WorldWideScience

Sample records for strong genetic structure

  1. Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

    Science.gov (United States)

    Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

    2017-06-01

    Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

  2. Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

    Directory of Open Access Journals (Sweden)

    Wouter Dekoninck

    2014-12-01

    Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

  3. Strong population genetic structure and larval dispersal capability of the burrowing ghost shrimp (Neotrypaea californiensis)

    Science.gov (United States)

    The burrowing ghost shrimp, Neotrypaea californiensis, is a vital member of the estuarine benthic community. Dense populations of shrimp are found in the major estuaries of Washington and Oregon. Our study determines the genetic structure of shrimp populations in order to gain ...

  4. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Changtragoon, Suchitra; Ponoy, Bundit

    2015-01-01

    had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern......) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using...

  5. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

    Science.gov (United States)

    Bergström, Anders; Oppenheimer, Stephen J; Mentzer, Alexander J; Auckland, Kathryn; Robson, Kathryn; Attenborough, Robert; Alpers, Michael P; Koki, George; Pomat, William; Siba, Peter; Xue, Yali; Sandhu, Manjinder S; Tyler-Smith, Chris

    2017-09-15

    New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies. Copyright © 2017, American Association for the Advancement of Science.

  6. Strong spatial genetic structure in five tropical Piper species: should the Baker–Fedorov hypothesis be revived for tropical shrubs?

    Science.gov (United States)

    Lasso, E; Dalling, J W; Bermingham, E

    2011-01-01

    Fifty years ago, Baker and Fedorov proposed that the high species diversity of tropical forests could arise from the combined effects of inbreeding and genetic drift leading to population differentiation and eventually to sympatric speciation. Decades of research, however have failed to support the Baker–Fedorov hypothesis (BFH), and it has now been discarded in favor of a paradigm where most trees are self-incompatible or strongly outcrossing, and where long-distance pollen dispersal prevents population drift. Here, we propose that several hyper-diverse genera of tropical herbs and shrubs, including Piper (>1,000 species), may provide an exception. Species in this genus often have aggregated, high-density populations with self-compatible breeding systems; characteristics which the BFH would predict lead to high local genetic differentiation. We test this prediction for five Piper species on Barro Colorado Island, Panama, using Amplified Fragment Length Polymorphism (AFLP) markers. All species showed strong genetic structure at both fine- and large-spatial scales. Over short distances (200–750 m) populations showed significant genetic differentiation (Fst 0.11–0.46, P < 0.05), with values of spatial genetic structure that exceed those reported for other tropical tree species (Sp = 0.03–0.136). This genetic structure probably results from the combined effects of limited seed and pollen dispersal, clonal spread, and selfing. These processes are likely to have facilitated the diversification of populations in response to local natural selection or genetic drift and may explain the remarkable diversity of this rich genus. PMID:22393518

  7. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.

    Science.gov (United States)

    Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, Kathrin; Cellerino, Alessandro; Bryja, Josef

    2013-09-12

    Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary

  8. Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp

    NARCIS (Netherlands)

    Luttikhuizen, P.C.; van den Heuvel, F.H.M.; Rebours, C.; Witte, H.J.; van Bleijswijk, J.D.L.; Timmermans, K.

    2018-01-01

    Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is Saccharina latissima, a northern hemisphere kelp inhabiting temperate to arctic rocky shores. To protect and document its natural genetic variation at the

  9. Seagrass radiation after Messinian salinity crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae.

    Directory of Open Access Journals (Sweden)

    Ludwig Triest

    Full Text Available Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies.

  10. Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

    Science.gov (United States)

    Stoelting, Ricka E.; Measey, G. John; Drewes, Robert C.

    2014-01-01

    Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities. PMID:25171066

  11. So far away, yet so close: strong genetic structure in Homonota uruguayensis (Squamata, Phyllodactylidae, a species with restricted geographic distribution in the Brazilian and Uruguayan Pampas.

    Directory of Open Access Journals (Sweden)

    Jéssica F Felappi

    Full Text Available The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings.

  12. Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

    DEFF Research Database (Denmark)

    Muwanka, V.B.; Nyakaana, S.; Siegismund, Hans Redlef

    2007-01-01

    populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection...

  13. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

    Czech Academy of Sciences Publication Activity Database

    Bartáková, V.; Reichard, M.; Janko, Karel; Polačik, M.; Blažek, R.; Reichwald, K.; Cellerino, A.; Bryja, J.

    2013-01-01

    Roč. 13, č. 196 (2013), s. 1-15 ISSN 1471-2148 Institutional support: RVO:67985904 Keywords : temporary pool * pyhlogeography * population genetics Subject RIV: EG - Zoology Impact factor: 3.407, year: 2013 http://www.biomedcentral.com/1471-2148/13/196

  14. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

    Czech Academy of Sciences Publication Activity Database

    Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, K.; Cellerino, A.; Bryja, Josef

    2013-01-01

    Roč. 13, č. 196 (2013), s. 196 ISSN 1471-2148 R&D Projects: GA ČR GA206/09/0815; GA ČR GBP505/12/G112 Institutional support: RVO:68081766 Keywords : Temporary pool * Phylogeography * Population genetics * Cyprinodontiformes * Senescence * Pluvials * Pleistocene climate changes * Dispersal * Founder effect * Killifish Subject RIV: EG - Zoology Impact factor: 3.407, year: 2013 http://www.biomedcentral.com/1471-2148/13/196

  15. Strong genetic overlap between executive functions and intelligence.

    Science.gov (United States)

    Engelhardt, Laura E; Mann, Frank D; Briley, Daniel A; Church, Jessica A; Harden, K Paige; Tucker-Drob, Elliot M

    2016-09-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic influences on EFs are very high, even in middle childhood, but the extent to which these genetic influences overlap with those on intelligence is unclear. We examined genetic and environmental overlap between EFs and intelligence in a racially and socioeconomically diverse sample of 811 twins ages 7 to 15 years (M = 10.91, SD = 1.74) from the Texas Twin Project. A general EF factor representing variance common to inhibition, switching, working memory, and updating domains accounted for substantial proportions of variance in intelligence, primarily via a genetic pathway. General EF continued to have a strong, genetically mediated association with intelligence even after controlling for processing speed. Residual variation in general intelligence was influenced only by shared and nonshared environmental factors, and there remained no genetic variance in general intelligence that was unique of EF. Genetic variance independent of EF did remain, however, in a more specific perceptual reasoning ability. These results provide evidence that genetic influences on general intelligence are highly overlapping with those on EF. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  16. Strong eukaryotic IRESs have weak secondary structure.

    Directory of Open Access Journals (Sweden)

    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  17. Electronic Structure of Strongly Correlated Materials

    CERN Document Server

    Anisimov, Vladimir

    2010-01-01

    Electronic structure and physical properties of strongly correlated materials containing elements with partially filled 3d, 4d, 4f and 5f electronic shells is analyzed by Dynamical Mean-Field Theory (DMFT). DMFT is the most universal and effective tool used for the theoretical investigation of electronic states with strong correlation effects. In the present book the basics of the method are given and its application to various material classes is shown. The book is aimed at a broad readership: theoretical physicists and experimentalists studying strongly correlated systems. It also serves as a handbook for students and all those who want to be acquainted with fast developing filed of condensed matter physics.

  18. Many Body Structure of Strongly Interacting Systems

    CERN Document Server

    Arenhövel, Hartmuth; Drechsel, Dieter; Friedrich, Jörg; Kaiser, Karl-Heinz; Walcher, Thomas; Symposium on 20 Years of Physics at the Mainz Microtron MAMI

    2006-01-01

    This carefully edited proceedings volume provides an extensive review and analysis of the work carried out over the past 20 years at the Mainz Microtron (MAMI). This research centered around the application of Quantum Chromodynamics in the strictly nonperturbative regime at hadronic scales of about 1 fm. Due to the many degrees of freedom in hadrons at this scale the leitmotiv of this research is "Many body structure of strongly interacting systems". Further, an outlook on the research with the forthcoming upgrade of MAMI is given. This volume is an authoritative source of reference for everyone interested in the field of the electro-weak probing of the structure of hadrons.

  19. White Matter Hyperintensities Are Under Strong Genetic Influence.

    Science.gov (United States)

    Sachdev, Perminder S; Thalamuthu, Anbupalam; Mather, Karen A; Ames, David; Wright, Margaret J; Wen, Wei

    2016-06-01

    The genetic basis of white matter hyperintensities (WMH) is still unknown. This study examines the heritability of WMH in both sexes and in different brain regions, and the influence of age. Participants from the Older Australian Twins Study were recruited (n=320; 92 monozygotic and 68 dizygotic pairs) who volunteered for magnetic resonance imaging scans and medical assessments. Heritability, that is, the ratio of the additive genetic variance to the total phenotypic variance, was estimated using the twin design. Heritability was high for total WMH volume (0.76), and for periventricular WMH (0.64) and deep WMH (0.77), and varied from 0.18 for the cerebellum to 0.76 for the occipital lobe. The genetic correlation between deep and periventricular WMH regions was 0.85, with one additive genetics factor accounting for most of the shared variance. Heritability was consistently higher in women in the cerebral regions. Heritability in deep but not periventricular WMH declined with age, in particular after the age of 75. WMH have a strong genetic influence but this is not uniform through the brain, being higher for deep than periventricular WMH and in the cerebral regions. The genetic influence is higher in women, and there is an age-related decline, most markedly for deep WMH. The data suggest some heterogeneity in the pathogenesis of WMH for different brain regions and for men and women. © 2016 American Heart Association, Inc.

  20. Coalgebraic structure of genetic inheritance.

    Science.gov (United States)

    Tian, Jianjun; Li, Bai-Lian

    2004-09-01

    Although in the broadly defined genetic algebra, multiplication suggests a forward direction of from parents to progeny, when looking from the reverse direction, it also suggests to us a new algebraic structure-coalge- braic structure, which we call genetic coalgebras. It is not the dual coalgebraic structure and can be used in the construction of phylogenetic trees. Math- ematically, to construct phylogenetic trees means we need to solve equations x([n]) = a, or x([n]) = b. It is generally impossible to solve these equations inalgebras. However, we can solve them in coalgebras in the sense of tracing back for their ancestors. A thorough exploration of coalgebraic structure in genetics is apparently necessary. Here, we develop a theoretical framework of the coalgebraic structure of genetics. From biological viewpoint, we defined various fundamental concepts and examined their elementary properties that contain genetic significance. Mathematically, by genetic coalgebra, we mean any coalgebra that occurs in genetics. They are generally noncoassociative and without counit; and in the case of non-sex-linked inheritance, they are cocommutative. Each coalgebra with genetic realization has a baric property. We have also discussed the methods to construct new genetic coalgebras, including cocommutative duplication, the tensor product, linear combinations and the skew linear map, which allow us to describe complex genetic traits. We also put forward certain theorems that state the relationship between gametic coalgebra and gametic algebra. By Brower's theorem in topology, we prove the existence of equilibrium state for the in-evolution operator.

  1. Somatically acquired structural genetic differences

    DEFF Research Database (Denmark)

    Magaard Koldby, Kristina; Nygaard, Marianne; Christensen, Kaare

    2016-01-01

    Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested t...... with age.European Journal of Human Genetics advance online publication, 20 April 2016; doi:10.1038/ejhg.2016.34....

  2. Phase structure of strongly correlated Fermi gases

    International Nuclear Information System (INIS)

    Roscher, Dietrich

    2015-01-01

    Strongly correlated fermionic many-body systems are ubiquitous in nature. Their theoretical description poses challenging problems which are further complicated when imbalances in, e.g., the particle numbers of the involved species or their masses are introduced. In this thesis, a number of different approaches is developed and applied in order to obtain predictions for physical observables of such systems that mutually support and confirm each other. In a first step, analytically well-founded mean-field analyses are carried through. One- and three-dimensional ultracold Fermi gases with spin and mass imbalance as well as Gross-Neveu and NJL-type relativistic models at finite baryon chemical potential are investigated with respect to their analytic properties in general and the occurrence of spontaneous breaking of translational invariance in particular. Based on these studies, further methods are devised or adapted allowing for investigations also beyond the mean-field approximation. Lattice Monte Carlo simulations with imaginary imbalance parameters are employed to surmount the infamous sign problem and compute the equation of state of the respective unitary Fermi gases. Moreover, in-medium two-body analyses are used to confirm and explain the characteristics of inhomogeneously ordered phases. Finally, functional RG methods are applied to the unitary Fermi gas with spin and mass imbalance. Besides quantitatively competitive predictions for critical temperatures for the superfluid state, strong hints on the stability of inhomogeneous phases with respect to order parameter fluctuations in the regime of large mass imbalance are obtained. Combining the findings from these different theoretical studies suggests the possibility to find such phases in experiments presently in preparation.

  3. Strong Genetic Overlap Between Executive Functions and Intelligence

    OpenAIRE

    Engelhardt, Laura E.; Mann, Frank D.; Briley, Daniel A.; Church, Jessica A.; Harden, K. Paige; Tucker-Drob, Elliot M.

    2016-01-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision-making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic infl...

  4. A Strong Case for Viral Genetic Factors in HIV Virulence

    Directory of Open Access Journals (Sweden)

    Joshua T. Herbeck

    2011-03-01

    Full Text Available HIV infections show great variation in the rate of progression to disease, and the role of viral genetic factors in this variation had remained poorly characterized until recently. Now a series of four studies [1–4] published within a year has filled this important gap and has demonstrated a robust effect of the viral genotype on HIV virulence.

  5. Development of strongly coupled FSI technology involving thin walled structures

    CSIR Research Space (South Africa)

    Suliman, Ridhwaan

    2011-01-01

    Full Text Available A strongly coupled finite volume-finite element fluid-structure interaction (FSI) scheme is developed. Both an edge-based finite volume and Galerkin finite element scheme are implemented and evaluated for modelling the mechanics of solids...

  6. Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population

    Directory of Open Access Journals (Sweden)

    Larsson Mikael

    2010-02-01

    Full Text Available Abstract Background Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. Results The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers. Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. Conclusions Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

  7. Characterization of genetic structure of Podophyllum hexandrum ...

    African Journals Online (AJOL)

    Characterization of genetic structure of Podophyllum hexandrum populations, an endangered medicinal herb of Northwestern Himalaya, using ISSR-PCR markers and its relatedness with podophyllotoxin content.

  8. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

  9. Universal structure of a strongly interacting Fermi gas

    Energy Technology Data Exchange (ETDEWEB)

    Kuhnle, Eva; Dyke, Paul; Hoinka, Sascha; Mark, Michael; Hu Hui; Liu Xiaji; Drummond, Peter; Hannaford, Peter; Vale, Chris, E-mail: cvale@swin.edu.au [ARC Centre of Excellence for Quantum Atom Optics, Swinburne University of Technology, Hawthorn 3122 (Australia)

    2011-01-10

    This paper presents studies of the universal properties of strongly interacting Fermi gases using Bragg spectroscopy. We focus on pair-correlations, their relationship to the contact C introduced by Tan, and their dependence on both the momentum and temperature. We show that short-range pair correlations obey a universal law, first derived by Tan through measurements of the static structure factor, which displays a universal scaling with the ratio of the contact to the momentum C/q. Bragg spectroscopy of ultracold {sup 6}Li atoms is employed to measure the structure factor for a wide range of momenta and interaction strengths, providing broad confirmation of this universal law. We show that calibrating our Bragg spectra using the f-sum rule leads to a dramatic improvement in the accuracy of the structure factor measurement. We also measure the temperature dependence of the contact in a unitary gas and compare our results to calculations based on a virial expansion.

  10. Strongly correlated electron materials. I. Theory of the quasiparticle structure

    International Nuclear Information System (INIS)

    Lopez-Aguilar, F.; Costa-Quintana, J.; Puig-Puig, L.

    1993-01-01

    In this paper we give a method for analyzing the renormalized electronic structure of the Hubbard systems. The first step is the determination of effective interactions from the random-phase approximation (RPA) and from an extended RPA (ERPA) that introduces vertex effects within the bubble polarization. The second step is the determination of the density of states deduced from the spectral functions. Its analysis leads us to conclude that these systems can exhibit three types of resonances in their electronic structures: the lower-, middle-, and upper-energy resonances. Furthermore, we analyze the conditions for which there is only one type of resonance and the causes that lead to the disappearance of the heavy-fermion state. We finally introduce the RPA and ERPA effective interactions within the strong-coupling theory and we give the conditions for obtaining coupling and superconductivity

  11. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    Hibar, D.P.; Stein, J.L.; Renteria, M.E.; Arias-Vasquez, A.; Desrivières, S.; Jahanshad, N.; Toro, R.; Wittfeld, K.; Abramovic, L.; Andersson, M.; Aribisala, B.S.; Armstrong, N.J.; Bernard, M.; Bohlken, M.M.; Biks, M.P.; Bralten, J.; Brown, A.A.; Chakravarty, M.M.; Chen, Q.; Ching, C.R.K.; Cuellar-Partida, G.; den Braber, A.; Giddaluru, S.; Goldman, A.L.; Grimm, O.; Guadalupe, T.; Hass, J.; Woldehawariat, G.; Holmes, A.J.; Hoogman, M.; Janowitz, D.; Jia, T.; Kim, S.; Klein, M.; Kraemer, B.; Lee, P.H.; Olde Loohuis, L.M.; Luciano, M.; Macare, C.; Mather, K.A.; Mattheisen, M.; Milaneschi, Y.; Nho, K.; Papmeyer, M.; Ramasamy, A.; Risacher, S.L.; Roiz-Santiañez, R.; Rose, E.J.; Salami, A.; Sämann, P.G.; Schmaal, L.; Schork, A.J.; Shin, J.; Strike, L.T.; Teumer, A.; Donkelaar, M.M.J.; van Eijk, K.R.; Walters, R.K.; Westlye, L.T.; Welan, C.D.; Winkler, A.M.; Zwiers, M.P.; Alhusaini, S.; Athanasiu, L.; Ehrlich, S.; Hakobjan, M.M.H.; Hartberg, C.B.; Haukvik, U.K.; Heister, A.J.G.A.M.; Hoehn, D.; Kasperaviciute, D.; Liewald, D.C.M.; Lopez, L.M.; Makkinje, R.R.; Matarin, M.; Naber, M.A.M.; Reese McKay, D.; Needham, M.; Nugent, A.C.; Pütz, B.; Royle, N.A.; Shen, L.; Sprooten, E.; Trabzuni, D.; van der Marel, S.S.L.; van Hulzen, K.J.E.; Walton, E.; Wolf, C.; Almasy, L.; Ames, D.; Arepalli, S.; Assareh, A.A.; Bastin, M.E.; Brodaty, H.; Bulayeva, K.B.; Carless, M.A.; Cichon, S.; Corvin, A.; Curran, J.E.; Czisch, M.; de Zubicaray, G.I.; Dillman, A.; Duggirala, R.; Dyer, T.D.; Erk, S.; Fedko, I.O.; Ferrucci, L.; Foroud, T.M.; Fox, P.T.; Fukunaga, M.; Gibbs, J.R.; Göring, H.H.H.; Green, R.C.; Guelfi, S.; Hansell, N.K.; Hartman, C.A.; Hegenscheid, K.; Heinz, A.; Hernandez, D.G.; Heslenfeld, D.J.; Hoekstra, P.J.; Holsboer, F.; Homuth, G.; Hottenga, J.J.; Ikeda, M.; Jack, C.R., Jr.; Jenkinson, M.; Johnson, R.; Kanai, R.; Keil, M.; Kent, J.W. Jr.; Kochunov, P.; Kwok, J.B.; Lawrie, S.M.; Liu, X.; Longo, D.L.; McMahon, K.L.; Meisenzahl, E.; Melle, I.; Mohnke, S.; Montgomery, G.W.; Mostert, J.C.; Mühleisen, T.W.; Nalls, M.A.; Nichols, T.E.; Nilsson, L.G.; Nöthen, M.M.; Ohi, K.; Olvera, R.L.; Perez-Iglesias, R.; Pike, G.B.; Potkin, S.G.; Reinvang, I.; Reppermund, S.; Rietschel, M.; Romanczuk-Seiferth, N.; Rosen, G.D.; Rujescu, D.; Schnell, K.; Schofield, P.R.; Smith, C.; Steen, V.M.; Sussmann, J.E.; Thalamuthu, A.; Toga, A.W.; Traynor, B.J.; Troncoso, J.; Turner, J.A.; Valdés Hernández, M.C.; van t Ent, D.; van der Brug, M.; van der Wee, N.J.A.; van Tol, M.J.; Veltman, D.J.; Wassink, T.H.; Westmann, E.; Zielke, R.H.; Zonderman, A.B.; Ashbrook, D.G.; Hager, R.; Lu, L.; McMahon, F.J.; Morris, D.W.; Williams, R.W.; Brunner, H.G.; Buckner, R.L.; Buitelaar, J.K.; Cahn, W.; Calhoun, V.D.; Cavalleri, G.L.; Crespo-Facorro, B.; Dale, A.M.; Davies, G.E.; Delanty, N.; Depondt, C.; Djurovic, S.; Drevets, W.C.; Espeseth, T.; Gollub, R.L.; Ho, B.C.; Hoffmann, W.; Hosten, N.; Kahn, R.S.; Le Hellard, S.; Meyer-Lindenberg, A.; Müller-Myhsok, B.; Nauck, M.; Nyberg, L.; Pandolfo, M.; Penninx, B.W.J.H.; Roffman, J.L.; Sisodiya, SM; Smoller, J.W.; van Bokhoven, H.; van Haren, N.E.M.; Völzke, H.; Walter, H.; Weiner, M.W.; Wen, W.; White, T.; Agartz, I.; Andreassen, O.A.; Blangero, J.; Boomsma, D.I.; Brouwer, R.M.; Cannon, D.M.; Cookson, M.R.; de Geus, E.J.C.; Deary, I.J.; Donohoe, G.; Fernandez, G.; Fisher, S.E.; Francks, C.; Glahn, D.C.; Grabe, H.J.; Gruber, O.; Hardy, J.; Hashimoto, R.; Hulshoff Pol, H.E.; Jönsson, E.G.; Kloszewska, I.; Lovestone, S.; Mattay, V.S.; Mecocci, P.; McDonald, C.; McIntosh, A.M.; Ophoff, R.A.; Paus, T.; Pausova, Z.; Ryten, M.; Sachdev, P.S.; Saykin, A.J.; Simmons, A.; Singleton, A.; Soininen, H.; Wardlaw, J.M.; Weale, M.E.; Weinberger, D.R.; Adams, H.H.H.; Launer, L.J.; Seiler, S.; Schmidt, R.; Chauhan, G.; Satizabal, C.L.; Becker, J.T.; Yanek, L.; van der Lee, S.J.; Ebling, M.; Fischl, B.; Longstreth, Jr. W.T.; Greve, D.; Schmidt, H.; Nyquist, P.; Vinke, L.N.; van Duijn, C.M.; Xue, L.; Mazoyer, B.; Bis, J.C.; Gudnason, V.; Seshadri, S.; Arfan Ikram, M.; Martin, N.G.; Wright, M.J.; Schumann, G.; Franke, B.; Thompson, P.M.; Medland, S.E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common

  12. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    D.P. Hibar (Derrek); J.L. Stein; M.E. Rentería (Miguel); A. Arias-Vásquez (Alejandro); S. Desrivières (Sylvane); N. Jahanshad (Neda); R. Toro (Roberto); K. Wittfeld (Katharina); L. Abramovic (Lucija); M. Andersson (Micael); B. Aribisala (Benjamin); N.J. Armstrong (Nicola J.); M. Bernard (Manon); M.M. Bohlken (Marc M.); M.P.M. Boks (Marco); L.B.C. Bralten (Linda); A.A. Brown (Andrew); M.M. Chakravarty (M. Mallar); Q. Chen (Qiang); C.R.K. Ching (Christopher); G. Cuellar-Partida (Gabriel); A. den Braber (Anouk); S. Giddaluru (Sudheer); A.L. Goldman (Aaron L.); O. Grimm (Oliver); T. Guadalupe (Tulio); J. Hass (Johanna); G. Woldehawariat (Girma); A.J. Holmes (Avram); M. Hoogman (Martine); D. Janowitz (Deborah); T. Jia (Tianye); S. Kim (Shinseog); M. Klein (Marieke); B. Kraemer (Bernd); P.H. Lee (Phil H.); L.M. Olde Loohuis (Loes M.); M. Luciano (Michelle); C. MacAre (Christine); R. Mather; M. Mattheisen (Manuel); Y. Milaneschi (Yuri); K. Nho (Kwangsik); M. Papmeyer (Martina); A. Ramasamy (Adaikalavan); S.L. Risacher (Shannon); R. Roiz-Santiañez (Roberto); E.J. Rose (Emma); A. Salami (Alireza); P.G. Sämann (Philipp); L. Schmaal (Lianne); N.J. Schork (Nicholas); J. Shin (Jean); L.T. Strike (Lachlan); A. Teumer (Alexander); M.M.J. Van Donkelaar (Marjolein M. J.); K.R. van Eijk (Kristel); R.K. Walters (Raymond); L.T. Westlye (Lars); C.D. Whelan (Christopher); A.M. Winkler (Anderson); M.P. Zwiers (Marcel); S. Alhusaini (Saud); L. Athanasiu (Lavinia); S.M. Ehrlich (Stefan); M. Hakobjan (Marina); C.B. Hartberg (Cecilie B.); U.K. Haukvik (Unn); A.J.G.A.M. Heister (Angelien J. G. A. M.); D. Hoehn (David); D. Kasperaviciute (Dalia); D.C. Liewald (David C.); L.M. Lopez (Lorna); R.R.R. Makkinje (Remco R. R.); M. Matarin (Mar); M.A.M. Naber (Marlies A. M.); D. Reese McKay; M. Needham (Margaret); A.C. Nugent (Allison); B. Pütz (Benno); N.A. Royle (Natalie); L. Shen (Li); R. Sprooten (Roy); D. Trabzuni (Danyah); S.S.L. Van Der Marel (Saskia S. L.); K.J.E. Van Hulzen (Kimm J. E.); E. Walton (Esther); A. Björnsson (Asgeir); L. Almasy (Laura); D.J. Ames (David); S. Arepalli (Sampath); A.A. Assareh; M.E. Bastin (Mark); H. Brodaty (Henry); K. Bulayeva (Kazima); M.A. Carless (Melanie); S. Cichon (Sven); A. Corvin (Aiden); J.E. Curran (Joanne); M. Czisch (Michael); G.I. de Zubicaray (Greig); A. Dillman (Allissa); A. Duggirala (Aparna); M.D. Dyer (Matthew); S. Erk; I. Fedko (Iryna); L. Ferrucci (Luigi); T. Foroud (Tatiana); P.T. Fox (Peter); M. Fukunaga (Masaki); J. Raphael Gibbs; H.H.H. Göring (Harald H.); R.C. Green (Robert C.); S. Guelfi (Sebastian); N.K. Hansell (Narelle); C.A. Hartman (Catharina); K. Hegenscheid (Katrin); J. Heinz (Judith); D.G. Hernandez (Dena); D.J. Heslenfeld (Dirk); P.J. Hoekstra (Pieter); F. Holsboer; G. Homuth (Georg); J.J. Hottenga (Jouke Jan); M. Ikeda (Masashi); C.R. Jack Jr. (Clifford); S. Jenkinson (Sarah); R. Johnson (Robert); R. Kanai (Ryota); M. Keil (Maria); J.W. Kent (Jack W.); P. Kochunov (Peter); J.B. Kwok (John B.); S. Lawrie (Stephen); X. Liu (Xinmin); D.L. Longo (Dan L.); K.L. Mcmahon (Katie); E. Meisenzahl (Eva); I. Melle (Ingrid); S. Mohnke (Sebastian); G.W. Montgomery (Grant); J.C. Mostert (Jeanette C.); T.W. Mühleisen (Thomas); M.A. Nalls (Michael); T.E. Nichols (Thomas); L.G. Nilsson; M.M. Nöthen (Markus); K. Ohi (Kazutaka); R.L. Olvera (Rene); R. Perez-Iglesias (Rocio); G. Bruce Pike; S.G. Potkin (Steven); I. Reinvang (Ivar); S. Reppermund; M. Rietschel (Marcella); N. Seiferth (Nina); G.D. Rosen (Glenn D.); D. Rujescu (Dan); K. Schnell (Kerry); C.J. Schofield (Christopher); C. Smith (Colin); V.M. Steen (Vidar); J. Sussmann (Jessika); A. Thalamuthu (Anbupalam); A.W. Toga (Arthur W.); B. Traynor (Bryan); J.C. Troncoso (Juan); J. Turner (Jessica); M.C. Valdés Hernández (Maria); D. van 't Ent (Dennis); M.P. van der Brug (Marcel); N.J. van der Wee (Nic); M.J.D. van Tol (Marie-José); D.J. Veltman (Dick); A.M.J. Wassink (Annemarie); E. Westman (Eric); R.H. Zielke (Ronald H.); A.B. Zonderman (Alan B.); D.G. Ashbrook (David G.); R. Hager (Reinmar); L. Lu (Lu); F.J. Mcmahon (Francis J); D.W. Morris (Derek W); R.W. Williams (Robert W.); H.G. Brunner; M. Buckner; J.K. Buitelaar (Jan K.); W. Cahn (Wiepke); V.D. Calhoun Vince D. (V.); G. Cavalleri (Gianpiero); B. Crespo-Facorro (Benedicto); A.M. Dale (Anders); G.E. Davies (Gareth); N. Delanty; C. Depondt (Chantal); S. Djurovic (Srdjan); D.A. Drevets (Douglas); T. Espeseth (Thomas); R.L. Gollub (Randy); B.C. Ho (Beng ); W. Hoffmann (Wolfgang); N. Hosten (Norbert); R. Kahn (René); S. Le Hellard (Stephanie); A. Meyer-Lindenberg; B. Müller-Myhsok (B.); M. Nauck (Matthias); L. Nyberg (Lars); M. Pandolfo (Massimo); B.W.J.H. Penninx (Brenda); J.L. Roffman (Joshua); S.M. Sisodiya (Sanjay); J.W. Smoller; H. van Bokhoven (Hans); N.E.M. van Haren (Neeltje E.); H. Völzke (Henry); H.J. Walter (Henrik); M.W. Weiner (Michael); W. Wen (Wei); T.J.H. White (Tonya); I. Agartz (Ingrid); O.A. Andreassen (Ole); J. Blangero (John); D.I. Boomsma (Dorret); R.M. Brouwer (Rachel); D.M. Cannon (Dara); M.R. Cookson (Mark); E.J.C. de Geus (Eco); I.J. Deary (Ian J.); D.J. Donohoe (Dennis); G. Fernandez (Guillén); S.E. Fisher (Simon); C. Francks (Clyde); D.C. Glahn (David); H.J. Grabe (Hans Jörgen); O. Gruber (Oliver); J. Hardy (John); R. Hashimoto (Ryota); H.E. Hulshoff Pol (Hilleke); E.G. Jönsson (Erik); I. Kloszewska (Iwona); S. Lovestone (Simon); V.S. Mattay (Venkata S.); P. Mecocci (Patrizia); C. McDonald (Colm); A.M. McIntosh (Andrew); R.A. Ophoff (Roel); T. Paus (Tomas); Z. Pausova (Zdenka); M. Ryten (Mina); P.S. Sachdev (Perminder); A.J. Saykin (Andrew); A. Simmons (Andrew); A. Singleton (Andrew); H. Soininen (H.); J.M. Wardlaw (J.); M.E. Weale (Michael); D.R. Weinberger (Daniel); H.H.H. Adams (Hieab); L.J. Launer (Lenore); S. Seiler (Stephan); R. Schmidt (Reinhold); G. Chauhan (Ganesh); C.L. Satizabal (Claudia L.); J.T. Becker (James); L.R. Yanek (Lisa); S.J. van der Lee (Sven); M. Ebling (Maritza); B. Fischl (Bruce); W.T. Longstreth Jr; D. Greve (Douglas); R. Schmidt (Reinhold); P. Nyquist (Paul); L.N. Vinke (Louis N.); C.M. van Duijn (Cornelia); L. Xue (Luting); B. Mazoyer (Bernard); J.C. Bis (Joshua); V. Gudnason (Vilmundur); S. Seshadri (Sudha); M.A. Ikram (Arfan); N.G. Martin (Nicholas); M.J. Wright (Margaret); G. Schumann (Gunter); B. Franke (Barbara); P.M. Thompson (Paul); S.E. Medland (Sarah Elizabeth)

    2015-01-01

    textabstractThe highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate

  13. Common genetic variants influence human subcortical brain structures

    NARCIS (Netherlands)

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivieres, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Loohuis, Loes M. Olde; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santianez, Roberto; Rose, Emma J.; Salami, Alireza; Saemann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Puetz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Goering, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzah, Eva; Melle, Ingrid; Mahnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Muehleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Noethen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdes Hernandez, Maria C.; van't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffman, Wolfgang; Hosten, Norbert; Kahn, Rene S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Mueller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Voelzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernandez, Guillen; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Pol, Hilleke E. Hulshoff; Joensson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences(1). Subcortical brain regions form circuits with cortical areas to coordinate movement(2), learning, memory(3) and motivation(4), and altered circuits can lead to abnormal behaviour and disease(5). To

  14. Circulating anti-Mullerian hormone levels in adult men are under a strong genetic influence.

    Science.gov (United States)

    Pietiläinen, Kirsi H; Kaprio, Jaakko; Vaaralahti, Kirsi; Rissanen, Aila; Raivio, Taneli

    2012-01-01

    The determinants of serum anti-Müllerian hormone (AMH) levels in adult men remain unclear. The objective of the study was to investigate the genetic and environmental components in determining postpubertal AMH levels in healthy men. Serum AMH levels, body mass index (BMI), and fat mass (dual energy x-ray absorptiometry) were measured in 64 healthy male (23 monozygotic and 41 dizygotic) twin pairs. Postpubertal AMH levels were highly genetically determined (broad sense heritability 0.92, 95% confidence interval 0.83-0.96). AMH correlated negatively with BMI (r = -0.26, P = 0.030) and fat mass (r = -0.23, P = 0.048). As AMH, BMI had a high heritability (0.68, 95% confidence interval 0.39-0.83), but no genetic correlation was observed between them. AMH levels in men after puberty are under a strong genetic influence. Twin modeling suggests that AMH and BMI are influenced by different sets of genes.

  15. The 5-HT2A receptor binding pattern in the human brain is strongly genetically determined

    DEFF Research Database (Denmark)

    Pinborg, Lars H; Arfan, Haroon; Haugbol, Steven

    2007-01-01

    With the appropriate radiolabeled tracers, positron emission tomography (PET) enables in vivo human brain imaging of markers for neurotransmission, including neurotransmitter synthesis, receptors, and transporters. Whereas structural imaging studies have provided compelling evidence that the human...... brain anatomy is largely genetically determined, it is currently unknown to what degree neuromodulatory markers are subjected to genetic and environmental influence. Changes in serotonin 2A (5-HT(2A)) receptors have been reported to occur in various neuropsychiatric disorders and an association between...

  16. Caledonian scots pine: origins and genetic structure

    Science.gov (United States)

    Bohun B Kinloch; R. D. Westfall; G. I. Forrest

    1986-01-01

    Monoterpene and isozyme loci, used as markers to study the genetic structure of Scots pine (Pinus sylvestris L.) native to Scotland, showed that the endemic populations are not genetically impoverished, in spite of severe contraction in range and numbers as a result of both natural and anthropogenic causes. On the contrary, variability in the relict...

  17. Ionic charge transport in strongly structured molten salts

    International Nuclear Information System (INIS)

    Tatlipinar, H.; Amoruso, M.; Tosi, M.P.

