their overall seasonal patterns. The median date of peak gross primary productivity is close to the summer solstice in June, while ecosystem respiration has two most-common annual peaks, one in early spring and another in mid fall. These differences in peak timing point to systematic differences at the continental scale in the timing of light versus organic matter availability, with consequent seasonality in net ecosystem productivity.

  18. Computation of supersonic jet mixing noise for an axisymmetric convergent-divergent nozzle

    Science.gov (United States)

    Khavaran, Abbas; Krejsa, Eugene A.; Kim, Chan M.

    1994-05-01

    The turbulent mixing noise of a supersonic jet is calculated for an axisymmetric convergent-divergent nozzle at the design pressure ratio. Aerodynamic computations are performed using the PARC code with a k-epsilon turbulence model. Lighthill's acoustic analogy is adopted. The acoustics solution is based upon the methodology followed in the MGB code. The source correlation function is expressed as a linear combination of second-order tensors (Ribner's assumption). Assuming separable second-order correlations and incorporating Batchelor's isotropic turbulence model, the source term was calculated from the kinetic energy of turbulence. A Gaussian distribution for the time-delay of correlation was introduced. The CFD solution was used to obtain the source strength as well as the characteristic time-delay of correlation. The effect of sound/flow interaction was incorporated using the high frequency asymptotic solution to Lilley's equation for axisymmetric geometries. Acoustic results include sound pressure level directivity and spectra at different polar angles. The aerodynamic and acoustic results demonstrate favorable agreement with experimental data.

  19. Characterization and phylogenetic analysis of -gliadin gene sequences reveals significant genomic divergence in Triticeae species

    Indian Academy of Sciences (India)

    Guang-Rong Li; Tao Lang; En-Nian Yang; Cheng Liu; Zu-Jun Yang

    2014-12-01

    Although the unique properties of wheat -gliadin gene family are well characterized, little is known about the evolution and genomic divergence of -gliadin gene family within the Triticeae. We isolated a total of 203 -gliadin gene sequences from 11 representative diploid and polyploid Triticeae species, and found 108 sequences putatively functional. Our results indicate that -gliadin genes may have possibly originated from wild Secale species, where the sequences contain the shortest repetitive domains and display minimum variation. A miniature inverted-repeat transposable element insertion is reported for the first time in -gliadin gene sequence of Thinopyrum intermedium in this study, indicating that the transposable element might have contributed to the diversification of -gliadin genes family among Triticeae genomes. The phylogenetic analyses revealed that the -gliadin gene sequences of Dasypyrum, Australopyrum, Lophopyrum, Eremopyrum and Pseudoroengeria species have amplified several times. A search for four typical toxic epitopes for celiac disease within the Triticeae -gliadin gene sequences showed that the -gliadins of wild Secale, Australopyrum and Agropyron genomes lack all four epitopes, while other Triticeae species have accumulated these epitopes, suggesting that the evolution of these toxic epitopes sequences occurred during the course of speciation, domestication or polyploidization of Triticeae.

  20. Quenched Chiral Logarithm Diverge in Very Light Quark Region from the Overlap Lattice Quantum Chromodynamics

    Institute of Scientific and Technical Information of China (English)

    应和平; 董绍静; 张剑波

    2003-01-01

    With an exact chiral symmetry, overlap fermions allow us to reach very light quark region. In the minimummps = 179 MeV, the quenched chiral logarithm diverge is examined. The chiral logarithm parameter δ is calculatedfrom both the pseudo-scalar meson mass mp2s diverge channel and the pseudo-scalar decay constant f p channel.In both the cases, we obtain δ = 0.25 ± 0.03. We also observe that the quenchedchiral logarithm diverge occursonly in the mps ≤400 MeV region.