    1999-08-01

    Data on the d.c. ionic conductivity for strongly structured molten halides of divalent and trivalent metals near freezing are interpreted as mainly reflecting charge transport by the halogen ions. On this assumption the Nernst-Einstein relation allows an estimate of the translational diffusion coefficient D tr of the halogen. In at least one case (molten ZnCl 2 ) D tr is much smaller than the measured diffusion coefficient, pointing to substantial diffusion via neutral units. The values of D tr estimated from the Nernst-Einstein relation are analyzed on the basis of a model involving two parameters, i.e. a bond-stretching frequency ω and an average waiting time τ. With the help of Raman scattering data for ω, the values of τ are evaluated and found to mostly lie in the range 0.02 - 0.3 ps for a vast class of materials. (author)

  18. Mathematical structure of Rabi oscillations in the strong coupling regime

    International Nuclear Information System (INIS)

    Fujii, Kazuyuki

    2003-01-01

    In this paper, we generalize the Jaynes-Cummings Hamiltonian by making use of some operators based on Lie algebras su(1, 1) and su(2), and study a mathematical structure of Rabi floppings of these models in the strong coupling regime. We show that Rabi frequencies are given by matrix elements of generalized coherent operators (Fujii K 2002 Preprint quant-ph/0202081) under the rotating-wave approximation. In the first half, we make a general review of coherent operators and generalized coherent ones based on Lie algebras su(1, 1) and su(2). In the latter half, we carry out a detailed examination of Frasca (Frasca M 2001 Preprint quant-ph/0111134) and generalize his method, and moreover present some related problems. We also apply our results to the construction of controlled unitary gates in quantum computation. Lastly, we make a brief comment on application to holonomic quantum computation

  19. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  20. Strong sustainability in Nepal: A structural economics approach

    Science.gov (United States)

    Devkota, Surendra R.

    example of a poor country moving along a path toward strong sustainability. To this end, a sincere intervention at the social and natural capital along with economic growth is necessary. Poverty alleviation efforts should target the socio-economically deprived households by enriching their human capital. Since community based social structures, such as the forest user groups, are already setting an example of strong sustainability, such community based social capital initiatives should be encouraged by granting rights and other resources to augment further economic activities like harnessing hydropower that may eventually transform the socio-ecological-economic system.

  1. Nonlinear phononics and structural control of strongly correlated materials

    Energy Technology Data Exchange (ETDEWEB)

    Mankowsky, Roman

    2016-01-20

    Mid-infrared light pulses can be used to resonantly excite infrared-active vibrational modes for the phase control of strongly correlated materials on subpicosecond timescales. As the energy is transferred directly into atomic motions, dissipation into the electronic system is reduced, allowing for the emergence of unusual low energy collective properties. Light-induced superconductivity, insulator-metal transitions and melting of magnetic order demonstrate the potential of this method. An understanding of the mechanism, by which these transitions are driven, is however missing. The aim of this work is to uncover this process by investigating the nonlinear lattice dynamics induced by the excitation and to elucidate their contribution to the modulation of collective properties of strongly correlated materials. The first signature of nonlinear lattice dynamics was reported in the observation of coherent phonon oscillations, resonant with the excitation of an infrared-active phonon mode in a manganite. This nonlinear phononic coupling can be described within a model, which predicts not only oscillatory coherent phonons dynamics but also directional atomic displacements along the coupled modes on average, which could cause the previously observed transitions. We verified this directional response and quantified the anharmonic coupling constant by tracing the atomic motions in a time-resolved hard X-ray diffraction experiment with sub-picometer spatial and femtosecond temporal resolution. In a subsequent study, we investigated the role of nonlinear lattice dynamics in the emergence of superconductivity far above the equilibrium transition temperature, an intriguing effect found to follow lattice excitation of YBa{sub 2}Cu{sub 3}O{sub 6+x}. By combining density functional theory (DFT) calculations of the anharmonic coupling constants with time-resolved X-ray diffraction experiments, we identified a structural rearrangement, which appears and decays with the same temporal

  2. Fine-Scale Genetic Structure in Finland

    Directory of Open Access Journals (Sweden)

    Sini Kerminen

    2017-10-01

    Full Text Available Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP and FineSTRUCTURE (FS we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Nöteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.

  3. Assessing population genetic structure via the maximisation of genetic distance

    Directory of Open Access Journals (Sweden)

    Toro Miguel A

    2009-11-01

    Full Text Available Abstract Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy

  4. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  5. [Genetic structure of natural populations

    International Nuclear Information System (INIS)

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs

  6. Focusing light through strongly scattering media using genetic algorithm with SBR discriminant

    Science.gov (United States)

    Zhang, Bin; Zhang, Zhenfeng; Feng, Qi; Liu, Zhipeng; Lin, Chengyou; Ding, Yingchun

    2018-02-01

    In this paper, we have experimentally demonstrated light focusing through strongly scattering media by performing binary amplitude optimization with a genetic algorithm. In the experiments, we control 160 000 mirrors of digital micromirror device to modulate and optimize the light transmission paths in the strongly scattering media. We replace the universal target-position-intensity (TPI) discriminant with signal-to-background ratio (SBR) discriminant in genetic algorithm. With 400 incident segments, a relative enhancement value of 17.5% with a ground glass diffuser is achieved, which is higher than the theoretical value of 1/(2π )≈ 15.9 % for binary amplitude optimization. According to our repetitive experiments, we conclude that, with the same segment number, the enhancement for the SBR discriminant is always higher than that for the TPI discriminant, which results from the background-weakening effect of SBR discriminant. In addition, with the SBR discriminant, the diameters of the focus can be changed ranging from 7 to 70 μm at arbitrary positions. Besides, multiple foci with high enhancement are obtained. Our work provides a meaningful reference for the study of binary amplitude optimization in the wavefront shaping field.

  7. Stiff, Strong Splice For A Composite Sandwich Structure

    Science.gov (United States)

    Schmaling, D.

    1991-01-01

    New type of splice for composite sandwich structure reduces peak shear stress in structure. Layers of alternating fiber orientation interposed between thin ears in adhesive joint. Developed for structural joint in spar of helicopter rotor blade, increases precision of control over thickness of adhesive at joint. Joint easy to make, requires no additional pieces, and adds little weight.

  8. Genetic structure of Pseudococcus microcirculus (Hemiptera ...

    Indian Academy of Sciences (India)

    Department of Biology, Armstrong State University, Savannah, GA 31419, USA. Abstract ... [Zettler J. A., Adams K., Frederick B., Gutting A., Ingebretsen N., Ragsdale A. and Schrey A. 2017 Genetic structure of Pseudococcus ..... Park) and Larry Richardson (Florida Panther Wildlife Refuge) for ... University Press of Florida,.

  9. Genetic structure of Japanese Spanish mackerel ( Scomberomorus ...

    African Journals Online (AJOL)

    Genetic structure of Japanese Spanish mackerel ( Scomberomorus niphonius ) in the East China Sea and Yellow Sea inferred from AFLP data. ... Considering the high hydrological connectivity of this region and the species pelagic life history, retention of larvae, different migration route and different spawning season may ...

  10. Population genetics inference for longitudinally-sampled mutants under strong selection.

    Science.gov (United States)

    Lacerda, Miguel; Seoighe, Cathal

    2014-11-01

    Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright-Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright-Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright-Fisher model. Copyright © 2014 by the Genetics Society of America.

  11. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed.

    Science.gov (United States)

    Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

    2012-09-01

    Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.

  12. Common genetic variants influence human subcortical brain structures.

    Science.gov (United States)

    Hibar, Derrek P; Stein, Jason L; Renteria, Miguel E; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S; Armstrong, Nicola J; Bernard, Manon; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brown, Andrew A; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Olde Loohuis, Loes M; Luciano, Michelle; Macare, Christine; Mather, Karen A; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rose, Emma J; Salami, Alireza; Sämann, Philipp G; Schmaal, Lianne; Schork, Andrew J; Shin, Jean; Strike, Lachlan T; Teumer, Alexander; van Donkelaar, Marjolein M J; van Eijk, Kristel R; Walters, Raymond K; Westlye, Lars T; Whelan, Christopher D; Winkler, Anderson M; Zwiers, Marcel P; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M H; Hartberg, Cecilie B; Haukvik, Unn K; Heister, Angelien J G A M; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C M; Lopez, Lorna M; Makkinje, Remco R R; Matarin, Mar; Naber, Marlies A M; McKay, D Reese; Needham, Margaret; Nugent, Allison C; Pütz, Benno; Royle, Natalie A; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S L; van Hulzen, Kimm J E; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A; Bastin, Mark E; Brodaty, Henry; Bulayeva, Kazima B; Carless, Melanie A; Cichon, Sven; Corvin, Aiden; Curran, Joanne E; Czisch, Michael; de Zubicaray, Greig I; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D; Erk, Susanne; Fedko, Iryna O; Ferrucci, Luigi; Foroud, Tatiana M; Fox, Peter T; Fukunaga, Masaki; Gibbs, J Raphael; Göring, Harald H H; Green, Robert C; Guelfi, Sebastian; Hansell, Narelle K; Hartman, Catharina A; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G; Heslenfeld, Dirk J; Hoekstra, Pieter J; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Liu, Xinmin; Longo, Dan L; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W; Mostert, Jeanette C; Mühleisen, Thomas W; Nalls, Michael A; Nichols, Thomas E; Nilsson, Lars G; Nöthen, Markus M; Ohi, Kazutaka; Olvera, Rene L; Perez-Iglesias, Rocio; Pike, G Bruce; Potkin, Steven G; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D; Rujescu, Dan; Schnell, Knut; Schofield, Peter R; Smith, Colin; Steen, Vidar M; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Turner, Jessica A; Valdés Hernández, Maria C; van 't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J A; van Tol, Marie-Jose; Veltman, Dick J; Wassink, Thomas H; Westman, Eric; Zielke, Ronald H; Zonderman, Alan B; Ashbrook, David G; Hager, Reinmar; Lu, Lu; McMahon, Francis J; Morris, Derek W; Williams, Robert W; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Cahn, Wiepke; Calhoun, Vince D; Cavalleri, Gianpiero L; Crespo-Facorro, Benedicto; Dale, Anders M; Davies, Gareth E; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C; Espeseth, Thomas; Gollub, Randy L; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W J H; Roffman, Joshua L; Sisodiya, Sanjay M; Smoller, Jordan W; van Bokhoven, Hans; van Haren, Neeltje E M; Völzke, Henry; Walter, Henrik; Weiner, Michael W; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A; Blangero, John; Boomsma, Dorret I; Brouwer, Rachel M; Cannon, Dara M; Cookson, Mark R; de Geus, Eco J C; Deary, Ian J; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E; Francks, Clyde; Glahn, David C; Grabe, Hans J; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E; Jönsson, Erik G; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M; Ophoff, Roel A; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S; Saykin, Andrew J; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M; Weale, Michael E; Weinberger, Daniel R; Adams, Hieab H H; Launer, Lenore J; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L; Becker, James T; Yanek, Lisa; van der Lee, Sven J; Ebling, Maritza; Fischl, Bruce; Longstreth, W T; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N; van Duijn, Cornelia M; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M Arfan; Martin, Nicholas G; Wright, Margaret J; Schumann, Gunter; Franke, Barbara; Thompson, Paul M; Medland, Sarah E

    2015-04-09

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

  13. Common genetic variants influence human subcortical brain structures

    Science.gov (United States)

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Olde Loohuis, Loes M.; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santiañez, Roberto; Rose, Emma J.; Salami, Alireza; Sämann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Pütz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Göring, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Mühleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Nöthen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdés Hernández, Maria C.; van ’t Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Völzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E.; Jönsson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability inhuman brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  14. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

    Science.gov (United States)

    Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

    2016-01-01

    Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

  15. Nucleon quark structure and strong meson-nucleon form factors

    International Nuclear Information System (INIS)

    Efimov, G.V.; Ivanov, M.A.

    1987-01-01

    The nucleon is considered as a three-quark system in virton-quark model. The main statistic properties of proton and neutron are calculated: magnetic moments, electromagnetic radii, G A /G V ratio in weak neutron decay. Strong meson-nucleon form factors which determine nucleon-nucleon potential are obtained as a function of squared transfer momentum of mesons. The results are compared with phenomenological form factors used for description of phases of NN-scattering in the one-boson-, exchange model

  16. Early environmental exposures influence schizophrenia expression even in the presence of strong genetic predisposition.

    Science.gov (United States)

    Husted, Janice A; Ahmed, Rashid; Chow, Eva W C; Brzustowicz, Linda M; Bassett, Anne S

    2012-05-01

    There are few studies of environmental factors in familial forms of schizophrenia. We investigated whether childhood adversity or environmental factors were associated with schizophrenia in a familial sample where schizophrenia is associated with the NOSA1P gene. We found that a cumulative adversity index including childhood illness, family instability and cannabis use was significantly associated with narrow schizophrenia, independent of NOSA1P risk genotype, previously measured childhood trauma, covariates and familial clustering (adjusted odds ratio (95% confidence interval)=1.55 (1.01, 2.38)). The results provide further support that early environmental exposures influence schizophrenia expression even in the presence of strong genetic predisposition. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Influence of earthquake strong motion duration on nonlinear structural response

    International Nuclear Information System (INIS)

    Meskouris, K.

    1983-01-01

    The effects of motion duration on nonlinear structural response of high-rise, moment resisting frames are studied by subjecting shear beam models of a 10- and a 5-story frame to a series of synthetic accelerograms, all matching the same NEWMARK/HALL design spectrum. Two different hysteretic laws are used for the story springs, and calculations are carried out for target ductility values of 2 and 4. Maximum ductilities reached and energy-based damage indicators (maximum seismically input energy, hysteretically dissipated energy) are evaluated and correlated with the motion characteristics. A reasonable extrapolative determination of structural response characteristics based on these indicators seems possible. (orig.)

  18. Genetic and environmental contributions to cardiovascular disease risk in American Indians: the strong heart family study.

    Science.gov (United States)

    North, Kari E; Howard, Barbara V; Welty, Thomas K; Best, Lyle G; Lee, Elisa T; Yeh, J L; Fabsitz, Richard R; Roman, Mary J; MacCluer, Jean W

    2003-02-15

    The aims of the Strong Heart Family Study are to clarify the genetic determinants of cardiovascular disease (CVD) risk in American Indians and to map and identify genes for CVD susceptibility. The authors describe the design of the Strong Heart Family Study (conducted between 1998 and 1999) and evaluate the heritabilities of CVD risk factors in American Indians from this study. In the first phase of the study, approximately 950 individuals, aged 18 years or more, in 32 extended families, were examined. The examination consisted of a personal interview, physical examination, laboratory tests, and an ultrasound examination of the carotid arteries. The phenotypes measured during the physical examination included anthropometry, lipoproteins, blood pressure, glycemic status, and clotting factors. Heritabilities for CVD risk factor phenotypes were estimated using a variance component approach and the program SOLAR. After accounting for the effects of covariates, the authors detected significant heritabilities for many CVD risk factor phenotypes (e.g., high density lipoprotein cholesterol (heritability = 0.50) and diastolic blood pressure (heritability = 0.34)). These results suggest that heredity explains a substantial proportion of the variability of CVD risk factors and that these heritabilities are large enough to warrant a search for major risk factor genes.

  19. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

    Science.gov (United States)

    FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

    2016-01-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

  20. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

    Science.gov (United States)

    Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

    2016-05-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

  1. Analysis of genetic structure and relationship among nine ...

    Indian Academy of Sciences (India)

    These results indicated that the clustering analysis using the Structure program might provide an ..... of the current genetic relations among the breeds, and con- tribute to ... sis of the genetic structure of the Canary goat populations using.

  2. Associated genetic syndromes and extracardiac malformations strongly influence outcomes of fetuses with congenital heart diseases.

    Science.gov (United States)

    Bensemlali, Myriam; Bajolle, Fanny; Ladouceur, Magalie; Fermont, Laurent; Lévy, Marilyne; Le Bidois, Jérôme; Salomon, Laurent J; Bonnet, Damien

    2016-05-01

    Congenital heart disease (CHD) is often associated with extracardiac malformations (ECMs) and genetic syndromes. To determine the effect of cytogenetic anomalies and/or ECMs associated with CHD on parental decision to choose termination of pregnancy (TOP) or compassionate care (CC), as well as on the outcome of children born alive. This 10-year retrospective study included all prenatally diagnosed cases of CHD in a single tertiary referral centre. From January 2002 to December 2011, 2036 consecutive cases of fetal CHD (798 TOPs and 1238 live births, including 59 with postnatal CC) were included. CHD was associated with a known cytogenetic anomaly in 9.8% of cases and a major ECM in 11.7% of cases. The proportion of prenatally identified associated cytogenetic anomalies was significantly lower in the live-birth group than in the TOP plus CC group (4.2% vs 17.5%; P<0.001); this was also true for ECMs (8.1% vs 16.7%; P<0.001). The mortality rate was higher in the group with an associated cytogenetic anomaly or ECM (29.1%) than in cases with isolated CHD; a 2.4-fold increase in the death rate was observed (95% confidence interval 1.34-4.38; P=0.003). These associations remained significant after multivariable analysis, including the severity of the CHD (uni- or biventricular physiology). Prenatal diagnosis of a known cytogenetic anomaly or major ECM strongly influences parental decision to choose TOP or postnatal CC. Genetic syndromes and ECMs are associated with a higher mortality rate, independent of the complexity of the CHD. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  3. Three-dimensional electromagnetic strong turbulence. II. Wave packet collapse and structure of wave packets during strong turbulence

    International Nuclear Information System (INIS)

    Graham, D. B.; Robinson, P. A.; Cairns, Iver H.; Skjaeraasen, O.

    2011-01-01

    Large-scale simulations of wave packet collapse are performed by numerically solving the three-dimensional (3D) electromagnetic Zakharov equations, focusing on individual wave packet collapses and on wave packets that form in continuously driven strong turbulence. The collapse threshold is shown to decrease as the electron thermal speed ν e /c increases and as the temperature ratio T i /T e of ions to electrons decreases. Energy lost during wave packet collapse and dissipation is shown to depend on ν e /c. The dynamics of density perturbations after collapse are studied in 3D electromagnetic strong turbulence for a range of T i /T e . The structures of the Langmuir, transverse, and total electric field components of wave packets during strong turbulence are investigated over a range of ν e /c. For ν e /c e /c > or approx. 0.17, transverse modes become trapped in density wells and contribute significantly to the structure of the total electric field. At all ν e /c, the Langmuir energy density contours of wave packets are predominantly oblate (pancake shaped). The transverse energy density contours of wave packets are predominantly prolate (sausage shaped), with the major axis being perpendicular to the major axes of the Langmuir component. This results in the wave packet becoming more nearly spherical as ν e /c increases, and in turn generates more spherical density wells during collapse. The results obtained are compared with previous 3D electrostatic results and 2D electromagnetic results.

  4. The Genetic Structure of Marijuana and Hemp.

    Directory of Open Access Journals (Sweden)

    Jason Sawler

    Full Text Available Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana, which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC, are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.

  5. The Genetic Structure of Marijuana and Hemp.

    Science.gov (United States)

    Sawler, Jason; Stout, Jake M; Gardner, Kyle M; Hudson, Darryl; Vidmar, John; Butler, Laura; Page, Jonathan E; Myles, Sean

    2015-01-01

    Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.

  6. The Genetic Structure of Marijuana and Hemp

    Science.gov (United States)

    Sawler, Jason; Stout, Jake M.; Gardner, Kyle M.; Hudson, Darryl; Vidmar, John; Butler, Laura; Page, Jonathan E.; Myles, Sean

    2015-01-01

    Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ 9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains. PMID:26308334

  7. Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

    Science.gov (United States)

    Rico, Y; Wagner, H H

    2016-11-01

    Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

  8. Turbulent structure and dynamics of swirled, strongly pulsed jet diffusion flames

    KAUST Repository

    Liao, Ying-Hao; Hermanson, James C.

    2013-01-01

    The structure and dynamics of swirled, strongly pulsed, turbulent jet diffusion flames were examined experimentally in a co-flow swirl combustor. The dynamics of the large-scale flame structures, including variations in flame dimensions, the degree

  9. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... STRUCTURE analysis revealed 4 clusters of genetically ..... 10000 cycles and 50000 Markov Chain Monte Carlo (MCMC) iterations and 10 replicate runs performed for each K value to ..... WL, Lee M, Porter K (2000). Genetic ...

  10. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

    Science.gov (United States)

    Orsini, Luisa; Marshall, Hollie; Cuenca Cambronero, Maria; Chaturvedi, Anurag; Thomas, Kelley W; Pfrender, Michael E; Spanier, Katina I; De Meester, Luc

    2016-12-01

    Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank. © 2016 John Wiley & Sons Ltd.

  11. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-26

    Dec 26, 2011 ... relief, diuresis, blood pressure and lipid metabolism. (Kawasaki et al., 2000). ... Habitat. Longitude(N),. Latitude(E). Population size. Sample size. LY. Luoyang, Henan ..... Compared with the high genetic diversity at the species.

  12. Genetic structure of Potentilla acaulis (Rosaceae) populations ...

    African Journals Online (AJOL)

    Jane

    2011-07-18

    Jul 18, 2011 ... populations based on randomly amplified polymorphic. DNA (RAPD) in habitat ..... the correlation between ΦST values and genetic distances was highly ... Propagule recruitment from genets of perennial clonal plants could ...

  13. Strong plasma shock structures based on the Navier--Stokes equations

    International Nuclear Information System (INIS)

    Abe, K.

    1975-01-01

    The structure of a plasma collisional shock wave is examined on the basis of the Navier--Stokes equations and simultaneously on the basis of the Fokker--Planck equation. The resultant structures are compared to check the validity of the Navier--Stokes equations applied to the structures of strong shock waves. The Navier--Stokes equations give quite correct structures for weak shock waves. For the strong shock waves, the detailed structures obtained from the Navier--Stokes equations differ from the results of the Fokker--Planck equation, but the shock thicknesses of the two shock waves are in relatively close agreement

  14. Spatial and population genetic structure of microsatellites in white pine

    Science.gov (United States)

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  15. Genetic and other factors determining mannose-binding lectin levels in American Indians: the Strong Heart Study

    DEFF Research Database (Denmark)

    Best, Lyle G; Ferrell, Robert E; Decroo, Susan

    2009-01-01

    control of MBL2 expression is complex and genetic background effects in specific populations are largely unknown. METHODS: The Strong Heart Study is a longitudinal, cohort study of cardiovascular disease among American Indians. A subset of individuals genotyped for the above mentioned case-control study...... in Caucasian and other populations, result in markedly reduced expression of functional protein. Prospective epidemiologic studies, including a nested, case-control study from the present population, have demonstrated the ability of MBL2 genotypes to predict complications of atherosclerosis,. The genetic...

  16. Strong Migration Limit for Games in Structured Populations: Applications to Dominance Hierarchy and Set Structure

    Directory of Open Access Journals (Sweden)

    Dhaker Kroumi

    2015-09-01

    Full Text Available In this paper, we deduce a condition for a strategy S1 to be more abundant on average at equilibrium under weak selection than another strategy S2 in a population structured into a finite number of colonies of fixed proportions as the population size tends to infinity. It is assumed that one individual reproduces at a time with some probability depending on the payoff received in pairwise interactions within colonies and between colonies and that the offspring replaces one individual chosen at random in the colony into which the offspring migrates. It is shown that an expected weighted average equilibrium frequency of S1 under weak symmetric strategy mutation between S1 and S2 is increased by weak selection if an expected weighted payoff of S1 near neutrality exceeds the corresponding expected weighted payoff of S2. The weights are given in terms of reproductive values of individuals in the different colonies in the neutral model. This condition for S1 to be favoured by weak selection is obtained from a strong migration limit of the genealogical process under neutrality for a sample of individuals, which is proven using a two-time scale argument. The condition is applied to games between individuals in colonies with linear or cyclic dominance and between individuals belonging to groups represented by subsets of a given set.

  17. Flexibility of the genetic code with respect to DNA structure

    DEFF Research Database (Denmark)

    Baisnée, P. F.; Baldi, Pierre; Brunak, Søren

    2001-01-01

    Motivation. The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA...... structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding...... sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure? Results. We develop an index for code flexibility with respect to DNA structure. Using five different di- or tri-nucleotide models of sequence-dependent DNA structure, we show...

  18. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Directory of Open Access Journals (Sweden)

    Kathleen Semple Delaney

    2010-09-01

    Full Text Available Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  19. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  20. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  1. Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

    Directory of Open Access Journals (Sweden)

    Pernille Sarup

    2011-01-01

    Full Text Available Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

  2. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

    Science.gov (United States)

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-09-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

  3. Testing the structure of a hydrological model using Genetic Programming

    Science.gov (United States)

    Selle, Benny; Muttil, Nitin

    2011-01-01

    SummaryGenetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that Genetic Programming can be used to test the structure of hydrological models and to identify dominant processes in hydrological systems. To test this, Genetic Programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, watertable depths and water ponding times during surface irrigation. Using Genetic Programming, a simple model of deep percolation was recurrently evolved in multiple Genetic Programming runs. This simple and interpretable model supported the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that Genetic Programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

  4. Strongly enhanced colorectal cancer risk stratification by combining family history and genetic risk score

    Directory of Open Access Journals (Sweden)

    Weigl K

    2018-01-01

    Full Text Available Korbinian Weigl,1,2 Jenny Chang-Claude,3,4 Phillip Knebel,5 Li Hsu,6 Michael Hoffmeister,1 Hermann Brenner1,2,7 1Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ, Heidelberg, 2German Cancer Consortium (DKTK, German Cancer Research Center (DKFZ, Heidelberg, 3Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ, Heidelberg, 4University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, 5Department for General, Visceral and Transplantation Surgery, University Heidelberg, Heidelberg, Germany; 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; 7Division of Preventive Oncology, German Cancer Research Center (DKFZ and National Center for Tumor Diseases (NCT, Heidelberg, Germany Background and aim: Family history (FH and genetic risk scores (GRSs are increasingly used for risk stratification for colorectal cancer (CRC screening. However, they were mostly considered alternatively rather than jointly. The aim of this study was to assess the potential of individual and joint risk stratification for CRC by FH and GRS.Patients and methods: A GRS was built based on the number of risk alleles in 53 previously identified single-nucleotide polymorphisms among 2,363 patients with a first diagnosis of CRC and 2,198 controls in DACHS [colorectal cancer: chances for prevention through screening], a population-based case-control study in Germany. Associations between GRS and FH with CRC risk were quantified by multiple logistic regression.Results: A total of 316 cases (13.4% and 214 controls (9.7% had a first-degree relative (FDR with CRC (adjusted odds ratio [aOR] 1.86, 95% CI 1.52–2.29. A GRS in the highest decile was associated with a 3.0-fold increased risk of CRC (aOR 3.00, 95% CI 2.24–4.02 compared with the lowest decile. This association was tentatively more pronounced in older age groups. FH and GRS were essentially unrelated, and their

  5. Automatic Creation of Machine Learning Workflows with Strongly Typed Genetic Programming

    Czech Academy of Sciences Publication Activity Database

    Křen, T.; Pilát, M.; Neruda, Roman

    2017-01-01

    Roč. 26, č. 5 (2017), č. článku 1760020. ISSN 0218-2130 R&D Projects: GA ČR GA15-19877S Grant - others:GA MŠk(CZ) LM2015042 Institutional support: RVO:67985807 Keywords : genetic programming * machine learning workflows * asynchronous evolutionary algorithm Subject RIV: IN - Informatics, Computer Science OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.778, year: 2016

  6. Genetic structure of Pseudococcus microcirculus (Hemiptera ...

    Indian Academy of Sciences (India)

    J. A. ZETTLER

    Life Technologies, Carlsbad, USA) to ... N, genetic diversity estimates including sample size; Ar, allelic richness; pAr, private allelic richness; HE, expected heterozygosity; HO, .... Harrington D. 1985 Burton–Swartz cypress company of Florida.

  7. A Strong Impact of Genetic Background on Gut Microflora in Mice

    Directory of Open Access Journals (Sweden)

    R. Steven Esworthy

    2010-01-01

    Full Text Available Genetic background affects susceptibility to ileocolitis in mice deficient in two intracellular glutathione peroxidases, GPx1 and GPx2. The C57BL/6 (B6 GPx1/2 double-knockout (DKO mice have mild ileocolitis, and 129S1/Sv (129 DKO mice have severe inflammation. We used diet to modulate ileocolitis; a casein-based defined diet with AIN76A micronutrients (AIN attenuates inflammation compared to conventional LabDiets. Because luminal microbiota induce DKO ileocolitis, we assessed bacterial composition with automated ribosomal intergenic-spacer analysis (ARISA on cecal DNA. We found that mouse strain had the strongest impact on the composition of microbiota than diet and GPx genotypes. In comparing AIN and LabDiet, DKO mice were more resistant to change than the non-DKO or WT mice. However, supplementing yeast and inulin to AIN diet greatly altered microflora profiles in the DKO mice. From 129 DKO strictly, we found overgrowth of Escherichia coli. We conclude that genetic background predisposes mice to colonization of potentially pathogenic E. coli.

  8. Population Genetic Structure of the People of Qatar

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

    2010-01-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

  9. Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

    Science.gov (United States)

    Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

    2017-01-01

    Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

  10. Genetic structure and demographic history of brown trout ( Salmo trutta ) populations from the southern Balkans

    DEFF Research Database (Denmark)

    Apostolidis, A.P.; Madeira, M.J.; Hansen, Michael Møller

    2008-01-01

    1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci...... in seven supposedly non-admixed and three stocked brown trout populations. 2. The analyses confirmed the absence of immigration and extraordinarily strong genetic differentiation among the seven non-introgressed populations in parallel with low levels of intrapopulation genetic variability. In contrast...

  11. Strong coupling strategy for fluid-structure interaction problems in supersonic regime via fixed point iteration

    Science.gov (United States)

    Storti, Mario A.; Nigro, Norberto M.; Paz, Rodrigo R.; Dalcín, Lisandro D.

    2009-03-01

    In this paper some results on the convergence of the Gauss-Seidel iteration when solving fluid/structure interaction problems with strong coupling via fixed point iteration are presented. The flow-induced vibration of a flat plate aligned with the flow direction at supersonic Mach number is studied. The precision of different predictor schemes and the influence of the partitioned strong coupling on stability is discussed.

  12. Population genetic structure of the people of Qatar.

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

    2010-07-09

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  13. Response of base isolated structure during strong ground motions beyond design earthquakes

    International Nuclear Information System (INIS)

    Yabana, Shuichi; Ishida, Katsuhiko; Shiojiri, Hiroo

    1991-01-01

    In Japan, some base isolated structures for fast breeder reactors (FBR) are tried to design. When a base isolated structure are designed, the relative displacement of isolators are generally limited so sa to be remain in linear state of those during design earthquakes. But to estimate safety margin of a base isolated structure, the response of that until the failure must be obtained experimentally to analytically during strong ground motions of beyond design earthquake. The aim of this paper is to investigate the response of a base isolated structure when the stiffness of the isolators hardens and to simulate the response during strong ground motions of beyond design earthquakes. The optimum characteristics of isolators, with which the margin of the structure are increased, are discussed. (author)

  14. Testing strong factorial invariance using three-level structural equation modeling

    Directory of Open Access Journals (Sweden)

    Suzanne eJak

    2014-07-01

    Full Text Available Within structural equation modeling, the most prevalent model to investigate measurement bias is the multigroup model. Equal factor loadings and intercepts across groups in a multigroup model represent strong factorial invariance (absence of measurement bias across groups. Although this approach is possible in principle, it is hardly practical when the number of groups is large or when the group size is relatively small. Jak, Oort and Dolan (2013 showed how strong factorial invariance across large numbers of groups can be tested in a multilevel structural equation modeling framework, by treating group as a random instead of a fixed variable. In the present study, this model is extended for use with three-level data. The proposed method is illustrated with an investigation of strong factorial invariance across 156 school classes and 50 schools in a Dutch dyscalculia test, using three-level structural equation modeling.

  15. Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

    Science.gov (United States)

    Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

    2018-01-01

    Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

  16. Strong Motion Instrumentation of Seismically-Strengthened Port Structures in California by CSMIP

    Science.gov (United States)

    Huang, M.J.; Shakal, A.F.

    2009-01-01

    The California Strong Motion Instrumentation Program (CSMIP) has instrumented five port structures. Instrumentation of two more port structures is underway and another one is in planning. Two of the port structures have been seismically strengthened. The primary goals of the strong motion instrumentation are to obtain strong earthquake shaking data for verifying seismic analysis procedures and strengthening schemes, and for post-earthquake evaluations of port structures. The wharves instrumented by CSMIP were recommended by the Strong Motion Instrumentation Advisory Committee, a committee of the California Seismic Safety Commission. Extensive instrumentation of a wharf is difficult and would be impossible without the cooperation of the owners and the involvement of the design engineers. The instrumentation plan for a wharf is developed through study of the retrofit plans of the wharf, and the strong-motion sensors are installed at locations where specific instrumentation objectives can be achieved and access is possible. Some sensor locations have to be planned during design; otherwise they are not possible to install after construction. This paper summarizes the two seismically-strengthened wharves and discusses the instrumentation schemes and objectives. ?? 2009 ASCE.

  17. Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

    Directory of Open Access Journals (Sweden)

    John S K Kauwe

    Full Text Available Alzheimer's disease (AD is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date.We assessed the familiality of AD in The Utah Population Database (UPDB, a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF between AD individuals and randomly selected controls and estimated the Relative Risk (RR for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths.The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths.These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.

  18. Testing the Structure of Hydrological Models using Genetic Programming

    Science.gov (United States)

    Selle, B.; Muttil, N.

    2009-04-01

    Genetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that genetic programming can be used to test the structure hydrological models and to identify dominant processes in hydrological systems. To test this, genetic programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, water table depths and water ponding times during surface irrigation. Using genetic programming, a simple model of deep percolation was consistently evolved in multiple model runs. This simple and interpretable model confirmed the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that genetic programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

  19. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  20. Genetic structure of populations and differentiation in forest trees

    Science.gov (United States)

    Raymond P. Guries; F. Thomas Ledig

    1981-01-01

    Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

  1. Genetic structure and diversity of the Neem Germplasm Bank from ...

    African Journals Online (AJOL)

    Particular

    2013-05-15

    May 15, 2013 ... ... fragment length polymorphism; AMOVA, molecular variance analysis. ... are technically simple, suitable for large-scale germplasm ... Brazil, our study aims to evaluate the genetic structure and genetic ... voltage of 100 V for 90 min. Gel was .... which does not justify an extra effort in labor (Bekessy et.

  2. Population Genetic Structure and Gene Flow Among Nigerian Goats ...

    African Journals Online (AJOL)

    Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

  3. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  4. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  5. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  6. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  7. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

    Science.gov (United States)

    Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

    2009-07-14

    The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites). Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 +/- 0.17), where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic

  8. Genetic structure and variability within and among populations of the ...

    African Journals Online (AJOL)

    Lalouta

    2014-01-01

    Jan 1, 2014 ... The clustering analysis performed with 'structure' detected the absence of .... tance of molecular information in the establishment of genetic improvement ... applied using a Markov Chain Monte Carlo simulation (100 batches,.

  9. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... useful in selection. The cross between two individuals from different groups might help exploit the ... primers used are labeled with different colored .... with a view to detect a structuring of accessions in genetically different ...

  10. Study of rare earth local moment magnetism and strongly correlated phenomena in various crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Tai [Iowa State Univ., Ames, IA (United States)

    2016-12-17

    Benefiting from unique properties of 4f electrons, rare earth based compounds are known for offering a versatile playground for condensed matter physics research as well as industrial applications. This thesis focuses on three specific examples that further explore the rare earth local moment magnetism and strongly correlated phenomena in various crystal structures.

  11. Structure of Vocational Interests for Diverse Groups on the 2005 Strong Interest Inventory

    Science.gov (United States)

    Kantamneni, Neeta; Fouad, Nadya

    2011-01-01

    This study was designed to examine the structure of vocational interests in a diverse sample of individuals who completed the 2005 revision of the Strong Interest Inventory. We examined the fit of three racial/ethnic groups (African American, Caucasian, and Latino/a), both genders, and three levels of professional status (GRS participant, student,…

  12. Testing strong factorial invariance using three-level structural equation modeling

    NARCIS (Netherlands)

    Jak, Suzanne

    Within structural equation modeling, the most prevalent model to investigate measurement bias is the multigroup model. Equal factor loadings and intercepts across groups in a multigroup model represent strong factorial invariance (absence of measurement bias) across groups. Although this approach is

  13. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  14. Diabetes-specific genetic effects on obesity traits in American Indian populations: the Strong Heart Family Study

    Directory of Open Access Journals (Sweden)

    Howard Barbara V

    2008-10-01

    Full Text Available Abstract Background Body fat mass distribution and deposition are determined by multiple environmental and genetic factors. Obesity is associated with insulin resistance, hyperinsulinemia, and type 2 diabetes. We previously identified evidence for genotype-by-diabetes interaction on obesity traits in Strong Heart Family Study (SHFS participants. To localize these genetic effects, we conducted genome-wide linkage scans of obesity traits in individuals with and without type 2 diabetes, and in the combined sample while modeling interaction with diabetes using maximum likelihood methods (SOLAR 2.1.4. Methods SHFS recruited American Indians from Arizona, North and South Dakota, and Oklahoma. Anthropometric measures and diabetes status were obtained during a clinic visit. Marker allele frequencies were derived using maximum likelihood methods estimated from all individuals and multipoint identity by descent sharing was estimated using Loki. We used variance component linkage analysis to localize quantitative trait loci (QTLs influencing obesity traits. We tested for evidence of additive and QTL-specific genotype-by-diabetes interactions using the regions identified in the diabetes-stratified analyses. Results Among 245 diabetic and 704 non-diabetic American Indian individuals, we detected significant additive gene-by-diabetes interaction for weight and BMI (P P Conclusion These results suggest distinct genetic effects on body mass in individuals with diabetes compared to those without diabetes, and a possible role for one or more genes on chromosome 1 in the pathogenesis of obesity.

  15. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

    Full Text Available Abstract Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

  16. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  17. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Science.gov (United States)

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  18. Phase Structure of Strong-Field Tunneling Wave Packets from Molecules.

    Science.gov (United States)

    Liu, Ming-Ming; Li, Min; Wu, Chengyin; Gong, Qihuang; Staudte, André; Liu, Yunquan

    2016-04-22

    We study the phase structure of the tunneling wave packets from strong-field ionization of molecules and present a molecular quantum-trajectory Monte Carlo model to describe the laser-driven dynamics of photoelectron momentum distributions of molecules. Using our model, we reproduce and explain the alignment-dependent molecular frame photoelectron spectra of strong-field tunneling ionization of N_{2} reported by M. Meckel et al. [Nat. Phys. 10, 594 (2014)]. In addition to modeling the low-energy photoelectron angular distributions quantitatively, we extract the phase structure of strong-field molecular tunneling wave packets, shedding light on its physical origin. The initial phase of the tunneling wave packets at the tunnel exit depends on both the initial transverse momentum distribution and the molecular internuclear distance. We further show that the ionizing molecular orbital has a critical effect on the initial phase of the tunneling wave packets. The phase structure of the photoelectron wave packet is a key ingredient for modeling strong-field molecular photoelectron holography, high-harmonic generation, and molecular orbital imaging.

  19. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... 1The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao. 266003 P. R. ... marginal sea of Western Pacific, which was an enclosed inland sea ... coral islands and reefs in South China Sea. There are ..... strong genetic divergence in Southeast Asia (Liu et al., 2006).

  20. Identifying Associations Between Brain Imaging Phenotypes and Genetic Factors via A Novel Structured SCCA Approach.

    Science.gov (United States)

    Du, Lei; Zhang, Tuo; Liu, Kefei; Yan, Jingwen; Yao, Xiaohui; Risacher, Shannon L; Saykin, Andrew J; Han, Junwei; Guo, Lei; Shen, Li

    2017-06-01

    Brain imaging genetics attracts more and more attention since it can reveal associations between genetic factors and the structures or functions of human brain. Sparse canonical correlation analysis (SCCA) is a powerful bi-multivariate association identification technique in imaging genetics. There have been many SCCA methods which could capture different types of structured imaging genetic relationships. These methods either use the group lasso to recover the group structure, or employ the graph/network guided fused lasso to find out the network structure. However, the group lasso methods have limitation in generalization because of the incomplete or unavailable prior knowledge in real world. The graph/network guided methods are sensitive to the sign of the sample correlation which may be incorrectly estimated. We introduce a new SCCA model using a novel graph guided pairwise group lasso penalty, and propose an efficient optimization algorithm. The proposed method has a strong upper bound for the grouping effect for both positively and negatively correlated variables. We show that our method performs better than or equally to two state-of-the-art SCCA methods on both synthetic and real neuroimaging genetics data. In particular, our method identifies stronger canonical correlations and captures better canonical loading profiles, showing its promise for revealing biologically meaningful imaging genetic associations.

  1. On the Contribution of Large-Scale Structure to Strong Gravitational Lensing

    Science.gov (United States)

    Faure, C.; Kneib, J.-P.; Hilbert, S.; Massey, R.; Covone, G.; Finoguenov, A.; Leauthaud, A.; Taylor, J. E.; Pires, S.; Scoville, N.; Koekemoer, Anton M.

    2009-04-01

    We study the correlation between the locations of galaxy-galaxy strong-lensing candidates and tracers of large-scale structure from both weak lensing (WL) or X-ray emission. The Cosmological Evolution Survey (COSMOS) is a unique data set, combining deep, high resolution and contiguous imaging in which strong lenses have been discovered, plus unparalleled multiwavelength coverage. To help interpret the COSMOS data, we have also produced mock COSMOS strong- and WL observations, based on ray-tracing through the Millennium Simulation. In agreement with the simulations, we find that strongly lensed images with the largest angular separations are found in the densest regions of the COSMOS field. This is explained by a prevalence among the lens population in dense environments of elliptical galaxies with high total-to-stellar mass ratios, which can deflect light through larger angles. However, we also find that the overall fraction of elliptical galaxies with strong gravitational lensing is independent of the local mass density; this observation is not true of the simulations, which predict an increasing fraction of strong lenses in dense environments. The discrepancy may be a real effect, but could also be explained by various limitations of our analysis. For example, our visual search of strong lens systems could be incomplete and suffer from selection bias; the luminosity function of elliptical galaxies may differ between our real and simulated data; or the simplifying assumptions and approximations used in our lensing simulations may be inadequate. Work is therefore ongoing. Automated searches for strong lens systems will be particularly important in better constraining the selection function.

  2. Genetic population structure of muskellunge in the Great Lakes

    Science.gov (United States)

    Kapuscinski, Kevin L.; Sloss, Brian L.; Farrell, John M.

    2013-01-01

    We quantified genetic relationships among Muskellunge Esox masquinongy from 15 locations in the Great Lakes to determine the extent and distribution of measurable population structure and to identify appropriate spatial scales for fishery management and genetic conservation. We hypothesized that Muskellunge from each area represented genetically distinct populations, which would be evident from analyses of genotype data. A total of 691 Muskellunge were sampled (n = 10–127/site) and genetic data were collected at 13 microsatellite loci. Results from a suite of analyses (including pairwise genetic differentiation, Bayesian admixture prediction, analysis of molecular variance, and tests of isolation by distance) indicated the presence of nine distinct genetic groups, including two that were approximately 50 km apart. Geographic proximity and low habitat complexity seemed to facilitate genetic similarity among areas, whereas Muskellunge from areas of greater habitat heterogeneity exhibited high differentiation. Muskellunge from most areas contained private alleles, and mean within-area genetic variation was similar to that reported for other freshwater fishes. Management programs aimed at conserving the broader diversity and long-term sustainability of Muskellunge could benefit by considering the genetically distinct groups as independent fisheries, and individual spawning and nursery habitats could subsequently be protected to conserve the evolutionary potential of Muskellunge.

  3. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Dong-Xiu Xue

    Full Text Available The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure. Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene and current gene flow (through larval dispersal were responsible for the weak level of genetic structure detected in A. pectinata.

  4. Multiscale Genetic Structure of Yellowstone Cutthroat Trout in the Upper Snake River Basin.

    Energy Technology Data Exchange (ETDEWEB)

    Cegelski, Christine C.; Campbell, Matthew R.

    2006-05-30

    Populations of Yellowstone cutthroat trout Oncorhynchus clarkii bouvierii have declined throughout their native range as a result of habitat fragmentation, overharvest, and introductions of nonnative trout that have hybridized with or displaced native populations. The degree to which these factors have impacted the current genetic population structure of Yellowstone cutthroat trout populations is of primary interest for their conservation. In this study, we examined the genetic diversity and genetic population structure of Yellowstone cutthroat trout in Idaho and Nevada with data from six polymorphic microsatellite loci. A total of 1,392 samples were analyzed from 45 sample locations throughout 11 major river drainages. We found that levels of genetic diversity and genetic differentiation varied extensively. The Salt River drainage, which is representative of the least impacted migration corridors in Idaho, had the highest levels of genetic diversity and low levels of genetic differentiation. High levels of genetic differentiation were observed at similar or smaller geographic scales in the Portneuf River, Raft River, and Teton River drainages, which are more altered by anthropogenic disturbances. Results suggested that Yellowstone cutthroat trout are naturally structured at the major river drainage level but that habitat fragmentation has altered this structuring. Connectivity should be restored via habitat restoration whenever possible to minimize losses in genetic diversity and to preserve historical processes of gene flow, life history variation, and metapopulation dynamics. However, alternative strategies for management and conservation should also be considered in areas where there is a strong likelihood of nonnative invasions or extensive habitat fragmentation that cannot be easily ameliorated.

  5. Strongly correlated electron systems and neutron scattering. Magnetism, superconductivity, structural phase transition

    Energy Technology Data Exchange (ETDEWEB)

    Katano, Susumu [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-03-01

    Neutron scattering experiments in our group on strongly correlated electron systems are reviewed Metal-insulator transitions caused by structural phase transitions in (La{sub 1-x}Sr{sub x}) MnO{sub 3}, a novel magnetic transition in the CeP compound, correlations between antiferromagnetism and superconductivity in UPd{sub 2}Al{sub 3} and so forth are discussed. Here, in this note, the phase transition of Mn-oxides was mainly described. (author)

  6. Structure of the strongly coupled classical plasma in the self-consistent mean spherical approximation

    International Nuclear Information System (INIS)

    Chaturvedi, D.K.; Senatore, G.; Tosi, M.P.

    1980-10-01

    An analytic theory is presented for the static structure factor of the one-component classical plasma at strong couplings. The theory combines the hard-core model of Gillan for short-range correlations in the Coulomb fluid with a semiempirical representation of intermediate-range correlations, through which the requirement of thermodynamic consistency on the ''compressibility'' and the known equation of state of the system are satisfied. Excellent agreement is found with the available computer simulation data on the structure of the fluid. The approach becomes inapplicable at intermediate and weak couplings where effects of penetration in the Coulomb hole of each particle become important. (author)

  7. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

    Science.gov (United States)

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis , which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

  8. A genome-wide association study identifies rs2000999 as a strong genetic determinant of circulating haptoglobin levels.

    Directory of Open Access Journals (Sweden)

    Philippe Froguel

    Full Text Available Haptoglobin is an acute phase inflammatory marker. Its main function is to bind hemoglobin released from erythrocytes to aid its elimination, and thereby haptoglobin prevents the generation of reactive oxygen species in the blood. Haptoglobin levels have been repeatedly associated with a variety of inflammation-linked infectious and non-infectious diseases, including malaria, tuberculosis, human immunodeficiency virus, hepatitis C, diabetes, carotid atherosclerosis, and acute myocardial infarction. However, a comprehensive genetic assessment of the inter-individual variability of circulating haptoglobin levels has not been conducted so far.We used a genome-wide association study initially conducted in 631 French children followed by a replication in three additional European sample sets and we identified a common single nucleotide polymorphism (SNP, rs2000999 located in the Haptoglobin gene (HP as a strong genetic predictor of circulating Haptoglobin levels (P(overall = 8.1 × 10(-59, explaining 45.4% of its genetic variability (11.8% of Hp global variance. The functional relevance of rs2000999 was further demonstrated by its specific association with HP mRNA levels (β = 0.23 ± 0.08, P = 0.007. Finally, SNP rs2000999 was associated with decreased total and low-density lipoprotein cholesterol in 8,789 European children (P(total cholesterol = 0.002 and P(LDL = 0.0008.Given the central position of haptoglobin in many inflammation-related metabolic pathways, the relevance of rs2000999 genotyping when evaluating haptoglobin concentration should be further investigated in order to improve its diagnostic/therapeutic and/or prevention impact.

  9. Chymotrypsinogen C Genetic Variants, Including c.180TT, Are Strongly Associated With Chronic Pancreatitis in Pediatric Patients.

    Science.gov (United States)

    Grabarczyk, Alicja Monika; Oracz, Grzegorz; Wertheim-Tysarowska, Katarzyna; Kujko, Aleksandra Anna; Wejnarska, Karolina; Kolodziejczyk, Elwira; Bal, Jerzy; Koziel, Dorota; Kowalik, Artur; Gluszek, Stanislaw; Rygiel, Agnieszka Magdalena

    2017-12-01

    Genetic studies in adults/adolescent patients with chronic pancreatitis (CP) identified chymotrypsinogen C (CTRC) genetic variants but their association with CP risk has been difficult to replicate. To evaluate the risk of CP associated with CTRC variants in CP pediatric patients-control study. The distribution of CTRC variants in CP pediatric cohort (n = 136, median age at CP onset 8 years) with no history of alcohol/smoking abuse was compared with controls (n = 401, median age 45). We showed that p.Arg254Trp (4.6%) and p.Lys247_Arg254del (5.3%) heterozygous mutations are frequent and significantly associated with CP risk in pediatric patients (odds ratio [OR] = 19.1; 95% CI 2.8-160; P = 0.001 and OR = 5.5; 95% CI 1.6-19.4; P = 0.001, respectively). For the first time, we demonstrated that the c.180TT genotype of common p.Gly60Gly variant is strong, an independent CP risk factor (OR = 23; 95% CI 7.7-70; P A variant, both CA and AA genotype, is significantly underrepresented in CP compared with controls (15% vs 35%; OR = 0.33; 95% CI 0.19-0.59; P risk factors. The c.493+51C>A variant may play a protective role against CP development.

  10. Stochastic search in structural optimization - Genetic algorithms and simulated annealing

    Science.gov (United States)

    Hajela, Prabhat

    1993-01-01

    An account is given of illustrative applications of genetic algorithms and simulated annealing methods in structural optimization. The advantages of such stochastic search methods over traditional mathematical programming strategies are emphasized; it is noted that these methods offer a significantly higher probability of locating the global optimum in a multimodal design space. Both genetic-search and simulated annealing can be effectively used in problems with a mix of continuous, discrete, and integer design variables.

  11. SSR-based genetic diversity and structure of garlic accessions from Brazil.

    Science.gov (United States)

    da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2014-10-01

    Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

  12. The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination

    Directory of Open Access Journals (Sweden)

    Alessia Viel

    2017-08-01

    Full Text Available In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota.

  13. Allocating structure to function: the strong links between neuroplasticity and natural selection

    Directory of Open Access Journals (Sweden)

    Michael L Anderson

    2014-01-01

    Full Text Available A central question in brain evolution is how species-typical behaviors, and the neural function-structure mappings supporting them, can be acquired and inherited. Advocates of brain modularity, in its different incarnations across scientific subfields, argue that natural selection must target domain-dedicated, separately modifiable neural subsystems, resulting in genetically-specified functional modules. In such modular systems, specification of neuron number and functional connectivity are necessarily linked. Mounting evidence, however, from allometric, developmental, comparative, systems-physiological, neuroimaging and neurological studies suggests that brain elements are used and reused in multiple functional systems. This variable allocation can be seen in short-term neuromodulation, in neuroplasticity over the lifespan and in response to damage. We argue that the same processes are evident in brain evolution. Natural selection must preserve behavioral functions that may co-locate in variable amounts with other functions. In genetics, the uses and problems of pleiotropy, the re-use of genes in multiple networks have been much discussed, but this issue has been sidestepped in neural systems by the invocation of modules. Here we highlight the interaction between evolutionary and developmental mechanisms to produce distributed and overlapping functional architectures in the brain. These adaptive mechanisms must be robust to perturbations that might disrupt critical information processing and action selection, but must also recognize useful new sources of information arising from internal genetic or environmental variability, when those appear. These contrasting properties of robustness and evolvability have been discussed for the basic organization of body plan and fundamental cell physiology. Here we extend them to the evolution and development, evo-devo, of brain structure.

  14. How spatio-temporal habitat connectivity affects amphibian genetic structure.

    Science.gov (United States)

    Watts, Alexander G; Schlichting, Peter E; Billerman, Shawn M; Jesmer, Brett R; Micheletti, Steven; Fortin, Marie-Josée; Funk, W Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

  15. How spatio-temporal habitat connectivity affects amphibian genetic structure

    Science.gov (United States)

    Watts, Alexander G.; Schlichting, P; Billerman, S; Jesmer, B; Micheletti, S; Fortin, M.-J.; Funk, W.C.; Hapeman, P; Muths, Erin L.; Murphy, M.A.

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

  16. Strong influence of regional species pools on continent-wide structuring of local communities.

    Science.gov (United States)

    Lessard, Jean-Philippe; Borregaard, Michael K; Fordyce, James A; Rahbek, Carsten; Weiser, Michael D; Dunn, Robert R; Sanders, Nathan J

    2012-01-22

    There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.

  17. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

  18. Structure of large spin expansion of anomalous dimensions at strong coupling

    Energy Technology Data Exchange (ETDEWEB)

    Beccaria, M. [Physics Department, Salento University and INFN, 73100 Lecce (Italy)], E-mail: matteo.beccaria@le.infn.it; Forini, V. [Humboldt-Universitaet zu Berlin, Institut fuer Physik, D-12489 Berlin (Germany)], E-mail: forini@aei.mpg.de; Tirziu, A. [Department of Physics, Purdue University, W. Lafayette, IN 47907-2036 (United States)], E-mail: atirziu@purdue.edu; Tseytlin, A.A. [Blackett Laboratory, Imperial College, London SW7 2AZ (United Kingdom)], E-mail: tseytlin@imperial.ac.uk

    2009-05-01

    The anomalous dimensions of planar N=4 SYM theory operators like tr({phi}D{sub +}{sup S}{phi}) expanded in large spin S have the asymptotics {gamma}=flnS+f{sub c}+1/S (f{sub 11}lnS+f{sub 10})+..., where f (the universal scaling function or cusp anomaly), f{sub c} and f{sub mn} are given by power series in the 't Hooft coupling {lambda}. The subleading coefficients appear to be related by the so-called functional relation and parity (reciprocity) property of the function expressing {gamma} in terms of the conformal spin of the collinear group. Here we study the structure of such large spin expansion at strong coupling via AdS/CFT, i.e. by using the dual description in terms of folded spinning string in AdS{sub 5}. The large spin expansion of the classical string energy happens to have exactly the same structure as that of {gamma} in the perturbative gauge theory. Moreover, the functional relation and the reciprocity constraints on the coefficients are also satisfied. We compute the leading string 1-loop corrections to the coefficients f{sub c}, f{sub 11}, f{sub 10} and verify the functional/reciprocity relations at subleading 1/({radical}({lambda})) order. This provides a strong indication that these relations hold not only in weak coupling (gauge-theory) but also in strong coupling (string-theory) perturbative expansions.

  19. Structure of large spin expansion of anomalous dimensions at strong coupling

    International Nuclear Information System (INIS)

    Beccaria, M.; Forini, V.; Tirziu, A.; Tseytlin, A.A.

    2009-01-01

    The anomalous dimensions of planar N=4 SYM theory operators like tr(ΦD + S Φ) expanded in large spin S have the asymptotics γ=flnS+f c +1/S (f 11 lnS+f 10 )+..., where f (the universal scaling function or cusp anomaly), f c and f mn are given by power series in the 't Hooft coupling λ. The subleading coefficients appear to be related by the so-called functional relation and parity (reciprocity) property of the function expressing γ in terms of the conformal spin of the collinear group. Here we study the structure of such large spin expansion at strong coupling via AdS/CFT, i.e. by using the dual description in terms of folded spinning string in AdS 5 . The large spin expansion of the classical string energy happens to have exactly the same structure as that of γ in the perturbative gauge theory. Moreover, the functional relation and the reciprocity constraints on the coefficients are also satisfied. We compute the leading string 1-loop corrections to the coefficients f c , f 11 , f 10 and verify the functional/reciprocity relations at subleading 1/(√(λ)) order. This provides a strong indication that these relations hold not only in weak coupling (gauge-theory) but also in strong coupling (string-theory) perturbative expansions

  20. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  1. Strong influence of regional species pools on continent-wide structuring of local communities

    DEFF Research Database (Denmark)

    Lessard, Jean-Philippe; Borregaard, Michael Krabbe; Fordyce, James A.

    2012-01-01

    pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use...... of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution...... of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong....

  2. Turbulent structure and emissions of strongly-pulsed jet diffusion flames

    Science.gov (United States)

    Fregeau, Mathieu

    This current research project studied the turbulent flame structure, the fuel/air mixing, the combustion characteristics of a nonpremixed pulsed (unsteady) and unpulsed (steady) flame configuration for both normal- and microgravity conditions, as well as the flame emissions in normal gravity. The unsteady flames were fully-modulated, with the fuel flow completely shut off between injection pulses using an externally controlled valve, resulting in the generation of compact puff-like flame structures. Conducting experiments in normal and microgravity environments enabled separate control over the relevant Richardson and Reynolds numbers to clarify the influence of buoyancy on the flame behavior, mixing, and structure. Experiments were performed in normal gravity in the laboratory at the University of Washington and in microgravity using the NASA GRC 2.2-second Drop Tower facility. High-speed imaging, as well as temperature and emissions probes were used to determine the large-scale structure dynamics, the details of the flame structure and oxidizer entrainment, the combustion temperatures, and the exhaust emissions of the pulsed and steady flames. Of particular interest was the impact of changes in flame structure due to pulsing on the combustion characteristics of this system. The turbulent flame puff celerity (i.e., the bulk velocity of the puffs) was strongly impacted by the jet-off time, increasing markedly as the time between pulses was decreased, which caused the degree of puff interaction to increase and the strongly-pulsed flame to more closely resemble a steady flame. This increase occurred for all values of injection time as well as for constant fuelling rate and in both the presence and absence of buoyancy. The removal of positive buoyancy in microgravity resulted in a decrease in the flame puff celerity in all cases, amounting to as much as 40%, for both constant jet injection velocity and constant fuelling rate. The mean flame length of the strongly

  3. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  4. Genetic manipulation of structural color in bacterial colonies

    DEFF Research Database (Denmark)

    Johansen, Villads Egede; Catón, Laura; Hamidjaja, Raditijo

    2018-01-01

    analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.......Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved...

  5. Higher Order QED Contributions to the Atomic Structure at Strong Central Fields

    International Nuclear Information System (INIS)

    Mokler, P H

    2007-01-01

    An accurate determination of the precise structure of highly charged, very heavy ions is crucial for understanding QED at strong fields. The experimental advances in the spectroscopy of very heavy, highly charged ions-in particular H-, He- and Li-like species-are reviewed: Presently the ground state Lamb shift for H-like U ions is measured on a 1% level of accuracy; the screening terms in two-electron QED have just been touched by experiments for He-like U; and two-loop QED terms have been determined with ultimate accuracy for Li-like heavy species. The different approaches on QED measurements in strong fields will be discussed and the results compared to theory

  6. Genetic population structure of the vulnerable bog fritillary butterfly.

    Science.gov (United States)

    Vandewoestijne, S; Baguette, M

    2004-01-01

    Populations of the bog fritillary butterfly Proclossiana eunomia (Lepidoptera, Nymphalidae) occur in patchy habitat in central and western Europe. P. eunomia is a vulnerable species in the Belgian Ardennes and the number of occupied sites has significantly decreased in this region since the 1960s. RAPD (random amplified polymorphic DNA) markers were used to study the consequences of habitat loss and fragmentation on the genetic population structure of this species. Gene diversity was lower in populations with smaller population sizes. Genetic subdivision was high (Fst=0.0887) considering the small spatial scale of this study (150 km2). The most geographically isolated population was also the most genetically differentiated one. The genetic population structure and genetic differentiation detected in this study were explained by (1) differences in altitude of the sampled locations and, (2) lower dispersal propensity and dispersal rate in fragmented landscapes versus continuous landscapes. Results from the RAPD analyses were compared with a previous allozyme based study on the same populations. The results of this study suggest that increased fragmentation has lead to a greater genetic differentiation between remaining P. eunomia populations.

  7. Nonuniform Internal Structure of Fibrin Fibers: Protein Density and Bond Density Strongly Decrease with Increasing Diameter

    Directory of Open Access Journals (Sweden)

    Wei Li

    2017-01-01

    Full Text Available The major structural component of a blood clot is a meshwork of fibrin fibers. It has long been thought that the internal structure of fibrin fibers is homogeneous; that is, the protein density and the bond density between protofibrils are uniform and do not depend on fiber diameter. We performed experiments to investigate the internal structure of fibrin fibers. We formed fibrin fibers with fluorescently labeled fibrinogen and determined the light intensity of a fiber, I, as a function of fiber diameter, D. The intensity and, thus, the total number of fibrin molecules in a cross-section scaled as D1.4. This means that the protein density (fibrin per cross-sectional area, ρp, is not homogeneous but instead strongly decreases with fiber diameter as D-0.6. Thinner fibers are denser than thicker fibers. We also determined Young’s modulus, Y, as a function of fiber diameter. Y decreased strongly with increasing D; Y scaled as D-1.5. This implies that the bond density, ρb, also scales as D-1.5. Thinner fibers are stiffer than thicker fibers. Our data suggest that fibrin fibers have a dense, well-connected core and a sparse, loosely connected periphery. In contrast, electrospun fibrinogen fibers, used as a control, have a homogeneous cross-section.

  8. Fault Structural Control on Earthquake Strong Ground Motions: The 2008 Wenchuan Earthquake as an Example

    Science.gov (United States)

    Zhang, Yan; Zhang, Dongli; Li, Xiaojun; Huang, Bei; Zheng, Wenjun; Wang, Yuejun

    2018-02-01

    Continental thrust faulting earthquakes pose severe threats to megacities across the world. Recent events show the possible control of fault structures on strong ground motions. The seismogenic structure of the 2008 Wenchuan earthquake is associated with high-angle listric reverse fault zones. Its peak ground accelerations (PGAs) show a prominent feature of fault zone amplification: the values within the 30- to 40-km-wide fault zone block are significantly larger than those on both the hanging wall and the footwall. The PGA values attenuate asymmetrically: they decay much more rapidly in the footwall than in the hanging wall. The hanging wall effects can be seen on both the vertical and horizontal components of the PGAs, with the former significantly more prominent than the latter. All these characteristics can be adequately interpreted by upward extrusion of the high-angle listric reverse fault zone block. Through comparison with a low-angle planar thrust fault associated with the 1999 Chi-Chi earthquake, we conclude that different fault structures might have controlled different patterns of strong ground motion, which should be taken into account in seismic design and construction.

  9. Revealing strong bias in common measures of galaxy properties using new inclination-independent structures

    Science.gov (United States)

    Devour, Brian M.; Bell, Eric F.

    2017-06-01

    Accurate measurement of galaxy structures is a prerequisite for quantitative investigation of galaxy properties or evolution. Yet, the impact of galaxy inclination and dust on commonly used metrics of galaxy structure is poorly quantified. We use infrared data sets to select inclination-independent samples of disc and flattened elliptical galaxies. These samples show strong variation in Sérsic index, concentration and half-light radii with inclination. We develop novel inclination-independent galaxy structures by collapsing the light distribution in the near-infrared on to the major axis, yielding inclination-independent 'linear' measures of size and concentration. With these new metrics we select a sample of Milky Way analogue galaxies with similar stellar masses, star formation rates, sizes and concentrations. Optical luminosities, light distributions and spectral properties are all found to vary strongly with inclination: When inclining to edge-on, r-band luminosities dim by >1 magnitude, sizes decrease by a factor of 2, 'dust-corrected' estimates of star formation rate drop threefold, metallicities decrease by 0.1 dex and edge-on galaxies are half as likely to be classified as star forming. These systematic effects should be accounted for in analyses of galaxy properties.

  10. How does farmer connectivity influence livestock genetic structure?

    DEFF Research Database (Denmark)

    Berthouly, C; Do, Duy Ngoc; Thévenon, S

    2009-01-01

    Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between...... farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were......, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies....

  11. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation.

    Science.gov (United States)

    Yang, Ye; Christensen, Ole F; Sorensen, Daniel

    2011-02-01

    Over recent years, statistical support for the presence of genetic factors operating at the level of the environmental variance has come from fitting a genetically structured heterogeneous variance model to field or experimental data in various species. Misleading results may arise due to skewness of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box-Cox transformations. Litter size data in rabbits and pigs that had previously been analysed in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box-Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected by the presence of asymmetry in the distribution of data. We recommend that to avoid one important source of spurious inferences, future work seeking support for a genetic component acting on environmental variation using a parametric approach based on normality assumptions confirms that these are met.

  12. Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

    Science.gov (United States)

    M. Aradhya; K. Woeste; D. Velasco

    2012-01-01

    An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

  13. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    Science.gov (United States)

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  14. Theorising big IT programmes in healthcare: strong structuration theory meets actor-network theory.

    Science.gov (United States)

    Greenhalgh, Trisha; Stones, Rob

    2010-05-01

    The UK National Health Service is grappling with various large and controversial IT programmes. We sought to develop a sharper theoretical perspective on the question "What happens - at macro-, meso- and micro-level - when government tries to modernise a health service with the help of big IT?" Using examples from data fragments at the micro-level of clinical work, we considered how structuration theory and actor-network theory (ANT) might be combined to inform empirical investigation. Giddens (1984) argued that social structures and human agency are recursively linked and co-evolve. ANT studies the relationships that link people and technologies in dynamic networks. It considers how discourses become inscribed in data structures and decision models of software, making certain network relations irreversible. Stones' (2005) strong structuration theory (SST) is a refinement of Giddens' work, systematically concerned with empirical research. It views human agents as linked in dynamic networks of position-practices. A quadripartite approcach considers [a] external social structures (conditions for action); [b] internal social structures (agents' capabilities and what they 'know' about the social world); [c] active agency and actions and [d] outcomes as they feed back on the position-practice network. In contrast to early structuration theory and ANT, SST insists on disciplined conceptual methodology and linking this with empirical evidence. In this paper, we adapt SST for the study of technology programmes, integrating elements from material interactionism and ANT. We argue, for example, that the position-practice network can be a socio-technical one in which technologies in conjunction with humans can be studied as 'actants'. Human agents, with their complex socio-cultural frames, are required to instantiate technology in social practices. Structurally relevant properties inscribed and embedded in technological artefacts constrain and enable human agency. The fortunes

  15. Survey of genetic structure of geese using novel microsatellite markers

    Directory of Open Access Journals (Sweden)

    Fang-Yu Lai

    2018-02-01

    Full Text Available Objective The aim of this study was to create a set of microsatellite markers with high polymorphism for the genetic monitoring and genetic structure analysis of local goose populations. Methods Novel microsatellite markers were isolated from the genomic DNA of white Roman geese using short tandem repeated probes. The DNA segments, including short tandem repeats, were tested for their variability among four populations of geese from the Changhua Animal Propagation Station (CAPS. The selected microsatellite markers could then be used to monitor genetic variability and study the genetic structures of geese from local geese farms. Results 14 novel microsatellite loci were isolated. In addition to seven known loci, two multiplex sets were constructed for the detection of genetic variations in geese populations. The average of allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.09, 5.145, 0.499, 0.745, and 0.705, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting white Roman cluster and a spreading Chinese cluster. In white Roman populations, the CAPS populations were depleted to roughly two clusters when K was set equal to 6 in the Bayesian cluster analysis. The founders of private farm populations had a similar genetic structure. Among the Chinese geese populations, the CAPS populations and private populations represented different clads of the phylogenetic tree and individuals from the private populations had uneven genetic characteristics according to various analyses. Conclusion Based on this study’s analyses, we suggest that the CAPS should institute a proper breeding strategy for white Roman geese to avoid further clustering. In addition, for preservation and stable quality, the Chinese geese in the CAPS and the aforementioned proper breeding scheme should be introduced to

  16. Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama

    Directory of Open Access Journals (Sweden)

    Cerón-Souza Ivania

    2012-10-01

    Full Text Available Abstract Background Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 Avicennia germinans for 11 microsatellite loci and 940 Rhizophora mangle for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama. Results Both species showed similar rates of outcrossing (t= 0.7 in A. germinans and 0.8 in R. mangle and strong patterns of spatial genetic structure within estuaries, although A. germinans had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and Sp= 0.02 > 0.002, and much greater cpDNA diversity (Hd= 0.8 > 0.2 than R. mangle. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (FST= 0.3-0.5 and plastid (FST= 0.5-0.8 genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = −0.6 in A. germinans and 7.7 in R. mangle, coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species. Conclusions We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure.

  17. Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama

    Science.gov (United States)

    2012-01-01

    Background Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 Avicennia germinans for 11 microsatellite loci and 940 Rhizophora mangle for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama. Results Both species showed similar rates of outcrossing (t= 0.7 in A. germinans and 0.8 in R. mangle) and strong patterns of spatial genetic structure within estuaries, although A. germinans had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and Sp= 0.02 > 0.002), and much greater cpDNA diversity (Hd= 0.8 > 0.2) than R. mangle. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (FST= 0.3-0.5) and plastid (FST= 0.5-0.8) genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = −0.6 in A. germinans and 7.7 in R. mangle), coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species. Conclusions We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure. PMID:23078287

  18. Flame Structure and Emissions of Strongly-Pulsed Turbulent Diffusion Flames with Swirl

    Science.gov (United States)

    Liao, Ying-Hao

    This work studies the turbulent flame structure, the reaction-zone structure and the exhaust emissions of strongly-pulsed, non-premixed flames with co-flow swirl. The fuel injection is controlled by strongly-pulsing the fuel flow by a fast-response solenoid valve such that the fuel flow is completely shut off between pulses. This control strategy allows the fuel injection to be controlled over a wide range of operating conditions, allowing the flame structure to range from isolated fully-modulated puffs to interacting puffs to steady flames. The swirl level is controlled by varying the ratio of the volumetric flow rate of the tangential air to that of the axial air. For strongly-pulsed flames, both with and without swirl, the flame geometry is strongly impacted by the injection time. Flames appear to exhibit compact, puff-like structures for short injection times, while elongated flames, similar in behaviors to steady flames, occur for long injection times. The flames with swirl are found to be shorter for the same fuel injection conditions. The separation/interaction level between flame puffs in these flames is essentially governed by the jet-off time. The separation between flame puffs decreases as swirl is imposed, consistent with the decrease in flame puff celerity due to swirl. The decreased flame length and flame puff celerity are consistent with an increased rate of air entrainment due to swirl. The highest levels of CO emissions are generally found for compact, isolated flame puffs, consistent with the rapid quenching due to rapid dilution with excess air. The imposition of swirl generally results in a decrease in CO levels, suggesting more rapid and complete fuel/air mixing by imposing swirl in the co-flow stream. The levels of NO emissions for most cases are generally below the steady-flame value. The NO levels become comparable to the steady-flame value for sufficiently short jet-off time. The swirled co-flow air can, in some cases, increase the NO

  19. Polarization-gradient laser cooling as a way to create strongly localized structures for atom lithography

    International Nuclear Information System (INIS)

    Prudnikov, O. N.; Taichenachev, A. V.; Tumaikin, A. M.; Yudin, V. I.

    2007-01-01

    Generally, conditions for deep sub-Doppler laser cooling do not match conditions for strong atomic localization, that takes place in a deeper optical potential and leads to higher temperature. Moreover, for a given detuning in a deep optical potential the secular approximation, which is frequently used for a quantum description of laser cooling, fails. Here we investigate the atomic localization in optical potential, using a full quantum approach for atomic density matrix beyond the secular approximation. It is shown that laser cooling in a deep optical potential, created by a light field with polarization gradients, can be used as an alternative method for the formation of high contrast spatially localized structures of atoms for the purposes of atom lithography and atomic nanofabrication. Finally, we analyze possible limits for the width and contrast of localized atomic structures that can be reached in this type of light mask

  20. Classical integrability for three-point functions: cognate structure at weak and strong couplings

    Energy Technology Data Exchange (ETDEWEB)

    Kazama, Yoichi [Research Center for Mathematical Physics, Rikkyo University,Toshima-ku, Tokyo 171-8501 (Japan); Quantum Hadron Physics Laboratory, RIKEN Nishina Center, Wako 351-0198 (Japan); Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Komatsu, Shota [Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, Ontario, N2L 2Y5 (Canada); Nishimura, Takuya [Institute of Physics, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2016-10-10

    In this paper, we develop a new method of computing three-point functions in the SU(2) sector of the N=4 super Yang-Mills theory in the semi-classical regime at weak coupling, which closely parallels the strong coupling analysis. The structure threading two disparate regimes is the so-called monodromy relation, an identity connecting the three-point functions with and without the insertion of the monodromy matrix. We shall show that this relation can be put to use directly for the semi-classical regime, where the dynamics is governed by the classical Landau-Lifshitz sigma model. Specifically, it reduces the problem to a set of functional equations, which can be solved once the analyticity in the spectral parameter space is specified. To determine the analyticity, we develop a new universal logic applicable at both weak and strong couplings. As a result, compact semi-classical formulas are obtained for a general class of three-point functions at weak coupling including the ones whose semi-classical behaviors were not known before. In addition, the new analyticity argument applied to the strong coupling analysis leads to a modification of the integration contour, producing the results consistent with the recent hexagon bootstrap approach. This modification also makes the Frolov-Tseytlin limit perfectly agree with the weak coupling form.

  1. The strong coupling constant: its theoretical derivation from a geometric approach to hadron structure

    International Nuclear Information System (INIS)

    Recami, E.; Tonin-Zanchin, V.

    1991-01-01

    Since more than a decade, a bi-scale, unified approach to strong and gravitational interactions has been proposed, that uses the geometrical methods of general relativity, and yielded results similar to strong gravity theory's. We fix our attention, in this note, on hadron structure, and show that also the strong interaction strength α s, ordinarily called the (perturbative) coupling-constant square, can be evaluated within our theory, and found to decrease (increase) as the distance r decreases (increases). This yields both the confinement of the hadron constituents for large values of r, and their asymptotic freedom [for small values of r inside the hadron]: in qualitative agreement with the experimental evidence. In other words, our approach leads us, on a purely theoretical ground, to a dependence of α s on r which had been previously found only on phenomenological and heuristical grounds. We expect the above agreement to be also quantitative, on the basis of a few checks performed in this paper, and of further work of ours about calculating meson mass-spectra. (author)

  2. Global structural optimizations of surface systems with a genetic algorithm

    International Nuclear Information System (INIS)

    Chuang, Feng-Chuan

    2005-01-01

    Global structural optimizations with a genetic algorithm were performed for atomic cluster and surface systems including aluminum atomic clusters, Si magic clusters on the Si(111) 7 x 7 surface, silicon high-index surfaces, and Ag-induced Si(111) reconstructions. First, the global structural optimizations of neutral aluminum clusters Al n (n up to 23) were performed using a genetic algorithm coupled with a tight-binding potential. Second, a genetic algorithm in combination with tight-binding and first-principles calculations were performed to study the structures of magic clusters on the Si(111) 7 x 7 surface. Extensive calculations show that the magic cluster observed in scanning tunneling microscopy (STM) experiments consist of eight Si atoms. Simulated STM images of the Si magic cluster exhibit a ring-like feature similar to STM experiments. Third, a genetic algorithm coupled with a highly optimized empirical potential were used to determine the lowest energy structure of high-index semiconductor surfaces. The lowest energy structures of Si(105) and Si(114) were determined successfully. The results of Si(105) and Si(114) are reported within the framework of highly optimized empirical potential and first-principles calculations. Finally, a genetic algorithm coupled with Si and Ag tight-binding potentials were used to search for Ag-induced Si(111) reconstructions at various Ag and Si coverages. The optimized structural models of √3 x √3, 3 x 1, and 5 x 2 phases were reported using first-principles calculations. A novel model is found to have lower surface energy than the proposed double-honeycomb chained (DHC) model both for Au/Si(111) 5 x 2 and Ag/Si(111) 5 x 2 systems

  3. Genetic population structure of Shoal Bass within their native range

    Science.gov (United States)

    Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

    2018-01-01

    Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is

  4. Strong composite films with layered structures prepared by casting silk fibroin-graphene oxide hydrogels

    Science.gov (United States)

    Huang, Liang; Li, Chun; Yuan, Wenjing; Shi, Gaoquan

    2013-04-01

    Composite films of graphene oxide (GO) sheets and silk fibroin (SF) with layered structures have been prepared by facile solution casting of SF-GO hydrogels. The as-prepared composite film containing 15% (by weight, wt%) of SF shows a high tensile strength of 221 +/- 16 MPa and a failure strain of 1.8 +/- 0.4%, which partially surpass those of natural nacre. Particularly, this composite film also has a high modulus of 17.2 +/- 1.9 GPa. The high mechanical properties of this composite film can be attributed to its high content of GO (85 wt%), compact layered structure and the strong hydrogen bonding interaction between SF chains and GO sheets.Composite films of graphene oxide (GO) sheets and silk fibroin (SF) with layered structures have been prepared by facile solution casting of SF-GO hydrogels. The as-prepared composite film containing 15% (by weight, wt%) of SF shows a high tensile strength of 221 +/- 16 MPa and a failure strain of 1.8 +/- 0.4%, which partially surpass those of natural nacre. Particularly, this composite film also has a high modulus of 17.2 +/- 1.9 GPa. The high mechanical properties of this composite film can be attributed to its high content of GO (85 wt%), compact layered structure and the strong hydrogen bonding interaction between SF chains and GO sheets. Electronic supplementary information (ESI) available: XPS spectrum of the SF-GO hybrid film, SEM images of lyophilized GO dispersion and the failure surface of GO film. See DOI: 10.1039/c3nr00196b

  5. Population genetic structure and demographic history of small ...

    African Journals Online (AJOL)

    Population genetic structure and demographic history of small yellow croaker, ... diversity (0.0112 ± 0.0061 to 0.0141 ± 0.0075) were detected in the species. ... into two closely related clades, but did not appear to have any geographic ...

  6. Genetic structure among the local chicken ecotypes of Tanzania ...

    African Journals Online (AJOL)

    A study was conducted to evaluate the genetic structure of local chicken ecotypes of Tanzania using 20 polymorphic microsatellite DNA markers. A standard PCR was followed by manual genotyping (6% native polyacrylamide gel visualized by silver staining). Phylogenetic analysis of 13 individuals from each of the nine ...

  7. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  8. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  9. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

  10. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

  11. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

  12. Genetic modification and its impact on industry structure and performance

    NARCIS (Netherlands)

    Vlaar, P.W.L.; van Beek, P.; Visser, R.G.F.

    2007-01-01

    Genetic modification has led to fierce debates around the world. Nevertheless, scientific evidence for its potential effects on the structure and performance of industries has hitherto remained rather meagre. In this article, we take some preliminary steps towards closing this gap by exploring the

  13. Triplet repeat DNA structures and human genetic disease

    Indian Academy of Sciences (India)

    Laboratory of DNA Structure and Mutagenesis, Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Sciences Center, 2121 West Holcombe Blvd., Houston, TX 77030-3303, USA; Hospital for Sick Children, Department of Genetics, 555 University Avenue, Elm Wing, ...

  14. Fine-scaled human genetic structure revealed by SNP microarrays.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

    2009-05-01

    We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

  15. Strong quantum-confined stark effect in germanium quantum-well structures on silicon

    International Nuclear Information System (INIS)

    Kuo, Y.; Lee, Y. K.; Gei, Y.; Ren, S; Roth, J. E.; Miller, D. A.; Harris, J. S.

    2006-01-01

    Silicon is the dominant semiconductor for electronics, but there is now a growing need to integrate such component with optoelectronics for telecommunications and computer interconnections. Silicon-based optical modulators have recently been successfully demonstrated but because the light modulation mechanisms in silicon are relatively weak, long (for example, several millimeters) devices or sophisticated high-quality-factor resonators have been necessary. Thin quantum-well structures made from III-V semiconductors such as GaAs, InP and their alloys exhibit the much stronger Quantum-Confined Stark Effect (QCSE) mechanism, which allows modulator structures with only micrometers of optical path length. Such III-V materials are unfortunately difficult to integrate with silicon electronic devices. Germanium is routinely integrated with silicon in electronics, but previous silicon-germanium structures have also not shown strong modulation effects. Here we report the discovery of the QCSE, at room temperature, in thin germanium quantum-well structures grown on silicon. The QCSE here has strengths comparable to that in III-V materials. Its clarity and strength are particularly surprising because germanium is an indirect gap semiconductor, such semiconductors often display much weak optical effects than direct gap materials (such as the III-V materials typically used for optoelectronics). This discovery is very promising for small, high-speed, low-power optical output devices fully compatible with silicon electronics manufacture. (author)

  16. Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry.

    Science.gov (United States)

    Chang, Po-Chih; Reddy, P Muralidhar; Ho, Yen-Peng

    2014-09-01

    Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H2 or -D2. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H2 and formaldehyde-D2, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R (2) of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.

  17. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  18. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box–Cox transformations. Litter size data in rabbits and pigs that had previously been analysed...... in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box–Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis...... in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected...

  19. Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus.

    Directory of Open Access Journals (Sweden)

    Natalia Rosetti

    Full Text Available Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD and partial sequences of the cytochrome oxydase 1 (COI mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the

  20. Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

    Science.gov (United States)

    Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

    2016-10-24

    Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (N A = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise F ST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising

  1. Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

    Science.gov (United States)

    Pressoir, G; Berthaud, J

    2004-02-01

    To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

  2. Tough and strong porous bioactive glass-PLA composites for structural bone repair.

    Science.gov (United States)

    Xiao, Wei; Zaeem, Mohsen Asle; Li, Guangda; Bal, B Sonny; Rahaman, Mohamed N

    2017-08-01

    Bioactive glass scaffolds have been used to heal small contained bone defects but their application to repairing structural bone is limited by concerns about their mechanical reliability. In the present study, the addition of an adherent polymer layer to the external surface of strong porous bioactive glass (13-93) scaffolds was investigated to improve their toughness. Finite element modeling (FEM) of the flexural mechanical response of beams composed of a porous glass and an adherent polymer layer predicted a reduction in the tensile stress in the glass with increasing thickness and elastic modulus of the polymer layer. Mechanical testing of composites with structures similar to the models, formed from 13-93 glass and polylactic acid (PLA), showed trends predicted by the FEM simulations but the observed effects were considerably more dramatic. A PLA layer of thickness -400 µm, equal to -12.5% of the scaffold thickness, increased the load-bearing capacity of the scaffold in four-point bending by ~50%. The work of fracture increased by more than 10,000%, resulting in a non-brittle mechanical response. These bioactive glass-PLA composites, combining bioactivity, high strength, high work of fracture and an internal architecture shown to be conducive to bone infiltration, could provide optimal implants for healing structural bone defects.

  3. Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; González, Angélica L; Doebeli, Michael; Farjalla, Vinicius F

    2017-08-01

    Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

    Science.gov (United States)

    Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

    2005-04-01

    Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

  5. Finite Elements Based on Strong and Weak Formulations for Structural Mechanics: Stability, Accuracy and Reliability

    Directory of Open Access Journals (Sweden)

    Francesco Tornabene

    2017-07-01

    Full Text Available The authors are presenting a novel formulation based on the Differential Quadrature (DQ method which is used to approximate derivatives and integrals. The resulting scheme has been termed strong and weak form finite elements (SFEM or WFEM, according to the numerical scheme employed in the computation. Such numerical methods are applied to solve some structural problems related to the mechanical behavior of plates and shells, made of isotropic or composite materials. The main differences between these two approaches rely on the initial formulation – which is strong or weak (variational – and the implementation of the boundary conditions, that for the former include the continuity of stresses and displacements, whereas in the latter can consider the continuity of the displacements or both. The two methodologies consider also a mapping technique to transform an element of general shape described in Cartesian coordinates into the same element in the computational space. Such technique can be implemented by employing the classic Lagrangian-shaped elements with a fixed number of nodes along the element edges or blending functions which allow an “exact mapping” of the element. In particular, the authors are employing NURBS (Not-Uniform Rational B-Splines for such nonlinear mapping in order to use the “exact” shape of CAD designs.

  6. The angular structure of jet quenching within a hybrid strong/weak coupling model

    Science.gov (United States)

    Casalderrey-Solana, Jorge; Gulhan, Doga Can; Milhano, José Guilherme; Pablos, Daniel; Rajagopal, Krishna

    2017-08-01

    Building upon the hybrid strong/weak coupling model for jet quenching, we incorporate and study the effects of transverse momentum broadening and medium response of the plasma to jets on a variety of observables. For inclusive jet observables, we find little sensitivity to the strength of broadening. To constrain those dynamics, we propose new observables constructed from ratios of differential jet shapes, in which particles are binned in momentum, which are sensitive to the in-medium broadening parameter. We also investigate the effect of the back-reaction of the medium on the angular structure of jets as reconstructed with different cone radii R. Finally we provide results for the so called ;missing-pt;, finding a qualitative agreement between our model calculations and data in many respects, although a quantitative agreement is beyond our simplified treatment of the hadrons originating from the hydrodynamic wake.

  7. Correlation between genetic and geographic structure in Europe

    DEFF Research Database (Denmark)

    Lao, Oscar; Lu, Timothy T; Nothnagel, Michael

    2008-01-01

    geographic but narrow genomic coverage [1, 2], or vice versa [3-6]. We therefore investigated Affymetrix GeneChip 500K genotype data from 2,514 individuals belonging to 23 different subpopulations, widely spread over Europe. Although we found only a low level of genetic differentiation between subpopulations......, the existing differences were characterized by a strong continent-wide correlation between geographic and genetic distance. Furthermore, mean heterozygosity was larger, and mean linkage disequilibrium smaller, in southern as compared to northern Europe. Both parameters clearly showed a clinal distribution...... Europe. By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry....

  8. Numerical methods and parallel algorithms for fast transient strongly coupled fluid-structure dynamics

    International Nuclear Information System (INIS)

    Faucher, V.

    2014-01-01

    This HDR is dedicated to the research in the framework of fast transient dynamics for industrial fluid-structure systems carried in the Laboratory of Dynamic Studies from CEA, implementing new numerical methods for the modelling of complex systems and the parallel solution of large coupled problems on supercomputers. One key issue for the proposed approaches is the limitation to its minimum of the number of non-physical parameters, to cope with constraints arising from the area of usage of the concepts: safety for both nuclear applications (CEA, EDF) and aeronautics (ONERA), protection of the citizen (EC/JRC) in particular. Kinematic constraints strongly coupling structures (namely through unilateral contact) or fluid and structures (with both conformant or non-conformant meshes depending on the geometrical situation) are handled through exact methods including Lagrange Multipliers, with consequences on the solution strategy to be dealt with. This latter aspect makes EPX, the simulation code where the methods are integrated, a singular tool in the community of fast transient dynamics software. The document mainly relies on a description of the modelling needs for industrial fast transient scenarios, for nuclear applications in particular, and the proposed solutions built in the framework of the collaboration between CEA, EDF (via the LaMSID laboratory) and the LaMCoS laboratory from INSA Lyon. The main considered examples are the tearing of the fluid-filled tank after impact, the Code Disruptive Accident for a Generation IV reactor or the ruin of reinforced concrete structures under impact. Innovative models and parallel algorithms are thus proposed, allowing to carry out with robustness and performance the corresponding simulations on supercomputers made of interconnected multi-core nodes, with a strict preservation of the quality of the physical solution. This was particularly the main point of the ANR RePDyn project (2010-2013), with CEA as the pilot. (author

  9. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity.

    Directory of Open Access Journals (Sweden)

    Rongman Cai

    2011-08-01

    Full Text Available Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced isolates in 3,543,009 nt of analyzed genome sequence, which suggests a recent evolutionary origin of this pathogen. Further analysis with genome-derived markers of 89 world-wide isolates showed that several genotypes exist in North America and in Europe indicating frequent pathogen movement between these world regions. Genome-derived markers and molecular analyses of key pathogen loci important for virulence and motility both suggest ongoing adaptation to the tomato host. A mutational hotspot was found in the type III-secreted effector gene hopM1. These mutations abolish the cell death triggering activity of the full-length protein indicating strong selection for loss of function of this effector, which was previously considered a virulence factor. Two non-synonymous mutations in the flagellin-encoding gene fliC allowed identifying a new microbe associated molecular pattern (MAMP in a region distinct from the known MAMP flg22. Interestingly, the ancestral allele of this MAMP induces a stronger tomato immune response than the derived alleles. The ancestral allele has largely disappeared from today's Pto populations suggesting that flagellin-triggered immunity limits pathogen fitness even in highly virulent pathogens. An additional non-synonymous mutation was identified in flg22 in South American isolates. Therefore, MAMPs are more variable than expected differing even between otherwise almost identical isolates of the same pathogen strain.

  10. Methodological approach for substantiating disease freedom in a heterogeneous small population. Application to ovine scrapie, a disease with a strong genetic susceptibility.

    Science.gov (United States)

    Martinez, Marie-José; Durand, Benoit; Calavas, Didier; Ducrot, Christian

    2010-06-01

    Demonstrating disease freedom is becoming important in different fields including animal disease control. Most methods consider sampling only from a homogeneous population in which each animal has the same probability of becoming infected. In this paper, we propose a new methodology to calculate the probability of detecting the disease if it is present in a heterogeneous population of small size with potentially different risk groups, differences in risk being defined using relative risks. To calculate this probability, for each possible arrangement of the infected animals in the different groups, the probability that all the animals tested are test-negative given this arrangement is multiplied by the probability that this arrangement occurs. The probability formula is developed using the assumption of a perfect test and hypergeometric sampling for finite small size populations. The methodology is applied to scrapie, a disease affecting small ruminants and characterized in sheep by a strong genetic susceptibility defining different risk groups. It illustrates that the genotypes of the tested animals influence heavily the confidence level of detecting scrapie. The results present the statistical power for substantiating disease freedom in a small heterogeneous population as a function of the design prevalence, the structure of the sample tested, the structure of the herd and the associated relative risks. (c) 2010 Elsevier B.V. All rights reserved.

  11. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

    NARCIS (Netherlands)

    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  12. Turbulent structure and dynamics of swirled, strongly pulsed jet diffusion flames

    KAUST Repository

    Liao, Ying-Hao

    2013-11-02

    The structure and dynamics of swirled, strongly pulsed, turbulent jet diffusion flames were examined experimentally in a co-flow swirl combustor. The dynamics of the large-scale flame structures, including variations in flame dimensions, the degree of turbulent flame puff interaction, and the turbulent flame puff celerity were determined from high-speed imaging of the luminous flame. All of the tests presented here were conducted with a fixed fuel injection velocity at a Reynolds number of 5000. The flame dimensions were generally found to be more impacted by swirl for the cases of longer injection time and faster co-flow flow rate. Flames with swirl exhibited a flame length up to 34% shorter compared to nonswirled flames. Both the turbulent flame puff separation and the flame puff celerity generally decreased when swirl was imposed. The decreased flame length, flame puff separation, and flame puff celerity are consistent with a greater momentum exchange between the flame and the surrounding co-flow, resulting from an increased rate of air entrainment due to swirl. Three scaling relations were developed to account for the impact of the injection time, the volumetric fuel-to-air flow rate ratio, and the jet-on fraction on the visible flame length. © 2013 Copyright Taylor and Francis Group, LLC.

  13. Structural change of cooper pairs in color superconductivity. Crossover from weak coupling to strong coupling

    Energy Technology Data Exchange (ETDEWEB)

    Abuki, Hiroaki; Hatsuda, Tetsuo [Tokyo Univ., Dept. of Physics, Tokyo (Japan); Itakura, Kazunori [Brookhaven National Laboratory, RIKEN BNL Research Center, Upton, NY (United States)

    2002-09-01

    The two-flavor color superconductivity is studied over a wide range of baryon density with a single model. We pay a special attention to the spatial-momentum dependence of the gap and to the spatial-structure of Cooper pairs. At extremely high baryon density ({approx}O(10{sup 10} {rho}{sub 0}) with {rho}{sub 0} being the normal nuclear matter density), our model becomes equivalent to the usual perturbative QCD treatment and the gap is shown to have a sharp peak near the Fermi surface due to the weak-coupling nature of QCD. On the other hand, the gap is a smooth function of the momentum at lower densities ({approx}O(10{sup 10} {rho}{sub 0})) due to strong color magnetic and electric interactions. To study the structural change of Cooper pairs from high density to lower density, quark correlation in the color superconductor is studied both in the momentum space and in the coordinate space. The size of the Cooper pair is shown to become comparable to the averaged inter-quark distance at low densities. Also, effects of the momentum-dependent running coupling and the antiquark pairing, which are both small at high density, are shown to be non-negligible at low densities. These features are highly contrasted to the standard BCS superconductivity in metals. (author)

  14. Radiation-induced structural transitions in composite materials with strong interaction of polymer components

    International Nuclear Information System (INIS)

    Zaikin, Yu.A.; Koztaeva, U.P.

    2002-01-01

    In earlier papers the internal friction (IF) method was applied to studies of structural relaxation in different types of polymer-based composite materials (glass-cloth, paper-based and foiled laminates impregnated by epoxy and phenolic resins) irradiated by 2 MeV electrons in the dose range of 0.1-50.0 MGy. Selectivity and high sensibility of the internal friction method allowed to distinguish glassy transitions in different structural components of the composites. The relaxation processes observed were identified and attributed to structural alterations in the polymer filler, the binder and the boundary layers. It was shown that changes in the parameters of relaxation maximums during irradiation can be considered as quantitative characteristics for the degree of radiation-induced degradation or cross-linking of polymer molecules. This paper deals with specific features of IF spectra in paper-based laminates where both the filler fibers and the binder are strongly interacting polymers. Anisotropy of viscous and elastic properties is very weak for this kind of materials, so that IF measurements give nearly the same result independently on the filler fiber orientation in the sample. The main reasons for it are the rigid chain structure of fillers (polyethylene-terephthalate and cellulose) and the good adhesion strengthened by diffusion of the epoxy or phenolic binder to defect regions of the filler.The IF temperature dependence observed in paper-based laminates is represented by superposition of two very broad relaxation maximums associated with transitions from glassy to high-elastic state in structural components, each based on one of the polymers. The inflection points characteristic for IF temperature dependence in paper-based laminates give a reason to treat them as a superposition of α-peaks associated with transitions from glassy to high-elastic state in structural components of a composite based on the binder and the filler, respectively. Another

  15. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    of the time series under consideration is available. Therefore, a black-box optimization approach is our method of choice for detecting structural breaks. We describe a genetic algorithm framework which easily adapts to a large number of statistical settings. To evaluate the usefulness of different crossover...... and mutation operations for this problem, we conduct extensive experiments to determine good choices for the parameters and operators of the genetic algorithm. One surprising observation is that use of uniform and one-point crossover together gave significantly better results than using either crossover...... operator alone. Moreover, we present a specific fitness function which exploits the sparse structure of the break points and which can be evaluated particularly efficiently. The experiments on artificial and real-world time series show that the resulting algorithm detects break points with high precision...

  16. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  17. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  18. MICRONEEDLE STRUCTURE DESIGN AND OPTIMIZATION USING GENETIC ALGORITHM

    OpenAIRE

    N. A. ISMAIL; S. C. NEOH; N. SABANI; B. N. TAIB

    2015-01-01

    This paper presents a Genetic Algorithm (GA) based microneedle design and analysis. GA is an evolutionary optimization technique that mimics the natural biological evolution. The design of microneedle structure considers the shape of microneedle, material used, size of the array, the base of microneedle, the lumen base, the height of microneedle, the height of the lumen, and the height of the drug container or reservoir. The GA is executed in conjunction with ANSYS simulation system to assess...

  19. The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

    Science.gov (United States)

    Shaw, Robyn E; Banks, Sam C; Peakall, Rod

    2018-01-01

    For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure. © 2017 John Wiley & Sons Ltd.

  20. Individual genetic variations related to satiety and appetite control increase risk of obesity in preschool-age children in the STRONG kids program.

    Science.gov (United States)

    Wang, Yingying; Wang, Anthony; Donovan, Sharon M; Teran-Garcia, Margarita

    2013-01-01

    The burden of the childhood obesity epidemic is well recognized; nevertheless, the genetic markers and gene-environment interactions associated with the development of common obesity are still unknown. In this study, candidate genes associated to satiety and appetite control pathways with obesity-related traits were tested in Caucasian preschoolers from the STRONG Kids project. Eight genetic variants in genes related to obesity (BDNF, LEPR, FTO, PCSK1, POMC, TUB, LEP, and MC4R) were genotyped in 128 children from the STRONG Kids project (mean age 39.7 months). Data were analyzed for individual associations and to test for genetic predisposition scores (GPSs) with body mass index (BMI) and anthropometric traits (Z-scores, e.g. height-for-age Z-score, HAZ). Covariates included age, sex, and breastfeeding (BF) duration. Obesity and overweight prevalence was 6.3 and 19.5%, respectively, according to age- and sex-specific BMI percentiles. Individual genetic associations of MC4R and LEPR markers with HAZ were strengthened when BF duration was included as a covariate. Our GPSs show that, as the number of risk alleles increased, the risk of higher BMI and HAZ also increased. Overall, the GPSs assembled were able to explain 2-3% of the variability in BMI and HAZ phenotypes. Genetic associations with common obesity-related phenotypes were found in the STRONG Kids project. GPSs assembled for specific candidate genes were associated with BMI and HAZ phenotypes. © 2013 S. Karger AG, Basel.

  1. Constant, cycling, hot and cold thermal environments: strong effects on mean viability but not on genetic estimates

    DEFF Research Database (Denmark)

    Ketola, Tarmo; Kellermann, Vanessa; Kristensen, Torsten Nygård

    2012-01-01

    and their fluctuations. How species will respond to these changes is uncertain, particularly as there is a lack of studies which compare genetic performances in constant vs. fluctuating environments. In this study, we used a nested full-sib/half-sib breeding design to examine how the genetic variances and heritabilities...

  2. Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

    Directory of Open Access Journals (Sweden)

    Magni Olsen Kyrkjeeide

    Full Text Available Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America. The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.

  3. Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

    Science.gov (United States)

    Kyrkjeeide, Magni Olsen; Hassel, Kristian; Flatberg, Kjell Ivar; Shaw, A Jonathan; Yousefi, Narjes; Stenøien, Hans K

    2016-01-01

    Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.

  4. Angular structure of jet quenching within a hybrid strong/weak coupling model

    Energy Technology Data Exchange (ETDEWEB)

    Casalderrey-Solana, Jorge [Rudolf Peierls Centre for Theoretical Physics, University of Oxford,1 Keble Road, Oxford OX1 3NP (United Kingdom); Departament de Física Quàntica i Astrofísica & Institut de Ciències del Cosmos (ICC),Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Gulhan, Doga Can [CERN, EP Department,CH-1211 Geneva 23 (Switzerland); Milhano, José Guilherme [CENTRA, Instituto Superior Técnico, Universidade de Lisboa,Av. Rovisco Pais, P-1049-001 Lisboa (Portugal); Laboratório de Instrumentação e Física Experimental de Partículas (LIP),Av. Elias Garcia 14-1, P-1000-149 Lisboa (Portugal); Theoretical Physics Department, CERN,Geneva (Switzerland); Pablos, Daniel [Departament de Física Quàntica i Astrofísica & Institut de Ciències del Cosmos (ICC),Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Rajagopal, Krishna [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States)

    2017-03-27

    Within the context of a hybrid strong/weak coupling model of jet quenching, we study the modification of the angular distribution of the energy within jets in heavy ion collisions, as partons within jet showers lose energy and get kicked as they traverse the strongly coupled plasma produced in the collision. To describe the dynamics transverse to the jet axis, we add the effects of transverse momentum broadening into our hybrid construction, introducing a parameter K≡q̂/T{sup 3} that governs its magnitude. We show that, because of the quenching of the energy of partons within a jet, even when K≠0 the jets that survive with some specified energy in the final state are narrower than jets with that energy in proton-proton collisions. For this reason, many standard observables are rather insensitive to K. We propose a new differential jet shape ratio observable in which the effects of transverse momentum broadening are apparent. We also analyze the response of the medium to the passage of the jet through it, noting that the momentum lost by the jet appears as the momentum of a wake in the medium. After freezeout this wake becomes soft particles with a broad angular distribution but with net momentum in the jet direction, meaning that the wake contributes to what is reconstructed as a jet. This effect must therefore be included in any description of the angular structure of the soft component of a jet. We show that the particles coming from the response of the medium to the momentum and energy deposited in it leads to a correlation between the momentum of soft particles well separated from the jet in angle with the direction of the jet momentum, and find qualitative but not quantitative agreement with experimental data on observables designed to extract such a correlation. More generally, by confronting the results that we obtain upon introducing transverse momentum broadening and the response of the medium to the jet with available jet data, we highlight the

  5. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  6. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  7. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Science.gov (United States)

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

  8. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    Science.gov (United States)

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

    2014-01-01

    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  9. Electronic structure calculations of atomic transport properties in uranium dioxide: influence of strong correlations

    International Nuclear Information System (INIS)

    Dorado, B.

    2010-09-01

    Uranium dioxide UO 2 is the standard nuclear fuel used in pressurized water reactors. During in-reactor operation, the fission of uranium atoms yields a wide variety of fission products (FP) which create numerous point defects while slowing down in the material. Point defects and FP govern in turn the evolution of the fuel physical properties under irradiation. In this study, we use electronic structure calculations in order to better understand the fuel behavior under irradiation. In particular, we investigate point defect behavior, as well as the stability of three volatile FP: iodine, krypton and xenon. In order to take into account the strong correlations of uranium 5f electrons in UO 2 , we use the DFT+U approximation, based on the density functional theory. This approximation, however, creates numerous metastable states which trap the system and induce discrepancies in the results reported in the literature. To solve this issue and to ensure the ground state is systematically approached as much as possible, we use a method based on electronic occupancy control of the correlated orbitals. We show that the DFT+U approximation, when used with electronic occupancy control, can describe accurately point defect and fission product behavior in UO 2 and provide quantitative information regarding point defect transport properties in the oxide fuel. (author)

  10. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

  11. Genetics-based interactions among plants, pathogens, and herbivores define arthropod community structure.

    Science.gov (United States)

    Busby, Posy E; Lamit, Louis J; Keith, Arthur R; Newcombe, George; Gehring, Catherine A; Whitham, Thomas G; Dirzo, Rodolfo

    2015-07-01

    Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens' indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens' indirect effects on arthropod communities and insect herbivory. First, due in part to the pathogens' differential impacts on leaf biomass among the two Populus species and the hybrids, the pathogen most strongly impacted arthropod community composition, richness, and abundance on the pathogen-susceptible tree species. Second, we found similar patterns comparing pathogen-susceptible and pathogen-resistant genotypes within species. Third, within a plant species, pathogens caused a fivefold greater reduction in herbivory on insect-herbivore-susceptible plant genotypes than on herbivore-resistant genotypes, demonstrating that the pathogen-herbivore interaction is genotype dependent. We conclude that interactions among plants, pathogens, and herbivores can structure multitrophic communities, supporting the interacting foundation species hypothesis. Because these interactions are genetically based, evolutionary changes in genetic resistance could result in ecological changes in associated communities, which may in turn feed back to affect plant fitness.

  12. Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae).

    Science.gov (United States)

    Austin, James D.; Jelks, Howard L.; Tate, Bill; Johnson, Aria R.; Jordan, Frank

    2011-01-01

    Imperiled Okaloosa darters (Etheostoma okaloosae) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom's, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

  13. Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.

    Science.gov (United States)

    Meng, Lixue; Wang, Yongmo; Wei, Wen-Hua; Zhang, Hongyu

    2018-01-24

    The Asian citrus psyllid Diaphorina citri Kuwayama is a major pest in citrus production, transmitting Candidatus Liberibacter asiaticus. It has spread widely across eastern and southern China. Unfortunately, little is known about the genetic diversity and population structure of D. citri, making pest control difficult. In this study, nine specifically developed SSR markers and three known mitochondrial DNA were used for population genetics study of D. citri using 225 samples collected from all 7 distribution regions in China. Based on the SSR data, D. citri was found highly diverse with a mean observed heterozygosity of 0.50, and three subgroups were structured by host plant: (i) Shatangju, NF mandarin and Ponkan; (ii) Murraya paniculata and Lemon; (iii) Citrus unshiu, Bingtangcheng, Summer orange and Navel. No significant genetic differences were found with mtDNA data. We suggested the host-associated divergence is likely to have occurred very recently. A unimodal distribution of paired differences, the negative and significant Tajima's D and Fu's F S parameters among mtDNA suggested a recent demographic expansion. The extensive citrus cultivation and increased suitable living habitat was recommended as a key for this expansion event.

  14. Evidence for strong genetic structure in European populations of the little owl Athene noctua

    Czech Academy of Sciences Publication Activity Database

    Pellegrino, I.; Negri, A.; Boano, G.; Cucco, M.; Kristensen, T. N.; Pertoldi, C.; Randi, E.; Šálek, Martin; Mucci, N.

    2015-01-01

    Roč. 46, č. 5 (2015), s. 462-475 ISSN 0908-8857 Institutional support: RVO:68081766 Keywords : postglacial range expansion * microsatellite DNA markers * multilocus genotype data * mitochondrial-DNA * glacial refugia * hybride zones * phenotypic divergence * Pleistocene refugia * woodpecker complex * climate change Subject RIV: EG - Zoology Impact factor: 2.192, year: 2015

  15. Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus across Africa

    Directory of Open Access Journals (Sweden)

    Bezault Etienne

    2011-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian (RST = 0.38 - 0.69. This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (RST = 0.24 - 0.32. The lowest differentiations were observed among connected populations within a basin (RST = 0.015 in the Volta basin. Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053. The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m ~ 0.094 - 0.097 in the Volta populations. Conclusions This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were

  16. Quantum Monte Carlo methods and strongly correlated electrons on honeycomb structures

    Energy Technology Data Exchange (ETDEWEB)

    Lang, Thomas C.

    2010-12-16

    In this thesis we apply recently developed, as well as sophisticated quantum Monte Carlo methods to numerically investigate models of strongly correlated electron systems on honeycomb structures. The latter are of particular interest owing to their unique properties when simulating electrons on them, like the relativistic dispersion, strong quantum fluctuations and their resistance against instabilities. This work covers several projects including the advancement of the weak-coupling continuous time quantum Monte Carlo and its application to zero temperature and phonons, quantum phase transitions of valence bond solids in spin-1/2 Heisenberg systems using projector quantum Monte Carlo in the valence bond basis, and the magnetic field induced transition to a canted antiferromagnet of the Hubbard model on the honeycomb lattice. The emphasis lies on two projects investigating the phase diagram of the SU(2) and the SU(N)-symmetric Hubbard model on the hexagonal lattice. At sufficiently low temperatures, condensed-matter systems tend to develop order. An exception are quantum spin-liquids, where fluctuations prevent a transition to an ordered state down to the lowest temperatures. Previously elusive in experimentally relevant microscopic two-dimensional models, we show by means of large-scale quantum Monte Carlo simulations of the SU(2) Hubbard model on the honeycomb lattice, that a quantum spin-liquid emerges between the state described by massless Dirac fermions and an antiferromagnetically ordered Mott insulator. This unexpected quantum-disordered state is found to be a short-range resonating valence bond liquid, akin to the one proposed for high temperature superconductors. Inspired by the rich phase diagrams of SU(N) models we study the SU(N)-symmetric Hubbard Heisenberg quantum antiferromagnet on the honeycomb lattice to investigate the reliability of 1/N corrections to large-N results by means of numerically exact QMC simulations. We study the melting of phases

  17. Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers.

    Science.gov (United States)

    Fan, Yan; Zhang, Chenglin; Wu, Wendan; He, Wei; Zhang, Li; Ma, Xiao

    2017-10-16

    Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I. pseudotinctoria from 15 natural locations in Wushan Montain, a highly structured mountain with typical karst landforms in Southwest China. We also tested whether eco-climate factors has affected genetic structure by correlating genetic diversity with habitat features. A total of 515 distinctly scoreable bands were generated, and 324 of them were polymorphic. The polymorphic information content (PIC) ranged from 0.694 to 0.890 with an average of 0.789 per primer pair. On species level, Nei's gene diversity ( H j ), the Bayesian genetic diversity index ( H B ) and the Shannon information index ( I ) were 0.2465, 0.2363 and 0.3772, respectively. The high differentiation among all sampling sites was detected ( F ST = 0.2217, G ST = 0.1746, G' ST = 0.2060, θ B = 0.1844), and instead, gene flow among accessions ( N m = 1.1819) was restricted. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. This structure pattern may indicate joint effects by the neutral evolution and natural selection. Restricted N m was

  18. Genetic algorithms for optimal design and control of adaptive structures

    CERN Document Server

    Ribeiro, R; Dias-Rodrigues, J; Vaz, M

    2000-01-01

    Future High Energy Physics experiments require the use of light and stable structures to support their most precise radiation detection elements. These large structures must be light, highly stable, stiff and radiation tolerant in an environment where external vibrations, high radiation levels, material aging, temperature and humidity gradients are not negligible. Unforeseen factors and the unknown result of the coupling of environmental conditions, together with external vibrations, may affect the position stability of the detectors and their support structures compromising their physics performance. Careful optimization of static and dynamic behavior must be an essential part of the engineering design. Genetic Algorithms ( GA) belong to the group of probabilistic algorithms, combining elements of direct and stochastic search. They are more robust than existing directed search methods with the advantage of maintaining a population of potential solutions. There is a class of optimization problems for which Ge...

  19. Strong tough low-carbon bainite structural steels exposed to heat treatment and mechanical working

    International Nuclear Information System (INIS)

    Lauprecht, W.; Imgrund, H.; Coldren, P.

    1975-01-01

    A review of results of studying the mechanical properties and structure of extremely strong construction low-pearlite and pearlite-free steels subjected to thermomechanical processing (TMP) is presented. The development of TMP of low-pearlite and pearlite-free steels has led to creation of steel of the following composition: 0.06% of C; 1.8% of Mn; 0.3% of Mo; 0.05-0.09% of Nb. Depending on the kind of TMP the most important parameters of which are the temperature of the termination of rolling and the total deformation below 900 deg C, transformation in these steels occurs partially or completely in the intermediate domain. The increased density of dislocations of beinite structure affects substantially the increase in the yield limit. High degrees of squeezing at temperatures below 870 deg C promote formation of ferrite nuclei. The laboratory rolling demonstrates that by selecting the conditions of TMP one can control the mechanical properties of a steel. The sheets of 13 mm thick allow to obtain the guaranteed values of the yield limit of 70 kgf/mm 2 the transition temperature T 50 = -25 deg C, whereas after rolling under different conditions the low-temperature limit of cold shortness is - 125 deg C, and the yield limit - 45 kgf/mm 2 . As followed from the estimate of numerous industrial experiments, with sheets 20 mm thick in hot-rolled state one can obtain the yield limit no less than 50 kgf/mm 2 . On rolling mills that make possible to produce large deformation at low temperature these values can be increased. For instance, with sheets 30 mm thick one can obtain the yield limit of 56 kgf/mm 2 and the transition temperature of - 60 deg C. The dependence of the yield limit on the holding time in steel tempering is given. The steel possesses a considerable reserve of the increase of strength due to dispersion hardening, which after tempering at 600-625 deg C constitutes 8-12 kgf/mm 2 . Because of low carbon content, this steel is characterized by good

  20. Genetic variation and phylogeographic structure of the cotton aphid, Aphis gossypii, based on mitochondrial DNA and microsatellite markers.

    Science.gov (United States)

    Wang, Xing-Ya; Yang, Xian-Ming; Lu, Bin; Zhou, Li-Hong; Wu, Kong-Ming

    2017-05-15

    Aphis gossypii, one of the most important agricultural pests in the world, can cause serious economic losses in the main crop-producing areas. To clarify issues such as the genetic differentiation, genetic structure, and demographic history of A. gossypii populations, we used 10 nuclear microsatellite loci (SSR) and two mitochondrial gene sequences (COI and Cytb) to investigate genetic diversity and population structure of A. gossypii populations that were collected from 33 sampling sites in China from different climatic zones. SSR and mtDNA data suggested low to moderate levels of genetic diversity. A star-shaped network of mtDNA haplotypes indicated that the maternal ancestor of China cotton aphids likely originated in Xinjiang. The POPTREE, STRUCTURE and principal coordinate analysis (PCoA) revealed two genetic clusters: an eastern and a western region group. Isolation by distance (IBD) results showed a positive correlation between geographic distance and genetic distance in the vast eastern region but not in the western region. Neutrality testing and mismatch distribution analysis provided strong evidence for a recent rapid expansion in most populations. Genetic bottleneck was not detected in A. gossypii populations of China. The present work can help us to develop strategies for managing this pest.

  1. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

    Directory of Open Access Journals (Sweden)

    AB Choupina

    Full Text Available Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia, are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal, there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates, as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

  2. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... RESEARCH ARTICLE. Genetic diversity, phylogeographic ... chickens as genetic resources towards ensuring food security. Keywords. genetic diversity ... PCR product as template DNA, 3.2 pmol of primer and. 8 μL of Big Dye ...

  3. Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

    Science.gov (United States)

    Brutsaert, Tom

    Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise.

  4. Genetic structure and genetic diversity of Swietenia macrophylla in areas subjected to selective logging in Quintana Roo, Mexico

    OpenAIRE

    Alcalá, Raúl Ernesto; Cruz, Silvia De la; Gutiérrez-Granados, Gabriel

    2015-01-01

    The hypothesis that selective logging has a negative effect by altering the genetic parameters of tropical tree species was evaluated. The genetic diversity and genetic structure between adult trees (N = 47) and saplings (N = 50) of Swietenia macrophylla were contrasted within an area subjected to selective logging in the Mayan zone. Although differences in the number of alleles and in their frequencies were detected between both groups, the observed and expected heterozygosity and the coeffi...

  5. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

    Science.gov (United States)

    Sun, Ye; Vargas-Mendoza, Carlos F

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  6. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

    Directory of Open Access Journals (Sweden)

    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  7. Chronic irradiation as an ecological factor affecting genetic population structure

    International Nuclear Information System (INIS)

    Kal'chenko, V.A.; Kalabushkin, B.A.; Rubanovich, A.V.

    1991-01-01

    Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

  8. MICRONEEDLE STRUCTURE DESIGN AND OPTIMIZATION USING GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    N. A. ISMAIL

    2015-07-01

    Full Text Available This paper presents a Genetic Algorithm (GA based microneedle design and analysis. GA is an evolutionary optimization technique that mimics the natural biological evolution. The design of microneedle structure considers the shape of microneedle, material used, size of the array, the base of microneedle, the lumen base, the height of microneedle, the height of the lumen, and the height of the drug container or reservoir. The GA is executed in conjunction with ANSYS simulation system to assess the design specifications. The GA uses three operators which are reproduction, crossover and mutation to manipulate the genetic composition of the population. In this research, the microneedle is designed to meet a number of significant specifications such as nodal displacement, strain energy, equivalent stress and flow rate of the fluid / drug that flow through its channel / lumen. A comparison study is conducted to investigate the design of microneedle structure with and without the implementation of GA model. The results showed that GA is able to optimize the design parameters of microneedle and is capable to achieve the required specifications with better performance.

  9. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    Science.gov (United States)

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  10. Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis in a Fragmented Landscape

    Directory of Open Access Journals (Sweden)

    Marina G. Figueiredo

    2015-07-01

    Full Text Available Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis, originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars, we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD and Iguaçu Region (IR. Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883. Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i larger effective population size of ocelots (relative to jaguars in each fragment, implying a slower effect of drift-induced differentiation; and (ii potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

  11. Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers.

    Science.gov (United States)

    Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade; Pinto, Luciana Rossini

    2018-01-01

    The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: [Formula: see text] = 0.211 and S. spontaneum: [Formula: see text] = 0.216, Pcommercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.

  12. Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

    DEFF Research Database (Denmark)

    Mucci, Nadia; Arrendal, Johanna; Ansorge, Hermann

    2010-01-01

    Eurasian otter populations strongly declined and partially disappeared due to global and local causes (habitat destruction, water pollution, human persecution) in parts of their continental range. Conservation strategies, based on reintroduction projects or restoration of dispersal corridors...... and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly...

  13. Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

    Directory of Open Access Journals (Sweden)

    Alison K. S. Wee

    2017-12-01

    Full Text Available Patterns of genetic structure are essential for a comprehensive understanding of the evolution and biogeography of a species. Here, we investigated the genetic patterns of one of the most widespread and abundant mangrove species in the Indo-West Pacific, Sonneratia alba J. Sm., in order to gain insights into the ecological and evolutionary drivers of genetic structure in mangroves. We employed 11 nuclear microsatellite loci and two chloroplast regions to genotyped 25 S. alba populations. Our objectives were to (1 assess the level of genetic diversity and its geographic distribution; and (2 determine the genetic structure of the populations. Our results revealed significant genetic differentiation among populations. We detected a major genetic break between Indo-Malesia and Australasia, and further population subdivision within each oceanic region in these two major clusters. The phylogeographic patterns indicated a strong influence of vicariance, oceanic barriers and geographic distance on genetic structure. In addition, we found low genetic diversity and high genetic drift at range edge. This study advances the scope of mangrove biogeography by demonstrating a unique scenario whereby a widespread species has limited dispersal and high genetic divergence among populations.

  14. Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment.

    Science.gov (United States)

    Gouskov, Alexandre; Reyes, Marta; Wirthner-Bitterlin, Lisa; Vorburger, Christoph

    2016-02-01

    The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man-made barriers without fishpasses. The Rhine Falls as the only long-standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man-made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.

  15. Hierarchical spatial genetic structure of Common Eiders (Somateria mollissima) breeding along a migratory corridor

    Science.gov (United States)

    Sonsthagen, S.A.; Talbot, S.L.; Lanctot, Richard B.; Scribner, K.T.; McCracken, K.G.

    2009-01-01

    Documentation of spatial genetic discordance among breeding populations of Arctic-nesting avian species is important, because anthropogenic change is altering environmental linkages at micro- and macrogeographic scales. We estimated levels of population subdivision within Pacific Common Eiders (Somateria mollissima v-nigrum) breeding on 12 barrier islands in the western Beaufort Sea, Alaska, using molecular markers and capture—mark—recapture (CMR) data. Common Eider populations were genetically structured on a microgeographic scale. Regional comparisons between populations breeding on island groups separated by 90 km (Mikkelsen Bay and Simpson Lagoon) revealed structuring at 14 microsatellite loci (F ST = 0.004, P Sea are strongly philopatric to island groups rather than to a particular island. Despite the apparent high site fidelity of females, coalescence-based models of gene flow suggest that asymmetrical western dispersal occurs between island groups and is likely mediated by Mikkelsen Bay females stopping early on spring migration at Simpson Lagoon to breed. Alternatively, late-arriving females may be predisposed to nest in Simpson Lagoon because of the greater availability and wider distribution of nesting habitat. Our results indicate that genetic discontinuities, mediated by female philopatry, can exist at microgeographic scales along established migratory corridors.

  16. Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

    Science.gov (United States)

    Putz, Christina M; Schmid, Christoph; Reisch, Christoph

    2015-09-01

    The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

  17. Genetic Variation in Schizophrenia Liability is Shared With Intellectual Ability and Brain Structure

    NARCIS (Netherlands)

    Bohlken, Marc M; Brouwer, Rachel M; Mandl, René C W; Kahn, René S; Hulshoff Pol, Hilleke E

    2016-01-01

    BACKGROUND: Alterations in intellectual ability and brain structure are important genetic markers for schizophrenia liability. How variations in these phenotypes interact with variance in schizophrenia liability due to genetic or environmental factors is an area of active investigation. Studying

  18. Structural health monitoring feature design by genetic programming

    International Nuclear Information System (INIS)

    Harvey, Dustin Y; Todd, Michael D

    2014-01-01

    Structural health monitoring (SHM) systems provide real-time damage and performance information for civil, aerospace, and other high-capital or life-safety critical structures. Conventional data processing involves pre-processing and extraction of low-dimensional features from in situ time series measurements. The features are then input to a statistical pattern recognition algorithm to perform the relevant classification or regression task necessary to facilitate decisions by the SHM system. Traditional design of signal processing and feature extraction algorithms can be an expensive and time-consuming process requiring extensive system knowledge and domain expertise. Genetic programming, a heuristic program search method from evolutionary computation, was recently adapted by the authors to perform automated, data-driven design of signal processing and feature extraction algorithms for statistical pattern recognition applications. The proposed method, called Autofead, is particularly suitable to handle the challenges inherent in algorithm design for SHM problems where the manifestation of damage in structural response measurements is often unclear or unknown. Autofead mines a training database of response measurements to discover information-rich features specific to the problem at hand. This study provides experimental validation on three SHM applications including ultrasonic damage detection, bearing damage classification for rotating machinery, and vibration-based structural health monitoring. Performance comparisons with common feature choices for each problem area are provided demonstrating the versatility of Autofead to produce significant algorithm improvements on a wide range of problems. (paper)

  19. The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis.

    Science.gov (United States)

    Schuller, Dorit; Casal, Margarida

    2007-02-01

    From the analysis of six polymorphic microsatellite loci performed in 361 Saccharomyces cerevisiae isolates, 93 alleles were identified, 52 of them being described for the first time. All these isolates have a distinct mtDNA RFLP pattern. They are derived from a pool of 1620 isolates obtained from spontaneous fermentations of grapes collected in three vineyards of the Vinho Verde Region in Portugal, during the 2001-2003 harvest seasons. For all loci analyzed, observed heterozygosity was 3-4 times lower than the expected value supposing a Hardy-Weinberg equilibrium (random mating and no evolutionary mechanisms acting), indicating a clonal structure and strong populational substructuring. Genetic differences among S. cerevisiae populations were apparent mainly from gradations in allele frequencies rather than from distinctive "diagnostic" genotypes, and the accumulation of small allele-frequency differences across six loci allowed the identification of population structures. Genetic differentiation in the same vineyard in consecutive years was of the same order of magnitude as the differences verified among the different vineyards. Correlation of genetic differentiation with the distance between sampling points within a vineyard suggested a pattern of isolation-by-distance, where genetic divergence in a vineyard increased with size. The continuous use of commercial yeasts has a limited influence on the autochthonous fermentative yeast population collected from grapes and may just slightly change populational structures of strains isolated from sites very close to the winery where they have been used. The present work is the first large-scale approach using microsatellite typing allowing a very fine resolution of indigenous S. cerevisiae populations isolated from vineyards.

  20. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    Directory of Open Access Journals (Sweden)

    Yan Zheng

    Full Text Available The oriental fruit moth Grapholita ( = Cydia molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

  1. Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae).

    Science.gov (United States)

    Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

    2013-05-01

    Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.

  2. Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

    Science.gov (United States)

    Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

    2018-01-01

    Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

  3. Global search in photoelectron diffraction structure determination using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Viana, M L [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Muino, R Diez [Donostia International Physics Center DIPC, Paseo Manuel de Lardizabal 4, 20018 San Sebastian (Spain); Soares, E A [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Hove, M A Van [Department of Physics and Materials Science, City University of Hong Kong, Hong Kong (China); Carvalho, V E de [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil)

    2007-11-07

    Photoelectron diffraction (PED) is an experimental technique widely used to perform structural determinations of solid surfaces. Similarly to low-energy electron diffraction (LEED), structural determination by PED requires a fitting procedure between the experimental intensities and theoretical results obtained through simulations. Multiple scattering has been shown to be an effective approach for making such simulations. The quality of the fit can be quantified through the so-called R-factor. Therefore, the fitting procedure is, indeed, an R-factor minimization problem. However, the topography of the R-factor as a function of the structural and non-structural surface parameters to be determined is complex, and the task of finding the global minimum becomes tough, particularly for complex structures in which many parameters have to be adjusted. In this work we investigate the applicability of the genetic algorithm (GA) global optimization method to this problem. The GA is based on the evolution of species, and makes use of concepts such as crossover, elitism and mutation to perform the search. We show results of its application in the structural determination of three different systems: the Cu(111) surface through the use of energy-scanned experimental curves; the Ag(110)-c(2 x 2)-Sb system, in which a theory-theory fit was performed; and the Ag(111) surface for which angle-scanned experimental curves were used. We conclude that the GA is a highly efficient method to search for global minima in the optimization of the parameters that best fit the experimental photoelectron diffraction intensities to the theoretical ones.

  4. Genetic structure in the coral, Montastraea cavernosa: assessing genetic differentiation among and within Mesophotic reefs.

    Directory of Open Access Journals (Sweden)

    Daniel A Brazeau

    Full Text Available Mesophotic coral reefs (30-150 m have recently received increased attention as a potential source of larvae (e.g., the refugia hypothesis to repopulate a select subset of the shallow water (<30 m coral fauna. To test the refugia hypothesis we used highly polymorphic Amplified Fragment Length Polymorphism (AFLP markers as a means to assess small-scale genetic heterogeneity between geographic locations and across depth clines in the Caribbean coral, Montastraea cavernosa. Zooxanthellae-free DNA extracts of coral samples (N = 105 were analyzed from four depths, shallow (3-10 m, medium (15-25 m, deep (30-50 m and very deep (60-90 m from Little Cayman Island (LCI, Lee Stocking Island (LSI, Bahamas and San Salvador (SS, Bahamas which range in distance from 170 to 1,600 km apart. Using AMOVA analysis there were significant differences in ΦST values in pair wise comparisons between LCI and LSI. Among depths at LCI, there was significant genetic differentiation between shallow and medium versus deep and very deep depths in contrast there were no significant differences in ΦST values among depths at LSI. The assignment program AFLPOP, however, correctly assigned 95.7% of the LCI and LSI samples to the depths from which they were collected, differentiating among populations as little as 10 to 20 m in depth from one another. Discriminant function analysis of the data showed significant differentiation among samples when categorized by collection site as well as collection depth. FST outlier analyses identified 2 loci under positive selection and 3 under balancing selection at LCI. At LSI 2 loci were identified, both showing balancing selection. This data shows that adult populations of M. cavernosa separated by depths of tens of meters exhibits significant genetic structure, indicative of low population connectivity among and within sites and are not supplying successful recruits to adjacent coral reefs less than 30 m in depth.

  5. Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

    Science.gov (United States)

    Planes, S; Fauvelot, C

    2002-02-01

    We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead

  6. Fracture mechanism of a dispersion-hardened molybdenum alloy with strong structural interfaces

    International Nuclear Information System (INIS)

    Vasil'ev, A.D.; Malashenko, I.S.; Moiseev, V.F.; Pechkovskij, Eh.P.; Sul'zhenko, V.K.; Trefilov, V.I.; AN Ukrainskoj SSR, Kiev. Inst. Ehlektrosvarki)

    1978-01-01

    Fracture mechanism in the two-phase Mo-15wt.%Nb-3.5 vol.% TiN alloy known to be of ''brittle matrix-strong interfaces'' type has been investigated depending on tensile test temperature. Several temperature intervals of fracture have been found, each of them having its own peculiarities. A scheme is suggested for fracture mechanism changes in dispersion-hardened alloys with strong interfaces. At low test temperatures brittle cleavage fracture takes place. With temperature increase fracture mechanisms change in the following way: brittle intergranular fracture; fracture of ''microvoid coalescence'' type; fracture typical for reinforced materials with ductile matrix; intergran laru fracture. Particles of strengthening phase have been shown to play different roles depending on the test temperature in the fracture of the alloys studied

  7. The structural role of weak and strong links in a financial market network

    Science.gov (United States)

    Garas, A.; Argyrakis, P.; Havlin, S.

    2008-05-01

    We investigate the properties of correlation based networks originating from economic complex systems, such as the network of stocks traded at the New York Stock Exchange (NYSE). The weaker links (low correlation) of the system are found to contribute to the overall connectivity of the network significantly more than the strong links (high correlation). We find that nodes connected through strong links form well defined communities. These communities are clustered together in more complex ways compared to the widely used classification according to the economic activity. We find that some companies, such as General Electric (GE), Coca Cola (KO), and others, can be involved in different communities. The communities are found to be quite stable over time. Similar results were obtained by investigating markets completely different in size and properties, such as the Athens Stock Exchange (ASE). The present method may be also useful for other networks generated through correlations.

  8. Aphid-parasitoid community structure on genetically modified wheat.

    Science.gov (United States)

    von Burg, Simone; van Veen, Frank J F; Álvarez-Alfageme, Fernando; Romeis, Jörg

    2011-06-23

    Since the introduction of genetically modified (GM) plants, one of the main concerns has been their potential effect on non-target insects. Many studies have looked at GM plant effects on single non-target herbivore species or on simple herbivore-natural enemy food chains. Agro-ecosystems, however, are characterized by numerous insect species which are involved in complex interactions, forming food webs. In this study, we looked at transgenic disease-resistant wheat (Triticum aestivum) and its effect on aphid-parasitoid food webs. We hypothesized that the GM of the wheat lines directly or indirectly affect aphids and that these effects cascade up to change the structure of the associated food webs. Over 2 years, we studied different experimental wheat lines under semi-field conditions. We constructed quantitative food webs to compare their properties on GM lines with the properties on corresponding non-transgenic controls. We found significant effects of the different wheat lines on insect community structure up to the fourth trophic level. However, the observed effects were inconsistent between study years and the variation between wheat varieties was as big as between GM plants and their controls. This suggests that the impact of our powdery mildew-resistant GM wheat plants on food web structure may be negligible and potential ecological effects on non-target insects limited.

  9. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    Science.gov (United States)

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  10. Genetic population structure of the desert shrub species lycium ruthenicum inferred from chloroplast dna

    International Nuclear Information System (INIS)

    Chen, H.; Yonezawa, T.

    2014-01-01

    Lycium ruthenicum (Solananeae), a spiny shrub mostly distributed in the desert regions of north and northwest China, has been shown to exhibit high tolerance to the extreme environment. In this study, the phylogeography and evolutionary history of L. ruthenicum were examined, on the basis of 80 individuals from eight populations. Using the sequence variations of two spacer regions of chloroplast DNA (trnH-psbA and rps16-trnK) , the absence of a geographic component in the chloroplast DNA genetic structure was identified (GST = 0.351, NST = 0.304, NST< GST), which was consisted with the result of SAMOVA, suggesting weak phylogeographic structure of this species. Phylogenetic and network analyses showed that a total of 10 haplotypes identified in the present study clustered into two clades, in which clade I harbored the ancestral haplotypes that inferred two independent glacial refugia in the middle of Qaidam Basin and the western Inner Mongolia. The existence of regional evolutionary differences was supported by GENETREE, which revealed that one of the population in Qaidam Basin and the two populations in Tarim Basin had experienced rapid expansion, and the other populations retained relatively stable population size during the Pleistocene . Given the results of long-term gene flow and pairwise differences, strong gene flow was insufficient to reduce the genetic differentiation among populations or within populations, probably due to the genetic composition containing a common haplotype and the high number of private haplotypes fixed for most of the population. The divergence times of different lineages were consistent with the rapid uplift phases of the Qinghai-Tibetan Plateau and the initiation and expansion of deserts in northern China, suggesting that the origin and evolution of L. ruthenicum were strongly influenced by Quaternary environment changes. (author)

  11. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  12. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Science.gov (United States)

    Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

    2012-01-01

    Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  13. Strong influence of regional species pools on continent-wide structuring of local communities

    OpenAIRE

    Lessard, Jean-Philippe; Borregaard, Michael K.; Fordyce, James A.; Rahbek, Carsten; Weiser, Michael D.; Dunn, Robert R.; Sanders, Nathan J.

    2011-01-01

    There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that...

  14. Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication

    Directory of Open Access Journals (Sweden)

    Pantano Thais

    2008-11-01

    Full Text Available Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers. The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.

  15. Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

    Science.gov (United States)

    Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

    2018-04-23

    The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure

  16. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    ... phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data ... thus, impact on community genetics (Bittles 2001, 2002). ... reflect an interaction between evolutionary and demographic.

  17. Atomic-structure effects in strong-field multiphoton detachment and ionization

    International Nuclear Information System (INIS)

    AAberg, T.; Mu, X.; Ruscheinski, J.; Crasemann, B.

    1994-01-01

    Above-threshold photoelectron detachment and ionization spectra are investigated theoretically in the tunneling and over-barrier regime as a function of wavelength (≥ 1.064 μm) and polarization of the electromagnetic field. It is found that the zeros in the initial-state wave function can drastically affect the shape of the high-energy photoelectron distribution. The phenomenon is not predicted by tunneling and related models and hence can test their validity and reveal whether Keldysh-type theories are in general applicable to strong-field multiphoton dynamics. (orig.)

  18. Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

    Science.gov (United States)

    Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

    2018-02-01

    Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

  19. Directed emission of CdSe nanoplatelets originating from strongly anisotropic 2D electronic structure

    Science.gov (United States)

    Scott, Riccardo; Heckmann, Jan; Prudnikau, Anatol V.; Antanovich, Artsiom; Mikhailov, Aleksandr; Owschimikow, Nina; Artemyev, Mikhail; Climente, Juan I.; Woggon, Ulrike; Grosse, Nicolai B.; Achtstein, Alexander W.

    2017-12-01

    Intrinsically directional light emitters are potentially important for applications in photonics including lasing and energy-efficient display technology. Here, we propose a new route to overcome intrinsic efficiency limitations in light-emitting devices by studying a CdSe nanoplatelets monolayer that exhibits strongly anisotropic, directed photoluminescence. Analysis of the two-dimensional k-space distribution reveals the underlying internal transition dipole distribution. The observed directed emission is related to the anisotropy of the electronic Bloch states governing the exciton transition dipole moment and forming a bright plane. The strongly directed emission perpendicular to the platelet is further enhanced by the optical local density of states and local fields. In contrast to the emission directionality, the off-resonant absorption into the energetically higher 2D-continuum of states is isotropic. These contrasting optical properties make the oriented CdSe nanoplatelets, or superstructures of parallel-oriented platelets, an interesting and potentially useful class of semiconductor-based emitters.

  20. Sensor placement optimization for structural modal identification of flexible structures using genetic algorithm

    International Nuclear Information System (INIS)

    Jung, B. K.; Cho, J. R.; Jeong, W. B.

    2015-01-01

    The position of vibration sensors influences the modal identification quality of flexible structures for a given number of sensors, and the quality of modal identification is usually estimated in terms of correlation between the natural modes using the modal assurance criterion (MAC). The sensor placement optimization is characterized by the fact that the design variables are not continuous but discrete, implying that the conventional sensitivity-driven optimization methods are not applicable. In this context, this paper presents the application of genetic algorithm to the sensor placement optimization for improving the modal identification quality of flexible structures. A discrete-type optimization problem using genetic algorithm is formulated by defining the sensor positions and the MAC as the design variables and the objective function, respectively. The proposed GA-based evolutionary optimization method is validated through the numerical experiment with a rectangular plate, and its excellence is verified from the comparison with the cases using different modal correlation measures.

  1. Population Genetic Structure and Evidence of Demographic Expansion of the Ayu (Plecoglossus altivelis in East Asia

    Directory of Open Access Journals (Sweden)

    Ye-Seul Kwan

    2012-10-01

    Full Text Available Plecoglossus altivelis (ayu is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region.

  2. Management applications of genetic structure of anadromous sturgeon populations in the Lower Danube River (LDR, Romania

    Directory of Open Access Journals (Sweden)

    ONĂRĂ Dalia Florentina

    2013-12-01

    Full Text Available During the last decades, the over-exploitation of sturgeon stocks for caviar production simultaneously with severe habitat deteriorations has led to drastic declines in the natural populations of the Danube River. As a result of (i decrease of sturgeon catches from 37.5 tons in year 2002 to 11.8 tons in year 2005, (ii disrupted age class structure of sturgeon adult cohorts in years 2003 and 2004, and (iii lack or low recruitment in the period 2001 – 2004, in 2005 the Romanian Government started the Supportive Stocking Program of Lower Danube River with hatchery-produced young sturgeons in Romania. Subsequently, in 2006 the commercial sturgeon fishing in Romania was banned for a 10-year period. Genetic investigations were undertaken as an attempt to assess the genetic variability of the sturgeon brood fish, captured from the wild, used in two aquaculture facilities in Romania for obtaining juveniles for supportive stocking of LDR with young sturgeons produced by artificial propagation in year 2007. Our data indicate strong genetic diversity in case of stellate sturgeon and lack of diversity within the batch of beluga sturgeon brood fish captured in 2007, analyzed in the current study. Specific measures that could improve the management plan of sturgeon brood fish in the Romanian part of LDR in the light of recent FAO guidelines regarding the sturgeon hatchery practices and management for release were suggested

  3. Structural modification of polysaccharides: A biochemical-genetic approach

    Science.gov (United States)

    Kern, Roger G.; Petersen, Gene R.

    1991-01-01

    Polysaccharides have a wide range of industrial and biomedical applications. An industry trend is underway towards the increased use of bacteria to produce polysaccharides. Long term goals of this work are the adaptation and enhancement of saccharide properties for electronic and optic applications. In this report we illustrate the application of enzyme-bearing bacteriophage on strains of the enteric bacterium Klebsiella pneumoniae, which produces a polysaccharide with the relatively rare rheological property of drag-reduction. This has resulted in the production of new polysaccharides with enhanced rheological properties. Our laboratory is developing techniques for processing and structurally modifying bacterial polysaccharides and oligosaccharides which comprise their basic polymeric repeat units. Our research has focused on bacteriophage which produce specific polysaccharide degrading enzymes. This has lead to the development of enzymes generated by bacteriophage as tools for polysaccharide modification and purification. These enzymes were used to efficiently convert the native material to uniform-sized high molecular weight polymers, or alternatively into high-purity oligosaccharides. Enzyme-bearing bacteriophage also serve as genetic selection tools for bacteria that produce new families of polysaccharides with modified structures.

  4. Comparison of the electronic structure of two polymers with strong dipole ordering

    International Nuclear Information System (INIS)

    Xiao Jie; Rosa, Luis G; Poulsen, Matt; Feng, D-Q; Reddy, D Sahadeva; Takacs, James M; Cai, Lei; Zhang, Jiandi; Ducharme, Stephen; Dowben, P A

    2006-01-01

    Two different polymers, with large local electric dipoles, are compared: copolymers of polyvinylidene fluoride with trifluoroethylene [P(VDF-TrFE, 70%:30%)] and polymethylvinylidenecyanide (PMVC). While the different local point group symmetries play a key role, both crystalline polymers exhibit intra-molecular band structure, though the Brillouin zone critical points differ. (letter to the editor)

  5. Structural study of liquids with strong short-range correlation in the atomic distribution

    International Nuclear Information System (INIS)

    Uzuki, Kenji

    1976-01-01

    Structure factors of liquids and amorphous solids having a relatively high degree of ordering in their short-range structures have been measured over a wide range of scattering vectors by means of the T-O-F neutron diffraction using epithermal pulsed neutrons generated by an electron linear accelerator. It has been shown in the case of liquid CS 2 that the size and shape of a molecule existing in the liquid phase are determined from the behaviour of the structure factor in the range of high scattering vectors, and that the structure factor in the region of low scattering vectors informs on inter-molecular orientational and center-center correlations in the liquid state. Moreover, based on highly resoluted radial distribution functions, a free rotating chain model has been discussed for chain molecules contained in liquid Se, and a splitting of the nearest neighbour Pd-Pd and Pd-Si correlation has been clearly found in the amorphous Pdsub(0.8) - Sisub(0.2) alloy. (orig./HK) [de

  6. Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers

    NARCIS (Netherlands)

    Tang, N.; Shahin, A.; Bijman, P.J.J.; Liu, J.; Tuyl, van J.M.; Arens, P.

    2013-01-01

    Although tulip is one of the most important bulbous crops worldwide, the genetic background of most cultivars is unclear at present. The purposes of this study are to investigate genetic diversity and to identify the genetic structure and relationships among tulip cultivars. A total of 236

  7. Genetic structure and diversity of the black and rufous sengiin Tanzanian coastal forests

    Czech Academy of Sciences Publication Activity Database

    Sabuni, C. A.; Van Houtte, N.; Gryseels, S.; Maganga, S. L. S.; Makundi, R. H.; Leirs, H.; Goüy de Bellocq, Joëlle

    2016-01-01

    Roč. 300, č. 4 (2016), s. 305-313 ISSN 0952-8369 Institutional support: RVO:68081766 Keywords : Rhynchocyon petersi * vulnerable * conservation genetics * coastal forests * Beamys hindei * genetic structure * genetic diversity * habitat fragmentation Subject RIV: EH - Ecology, Behaviour Impact factor: 2.186, year: 2016

  8. Long term human impacts on genetic structure of Italian walnut inferred by SSR markers

    Science.gov (United States)

    Paola Pollegioni; Keith Woeste; Irene Olimpieri; Danilo Marandola; Francesco Cannata; Maria E Malvolti

    2011-01-01

    Life history traits, historic factors, and human activities can all shape the genetic diversity of a species. In Italy, walnut (Juglans regia L.) has a long history of cultivation both for wood and edible nuts. To better understand the genetic variability of current Italian walnut resources, we analyzed the relationships among the genetic structure...

  9. Structured Parenting of Toddlers at High versus Low Genetic Risk: Two Pathways to Child Problems

    Science.gov (United States)

    Leve, Leslie D.; Harold, Gordon T.; Ge, Xiaojia; Neiderhiser, Jenae M.; Shaw, Daniel; Scaramella, Laura V.; Reiss, David

    2009-01-01

    Objective: Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for…

  10. Nonlinear physics of plasmas. Spatiotemporal structures in strong turbulence. Lecture notes

    International Nuclear Information System (INIS)

    Skoric, Milos M.

    2008-05-01

    This material has been prepared and partly delivered in a series of lectures given at NIFS to Doctor course students of the SOKENDAI (Graduate University of Advanced Studies, Japan) in academic 2007/08 year. Special gratitude is due to colleagues for fruitful collaboration: Profs. K. Mima, Lj. Hadzievski, S. Ishiguro, A. Maluckov, M. Rajkovic and Dr Li Baiwen and Dr Lj. Nikolic, in particular, and to Prof. Mitsuo Kono for motivating the work on this text. I wish to pay unique tribute to close friends and longtime collaborators, Prof. Dik ter Haar and Prof. Moma Jovanovic who are no longer with us. This report contains Chapter 1 (Strong Langmur Turbulence), Chapter 2 (Wave Collapse in Plasmas), Chapter 3 (Spatiotemporal Complexity in Plasmas), Chapter 4 (Relativistic Plasma Interactions) and Chapter 5 (Ponderomotive Potential and Magnetization). (J.P.N.)

  11. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  12. Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.

    Science.gov (United States)

    Samiotakis, Antonios; Dhar, Apratim; Ebbinghaus, Simon; Nienhaus, Lea; Homouz, Dirar; Gruebele, Martin; Cheung, Margaret

    2010-10-01

    We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal) and Sph (spherical compact). With an adjustment for viscosity, crowded wild type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a new solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates.

  13. Bound states in the continuum on periodic structures surrounded by strong resonances

    Science.gov (United States)

    Yuan, Lijun; Lu, Ya Yan

    2018-04-01

    Bound states in the continuum (BICs) are trapped or guided modes with their frequencies in the frequency intervals of the radiation modes. On periodic structures, a BIC is surrounded by a family of resonant modes with their quality factors approaching infinity. Typically the quality factors are proportional to 1 /|β - β*|2 , where β and β* are the Bloch wave vectors of the resonant modes and the BIC, respectively. But for some special BICs, the quality factors are proportional to 1 /|β - β*|4 . In this paper, a general condition is derived for such special BICs on two-dimensional periodic structures. As a numerical example, we use the general condition to calculate special BICs, which are antisymmetric standing waves, on a periodic array of circular cylinders, and show their dependence on parameters. The special BICs are important for practical applications, because they produce resonances with large quality factors for a very large range of β .

  14. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  15. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  16. Monogamy, strongly bonded groups, and the evolution of human social structure.

    Science.gov (United States)

    Chapais, Bernard

    2013-01-01

    Human social evolution has most often been treated in a piecemeal fashion, with studies focusing on the evolution of specific components of human society such as pair-bonding, cooperative hunting, male provisioning, grandmothering, cooperative breeding, food sharing, male competition, male violence, sexual coercion, territoriality, and between-group conflicts. Evolutionary models about any one of those components are usually concerned with two categories of questions, one relating to the origins of the component and the other to its impact on the evolution of human cognition and social life. Remarkably few studies have been concerned with the evolution of the entity that integrates all components, the human social system itself. That social system has as its core feature human social structure, which I define here as the common denominator of all human societies in terms of group composition, mating system, residence patterns, and kinship structures. The paucity of information on the evolution of human social structure poses substantial problems because that information is useful, if not essential, to assess both the origins and impact of any particular aspect of human society. Copyright © 2013 Wiley Periodicals, Inc.

  17. Electrical Control of Structural and Physical Properties via Strong Spin-Orbit Interactions in Sr2IrO4

    Science.gov (United States)

    Cao, G.; Terzic, J.; Zhao, H. D.; Zheng, H.; De Long, L. E.; Riseborough, Peter S.

    2018-01-01

    Electrical control of structural and physical properties is a long-sought, but elusive goal of contemporary science and technology. We demonstrate that a combination of strong spin-orbit interactions (SOI) and a canted antiferromagnetic Mott state is sufficient to attain that goal. The antiferromagnetic insulator Sr2IrO4 provides a model system in which strong SOI lock canted Ir magnetic moments to IrO6 octahedra, causing them to rigidly rotate together. A novel coupling between an applied electrical current and the canting angle reduces the Néel temperature and drives a large, nonlinear lattice expansion that closely tracks the magnetization, increases the electron mobility, and precipitates a unique resistive switching effect. Our observations open new avenues for understanding fundamental physics driven by strong SOI in condensed matter, and provide a new paradigm for functional materials and devices.

  18. SU(6)-strong breaking: structure functions and small momentum transfer properties of the nucleon

    International Nuclear Information System (INIS)

    Le Yaouanc, A.; Oliver, L.; Pene, O.; Raynal, J.C.

    1975-01-01

    A new approach in the study of the SU(6) symmetry breaking (in particular in deep inelastic electron-nucleon scattering) is presented. It is shown that there is a connection between deep inelastic and low momentum transfer or static properties of the nucleon, which extends much beyond the common SU(6) 56-assignments of the nucleon in both cases. This connection is provided by the realistic quark model (in which quarks are considered as real entities moving inside the hadron). Using this connection it is shown that the breaking of the prediction Fsub(2)sup(en)/Fsub(2)sup(ep)=2/3 is not truly related to chiral configuration mixings. An alternative solution, based on a true modification of the 56-assignment of the nucleon to a (56,L=0)+(70,L=0) mixing (called SU(6) strong mixing) is proposed. It is shown that the 'good' predictions of SU(6) are not much changed by this mixing. A complete description of the deep inelastic scattering including gluons and pairs is presented

  19. Structure of Langmuir and electromagnetic collapsing wave packets in two-dimensional strong plasma turbulence

    International Nuclear Information System (INIS)

    Alinejad, H.; Robinson, P. A.; Cairns, I. H.; Skjaeraasen, O.; Sobhanian, S.

    2007-01-01

    Nucleating and collapsing wave packets relevant to electromagnetic strong plasma turbulence are studied theoretically in two dimensions. Model collapsing Langmuir and transverse potentials are constructed as superpositions of approximate eigenstates of a spherically symmetric density well. Electrostatic and electromagnetic potentials containing only components with azimuthal quantum numbers m=0, 1, 2 are found to give a good representation of the electric fields of nucleating collapsing wave packets in turbulence simulations. The length scales of these trapped states are related to the electron thermal speed v e and the length scale of the density well. It is shown analytically that the electromagnetic trapped states change with v e and that for v e e > or approx. 0.17c, the Langmuir and transverse modes remain coupled during collapse, with autocorrelation lengths in a constant ratio. An investigation of energy transfer to packets localized in density wells shows that the strongest power transfer to the nucleating state occurs for Langmuir waves. Energy transitions between different trapped and free states for collapsing wave packets are studied, and the transition rate from trapped Langmuir to free plane electromagnetic waves is calculated and related to the emission of electromagnetic waves at the plasma frequency

  20. Counter-rotating effects and entanglement dynamics in strongly coupled quantum-emitter-metallic-nanoparticle structures

    Science.gov (United States)

    Iliopoulos, Nikos; Thanopulos, Ioannis; Yannopapas, Vassilios; Paspalakis, Emmanuel

    2018-03-01

    We study the spontaneous emission of a two-level quantum emitter next to a plasmonic nanoparticle beyond the Markovian approximation and the rotating-wave approximation (RWA) by combining quantum dynamics and classical electromagnetic calculations. For emitters with decay times in the picosecond to nanosecond time regime, as well as located at distances from the nanoparticle up to its radius, the dynamics with and without the RWA and the transition from the non-Markovian to the Markovian regime are investigated. For emitters with longer decay times, the Markov approximation proves to be adequate for distances larger than half the nanoparticle radius. However, the RWA is correct for all distances of the emitter from the nanoparticle. For short decay time emitters, the Markov approximation and RWA are both inadequate, with only the RWA becoming valid again at a distance larger than half the nanoparticle radius. We also show that the entanglement dynamics of two initially entangled qubits interacting independently with the nanoparticle may have a strong non-Markovian character when counter-rotating effects are included. Interesting effects such as entanglement sudden death, periodic entanglement revival, entanglement oscillations, and entanglement trapping are further observed when different initial two-qubit states and different distances between the qubit and the nanoparticle are considered.

  1. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient

    Directory of Open Access Journals (Sweden)

    Rossetto Maurizio

    2012-08-01

    an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Conclusions Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.

  2. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

    Science.gov (United States)

    Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

    2012-08-20

    corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.

  3. Two-step excitation structure changes of luminescence centers and strong tunable blue emission on surface of silica nanospheres

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Lei, E-mail: nanoyang@qq.com; Jiang, Zhongcheng; Dong, Jiazhang; Zhang, Liuqian [Hunan University, College of Materials Science and Engineering (China); Pan, Anlian, E-mail: anlian.pan@gmail.com; Zhuang, Xiujuan [Hunan University, Key Laboratory for Micro-Nano Physics and Technology of Hunan Province (China)

    2015-10-15

    We report a scheme for investigating two-step stimulated structure change of luminescence centers. Amorphous silica nanospheres with uniform diameter of 9–15 nm have been synthesized by Stöber method. Strong hydroxyl-related infrared-absorption band is observed in infrared spectrum. The surface hydroxyl groups exert great influence on the luminescent behavior of silica. They provide stable and intermediate energy states to accommodate excitation electrons. The existence of these surface states reduces the energy barrier of photochemical reactions, creating conditions for two-step excitation process. By carefully examining excitation and emission process, the nearest excitation band is absent in both optical absorption spectrum and excitation spectrum. This later generated state confirms the generation of new luminescence centers as well as the existence of photochemical reactions. Stimulated by different energies, two-step excitation process impels different photochemical reactions, prompting generation of different lattice defects on surface area of silica. Thereby, tunable luminescence is achieved. After thermal treatment, strong gap excitation band appears with the disappearance of strong surface excitation band. Strong blue luminescence also disappears. The research is significance to precise introducing structural defects and controlling position of luminescence peaks.

  4. Determination of the Bjorken Sum and Strong Coupling from Polarized Structure Functions

    CERN Document Server

    Altarelli, Guido; Forte, Stefano; Ridolfi, G; Altarelli, Guido; Ball, Richard D.; Forte, Stefano; Ridolfi, Giovanni

    1997-01-01

    We present a NLO perturbative analysis of all available data on the polarized structure function g_1(x,Q^2) with the aim of making a quantitative test of the validity of the Bjorken sum rule, of measuring \\alpha_s, and of deriving helicity fractions. We take particular care over the small x extrapolation, since it is now known that Regge behaviour is unreliable at perturbative scales. For fixed \\alpha_s we find that if all the most recent data are included g_A=1.18\\pm0.09, confirming the Bjorken sum rule at the 8% level. We further show that the value of \\alpha_s is now reasonably well constrained by scaling violations in the structure function data, despite the fact that it cannot yet be reliably fixed by the value of the Bjorken sum: our final result is \\alpha_s(m_Z) = 0.120+0.010-0.008. We also confirm earlier indications of a sizeable positive gluon polarization in the nucleon.

  5. Stiff, light, strong and ductile: nano-structured High Modulus Steel.

    Science.gov (United States)

    Springer, H; Baron, C; Szczepaniak, A; Uhlenwinkel, V; Raabe, D

    2017-06-05

    Structural material development for lightweight applications aims at improving the key parameters strength, stiffness and ductility at low density, but these properties are typically mutually exclusive. Here we present how we overcome this trade-off with a new class of nano-structured steel - TiB 2 composites synthesised in-situ via bulk metallurgical spray-forming. Owing to the nano-sized dispersion of the TiB 2 particles of extreme stiffness and low density - obtained by the in-situ formation with rapid solidification kinetics - the new material has the mechanical performance of advanced high strength steels, and a 25% higher stiffness/density ratio than any of the currently used high strength steels, aluminium, magnesium and titanium alloys. This renders this High Modulus Steel the first density-reduced, high stiffness, high strength and yet ductile material which can be produced on an industrial scale. Also ideally suited for 3D printing technology, this material addresses all key requirements for high performance and cost effective lightweight design.

  6. STRUCTURAL ASPECTS OF STRONG INHIBITION AND ROLE OF SCAFFOLD FOR SERINE PROTEASE INHIBITORS

    Directory of Open Access Journals (Sweden)

    Jhimli Dasgupta

    2011-12-01

    Full Text Available Canonical serine protease inhibitors inhibit their cognate enzymes by binding tightly at the enzyme active site in a substrate-like manner, being cleaved extremely slowly compared to a true substrate. They interact with cognate enzymes through P3-P2 region of the inhibitory loop while the scaffold hardly makes any contact. Neighbouring scaffolding residues like arginine or asparagine shape-up the inhibitory loop and religate the cleaved scissile bond. The specificity of the inhibitor can be altered by mutating the hyper solvent accessible P1 residue without changing loop-scaffold interactions. To understand the loop-scaffold compatibility, we prepared three chimeric proteins ECIL-WCIS , ETIL-WCIS , and STIL-WCIS , where the inhibitory loops of ECI, ETI, and STI were placed on the scaffold of their homologue WCI. Results showed that although ECIL-WCIS and STIL-WCIS behave like inhibitors, ETIL-WCIS behaves like a substrate. Crystal structure of ETIL-WCIS and its comparison with ETI indicated that three novel scaffolding residues Trp88, Arg74, and Tyr113 in ETI act as barrier to confine the inhibitory loop to canonical conformation. Absence of this barrier in the scaffold of WCI makes the inhibitory loop flexible in ETIL-WCIS leading to a loss of canonical conformation, explaining its substrate-like behaviour. Furthermore, complex structures of the inhibitors with their cognate enzymes indicate that rigidification of the inhibitory loop at the enzyme active site is necessary for efficient inhibition.

  7. Structural evolution during fragile-to-strong transition in CuZr(Al) glass-forming liquids

    DEFF Research Database (Denmark)

    Zhou, C.; Hu, L.N.; Sun, Q.J.

    2015-01-01

    In the present work, we show experimental evidence for the dynamic fragile-to-strong (F-S) transition in a series of CuZr(Al) glass-forming liquids (GFLs). A detailed analysis of the dynamics of 98 glass-forming liquids indicates that the F-S transition occurs around Tf-s ≈ 1.36 Tg. Using...... the hyperquenching-annealing-x-ray scattering approach, we have observed a three-stage evolution pattern of medium-range ordering (MRO) structures during the F-S transition, indicating a dramatic change of the MRO clusters around Tf-s upon cooling. The F-S transition in CuZr(Al) GFLs is attributed to the competition...... among the MRO clusters composed of different locally ordering configurations. A phenomenological scenario has been proposed to explain the structural evolution from the fragile to the strong phase in the CuZr(Al) GFLs....

  8. Heavy quarks and strong binding: A field theory of hadron structure

    International Nuclear Information System (INIS)

    Bardeen, W.A.; Chanowitz, M.S.; Drell, S.D.; Weinstein, M.; Yan, T.

    1975-01-01

    We investigate in canonical field theory the possibility that quarks may exist in isolation as very heavy particles, M/sub quark/) very-much-greater-than 1 GeV, yet form strongly bound hadronic states, M/sub hadron/) approx. 1 GeV. In a model with spin-1/2 quarks coupled to scalar gluons we find that a mechanism exists for the formation of bound states which are much lighter than the free constituents. Following Nambu, we introduce a color interaction mediated by gauge vector mesons to guarantee that all states with nonvanishing triality have masses much larger than 1 GeV. The possibility of such a solution to a stronly coupled field theory is exhibited by a calculation employing the variational principle in tree approximation. This procedure reduces the field-theoretical problem to a set of coupled differential equations for classical fields which are just the free parameters of the variational state. A striking property of the solution is that the quark wave function is confined to a thin shell at the surface of the hadronic bound state. Though the quantum corrections to this procedure remain to be investigated systematically, we explore some of the phenomenological implications of the trial wave functions so obtained. In particular, we exhibit the low-lying meson and baryon multiplets of SU(6); their magnetic moments, charge radii, and radiative decays, and the axial charge of the baryons. States of nonvanishing momenta are constructed and the softness of the hadron shell to deformations in scattering processes is discussed qualitatively along with the implications for deep-inelastic electron scattering and dual resonance models

  9. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations.

    Directory of Open Access Journals (Sweden)

    Rachael Y Dudaniec

    Full Text Available With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus in two core regions (Washington State, United States versus the species' northern peripheral region (British Columbia, Canada where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape, but at the periphery, topography (slope and elevation had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.

  10. Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

    Science.gov (United States)

    Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

    2017-09-01

    The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among

  11. The ordered network structure of M {>=} 6 strong earthquakes and its prediction in the Jiangsu-South Yellow Sea region

    Energy Technology Data Exchange (ETDEWEB)

    Men, Ke-Pei [Nanjing Univ. of Information Science and Technology (China). College of Mathematics and Statistics; Cui, Lei [California Univ., Santa Barbara, CA (United States). Applied Probability and Statistics Dept.

    2013-05-15

    The the Jiangsu-South Yellow Sea region is one of the key seismic monitoring defence areas in the eastern part of China. Since 1846, M {>=} 6 strong earthquakes have showed an obvious commensurability and orderliness in this region. The main orderly values are 74 {proportional_to} 75 a, 57 {proportional_to} 58 a, 11 {proportional_to} 12 a, and 5 {proportional_to} 6 a, wherein 74 {proportional_to} 75 a and 57 {proportional_to} 58 a with an outstanding predictive role. According to the information prediction theory of Wen-Bo Weng, we conceived the M {>=} 6 strong earthquake ordered network structure in the South Yellow Sea and the whole region. Based on this, we analyzed and discussed the variation of seismicity in detail and also made a trend prediction of M {>=} 6 strong earthquakes in the future. The results showed that since 1998 it has entered into a new quiet episode which may continue until about 2042; and the first M {>=} 6 strong earthquake in the next active episode will probably occur in 2053 pre and post, with the location likely in the sea area of the South Yellow Sea; also, the second and the third ones or strong earthquake swarm in the future will probably occur in 2058 and 2070 pre and post. (orig.)

  12. Effective collision frequency method in the theory of the conductivity of Coulomb systems. II. Strong interion interaction and plasma structure

    International Nuclear Information System (INIS)

    Bobrov, V.B.; Triger, S.A.

    1994-01-01

    The effective collision frequency method developed earlier by the authors for Coulomb systems characterized by strong interion interaction is developed further. An explicit expression is obtained for the effective electron collision frequency on the basis of the exact diagram representation obtained in Part I and the use of the model of a one-component plasma as initial approximation. The description of plasma structure in the corresponding approximation is considered. 25 refs

  13. The crystallochemical factor of strong keeping of radiogenic 187Os in the structure of rhenium-bearing molybdenites

    International Nuclear Information System (INIS)

    Val'ter, A.A.; Pisanskij, A.I.; Podberezskaya, N.V.

    2007-01-01

    To understand the possible cause of the strong keeping of radiogenic Os in comparison with initial Re in the molybdenite structure, we compare the cation positions in MoS 2 , ReS 2 , and OsS 2 and the geometry of 'empty' octahedra of the molybdenite structure. The similarity of 'empty' octahedra of MoS 2 and the Os environment in OsS 2 is determined. So, one can assume that knock-on atoms of 187 Os can be fixed in 'empty' octahedra by recoiling or the later thermal action

  14. Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris.

    Science.gov (United States)

    Beghè, D; Piotti, A; Satovic, Z; de la Rosa, R; Belaj, A

    2017-03-01

    Wild olive ( Olea europaea subsp. europaea var. sylvestris ) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources. © The Author 2016. Published by Oxford University Press on behalf

  15. Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation

    Science.gov (United States)

    Ochoa, Luz Eneida; Pereira, Luiz Henrique G; Costa-Silva, Guilherme Jose; Roxo, Fábio F; Batista, Jacqueline S; Formiga, Kyara; Foresti, Fausto; Oliveira, Claudio

    2015-01-01

    Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for FST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2–2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2–2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin. PMID:26045952

  16. Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system.

    Science.gov (United States)

    Kuhn, A; Bauman, D; Darras, H; Aron, S

    2017-10-01

    Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.

  17. Dynamics and genetic structure of Argentine ant supercolonies in their native range

    DEFF Research Database (Denmark)

    Vogel, Valérie; Pedersen, Jes S; d'Ettorre, Patrizia

    2009-01-01

    analyses revealed the presence of 11 supercolonies (width 1 to 515 m) over a 3-km transect. As in the introduced range, there was always strong aggression between but never within supercolonies. The genetic data were in perfect agreement with the behavioral tests, all nests being assigned to identical...... supercolonies with the different methods. There was strong genetic differentiation between supercolonies but no genetic differentiation among nests within supercolonies. We never found more than a single mitochondrial haplotype per supercolony, further supporting the view that supercolonies are closed breeding...

  18. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839

    Directory of Open Access Journals (Sweden)

    Beerli Peter

    2008-09-01

    Full Text Available Abstract Background Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour and physical (e.g. present-day ocean currents, past changes in sea temperature and levels factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II, which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. Results We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Conclusion Lack of congruence between mt and nuclear evidences, which

  19. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839).

    Science.gov (United States)

    Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

    2008-09-17

    Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects

  20. Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

    Science.gov (United States)

    Lindy B. Mullen; H. Arthur Woods; Michael K. Schwartz; Adam J. Sepulveda; Winsor H. Lowe

    2010-01-01

    The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho...

  1. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    Science.gov (United States)

    Gretchen H. Roffler; Sandra L. Talbot; Gordon Luikart; George K. Sage; Kristy L. Pilgrim; Layne G. Adams; Michael K. Schwartz

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale...

  2. Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri.

    Science.gov (United States)

    Magalhaes, Ivan L F; Oliveira, Ubirajara; Santos, Fabrício R; Vidigal, Teofânia H D A; Brescovit, Antonio D; Santos, Adalberto J

    2014-11-01

    The Brazilian Caatinga is part of the seasonally dry tropical forests, a vegetation type disjunctly distributed throughout the Neotropics. It has been suggested that during Pleistocene glacial periods, these dry forests had a continuous distribution, so that these climatic shifts may have acted as important driving forces of the Caatinga biota diversification. To address how these events affected the distribution of a dry forest species, we chose Sicarius cariri, a spider endemic to the Caatinga, as a model. We studied the phylogeography of one mitochondrial and one nuclear gene and reconstructed the paleodistribution of the species using modelling algorithms. We found two allopatric and deeply divergent clades within S. cariri, suggesting that this species as currently recognized might consist of more than one independently evolving lineage. Sicarius cariri populations are highly structured, with low haplotype sharing among localities, high fixation index and isolation by distance. Models of paleodistribution, Bayesian reconstructions and coalescent simulations suggest that this species experienced a reduction in its population size during glacial periods, rather than the expansion expected by previous hypotheses on the paleodistribution of dry forest taxa. In addition to that, major splits of intraspecific lineages of S. cariri took place in the Pliocene. Taken together, these results indicate S. cariri has a complex diversification history dating back to the Tertiary, suggesting the history of dry forest taxa may be significantly older than previously thought. © 2014 John Wiley & Sons Ltd.

  3. Genetic structure of Antioquia Holstein from two SNPs and association with dairy traits

    Directory of Open Access Journals (Sweden)

    Stephania Madrid G

    2015-11-01

    Full Text Available Objective. Analyze the structure and genetic differentiation of a population of Antioquia Holstein cows from the polymorphisms A192G of INHA and A-320T of FSHR, and explore the association of the genotypic combinations with milk traits. Materials and methods. 1240 lactations of 356 animals from 9 herds in 6 municipalities of Antioquia were analyzed. Genotyping was performed by PCR-RFLP. Structure and genetic diversity parameters were determined using GenAlex software. The association of genotypes combinations with productive and reproductive traits was explored through a linear mixed model. Results. SNP A192G showed a frequency of 0.534 and 0.466 for A and G alleles respectively and SNP A-320T had a frequency of 0.660 far A allele and 0.339 for T allele, this way the population is in HWE. The FST, FIS and FIT values were 0.059, 0.285 and 0.328 respectively indicating a moderate genetic differentiation between subpopulations. The A-320T SNP showed significant effect on milk yield. Fat and protein percentage, calving interval and services per conception were not affected by these polymorphisms or their interaction. Conclusions. Phenotypic selection made on this population has not been strong enough to generate noticeable changes in allele frequencies of these polymorphisms or deviations from Hardy-Weinberg equilibrium. The interaction of these polymorphisms has no significant effect on the characteristics of zootechnical interest, so its use in programs of molecular marker assisted selection is not recommended.

  4. Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain

    International Nuclear Information System (INIS)

    Moreno, I.M.; Malpica, J.M.; Diaz-Pendon, J.A.; Moriones, E.; Fraile, A.; Garcia-Arenal, F.

    2004-01-01

    The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection

  5. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis.

    Science.gov (United States)

    Malenfant, René M; Davis, Corey S; Cullingham, Catherine I; Coltman, David W

    2016-01-01

    Recently, an extensive study of 2,748 polar bears (Ursus maritimus) from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1) highly unbalanced sample sizes and large amounts of systematically missing data; (2) incorrect calculation of FST and of significance levels; (3) misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

  6. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis.

    Directory of Open Access Journals (Sweden)

    René M Malenfant

    Full Text Available Recently, an extensive study of 2,748 polar bears (Ursus maritimus from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1 highly unbalanced sample sizes and large amounts of systematically missing data; (2 incorrect calculation of FST and of significance levels; (3 misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

  7. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, ...

  8. Population genetic structure of the sidespot barb, Barbus neefi, from ...

    African Journals Online (AJOL)

    Allozyme analysis was used to determine patterns of genetic variation within and between populations of Barbus neefi. The products of 29 loci were analysed, with 17 loci being monomorphic in all populations. The genetic variability estimates compared well with values reported in the literature. The percentage of ...

  9. Population genetic structure of Rufous-Vented Prinia ( Prinia burnesii )

    African Journals Online (AJOL)

    The objective of the study is to ascertain genetic variation within Rufous-vented Prinia, Prinia burnesii an endemic species, by DNA fingerprinting applying random amplified polymorphic DNA (RAPD) technique. Genetic material was obtained from three distant sites along western bank of River Indus. These sites include ...

  10. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

  11. Genetic and environmental influences on last-year major depression in adulthood: a highly heritable stable liability but strong environmental effects on 1-year prevalence.

    Science.gov (United States)

    Kendler, K S; Gardner, C O

    2017-07-01

    This study seeks to clarify the contribution of temporally stable and occasion-specific genetic and environmental influences on risk for major depression (MD). Our sample was 2153 members of female-female twin pairs from the Virginia Twin Registry. We examined four personal interview waves conducted over an 8-year period with MD in the last year defined by DSM-IV criteria. We fitted a structural equation model to the data using classic Mx. The model included genetic and environmental risk factors for a latent, stable vulnerability to MD and for episodes in each of the four waves. The best-fit model was simple and included genetic and unique environmental influences on the latent liability to MD and unique wave-specific environmental effects. The path from latent liability to MD in the last year was constant over time, moderate in magnitude (+0.65) and weaker than the impact of occasion-specific environmental effects (+0.76). Heritability of the latent stable liability to MD was much higher (78%) than that estimated for last-year MD (32%). Of the total unique environmental influences on MD, 13% reflected enduring consequences of earlier environmental insults, 17% diagnostic error and 70% wave-specific short-lived environmental stressors. Both genetic influences on MD and MD heritability are stable over middle adulthood. However, the largest influence on last-year MD is short-lived environmental effects. As predicted by genetic theory, the heritability of MD is increased substantially by measurement at multiple time points largely through the reduction of the effects of measurement error and short-term environmental risk factors.

  12. Population genetic structure and natural selection of apical membrane antigen-1 in Plasmodium vivax Korean isolates.

    Science.gov (United States)

    Kang, Jung-Mi; Lee, Jinyoung; Cho, Pyo-Yun; Moon, Sung-Ung; Ju, Hye-Lim; Ahn, Seong Kyu; Sohn, Woon-Mok; Lee, Hyeong-Woo; Kim, Tong-Soo; Na, Byoung-Kuk

    2015-11-16

    Plasmodium vivax apical membrane antigen-1 (PvAMA-1) is a leading candidate antigen for blood stage malaria vaccine. However, antigenic variation is a major obstacle in the development of an effective vaccine based on this antigen. In this study, the genetic structure and the effect of natural selection of PvAMA-1 among Korean P. vivax isolates were analysed. Blood samples were collected from 66 Korean patients with vivax malaria. The entire PvAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. The PvAMA-1 sequence of each isolate was sequenced and the polymorphic characteristics and effect of natural selection were analysed using the DNASTAR, MEGA4, and DnaSP programs. Thirty haplotypes of PvAMA-1, which were further classified into seven different clusters, were identified in the 66 Korean P. vivax isolates. Domain II was highly conserved among the sequences, but substantial nucleotide diversity was observed in domains I and III. The difference between the rates of non-synonymous and synonymous mutations suggested that the gene has evolved under natural selection. No strong evidence indicating balancing or positive selection on PvAMA-1 was identified. Recombination may also play a role in the resulting genetic diversity of PvAMA-1. This study is the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene using a single population sample from Korea. Korean PvAMA-1 had limited genetic diversity compared to PvAMA-1 in global isolates. The overall pattern of genetic polymorphism of Korean PvAMA-1 differed from other global isolates and novel amino acid changes were also identified in Korean PvAMA-1. Evidences for natural selection and recombination event were observed, which is likely to play an important role in generating genetic diversity across the PvAMA-1. These results provide useful information for the understanding the population structure of P. vivax circulating in Korea and have important

  13. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands.

    Science.gov (United States)

    Wallace, Lisa E; Wheeler, Gregory L; McGlaughlin, Mitchell E; Bresowar, Gerald; Helenurm, Kaius

    2017-05-01

    Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. DNA sequences were collected from nuclear (ADH) and plastid genomes ( rpL16 , ndhA , psbD-trnT ) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus , we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems. © 2017 Botanical Society of America.

  14. Refining and defining riverscape genetics: How rivers influence population genetic structure

    Science.gov (United States)

    Chanté D. Davis; Clinton W. Epps; Rebecca L. Flitcroft; Michael A. Banks

    2018-01-01

    Traditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. Genetic variation of organisms in complex landscapes, seascapes, or riverine systems, however, may be shaped by many forces. Recent research has linked habitat heterogeneity and landscape...

  15. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)

    Science.gov (United States)

    Peucker, Amanda J.; Valautham, Sureen K.; Styan, Craig A.; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. PMID:25833231

  16. Structured parenting of toddlers at high versus low genetic risk: two pathways to child problems.

    Science.gov (United States)

    Leve, Leslie D; Harold, Gordon T; Ge, Xiaojia; Neiderhiser, Jenae M; Shaw, Daniel; Scaramella, Laura V; Reiss, David

    2009-11-01

    Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for psychopathology. The sample included 290 linked sets of adoptive families and birth mothers and 95 linked birth fathers. Genetic risk was assessed via birth mother and birth father psychopathology (anxiety, depression, antisociality, and drug use). Structured parenting was assessed via microsocial coding of adoptive mothers' behavior during a cleanup task. Toddler behavior problems were assessed with the Child Behavior Checklist. Controlling for temperamental risk at 9 months, there was an interaction between birth mother psychopathology and adoptive mothers' parenting on toddler behavior problems at 18 months. The interaction indicated two pathways to child problems: structured parenting was beneficial for toddlers at high genetic risk but was related to behavior problems for toddlers at low genetic risk. This crossover interaction pattern was replicated with birth father psychopathology as the index of genetic risk. The effects of structured parenting on toddler behavior problems varied as a function of genetic risk. Children at genetic risk might benefit from parenting interventions during toddlerhood that enhance structured parenting.

  17. Genetic structure of Rajaka caste and affinities with other caste populations of Andhra Pradesh, India.

    Science.gov (United States)

    Parvatheesam, C; Babu, B V; Babu, M C

    1997-01-01

    The present study gives an account of the genetic structure in terms of distribution of a few genetic markers, viz., A1A2B0, Rh(D), G6PD deficiency and haemoglobin among the Rajaka caste population of Andhra Pradesh, India. The genetic relationships of the Rajaka caste with other Andhra caste populations were investigated in terms of genetic distance, i.e., Sq B (mn) of Balakrishnan and Sanghvi. Relatively lesser distance was established between the Rajaka and two Panchama castes. Also, the pattern of genetic distance corroborates the hierarchical order of the Hindu varna system.

  18. Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI

    Science.gov (United States)

    López-Legentil, S.; Pawlik, J. R.

    2009-03-01

    In recent years, reports of sponge bleaching, disease, and subsequent mortality have increased alarmingly. Population recovery may depend strongly on colonization capabilities of the affected species. The giant barrel sponge Xestospongia muta is a dominant reef constituent in the Caribbean. However, little is known about its population structure and gene flow. The 5'-end fragment of the mitochondrial gene cytochrome oxidase subunit I is often used to address these kinds of questions, but it presents very low intraspecific nucleotide variability in sponges. In this study, the usefulness of the I3-M11 partition of COI to determine the genetic structure of X. muta was tested for seven populations from Florida, the Bahamas and Belize. A total of 116 sequences of 544 bp were obtained for the I3-M11 partition corresponding to four haplotypes. In order to make a comparison with the 5'-end partition, 10 sequences per haplotype were analyzed for this fragment. The 40 resulting sequences were of 569 bp and corresponded to two haplotypes. The nucleotide diversity of the I3-M11 partition (π = 0.00386) was higher than that of the 5'-end partition (π = 0.00058), indicating better resolution at the intraspecific level. Sponges with the most divergent external morphologies (smooth vs. digitate surface) had different haplotypes, while those with the most common external morphology (rough surface) presented a mixture of haplotypes. Pairwise tests for genetic differentiation among geographic locations based on F ST values showed significant genetic divergence between most populations, but this genetic differentiation was not due to isolation by distance. While limited larval dispersal may have led to differentiation among some of the populations, the patterns of genetic structure appear to be most strongly related to patterns of ocean currents. Therefore, hydrological features may play a major role in sponge colonization and need to be considered in future plans for management and

  19. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

    Directory of Open Access Journals (Sweden)

    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  20. RECENT STRONG EARTHQUAKES IN CENTRAL ASIA: REGULAR TECTONOPHYSICAL FEATURES OF LOCATIONS IN THE STRUCTURE AND GEODYNAMICS OF THE LITHOSPHERE. PART 1. MAIN GEODYNAMIC FACTORS PREDETERMINING LOCATIONS OF STRONG EARTHQUAKES IN THE STRUCTURE OF THE LITHOSPHER

    Directory of Open Access Journals (Sweden)

    S. I. Sherman

    2015-01-01

    Full Text Available Studying locations of strong earthquakes (М≥8 in space and time in Central Asia has been among top prob-lems for many years and still remains challenging for international research teams. The authors propose a new ap-proach that requires changing the paradigm of earthquake focus – solid rock relations, while this paradigm is a basis for practically all known physical models of earthquake foci. This paper describes the first step towards developing a new concept of the seismic process, including generation of strong earthquakes, with reference to specific geodynamic features of the part of the study region wherein strong earthquakes were recorded in the past two centuries. Our analysis of the locations of М≥8 earthquakes shows that in the past two centuries such earthquakes took place in areas of the dynamic influence of large deep faults in the western regions of Central Asia. In the continental Asia, there is a clear submeridional structural boundary (95–105°E between the western and eastern regions, and this is a factor controlling localization of strong seismic events in the western regions. Obviously, the Indostan plate’s pressure from the south is an energy source for such events. The strong earthquakes are located in a relatively small part of the territory of Central Asia (i.e. the western regions, which is significantly different from its neighbouring areas at the north, east and west, as evidenced by its specific geodynamic parameters. (1 The crust is twice as thick in the western regions than in the eastern regions. (2 In the western regions, the block structures re-sulting from the crust destruction, which are mainly represented by lense-shaped forms elongated in the submeridio-nal direction, tend to dominate. (3 Active faults bordering large block structures are characterized by significant slip velocities that reach maximum values in the central part of the Tibetan plateau. Further northward, slip velocities decrease

  1. The Genetic Structure of Milkfish (Chanos chanos) Stocks from ...

    African Journals Online (AJOL)

    Yudha T Adiputra

    2012-02-14

    Feb 14, 2012 ... Genetic diversity of Indonesia milkfish (Chanos chanos) using amplified ... into fish populations in a wide range of applications. (Verspoor ... The quality of extracted DNA was ..... egg, larval and adult stages (Lin et al., 2009).

  2. Short communication Population structure and genetic trends for ...

    African Journals Online (AJOL)

    user

    2016-05-23

    May 23, 2016 ... been reported to have negative effects on some production and fitness traits in ..... Drakensberger Handbook 2011, First Edition. www.drakensbergers,co.za ... of National Farm Animal Genetic Resources Management Plans.

  3. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  4. Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

    Science.gov (United States)

    Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

    2015-07-01

    Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

  5. Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method.

    Science.gov (United States)

    Du, Lei; Huang, Heng; Yan, Jingwen; Kim, Sungeun; Risacher, Shannon L; Inlow, Mark; Moore, Jason H; Saykin, Andrew J; Shen, Li

    2016-05-15

    Structured sparse canonical correlation analysis (SCCA) models have been used to identify imaging genetic associations. These models either use group lasso or graph-guided fused lasso to conduct feature selection and feature grouping simultaneously. The group lasso based methods require prior knowledge to define the groups, which limits the capability when prior knowledge is incomplete or unavailable. The graph-guided methods overcome this drawback by using the sample correlation to define the constraint. However, they are sensitive to the sign of the sample correlation, which could introduce undesirable bias if the sign is wrongly estimated. We introduce a novel SCCA model with a new penalty, and develop an efficient optimization algorithm. Our method has a strong upper bound for the grouping effect for both positively and negatively correlated features. We show that our method performs better than or equally to three competing SCCA models on both synthetic and real data. In particular, our method identifies stronger canonical correlations and better canonical loading patterns, showing its promise for revealing interesting imaging genetic associations. The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/angscca/ shenli@iu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

    Directory of Open Access Journals (Sweden)

    Martina Temunović

    Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

  7. Strong interactions

    International Nuclear Information System (INIS)

    Froissart, Marcel

    1976-01-01

    Strong interactions are introduced by their more obvious aspect: nuclear forces. In hadron family, the nucleon octet, OMEGA - decuplet, and quark triply are successively considered. Pion wave having been put at the origin of nuclear forces, low energy phenomena are described, the force being explained as an exchange of structure corresponding to a Regge trajectory in a variable rotating state instead of the exchange of a well defined particle. At high energies the concepts of pomeron, parton and stratons are introduced, pionization and fragmentation are briefly differentiated [fr

  8. Deep subsurface structure modeling and site amplification factor estimation in Niigata plain for broadband strong motion prediction

    International Nuclear Information System (INIS)

    Sato, Hiroaki

    2009-01-01

    This report addresses a methodology of deep subsurface structure modeling in Niigata plain, Japan to estimate site amplification factor in the broadband frequency range for broadband strong motion prediction. In order to investigate deep S-wave velocity structures, we conduct microtremor array measurements at nine sites in Niigata plain, which are important to estimate both long- and short-period ground motion. The estimated depths of the top of the basement layer agree well with those of the Green tuff formation as well as the Bouguer anomaly distribution. Dispersion characteristics derived from the observed long-period ground motion records are well explained by the theoretical dispersion curves of Love wave group velocities calculated from the estimated subsurface structures. These results demonstrate the deep subsurface structures from microtremor array measurements make it possible to estimate long-period ground motions in Niigata plain. Moreover an applicability of microtremor array exploration for inclined basement structure like a folding structure is shown from the two dimensional finite difference numerical simulations. The short-period site amplification factors in Niigata plain are empirically estimated by the spectral inversion analysis from S-wave parts of strong motion data. The resultant characteristics of site amplification are relative large in the frequency range of about 1.5-5 Hz, and decay significantly with the frequency increasing over about 5 Hz. However, these features can't be explained by the calculations from the deep subsurface structures. The estimation of site amplification factors in the frequency range of about 1.5-5 Hz are improved by introducing a shallow detailed structure down to GL-20m depth at a site. We also propose to consider random fluctuation in a modeling of deep S-wave velocity structure for broadband site amplification factor estimation. The Site amplification in the frequency range higher than about 5 Hz are filtered

  9. Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan.

    Science.gov (United States)

    Thormann, Imke; Reeves, Patrick; Reilley, Ann; Engels, Johannes M M; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M

    2016-01-01

    Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

  10. Imprints of the Molecular Electronic Structure in the Photoelectron Spectra of Strong-Field Ionized Asymmetric Triatomic Model Molecules

    Science.gov (United States)

    Paul, Matthias; Yue, Lun; Gräfe, Stefanie

    2018-06-01

    We examine the circular dichroism in the angular distribution of photoelectrons of triatomic model systems ionized by strong-field ionization. Following our recent work on this effect [Paul, Yue, and Gräfe, J. Mod. Opt. 64, 1104 (2017), 10.1080/09500340.2017.1299883], we demonstrate how the symmetry and electronic structure of the system is imprinted into the photoelectron momentum distribution. We use classical trajectories to reveal the origin of the threefolded pattern in the photoelectron momentum distribution, and show how an asymmetric nuclear configuration of the triatomic system effects the photoelectron spectra.

  11. Strong genetic differentiation among east Atlantic populations of the sword razor shell ( Ensis siliqua) assessed with mtDNA and RAPD markers

    Science.gov (United States)

    Arias, Alberto; Fernández-Moreno, Mercedes; Fernández-Tajes, Juan; Gaspar, Miguel B.; Méndez, Josefina

    2011-03-01

    The sword razor shell Ensis siliqua (Linnaeus, 1758) is a bivalve with a high commercial value being appreciated in fresh and processed markets. However, the genetic studies carried out in populations of E. siliqua are scarce. In this work, the genetic variability and differentiation of the sword razor shell was assessed using PCR-RFLPs of a fragment of the 16S rRNA mitochondrial gene and random amplified polymorphic loci (RAPD) in nine localities from Ireland, Spain, and Portugal. In the 314 individuals examined for the mitochondrial fragment, 12 composite haplotypes were observed; meanwhile, a unique phenotype was observed for each of the 242 individuals analyzed with 61 RAPD loci. Two of the mitochondrial composite haplotypes accounted for the majority of individuals (89.81%) and showed a remarkably disjoint distribution between Irish and Iberian samples, with the exception of Aveiro which exhibited as the most frequent haplotype the same found in Ireland. The level of variability observed for each sample was generally correlated with both types of markers and the results obtained suggest the existence of a strong population differentiation between Irish and Iberian localities, except for the Portuguese sample from Aveiro which is surprisingly closer to Irish individuals, although it is probably highly differentiated.

  12. Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords.

    Directory of Open Access Journals (Sweden)

    Cristian B Canales-Aguirre

    Full Text Available Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords, but no spatial isolation by distance (IBD pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone, and the local geographical configuration (i.e. embayment area, islands, archipelagos. We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA of continental Chile, which is the Tic-Toc MPA.

  13. Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords.

    Science.gov (United States)

    Canales-Aguirre, Cristian B; Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E

    2016-01-01

    Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA.

  14. Genetic structure of Suillus luteus populations in heavy metal polluted and nonpolluted habitats.

    Science.gov (United States)

    Muller, Ludo A H; Vangronsveld, Jaco; Colpaert, Jan V

    2007-11-01

    The genetic structure of populations of the ectomycorrhizal basidiomycete Suillus luteus in heavy metal polluted and nonpolluted areas was studied. Sporocarps were collected at nine different locations and genotyped at four microsatellite loci. Six of the sampling sites were severely contaminated with heavy metals and were dominated by heavy metal-tolerant individuals. Considerable genetic diversity was found within the geographical subpopulations, but no reduction of the genetic diversity, current or historic, was observed in subpopulations inhabiting polluted soils. The genetic differentiation between the geographical subpopulations was low, and no evidence for clustering of subpopulations from polluted soils vs. subpopulations from nonpolluted soils was found. These results indicate that heavy metal pollution has a limited effect on the genetic structure of S. luteus populations, and this may be due to the high frequency of sexual reproduction and extensive gene flow in S. luteus, which allows rapid evolution of the tolerance trait while maintaining high levels of genetic diversity.

  15. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

    Science.gov (United States)

    Peter, Benjamin M.; Basnyat, Buddha; Neupane, Maniraj; Beall, Cynthia M.; Childs, Geoff; Craig, Sienna R.; Novembre, John; Di Rienzo, Anna

    2017-01-01

    Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context. PMID:28448508

  16. Structural, evolutionary and genetic analysis of the histidine biosynthetic "core" in the genus Burkholderia.

    Science.gov (United States)

    Papaleo, Maria Cristiana; Russo, Edda; Fondi, Marco; Emiliani, Giovanni; Frandi, Antonio; Brilli, Matteo; Pastorelli, Roberta; Fani, Renato

    2009-12-01

    In this work a detailed analysis of the structure, the expression and the organization of his genes belonging to the core of histidine biosynthesis (hisBHAF) in 40 newly determined and 13 available sequences of Burkholderia strains was carried out. Data obtained revealed a strong conservation of the structure and organization of these genes through the entire genus. The phylogenetic analysis showed the monophyletic origin of this gene cluster and indicated that it did not undergo horizontal gene transfer events. The analysis of the intergenic regions, based on the substitution rate, entropy plot and bendability suggested the existence of a putative transcription promoter upstream of hisB, that was supported by the genetic analysis that showed that this cluster was able to complement Escherichia colihisA, hisB, and hisF mutations. Moreover, a preliminary transcriptional analysis and the analysis of microarray data revealed that the expression of the his core was constitutive. These findings are in agreement with the fact that the entire Burkholderiahis operon is heterogeneous, in that it contains "alien" genes apparently not involved in histidine biosynthesis. Besides, they also support the idea that the proteobacterial his operon was piece-wisely assembled, i.e. through accretion of smaller units containing only some of the genes (eventually together with their own promoters) involved in this biosynthetic route. The correlation existing between the structure, organization and regulation of his "core" genes and the function(s) they perform in cellular metabolism is discussed.

  17. Spatial genetic structure in natural populations of Phragmites australis in a mosaic of saline habitats in the Yellow River Delta, China.

    Directory of Open Access Journals (Sweden)

    Lexuan Gao

    Full Text Available Determination of spatial genetic structure (SGS in natural populations is important for both theoretical aspects of evolutionary genetics and their application in species conservation and ecological restoration. In this study, we examined genetic diversity within and among the natural populations of a cosmopolitan grass Phragmites australis (common reed in the Yellow River Delta (YRD, China, where a mosaic of habitat patches varying in soil salinity was detected. We demonstrated that, despite their close geographic proximity, the common reed populations in the YRD significantly diverged at six microsatellite loci, exhibiting a strong association of genetic variation with habitat heterogeneity. Genetic distances among populations were best explained as a function of environmental difference, rather than geographical distance. Although the level of genetic divergence among populations was relatively low (F'(ST =0.073, weak but significant genetic differentiation, as well as the concordance between ecological and genetic landscapes, suggests spatial structuring of genotypes in relation to patchy habitats. These findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.

  18. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  19. Variation and Genetic Structure in Platanus mexicana (Platanaceae along Riparian Altitudinal Gradient

    Directory of Open Access Journals (Sweden)

    Dulce M. Galván-Hernández

    2015-01-01

    Full Text Available Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l. using ten inter-simple sequence repeats (ISSR markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42 and polymorphism reached the top value at the middle altitude (% p = 88.57. Analysis of molecular variance (AMOVA and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems.

  20. Historical habitat connectivity affects current genetic structure in a grassland species.

    Science.gov (United States)

    Münzbergová, Z; Cousins, S A O; Herben, T; Plačková, I; Mildén, M; Ehrlén, J

    2013-01-01

    Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co-dominant markers to estimate genetic diversity and deviation from Hardy-Weinberg equilibrium in 31 populations distributed within a 5 km(2) agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. Extreme genetic structure in a social bird species despite high dispersal capacity.

    Science.gov (United States)

    Morinha, Francisco; Dávila, José A; Bastos, Estela; Cabral, João A; Frías, Óscar; González, José L; Travassos, Paulo; Carvalho, Diogo; Milá, Borja; Blanco, Guillermo

    2017-05-01

    Social barriers have been shown to reduce gene flow and contribute to genetic structure among populations in species with high cognitive capacity and complex societies, such as cetaceans, apes and humans. In birds, high dispersal capacity is thought to prevent population divergence unless major geographical or habitat barriers induce isolation patterns by dispersal, colonization or adaptation limitation. We report that Iberian populations of the red-billed chough, a social, gregarious corvid with high dispersal capacity, show a striking degree of genetic structure composed of at least 15 distinct genetic units. Monitoring of marked individuals over 30 years revealed that long-distance movements over hundreds of kilometres are common, yet recruitment into breeding populations is infrequent and highly philopatric. Genetic differentiation is weakly related to geographical distance, and habitat types used are overall qualitatively similar among regions and regularly shared by individuals of different populations, so that genetic structure is unlikely to be due solely to isolation by distance or isolation by adaptation. Moreover, most population nuclei showed relatively high levels of genetic diversity, suggesting a limited role for genetic drift in significantly differentiating populations. We propose that social mechanisms may underlie this unprecedented level of genetic structure in birds through a pattern of isolation by social barriers not yet described, which may have driven this remarkable population divergence in the absence of geographical and environmental barriers. © 2017 John Wiley & Sons Ltd.

  2. Evaluation of the genetic structure of the urban dwelling species of ...

    African Journals Online (AJOL)

    We used the random amplified polymorphic DNA (RAPD) technique to decipher the genetic structure of the Bank Myna (Acridotheres ginginisnus) in Pakistan. The samples were collected from four cities namely: Dera Ghazi Khan, Jahanian, Khanewal and Gujranwala. The analysis showed a high genetic diversity at species ...

  3. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

    Directory of Open Access Journals (Sweden)

    James W Kijas

    Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

  4. Genetic structure of arbuscular mycorrhizal populations in fallow and cultivated soils

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Matzen, Hans

    2008-01-01

    protein-coding genes GmFOX2 and GmTOR2 were used as co-dominant genetic markers together with the large subunit (LSU) rDNA. The gene diversity and genetic structure of Glomus mosseae, Glomus geosporum and Glomus caledonium were compared within and between the fields. •  Spores of G. caledonium and G...

  5. Clonal growth and fine-scale genetic structure in tanoak (Notholithocarpus densiflorus: Fagaceae)

    Science.gov (United States)

    Richard S. Dodd; Wasima Mayer; Alejandro Nettel; Zara Afzal-Rafii

    2013-01-01

    The combination of sprouting and reproduction by seed can have important consequences on fine-scale spatial distribution of genetic structure (SGS). SGS is an important consideration for species’ restoration because it determines the minimum distance among seed trees to maximize genetic diversity while not prejudicing locally adapted genotypes. Local environmental...

  6. Genetic structure and diversity of East African taro [ Colocasia ...

    African Journals Online (AJOL)

    Taro [Colocasia esculenta (L) Schott] is mainly produced in Africa by small holder farmers and plays an important role in the livelihood of millions of poor people in less developed countries. The genetic diversity of East African taro has not been determined. This study utilizes six microsatellite primers to analyze five ...

  7. Genetic covariance structure of reading, intelligence and memory in children

    NARCIS (Netherlands)

    van Leeuwen, Marieke; van den Berg, Stéphanie Martine; Peper, Jiska S.; Hulshoff Pol, Hilleke E.; Boomsma, Dorret I.

    2009-01-01

    This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained

  8. Genetic Covariance Structure of Reading, Intelligence and Memory in Children

    NARCIS (Netherlands)

    van Leeuwen, M.; van den Berg, S.M.; Peper, J.S.; Hulshoff Pol, H.E.; Boomsma, D.I.

    2009-01-01

    This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained

  9. Genetic Covariance Structure of Reading, Intelligence and Memory in Children

    NARCIS (Netherlands)

    van Leeuwen, Marieke; van den Berg, Stephanie M.; Peper, Jiska S.; Pol, Hilleke E. Hulshoff; Boomsma, Dorret I.

    This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained

  10. Genetic polymorphism and population structure of Echinococcus ortleppi.

    Science.gov (United States)

    Addy, F; Wassermann, M; Banda, F; Mbaya, H; Aschenborn, J; Aschenborn, O; Koskei, P; Umhang, G; DE LA Rue, M; Elmahdi, I E; Mackenstedt, U; Kern, P; Romig, T

    2017-04-01

    The zoonotic cestode Echinococcus ortleppi (Lopez-Neyra and Soler Planas, 1943) is mainly transmitted between dogs and cattle. It occurs worldwide but is only found sporadically in most regions, with the notable exception of parts of southern Africa and South America. Its epidemiology is little understood and the extent of intraspecific variability is unknown. We have analysed in the present study the genetic diversity among 178 E. ortleppi isolates from sub-Saharan Africa, Europe and South America using the complete mitochondrial cox1 (1608 bp) and nad1 (894 bp) DNA sequences. Genetic polymorphism within the loci revealed 15 cox1 and six nad1 haplotypes, respectively, and 20 haplotypes of the concatenated genes. Presence of most haplotypes was correlated to geographical regions, and only one haplotype had a wider spread in both eastern and southern Africa. Intraspecific microvariance was low in comparison with Echinococcus granulosus sensu stricto, despite the wide geographic range of examined isolates. In addition, the various sub-populations showed only subtle deviation from neutrality and were mostly genetically differentiated. This is the first insight into the population genetics of the enigmatic cattle adapted Echinococcus ortleppi. It, therefore, provides baseline data for biogeographical comparison among E. ortleppi endemic regions and for tracing its translocation paths.

  11. Analysis of genetic structure of white croaker using amplified ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... the genetic differentiation of P. argentata between China and Japan coastal waters. ... revealed that white croaker might choose the retention larval strategy within .... extension of 7 min at 72°C. PCR products were run on 6.0%.

  12. Assessing genetic diversity and phylogeographic structure of duck ...

    African Journals Online (AJOL)

    In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were ...

  13. Genetic variability and structure of an isolated population of ...

    Indian Academy of Sciences (India)

    Rosa-Laura Heredia-Bobadilla

    2017-11-15

    Nov 15, 2017 ... Journal of Genetics, Vol. 96, No. 6, December 2017 ... or international status of protection. The mole ... populations by a matrix of agriculture and urbanization, can be considered ...... BioScience 38, 471–479. Lemos-Espinal ...

  14. Population genetic structure and gene flow of Forsythia suspensa ...

    African Journals Online (AJOL)

    Forsythia suspensa (Thunb.) Vahl, is a climbing plant belonging to Oleaceae, which is widely distributed in China, North and South Korea and Japan. In this study, the genetic diversity of F. suspensa was analyzed using two noncoding chloroplast DNA regions (trnL-F and psbA-trnH) and nuclear ribosomal internal ...

  15. Genetic structure and domestication history of the grape

    Science.gov (United States)

    Myles, Sean; Boyko, Adam R.; Owens, Christopher L.; Brown, Patrick J.; Grassi, Fabrizio; Aradhya, Mallikarjuna K.; Prins, Bernard; Reynolds, Andy; Chia, Jer-Ming; Ware, Doreen; Bustamante, Carlos D.; Buckler, Edward S.

    2011-01-01

    The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity. PMID:21245334

  16. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  17. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  18. Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

    Science.gov (United States)

    The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europ...

  19. General asymmetric neutral networks and structure design by genetic algorithms: A learning rule for temporal patterns

    Energy Technology Data Exchange (ETDEWEB)

    Bornholdt, S. [Heidelberg Univ., (Germany). Inst., fuer Theoretische Physik; Graudenz, D. [Lawrence Berkeley Lab., CA (United States)

    1993-07-01

    A learning algorithm based on genetic algorithms for asymmetric neural networks with an arbitrary structure is presented. It is suited for the learning of temporal patterns and leads to stable neural networks with feedback.

  20. General asymmetric neutral networks and structure design by genetic algorithms: A learning rule for temporal patterns

    International Nuclear Information System (INIS)

    Bornholdt, S.

    1993-07-01

    A learning algorithm based on genetic algorithms for asymmetric neural networks with an arbitrary structure is presented. It is suited for the learning of temporal patterns and leads to stable neural networks with feedback

  1. Genetic structure of Leptopilina boulardi populations from different climatic zones of Iran

    NARCIS (Netherlands)

    Seyahooei, M.A.; van Alphen, J.J.M.; Kraaijeveld, K.

    2011-01-01

    Background The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in Leptopilina boulardi, a parasitoid of Drosophila of African origin and widely distributed over temperate and (sub) tropical climates.

  2. Comparisons of the genetic structure of populations of Turnip mosaic virus in west east Eurasia

    Czech Academy of Sciences Publication Activity Database

    Tomimura, K.; Špak, Josef; Katis, N.; Jenner, C. E.; Walsh, J.A.; Gibbs, A.J.; Ohshima, K.

    2004-01-01

    Roč. 330, - (2004), 408-423 ISSN 0042-6822 Institutional research plan: CEZ:AV0Z5051902 Keywords : mosaic virus * genetic structure Subject RIV: EE - Microbiology, Virology Impact factor: 3.071, year: 2004

  3. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES

    Directory of Open Access Journals (Sweden)

    Le Marchand Loic

    2009-11-01

    Full Text Available Abstract Background Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP, formed from a sample from the Multiethnic Cohort (MEC study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians. Sensitivity of ancestry estimates to relative sample size was considered. Results We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. Conclusion These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that

  4. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

    Science.gov (United States)

    Shtir, Corina J; Marjoram, Paul; Azen, Stanley; Conti, David V; Le Marchand, Loic; Haiman, Christopher A; Varma, Rohit

    2009-11-10

    Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD) risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP), formed from a sample from the Multiethnic Cohort (MEC) study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians). Sensitivity of ancestry estimates to relative sample size was considered. We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that it will be important to assess this heterogeneity

  5. Individual Differences in the Speed of Facial Emotion Recognition Show Little Specificity but Are Strongly Related with General Mental Speed: Psychometric, Neural and Genetic Evidence

    Directory of Open Access Journals (Sweden)

    Xinyang Liu

    2017-08-01

    Full Text Available Facial identity and facial expression processing are crucial socio-emotional abilities but seem to show only limited psychometric uniqueness when the processing speed is considered in easy tasks. We applied a comprehensive measurement of processing speed and contrasted performance specificity in socio-emotional, social and non-social stimuli from an individual differences perspective. Performance in a multivariate task battery could be best modeled by a general speed factor and a first-order factor capturing some specific variance due to processing emotional facial expressions. We further tested equivalence of the relationships between speed factors and polymorphisms of dopamine and serotonin transporter genes. Results show that the speed factors are not only psychometrically equivalent but invariant in their relation with the Catechol-O-Methyl-Transferase (COMT Val158Met polymorphism. However, the 5-HTTLPR/rs25531 serotonin polymorphism was related with the first-order factor of emotion perception speed, suggesting a specific genetic correlate of processing emotions. We further investigated the relationship between several components of event-related brain potentials with psychometric abilities, and tested emotion specific individual differences at the neurophysiological level. Results revealed swifter emotion perception abilities to go along with larger amplitudes of the P100 and the Early Posterior Negativity (EPN, when emotion processing was modeled on its own. However, after partialling out the shared variance of emotion perception speed with general processing speed-related abilities, brain-behavior relationships did not remain specific for emotion. Together, the present results suggest that speed abilities are strongly interrelated but show some specificity for emotion processing speed at the psychometric level. At both genetic and neurophysiological levels, emotion specificity depended on whether general cognition is taken into account

  6. Individual Differences in the Speed of Facial Emotion Recognition Show Little Specificity but Are Strongly Related with General Mental Speed: Psychometric, Neural and Genetic Evidence

    Science.gov (United States)

    Liu, Xinyang; Hildebrandt, Andrea; Recio, Guillermo; Sommer, Werner; Cai, Xinxia; Wilhelm, Oliver

    2017-01-01

    Facial identity and facial expression processing are crucial socio-emotional abilities but seem to show only limited psychometric uniqueness when the processing speed is considered in easy tasks. We applied a comprehensive measurement of processing speed and contrasted performance specificity in socio-emotional, social and non-social stimuli from an individual differences perspective. Performance in a multivariate task battery could be best modeled by a general speed factor and a first-order factor capturing some specific variance due to processing emotional facial expressions. We further tested equivalence of the relationships between speed factors and polymorphisms of dopamine and serotonin transporter genes. Results show that the speed factors are not only psychometrically equivalent but invariant in their relation with the Catechol-O-Methyl-Transferase (COMT) Val158Met polymorphism. However, the 5-HTTLPR/rs25531 serotonin polymorphism was related with the first-order factor of emotion perception speed, suggesting a specific genetic correlate of processing emotions. We further investigated the relationship between several components of event-related brain potentials with psychometric abilities, and tested emotion specific individual differences at the neurophysiological level. Results revealed swifter emotion perception abilities to go along with larger amplitudes of the P100 and the Early Posterior Negativity (EPN), when emotion processing was modeled on its own. However, after partialling out the shared variance of emotion perception speed with general processing speed-related abilities, brain-behavior relationships did not remain specific for emotion. Together, the present results suggest that speed abilities are strongly interrelated but show some specificity for emotion processing speed at the psychometric level. At both genetic and neurophysiological levels, emotion specificity depended on whether general cognition is taken into account or not. These

  7. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows

    Science.gov (United States)

    Cousseau, L; Husemann, M; Foppen, R; Vangestel, C; Lens, L

    2016-01-01

    Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns. PMID:27273323

  8. Farmers without borders-genetic structuring in century old barley (Hordeum vulgare).

    Science.gov (United States)

    Forsberg, N E G; Russell, J; Macaulay, M; Leino, M W; Hagenblad, J

    2015-02-01

    The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. FST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.

  9. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839)

    OpenAIRE

    Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

    2008-01-01

    Abstract Background Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitoc...

  10. Spatial genetic structure across a hybrid zone between European rabbit subspecies

    Directory of Open Access Journals (Sweden)

    Fernando Alda

    2014-09-01

    Full Text Available The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus, which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological

  11. The Structure of Trade in Genetic Resources: Implications for the International ABS Regime Negotiation

    Directory of Open Access Journals (Sweden)

    Mikyung Yun

    2010-06-01

    Full Text Available The intensive exploitation of genetic resources at the international level has led to a negotiation of an international regime on Access and Benefit-Sharing (ABS of genetic resources. Due to lack of systematic data, little is known about the structure of trade in genetic resources to inform the negotiators. This study attempts to shed a greater insight into genetic resources trade in the pharmaceutical sector in Korea, mainly relying on interviews of industry practitioners and scientists in related fields. The study finds that Korea is mainly a genetic resource importer, but that pharmaceutical firms rarely carry out bioprospecting directly, relying on semi-processed biochemicals imports trough agents. Therefore, the impact of the to-be negotiated international ABS negotiation will be larger if derivatives are included in its scope. However, the general impact on the economy as a whole would be small, given the small share of genetic resources trade compared to total trade volumes.

  12. Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Sangwon Suh

    2014-11-01

    Full Text Available Four Korean native cattle (KNC breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO. The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120 and exotic breeds (Holstein and Charolais, n = 56. Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

  13. Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank.

    Science.gov (United States)

    Cortes, Adrian; Dendrou, Calliope A; Motyer, Allan; Jostins, Luke; Vukcevic, Damjan; Dilthey, Alexander; Donnelly, Peter; Leslie, Stephen; Fugger, Lars; McVean, Gil

    2017-09-01

    Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform understanding of the human phenome and accelerate progress toward precision medicine. However, a critical question when analyzing high-dimensional and heterogeneous data is how best to interrogate increasingly specific subphenotypes while retaining statistical power to detect genetic associations. Here we develop and employ a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies new associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying the approach to genetic risk scores (GRSs), we show the extent of genetic sharing among IMDs and expose differences in disease perception or diagnosis with potential clinical implications.

  14. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

    Science.gov (United States)

    De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

    2017-07-01

    There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (Φ ST  = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

  15. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    Science.gov (United States)

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  16. Population genetic structure in wild and aquaculture populations of Hemibarbus maculates inferred from microsatellites markers

    Directory of Open Access Journals (Sweden)

    Linlin Li

    2017-03-01

    Full Text Available The objective of this study was to investigate 4 aquaculture populations Shanghai (SH, Hangzhou (HZ, Kaihua (KH and Xianju (XJ and one wild population Yingshan (YS of spotted barbell (Hemibarbus maculates to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

  17. The Genetic Structure and History of Africans and African Americans

    Science.gov (United States)

    Tishkoff, Sarah A.; Reed, Floyd A.; Friedlaender, Françoise R.; Ehret, Christopher; Ranciaro, Alessia; Froment, Alain; Hirbo, Jibril B.; Awomoyi, Agnes A.; Bodo, Jean-Marie; Doumbo, Ogobara; Ibrahim, Muntaser; Juma, Abdalla T.; Kotze, Maritha J.; Lema, Godfrey; Moore, Jason H.; Mortensen, Holly; Nyambo, Thomas B.; Omar, Sabah A.; Powell, Kweli; Pretorius, Gideon S.; Smith, Michael W.; Thera, Mahamadou A.; Wambebe, Charles; Weber, James L.; Williams, Scott M.

    2010-01-01

    Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (~71%), European (~13%), and other African (~8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies. PMID:19407144

  18. Structure of strongly underexpanded gas jets submerged in liquids – Application to the wastage of tubes by aggressive jets

    Energy Technology Data Exchange (ETDEWEB)

    Roger, Francis, E-mail: roger@ensma.fr [Institut PPRIME, Département Fluides, Thermique, Combustion CNRS ENSMA Université de Poitiers UPR 3346, ENSMA BP 109, 86960 Futuroscope Cedex (France); Carreau, Jean-Louis; Gbahoué, Laurent; Hobbes, Philippe [Institut PPRIME, Département Fluides, Thermique, Combustion CNRS ENSMA Université de Poitiers UPR 3346, ENSMA BP 109, 86960 Futuroscope Cedex (France); Allou, Alexandre; Beauchamp, François [CEA, DEN, Cadarache, DTN/STPA/LTRS, 13108 Saint-Paul lez, Durance Cedex (France)

    2014-07-01

    Highlights: • Underexpanded gas jets submerged in liquids behave similarly to homogeneous gas jets. • The counter rotating vortex pairs of jet produce discrete imprints on the targets. • The shape of hollows made on the targets is explained by the jet structure. • The erosion–corrosion phenomenon well explains the wastage of exchange tubes. - Abstract: Strongly underexpanded gas jets submerged in a liquid at rest behave similarly to underexpanded homogeneous gas jets. The existence of the Taylor-Görtler vortices around the inner zone of the gas jets is demonstrated in free gas jets submerged in water by means of optical probe. In the near field, the same phenomenon produces discrete imprints, approximately distributed in a circle, when underexpanded nitrogen jet submerged in liquid sodium hydroxide and underexpanded water vapour jet submerged in liquid sodium impact onto AU{sub 4}G-T{sub 4} and Incoloy 800{sup ®} alloy targets respectively. For a jet-target couple, the volume of the hollow is satisfactorily related to the strain energy density of the material and the kinetic energy of the gas jet. However, the comparison between volumes of hollows produced by both jets also indicates strong corrosive action of the medium on targets. This allows better understanding of the mechanism of wastage of tubes employed in steam generators integrated in liquid metal fast breeder reactors.

  19. Demography and genetic structure of a recovering grizzly bear population

    Science.gov (United States)

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  20. Genetic structure and evolved malaria resistance in Hawaiian honeycreepers

    Science.gov (United States)

    Foster, J.T.; Woodworth, B.L.; Eggert, L.E.; Hart, P.J.; Palmer, D.; Duffy, D.C.; Fleischer, R.C.

    2007-01-01

    Infectious diseases now threaten wildlife populations worldwide but population recovery following local extinction has rarely been observed. In such a case, do resistant individuals recolonize from a central remnant population, or do they spread from small, perhaps overlooked, populations of resistant individuals? Introduced avian malaria (Plasmodium relictum) has devastated low-elevation populations of native birds in Hawaii, but at least one species (Hawaii amakihi, Hemignathus virens) that was greatly reduced at elevations below about 1000 m tolerates malaria and has initiated a remarkable and rapid recovery. We assessed mitochondrial and nuclear DNA markers from amakihi and two other Hawaiian honeycreepers, apapane (Himatione sanguinea) and iiwi (Vestiaria coccinea), at nine primary study sites from 2001 to 2003 to determine the source of re-establishing birds. In addition, we obtained sequences from tissue from amakihi museum study skins (1898 and 1948-49) to assess temporal changes in allele distributions. We found that amakihi in lowland areas are, and have historically been, differentiated from birds at high elevations and had unique alleles retained through time; that is, their genetic signature was not a subset of the genetic variation at higher elevations. We suggest that high disease pressure rapidly selected for resistance to malaria at low elevation, leaving small pockets of resistant birds, and this resistance spread outward from the scattered remnant populations. Low-elevation amakihi are currently isolated from higher elevations (> 1000 m) where disease emergence and transmission rates appear to vary seasonally and annually. In contrast to results from amakihi, no genetic differentiation between elevations was found in apapane and iiwi, indicating that slight variation in genetic or life-history attributes can determine disease resistance and population recovery. Determining the conditions that allow for the development of resistance to disease is

  1. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis as Revealed by Mitochondrial and Microsatellite DNA

    Directory of Open Access Journals (Sweden)

    Minmin Chen

    2014-06-01

    Full Text Available Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS, and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY and Tongling (TL and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP.

  2. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis) as Revealed by Mitochondrial and Microsatellite DNA

    Science.gov (United States)

    Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

    2014-01-01

    Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

  3. Spontaneous chromosome aberrations in cancer cells. Evidence of existence of hidden genetic lesions in genetic structures

    International Nuclear Information System (INIS)

    Poryadkova-Luchnik, N.A.; Kuz'mina, E.G.

    1996-01-01

    Chromosome aberrations spontaneously observed in cancer cells were quantitively studied under the effect of non-mutagenic (suboptimal temperature, low content of propilgallate and caffeine) and mutagenic (ionizing radiation) factors. Human larynx cancer cells during several years or gamma-irradiation were used to carry out experiments. The experiments linked with cloning of the initial population and investigation into chromosome aberrations in 22 clones demonstrated persuasively the occurrence of latent genetic lesions in cancer cells

  4. Genuine multipartite entanglement of symmetric Gaussian states: Strong monogamy, unitary localization, scaling behavior, and molecular sharing structure

    Science.gov (United States)

    Adesso, Gerardo; Illuminati, Fabrizio

    2008-10-01

    We investigate the structural aspects of genuine multipartite entanglement in Gaussian states of continuous variable systems. Generalizing the results of Adesso and Illuminati [Phys. Rev. Lett. 99, 150501 (2007)], we analyze whether the entanglement shared by blocks of modes distributes according to a strong monogamy law. This property, once established, allows us to quantify the genuine N -partite entanglement not encoded into 2,…,K,…,(N-1) -partite quantum correlations. Strong monogamy is numerically verified, and the explicit expression of the measure of residual genuine multipartite entanglement is analytically derived, by a recursive formula, for a subclass of Gaussian states. These are fully symmetric (permutation-invariant) states that are multipartitioned into blocks, each consisting of an arbitrarily assigned number of modes. We compute the genuine multipartite entanglement shared by the blocks of modes and investigate its scaling properties with the number and size of the blocks, the total number of modes, the global mixedness of the state, and the squeezed resources needed for state engineering. To achieve the exact computation of the block entanglement, we introduce and prove a general result of symplectic analysis: Correlations among K blocks in N -mode multisymmetric and multipartite Gaussian states, which are locally invariant under permutation of modes within each block, can be transformed by a local (with respect to the partition) unitary operation into correlations shared by K single modes, one per block, in effective nonsymmetric states where N-K modes are completely uncorrelated. Due to this theorem, the above results, such as the derivation of the explicit expression for the residual multipartite entanglement, its nonnegativity, and its scaling properties, extend to the subclass of non-symmetric Gaussian states that are obtained by the unitary localization of the multipartite entanglement of symmetric states. These findings provide strong

  5. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

  6. Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicate potential for spread of herbicide resistance via gene flow.

    Science.gov (United States)

    Karn, Elizabeth; Jasieniuk, Marie

    2017-07-01

    Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggest the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne .

  7. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple...... sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic...... diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two...

  8. Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

    Science.gov (United States)

    Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

    2013-01-01

    Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

  9. Formation of non-equilibrium structures in R6M5 steel under strong pulse beams action

    International Nuclear Information System (INIS)

    Rusin, Yu.G.; Plotnikov, S.V.

    2001-01-01

    Formation of non-equilibrium structures in R6M5 steel surface layer in the supply state under irradiation by strong pulse beams (SPB) is examined. Cylindric samples with diameter 10 mm and height 15 mm of R6M5 fast-cutting steel with following content (weight %): 0.85% C, 0.4% Mn, 0.5% Si, 4.0 Cr; 2.1% V; 5.3% Mo, 6.0% W; 0.4% Ni, Fe (the rest) were examined. Irradiation by SPB was conducted on the 'TEMP' modified accelerator operating in a technological regime with carbon beams parameters: energy from 0.3 up o 0.4 MeV, beam density in an impulse from 20 to 250 A/cm 2 , pulse duration from 60 tp 100 ns. The beam consists of 70 % carbon ions and 30 % hydrogen ions. Phase identification and its structural phase analysis have been studied on the DRON-3 X-ray diffractometer of common assignment. Topography of metallographic specimen surface has been examined on the REM-200 scanning electron microscope. Doping elements redistribution and phases quantitative characteristics after SPB action were studied with help of the X-ray spectral microanalysis (XRSA) on the MS-46 Camebax microanalyzer. Character of doping elements redistribution in the alloy (XRSA data) show its appreciably redistribution, moreover in the melted zone the increased content of molybdenum, tungsten, vanadium is observing, and in the zone of thermal action its increase relatively to matrix values

  10. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    Science.gov (United States)

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  11. Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species.

    Science.gov (United States)

    van Schaik, J; Dekeukeleire, D; Kerth, G

    2015-05-01

    Host-parasite interactions are ubiquitous in nature. However, how parasite population genetic structure is shaped by the interaction between host and parasite life history remains understudied. Studies comparing multiple parasites infecting a single host can be used to investigate how different parasite life history traits interplay with host behaviour and life history. In this study, we used 10 newly developed microsatellite loci to investigate the genetic structure of a parasitic bat fly (Basilia nana). Its host, the Bechstein's bat (Myotis bechsteinii), has a social system and roosting behaviour that restrict opportunities for parasite transmission. We compared fly genetic structure to that of the host and another parasite, the wing-mite, Spinturnix bechsteini. We found little spatial or temporal genetic structure in B. nana, suggesting a large, stable population with frequent genetic exchange between fly populations from different bat colonies. This contrasts sharply with the genetic structure of the wing-mite, which is highly substructured between the same bat colonies as well as temporally unstable. Our results suggest that although host and parasite life history interact to yield similar transmission patterns in both parasite species, the level of gene flow and eventual spatiotemporal genetic stability is differentially affected. This can be explained by the differences in generation time and winter survival between the flies and wing-mites. Our study thus exemplifies that the population genetic structure of parasites on a single host can vary strongly as a result of how their individual life history characteristics interact with host behaviour and life history traits. © 2015 John Wiley & Sons Ltd.

  12. Linking the planktonic and benthic habitat: genetic structure of the marine diatom Skeletonema marinoi.

    Science.gov (United States)

    Godhe, Anna; Härnström, Karolina

    2010-10-01

    Dormant life stages are important strategies for many aquatic organisms. The formation of resting stages will provide a refuge from unfavourable conditions in the water column, and their successive accumulation in the benthos will constitute a genetic reservoir for future planktonic populations. We have determined the genetic structure of a common bloom-forming diatom, Skeletonema marinoi, in the sediment and the plankton during spring, summer and autumn two subsequent years (2007-2009) in Gullmar Fjord on the Swedish west coast. Eight polymorphic microsatellite loci were used to assess the level of genetic differentiation and the respective gene diversity of the two different habitats. We also determined the degree of genetic differentiation between the seed banks inside the fjord and the open sea. The results indicate that Gullmar Fjord has one dominant endogenous population of S. marinoi, which is genetically differentiated from the open sea population. The fjord population is encountered in the plankton and in the sediment. Shifts from the dominant population can happen, and in our study, two genetically differentiated plankton populations, displaying reduced genetic diversity, occurred in September 2007 and 2008. Based on our results, we suggest that sill fjords maintain local long-lived and well-adapted protist populations, which continuously shift between the planktonic and benthic habitats. Intermittently, short-lived and mainly asexually reproducing populations can replace the dominant population in the water column, without influencing the genetic structure of the benthic seed bank. © 2010 Blackwell Publishing Ltd.

  13. Population genetic structure of Taenia solium from Madagascar and Mexico: implications for clinical profile diversity and immunological technology.

    Science.gov (United States)

    Vega, Rodrigo; Piñero, Daniel; Ramanankandrasana, Bienvenue; Dumas, Michel; Bouteille, Bernard; Fleury, Agnes; Sciutto, Edda; Larralde, Carlos; Fragoso, Gladis

    2003-11-01

    Taenia solium is a cestode parasitic of humans and pigs that strongly impacts on public health in developing countries. Its larvae (cysticercus) lodge in the brain, causing neurocysticercosis, and in other tissues, like skeletal muscle and subcutaneous space, causing extraneuronal cysticercosis. Prevalences of these two clinical manifestations vary greatly among continents. Also, neurocysticercosis may be clinically heterogeneous, ranging from asymptomatic forms to severely incapacitating and even fatal presentation. Further, vaccine design and diagnosis technology have met with difficulties in sensitivity, specificity and reproducibility. Parasite diversity underlying clinical heterogeneity and technological difficulties is little explored. Here, T. solium genetic population structure and diversity was studied by way of random amplified polymorphic DNA in individual cysticerci collected from pigs in Madagascar and two regions in Mexico. The amplification profiles of T. solium were also compared with those of the murine cysticercus Taenia crassiceps (ORF strain). We show significant genetic differentiation between Madagascar and Mexico and between regions in Mexico, but less so between cysticerci from different localities in Mexico and none between cysticerci from different tissues from the same pig. We also found restricted genetic variability within populations and gene flow was estimated to be low between populations. Thus, genetic differentiation of T. solium suggests that different evolutionary paths have been taken and provides support for its involvement in the differential tissue distribution of cysticerci and varying degrees of severity of the disease. It may also explain difficulties in the development of vaccines and tools for immunodiagnosis.

  14. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

    Science.gov (United States)

    Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

    2012-01-01

    Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

  15. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  16. Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds.

    Science.gov (United States)

    Selepe, Mokhethi Matthews; Ceccobelli, Simone; Lasagna, Emiliano; Kunene, Nokuthula Winfred

    2018-01-01

    The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  17. Genetic structure of South African Nguni (Zulu sheep populations reveals admixture with exotic breeds.

    Directory of Open Access Journals (Sweden)

    Mokhethi Matthews Selepe

    Full Text Available The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69 and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  18. Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos).

    Science.gov (United States)

    Momigliano, P; Harcourt, R; Robbins, W D; Jaiteh, V; Mahardika, G N; Sembiring, A; Stow, A

    2017-09-01

    With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

  19. Coevolutionary and genetic algorithm based building spatial and structural design

    NARCIS (Netherlands)

    Hofmeyer, H.; Davila Delgado, J.M.

    2015-01-01

    In this article, two methods to develop and optimize accompanying building spatial and structural designs are compared. The first, a coevolutionary method, applies deterministic procedures, inspired by realistic design processes, to cyclically add a suitable structural design to the input of a

  20. Mapping the regional influence of genetics on brain structure variability--a tensor-based morphometry study.

    Science.gov (United States)

    Brun, Caroline C; Leporé, Natasha; Pennec, Xavier; Lee, Agatha D; Barysheva, Marina; Madsen, Sarah K; Avedissian, Christina; Chou, Yi-Yu; de Zubicaray, Greig I; McMahon, Katie L; Wright, Margaret J; Toga, Arthur W; Thompson, Paul M

    2009-10-15

    Genetic and environmental factors influence brain structure and function profoundly. The search for heritable anatomical features and their influencing genes would be accelerated with detailed 3D maps showing the degree to which brain morphometry is genetically determined. As part of an MRI study that will scan 1150 twins, we applied Tensor-Based Morphometry to compute morphometric differences in 23 pairs of identical twins and 23 pairs of same-sex fraternal twins (mean age: 23.8+/-1.8 SD years). All 92 twins' 3D brain MRI scans were nonlinearly registered to a common space using a Riemannian fluid-based warping approach to compute volumetric differences across subjects. A multi-template method was used to improve volume quantification. Vector fields driving each subject's anatomy onto the common template were analyzed to create maps of local volumetric excesses and deficits relative to the standard template. Using a new structural equation modeling method, we computed the voxelwise proportion of variance in volumes attributable to additive (A) or dominant (D) genetic factors versus shared environmental (C) or unique environmental factors (E). The method was also applied to various anatomical regions of interest (ROIs). As hypothesized, the overall volumes of the brain, basal ganglia, thalamus, and each lobe were under strong genetic control; local white matter volumes were mostly controlled by common environment. After adjusting for individual differences in overall brain scale, genetic influences were still relatively high in the corpus callosum and in early-maturing brain regions such as the occipital lobes, while environmental influences were greater in frontal brain regions that have a more protracted maturational time-course.

  1. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management.

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  2. Conceptual optimization using genetic algorithms for tube in tube structures

    International Nuclear Information System (INIS)

    Pârv, Bianca Roxana; Hulea, Radu; Mojolic, Cristian

    2015-01-01

    The purpose of this article is to optimize the tube in tube structural systems for tall buildings under the horizontal wind loads. It is well-known that the horizontal wind loads is the main criteria when choosing the structural system, the types and the dimensions of structural elements in the majority of tall buildings. Thus, the structural response of tall buildings under the horizontal wind loads will be analyzed for 40 story buildings and a total height of 120 meters; the horizontal dimensions will be 30m × 30m for the first two optimization problems and 15m × 15m for the third. The optimization problems will have the following as objective function the cross section area, as restrictions the displacement of the building< the admissible displacement (H/500), and as variables the cross section dimensions of the structural elements

  3. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

    Directory of Open Access Journals (Sweden)

    Nobushima Fuyuo

    2006-10-01

    Full Text Available Abstract Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a

  4. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

    Science.gov (United States)

    Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

    2006-10-11

    Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

  5. Modified genetic algorithms to model cluster structures in medium-size silicon clusters

    International Nuclear Information System (INIS)

    Bazterra, Victor E.; Ona, Ofelia; Caputo, Maria C.; Ferraro, Marta B.; Fuentealba, Patricio; Facelli, Julio C.

    2004-01-01

    This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of medium size silicon clusters. In this work the GA uses a semiempirical energy function to find the best cluster structures, which are further optimized using density-functional theory. For small clusters our results agree well with previously reported structures, but for larger ones different structures appear. This is the case of Si 36 where we report a different structure, with significant lower energy than those previously found using limited search approaches on common structural motifs. This demonstrates the need for global optimization schemes when searching for stable structures of medium-size silicon clusters

  6. Levitated superconductor ring trap (mini-RT) project - A new self-organized structure with strong plasma flow

    International Nuclear Information System (INIS)

    Ogawa, Y.; Himura, H.; Hishinuma, Y.

    2003-01-01

    Mahajan-Yoshida has theoretically developed a new relaxation state under the condition of a strong plasma flow, and proposed a possibility for confining high beta plasmas. In this self-organized state, two fluids (electron and ion) would relax to the condition given by the relation β + (V/V A ) 2 = const.. An internal coil device is suitable for studying a self-organized structure with strong plasma flow, because a strong toroidal flow is easily induced by introducing an appropriate radial electric field. We are constructing a Mini-RT device, which is equipping a floating coil with a high temperature superconductor (HTS) coil (R=0.15m, Ic=50kAturns). The magnetic field strength near the floating coil is around 0.1 T, and the plasma production with 2.45 GHz Electron Cyclotron Heating is planned. We are preparing several techniques to build up the radial electric field in the plasma such as the direct insertion of the electrode and so on. The utilization of direct orbit loss of high energy electrons produced by ECH might be an interesting method. The orbit calculation results show that the electrons with the energy of more than 10 keV would escape at the outer region of the plasma column, yielding the build-up of the radial electric field. The engineering aspect of the HTS coil is in progress. We have fabricated a small HTS coil (R=0.04 m and Ic= 2.6 kAturns), and succeeded in levitating it during four minutes with an accuracy of a few tens of micrometers. Since the HTS coil is excited by the external power supply, the persistent current switch for the HTS coil has been developed. The HTS coil system with the PCS coil has been fabricated and the excitation test has been carried out. We have succeeded in achieving a persistent current, and it is found that the decay constant of the coil current is evaluated to be around 40 hours and 6.5 hours at 20 K and 40 K, respectively. (author)

  7. Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

    Directory of Open Access Journals (Sweden)

    Panyu Hua

    Full Text Available Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

  8. Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

    Science.gov (United States)

    Hua, Panyu; Zhang, Libiao; Guo, Tingting; Flanders, Jon; Zhang, Shuyi

    2013-01-01

    Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

  9. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea.

    Science.gov (United States)

    Kim, Hye Ri; Park, Yung Chul

    2015-11-10

    The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (π=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. Copyright © 2015. Published by Elsevier B.V.

  10. Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

    Science.gov (United States)

    Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

    2017-01-01

    Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

  11. The role of river drainages in shaping the genetic structure of capybara populations.

    Science.gov (United States)

    Byrne, María Soledad; Quintana, Rubén Darío; Bolkovic, María Luisa; Cassini, Marcelo H; Túnez, Juan Ignacio

    2015-12-01

    The capybara, Hydrochoerus hydrochaeris, is an herbivorous rodent widely distributed throughout most of South American wetlands that lives closely associated with aquatic environments. In this work, we studied the genetic structure of the capybara throughout part of its geographic range in Argentina using a DNA fragment of the mitochondrial control region. Haplotypes obtained were compared with those available for populations from Paraguay and Venezuela. We found 22 haplotypes in 303 individuals. Hierarchical AMOVAs were performed to evaluate the role of river drainages in shaping the genetic structure of capybara populations at the regional and basin scales. In addition, two landscape genetic models, isolation by distance and isolation by resistance, were used to test whether genetic distance was associated with Euclidean distance (i.e. isolation by distance) or river corridor distance (i.e. isolation by resistance) at the basin scale. At the regional scale, the results of the AMOVA grouping populations by mayor river basins showed significant differences between them. At the basin scale, we also found significant differences between sub-basins in Paraguay, together with a significant correlation between genetic and river corridor distance. For Argentina and Venezuela, results were not significant. These results suggest that in Paraguay, the current genetic structure of capybaras is associated with the lack of dispersion corridors through permanent rivers. In contrast, limited structuring in Argentina and Venezuela is likely the result of periodic flooding facilitating dispersion.

  12. Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

    Science.gov (United States)

    Vickruck, J L; Richards, M H

    2017-05-01

    While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

  13. The Atlantic-Mediterranean watershed, river basins and glacial history shape the genetic structure of Iberian poplars.

    Science.gov (United States)

    Macaya-Sanz, D; Heuertz, M; López-de-Heredia, U; De-Lucas, A I; Hidalgo, E; Maestro, C; Prada, A; Alía, R; González-Martínez, S C

    2012-07-01

    Recent phylogeographic studies have elucidated the effects of Pleistocene glaciations and of Pre-Pleistocene events on populations from glacial refuge areas. This study investigates those effects in riparian trees (Populus spp.), whose particular features may convey enhanced resistance to climate fluctuations. We analysed the phylogeographic structure of 44 white (Populus alba), 13 black (Populus nigra) and two grey (Populus x canescens) poplar populations in the Iberian Peninsula using plastid DNA microsatellites and sequences. We also assessed fine-scale spatial genetic structure and the extent of clonality in four white and one grey poplar populations using nuclear microsatellites and we determined quantitative genetic differentiation (Q(ST) ) for growth traits in white poplar. Black poplar displayed higher regional diversity and lower differentiation than white poplar, reflecting its higher cold-tolerance. The dependence of white poplar on phreatic water was evidenced by strong differentiation between the Atlantic and Mediterranean drainage basins and among river basins, and by weaker isolation by distance within than among river basins. Our results suggest confinement to the lower river courses during glacial periods and moderate interglacial gene exchange along coastlines. In northern Iberian river basins, white poplar had lower diversity, fewer private haplotypes and larger clonal assemblies than in southern basins, indicating a stronger effect of glaciations in the north. Despite strong genetic structure and frequent asexual propagation in white poplar, some growth traits displayed adaptive divergence between drainage and river basins (Q(ST) >F(ST)), highlighting the remarkable capacity of riparian tree populations to adapt to regional environmental conditions. © 2012 Blackwell Publishing Ltd.

  14. A large-scale genetic analysis reveals a strong contribution of the HLA class II region to giant cell arteritis susceptibility.

    Science.gov (United States)

    Carmona, F David; Mackie, Sarah L; Martín, Jose-Ezequiel; Taylor, John C; Vaglio, Augusto; Eyre, Stephen; Bossini-Castillo, Lara; Castañeda, Santos; Cid, Maria C; Hernández-Rodríguez, José; Prieto-González, Sergio; Solans, Roser; Ramentol-Sintas, Marc; González-Escribano, M Francisca; Ortiz-Fernández, Lourdes; Morado, Inmaculada C; Narváez, Javier; Miranda-Filloy, José A; Beretta, Lorenzo; Lunardi, Claudio; Cimmino, Marco A; Gianfreda, Davide; Santilli, Daniele; Ramirez, Giuseppe A; Soriano, Alessandra; Muratore, Francesco; Pazzola, Giulia; Addimanda, Olga; Wijmenga, Cisca; Witte, Torsten; Schirmer, Jan H; Moosig, Frank; Schönau, Verena; Franke, Andre; Palm, Øyvind; Molberg, Øyvind; Diamantopoulos, Andreas P; Carette, Simon; Cuthbertson, David; Forbess, Lindsy J; Hoffman, Gary S; Khalidi, Nader A; Koening, Curry L; Langford, Carol A; McAlear, Carol A; Moreland, Larry; Monach, Paul A; Pagnoux, Christian; Seo, Philip; Spiera, Robert; Sreih, Antoine G; Warrington, Kenneth J; Ytterberg, Steven R; Gregersen, Peter K; Pease, Colin T; Gough, Andrew; Green, Michael; Hordon, Lesley; Jarrett, Stephen; Watts, Richard; Levy, Sarah; Patel, Yusuf; Kamath, Sanjeet; Dasgupta, Bhaskar; Worthington, Jane; Koeleman, Bobby P C; de Bakker, Paul I W; Barrett, Jennifer H; Salvarani, Carlo; Merkel, Peter A; González-Gay, Miguel A; Morgan, Ann W; Martín, Javier

    2015-04-02

    We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip array. We also imputed HLA data with a previously validated imputation method to perform a more comprehensive analysis of this genomic region. The strongest association signals were observed in the HLA region, with rs477515 representing the highest peak (p = 4.05 × 10(-40), OR = 1.73). A multivariate model including class II amino acids of HLA-DRβ1 and HLA-DQα1 and one class I amino acid of HLA-B explained most of the HLA association with GCA, consistent with previously reported associations of classical HLA alleles like HLA-DRB1(∗)04. An omnibus test on polymorphic amino acid positions highlighted DRβ1 13 (p = 4.08 × 10(-43)) and HLA-DQα1 47 (p = 4.02 × 10(-46)), 56, and 76 (both p = 1.84 × 10(-45)) as relevant positions for disease susceptibility. Outside the HLA region, the most significant loci included PTPN22 (rs2476601, p = 1.73 × 10(-6), OR = 1.38), LRRC32 (rs10160518, p = 4.39 × 10(-6), OR = 1.20), and REL (rs115674477, p = 1.10 × 10(-5), OR = 1.63). Our study provides evidence of a strong contribution of HLA class I and II molecules to susceptibility to GCA. In the non-HLA region, we confirmed a key role for the functional PTPN22 rs2476601 variant and proposed other putative risk loci for GCA involved in Th1, Th17, and Treg cell function. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  15. Applying genetic algorithms for calibrating a hexagonal cellular automata model for the simulation of debris flows characterised by strong inertial effects

    Science.gov (United States)

    Iovine, G.; D'Ambrosio, D.; Di Gregorio, S.

    2005-03-01

    In modelling complex a-centric phenomena which evolve through local interactions within a discrete time-space, cellular automata (CA) represent a valid alternative to standard solution methods based on differential equations. Flow-type phenomena (such as lava flows, pyroclastic flows, earth flows, and debris flows) can be viewed as a-centric dynamical systems, and they can therefore be properly investigated in CA terms. SCIDDICA S 4a is the last release of a two-dimensional hexagonal CA model for simulating debris flows characterised by strong inertial effects. S 4a has been obtained by progressively enriching an initial simplified model, originally derived for simulating very simple cases of slow-moving flow-type landslides. Using an empirical strategy, in S 4a, the inertial character of the flowing mass is translated into CA terms by means of local rules. In particular, in the transition function of the model, the distribution of landslide debris among the cells is obtained through a double cycle of computation. In the first phase, the inertial character of the landslide debris is taken into account by considering indicators of momentum. In the second phase, any remaining debris in the central cell is distributed among the adjacent cells, according to the principle of maximum possible equilibrium. The complexities of the model and of the phenomena to be simulated suggested the need for an automated technique of evaluation for the determination of the best set of global parameters. Accordingly, the model is calibrated using a genetic algorithm and by considering the May 1998 Curti-Sarno (Southern Italy) debris flow. The boundaries of the area affected by the debris flow are simulated well with the model. Errors computed by comparing the simulations with the mapped areal extent of the actual landslide are smaller than those previously obtained without genetic algorithms. As the experiments have been realised in a sequential computing environment, they could be

  16. Effects of strong interactions between Ti and ceria on the structures of Ti/CeO2.

    Science.gov (United States)

    Yao, Xiao-Dan; Zhu, Kong-Jie; Teng, Bo-Tao; Yu, Cao-Ming; Zhang, Yun-Lei; Liu, Ya; Fan, Maohong; Wen, Xiao-Dong

    2016-11-30

    The effects of strong interactions between Ti and ceria on the structures of Ti/CeO 2 (111) are systematically investigated by density functional theory calculation. To our best knowledge, the adsorption energy of a Ti atom at the hollow site of CeO 2 is the highest value (-7.99 eV) reported in the literature compared with those of Au (-0.88--1.26 eV), Ag (-1.42 eV), Cu (-2.69 eV), Pd (-1.75 eV), Pt (-2.62 eV) and Sn (-3.68 eV). It is very interesting to find that Ti adatoms disperse at the hollow site of CeO 2 (111) to form surface TiO x species, instead of aggregating to form Ti metal clusters for the Ti-CeO 2 interactions that are much stronger than those of Ti-Ti ones. Ti adatoms are completely oxidized to Ti 4+ ions if they are monatomically dispersed on the next near hollow sites of CeO 2 (111) (xTi-NN-hollow); while Ti 3+ ions are observed when they locate at the near hollow sites (xTi-N-hollow). Due to the electronic repulsive effects among Ti 3+ ions, the adsorption energies of xTi-N-hollow are slightly weaker than those of xTi-NN-hollow. Simultaneously, the existence of unstable Ti 3+ ions on xTi-N-hollow also leads to the restructuring of xTi-N-hollow by surface O atoms of ceria transferring to the top of Ti 3+ ions, or oxidation by O 2 adsorption and dissociation. Both processes improve the stability of the xTi/CeO 2 system by Ti 3+ oxidation. Correspondingly, surface TiO 2 -like species form. This work sheds light into the structures of metal/CeO 2 catalysts with strong interactions between the metal and the ceria support.

  17. Genetic structure of Mexican Mestizo women with breast cancer based on three STR loci.

    Science.gov (United States)

    Calderón-Garcidueñas, Ana L; Rivera-Prieto, Roxana A; Ortíz-Lopez, Rocio; Rivas, Fernando; Barrera-Saldaña, Hugo A; Peñaloza-Espinosa, Rosenda I; Cerda-Flores, Ricardo M

    2008-01-01

    The aim of this population genetics study was to compare the genetic structure of Mexican women with breast cancer (BrCa) with previously reported data of four random populations (Nuevo León, Hispanics, Chihuahua, and Central Region of Mexico). A sample of 115 unrelated women with BrCa and whose four grandparents were born in five zones of Mexico were interviewed at a reference hospital in Northeastern Mexico. Noncodifying STRs D7S820, D13S317, and D16S39 were analyzed; genotype distribution was in agreement with Hardy-Weinberg expectations for all three markers. Similar allele frequencies among four random populations and this selected population were found. According with this and previous studies using molecular and nonmolecular nuclear DNA markers not associated with any disease, Mexican Mestizo population is genetically homogeneous and therefore, genetic causes of BrCa are less heterogeneous, simplifying genetic epidemiologic studies.

  18. Genetic structure analysis of Eufriesea violacea (Hymenoptera, Apidae populations from southern Brazilian Atlantic rainforest remnants

    Directory of Open Access Journals (Sweden)

    Silvia H. Sofia

    2005-09-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to analyze the genetic structure of Eufriesea violacea populations in three fragments (85.47, 832.58 and 2800 ha of Atlantic rainforest located in the north of the Brazilian state of Paraná. A total of twelve primers produced 206 loci, of which 129 were polymorphic (95% criterion. The proportions of polymorphic loci in each population ranged from 57.28% to 59.2%, revealing very similar levels of genetic variability in the groups of bees from each fragment. Unbiased genetic distances between groups ranged from 0.0171 to 0.0284, the smallest genetic distance occurring between bees from the two larger fragments. These results suggest that the E. violacea populations from the three fragments have maintained themselves genetically similar to native populations of this species originally present in northern Paraná.

  19. Population genetic structure of urban malaria vector Anopheles stephensi in India.

    Science.gov (United States)

    Sharma, Richa; Sharma, Arvind; Kumar, Ashwani; Dube, Madhulika; Gakhar, S K

    2016-04-01

    Malaria is a major public health problem in India because climatic condition and geography of India provide an ideal environment for development of malaria vector. Anopheles stephensi is a major urban malaria vector in India and its control has been hampered by insecticide resistance. In present study population genetic structure of A. stephensi is analyzed at macro geographic level using 13 microsatellite markers. Significantly high genetic differentiation was found in all studied populations with differentiation values (FST) ranging from 0.0398 to 0.1808. The geographic distance was found to be playing a major role in genetic differentiation between different populations. Overall three genetic pools were observed and population of central India was found to be coexisting in two genetic pools. High effective population size (Ne) was found in all the studied populations. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland.

    Science.gov (United States)

    Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Arni; Räsänen, Katja

    2013-09-01

    Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments - favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.

  1. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Directory of Open Access Journals (Sweden)

    Sharat Kumar Pradhan

    Full Text Available Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  2. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    Science.gov (United States)

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  3. Transferrin variation and genetic structure of reindeer populations in Scandinavia

    Directory of Open Access Journals (Sweden)

    Knut H. Røed

    1987-06-01

    Full Text Available Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations.Transferrin-variasjon og genetisk struktur hos rein i Skandinavia.Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11 og heterozygositeten var tilsvarende høy med en

  4. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

    Science.gov (United States)

    Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

    2009-10-01

    This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

  5. Analysis of genetic diversity and population structure in upland ...

    Indian Academy of Sciences (India)

    Mulugeta Seyoum

    2018-06-09

    Jun 9, 2018 ... diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions ...... conservation of cotton germplasm in China (English abstract). ... and Alishah O. 2011 Inter simple sequence repeats (ISSR).

  6. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... polymorphic molecular markers for use in hybridization and variety development. Genomic ... The model-based cluster analysis of SSR diversity in the ...... clusters of individuals using the software STRUCTURE: A simulation.

  7. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... ... Aromatic and Economic Plants, CSIR - North-East Institute of Science and Technology ... and population structure is receiving tremendous attention for effective .... unreliable detection and to increase the quality of data. The.

  8. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

    KAUST Repository

    Vignaud, Thomas M.; Maynard, Jeffrey Allen; Leblois, Raphaë l; Meekan, Mark G.; Vá zquez-Juá rez, Ricardo; Ramí rez-Mací as, Dení ; Pierce, Simon J.; Rowat, David; Berumen, Michael L.; Beeravolu, Champak R.; Baksay, Sandra; Planes, Serge

    2014-01-01

    This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks

  9. Genetic Variation in Schizophrenia Liability is Shared With Intellectual Ability and Brain Structure.

    Science.gov (United States)

    Bohlken, Marc M; Brouwer, Rachel M; Mandl, René C W; Kahn, René S; Hulshoff Pol, Hilleke E

    2016-09-01

    Alterations in intellectual ability and brain structure are important genetic markers for schizophrenia liability. How variations in these phenotypes interact with variance in schizophrenia liability due to genetic or environmental factors is an area of active investigation. Studying these genetic markers using a multivariate twin modeling approach can provide novel leads for (genetic) pathways of schizophrenia development. In a sample of 70 twins discordant for schizophrenia and 130 healthy control twins, structural equation modeling was applied to quantify unique contributions of genetic and environmental factors on human brain structure (cortical thickness, cortical surface and global white matter fractional anisotropy [FA]), intellectual ability and schizophrenia liability. In total, up to 28.1% of the genetic variance (22.8% of total variance) in schizophrenia liability was shared with intelligence quotient (IQ), global-FA, cortical thickness, and cortical surface. The strongest contributor was IQ, sharing on average 16.4% of the genetic variance in schizophrenia liability, followed by cortical thickness (6.3%), global-FA (4.7%) and cortical surface (0.5%). Furthermore, we found that up to 57.4% of the variation due to environmental factors (4.6% of total variance) in schizophrenia was shared with IQ (34.2%) and cortical surface (13.4%). Intellectual ability, FA and cortical thickness show significant and independent shared genetic variance with schizophrenia liability. This suggests that measuring brain-imaging phenotypes helps explain genetic variance in schizophrenia liability that is not captured by variation in IQ. © The Author 2016. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  10. A novel structure-aware sparse learning algorithm for brain imaging genetics.

    Science.gov (United States)

    Du, Lei; Jingwen, Yan; Kim, Sungeun; Risacher, Shannon L; Huang, Heng; Inlow, Mark; Moore, Jason H; Saykin, Andrew J; Shen, Li

    2014-01-01

    Brain imaging genetics is an emergent research field where the association between genetic variations such as single nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is evaluated. Sparse canonical correlation analysis (SCCA) is a bi-multivariate analysis method that has the potential to reveal complex multi-SNP-multi-QT associations. Most existing SCCA algorithms are designed using the soft threshold strategy, which assumes that the features in the data are independent from each other. This independence assumption usually does not hold in imaging genetic data, and thus inevitably limits the capability of yielding optimal solutions. We propose a novel structure-aware SCCA (denoted as S2CCA) algorithm to not only eliminate the independence assumption for the input data, but also incorporate group-like structure in the model. Empirical comparison with a widely used SCCA implementation, on both simulated and real imaging genetic data, demonstrated that S2CCA could yield improved prediction performance and biologically meaningful findings.

  11. Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates.

    Science.gov (United States)

    Kang, Jung-Mi; Lee, Jinyoung; Moe, Mya; Jun, Hojong; Lê, Hương Giang; Kim, Tae Im; Thái, Thị Lam; Sohn, Woon-Mok; Myint, Moe Kyaw; Lin, Khin; Shin, Ho-Joon; Kim, Tong-Soo; Na, Byoung-Kuk

    2018-02-07

    Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is one of leading blood stage malaria vaccine candidates. However, genetic variation and antigenic diversity identified in global PfAMA-1 are major hurdles in the development of an effective vaccine based on this antigen. In this study, genetic structure and the effect of natural selection of PfAMA-1 among Myanmar P. falciparum isolates were analysed. Blood samples were collected from 58 Myanmar patients with falciparum malaria. Full-length PfAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. PfAMA-1 sequence of each isolate was sequenced. Polymorphic characteristics and effect of natural selection were analysed with using DNASTAR, MEGA4, and DnaSP programs. Polymorphic nature and natural selection in 459 global PfAMA-1 were also analysed. Thirty-seven different haplotypes of PfAMA-1 were identified in 58 Myanmar P. falciparum isolates. Most amino acid changes identified in Myanmar PfAMA-1 were found in domains I and III. Overall patterns of amino acid changes in Myanmar PfAMA-1 were similar to those in global PfAMA-1. However, frequencies of amino acid changes differed by country. Novel amino acid changes in Myanmar PfAMA-1 were also identified. Evidences for natural selection and recombination event were observed in global PfAMA-1. Among 51 commonly identified amino acid changes in global PfAMA-1 sequences, 43 were found in predicted RBC-binding sites, B-cell epitopes, or IUR regions. Myanmar PfAMA-1 showed similar patterns of nucleotide diversity and amino acid polymorphisms compared to those of global PfAMA-1. Balancing natural selection and intragenic recombination across PfAMA-1 are likely to play major roles in generating genetic diversity in global PfAMA-1. Most common amino acid changes in global PfAMA-1 were located in predicted B-cell epitopes where high levels of nucleotide diversity and balancing natural selection were found. These results highlight the

  12. What is the physical origin of strong Lyα emission? I. Demographics of Lyα emitter structures

    International Nuclear Information System (INIS)

    Shibuya, Takatoshi; Ouchi, Masami; Yuma, Suraphong; Nakajima, Kimihiko; Hashimoto, Takuya; Shimasaku, Kazuhiro; Mori, Masao; Umemura, Masayuki

    2014-01-01

    We present the results of structure analyses for a large sample of 426 Lyα emitters (LAEs) at z ∼ 2.2 that are observed with the Hubble Space Telescope/Advanced Camera for Surveys and WFC3-IR during deep extra-galactic legacy surveys. We confirm that the merger fraction and the average ellipticity of LAE's stellar component are 10%-30% and 0.4-0.6, respectively, that are comparable with previous study results. We successfully identify that some LAEs have a spatial offset between Lyα and stellar-continuum emission peaks, δ Lyα , by ∼2.5-4 kpc beyond our statistical errors. To uncover the physical origin of strong Lyα emission found in LAEs, we investigate the Lyα equivalent width (EW) dependences of three structural parameters: merger fraction, δ Lyα , and ellipticity of stellar distribution in the range of EW(Lyα) = 20-250 Å. Contrary to expectations, we find that the merger fraction does not significantly increase with Lyα EW. We reveal an anti-correlation between δ Lyα and EW(Lyα) using a Kolmogorov-Smirnov (K-S) test. There is a trend that the LAEs with a large Lyα EW have a small ellipticity. This is consistent with the recent theoretical claims that Lyα photons can more easily escape from face-on disks having a small ellipticity, due to less inter-stellar gas along the line of sight, although our K-S test indicates that this trend is not statistically significant. Our results of Lyα-EW dependence generally support the idea that an H I column density is a key quantity determining Lyα emissivity.

  13. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    Science.gov (United States)

    Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

  14. BNN-20, a synthetic microneurotrophin, strongly protects dopaminergic neurons in the "weaver" mouse, a genetic model of dopamine-denervation, acting through the TrkB neurotrophin receptor.

    Science.gov (United States)

    Botsakis, Konstantinos; Mourtzi, Theodora; Panagiotakopoulou, Vasiliki; Vreka, Malamati; Stathopoulos, Georgios T; Pediaditakis, Iosif; Charalampopoulos, Ioannis; Gravanis, Achilleas; Delis, Foteini; Antoniou, Katerina; Zisimopoulos, Dimitrios; Georgiou, Christos D; Panagopoulos, Nikolaos T; Matsokis, Nikolaos; Angelatou, Fevronia

    2017-07-15

    Neurotrophic factors are among the most promising treatments aiming at slowing or stopping and even reversing Parkinson's disease (PD). However, in most cases, they cannot readily cross the human blood-brain-barrier (BBB). Herein, we propose as a therapeutic for PD the small molecule 17-beta-spiro-[5-androsten-17,2'-oxiran]-3beta-ol (BNN-20), a synthetic analogue of DHEA, which crosses the BBB and is deprived of endocrine side-effects. Using the "weaver" mouse, a genetic model of PD, which exhibits progressive dopaminergic neurodegeneration in the Substantia Nigra (SN), we have shown that long-term administration (P1-P21) of BNN-20 almost fully protected the dopaminergic neurons and their terminals, via i) a strong anti-apoptotic effect, probably mediated through the Tropomyosin receptor kinase B (TrkB) neurotrophin receptor's PI3K-Akt-NF-κB signaling pathway, ii) by exerting an efficient antioxidant effect, iii) by inducing significant anti-inflammatory activity and iv) by restoring Brain-Derived Neurotrophic Factor (BDNF) levels. By intercrossing "weaver" with NGL mice (dual GFP/luciferase-NF-κΒ reporter mice, NF-κΒ.GFP.Luc), we obtained Weaver/NGL mice that express the NF-κB reporter in all somatic cells. Acute BNN-20 administration to Weaver/NGL mice induced a strong NF-κB-dependent transcriptional response in the brain as detected by bioluminescence imaging, which was abolished by co-administration of the TrkB inhibitor ANA-12. This indicates that BNN-20 exerts its beneficial action (at least in part) through the TrkB-PI3K-Akt-NF-κB signaling pathway. These results could be of clinical relevance, as they suggest BNN-20 as an important neuroprotective agent acting through the TrkB neurotrophin receptor pathway, mimicking the action of the endogenous neurotrophin BDNF. Thus BNN-20 could be proposed for treatment of PD. Copyright © 2017. Published by Elsevier Ltd.

  15. Self-gravito-acoustic shock structures in a self-gravitating, strongly coupled, multi-component, degenerate quantum plasma system

    Science.gov (United States)

    Mamun, A. A.

    2017-10-01

    The existence of self-gravito-acoustic (SGA) shock structures (SSs) associated with negative self-gravitational potential in a self-gravitating, strongly coupled, multi-component, degenerate quantum plasma (SGSCMCDQP) system is predicted for the first time. The modified Burgers (MB) equation, which is valid for both planar and non-planar (spherical) geometries, is derived analytically, and solved numerically. It is shown that the longitudinal viscous force acting on inertial plasma species of the plasma system is the source of dissipation and is responsible for the formation of these SGA SSs in the plasma system. The time evolution of these SGA SSs is also shown for different values (viz., 0.5, 1, and 2) of Γ, where Γ is the ratio of the nonlinear coefficient to the dissipative coefficient in the MB equation. The SGSCMCDQP model and the numerical analysis of the MB equation presented here are so general that they can be applied in any type of SGSCMCDQP systems like astrophysical compact objects having planar or non-planar (spherical) shape.

  16. Connectivity and genetic structure of the queen conch on the Mesoamerican Reef

    Science.gov (United States)

    Machkour-M'Rabet, Salima; Cruz-Medina, Jorge; García-De León, Francisco J.; De Jesús-Navarrete, Alberto; Hénaut, Yann

    2017-06-01

    The queen conch ( Strombus gigas) is a commercially important marine invertebrate that is widely distributed throughout the western Atlantic, from Bermuda to Brazil. Intense exploitation has resulted in a decrease in population numbers of this species, which is listed as protected from commercial exploitation under IUCN and CITES. Previous studies on population genetics have demonstrated contrasting results in terms of the population structure of S. gigas. This research analyzed the genetic connectivity of the queen conch over a wide area of the Mesoamerican Reef System to determine whether S. gigas presents one panmictic population or a more complex structure. Furthermore, we evaluated the risk of local extinction by establishing the genetic diversity of the studied populations. High resolution was obtained for the five ISSR markers used for a total of 190 individuals, from seven localities along the Mesoamerican Reef. Our results reject the panmictic structure hypothesis for the queen conch in the study area and demonstrate genetic patchiness, indicating general homogeneity among localities that present an isolation-by-distance pattern. However, some genetic temporal variation was confirmed for the Cozumel locality. Furthermore, our results reveal self-recruitment for the Alacranes Reef aggregation and suggest sufficient connectivity with localities on the Caribbean coast to maintain high genetic diversity. With regard to genetic diversity, the results demonstrate that the queen conch is not genetically threatened in the study area. This is probably due to high annual recruitment within Caribbean queen conch aggregations, and suggests that S. gigas is a highly resilient organism. We advocate that the appropriate management of S. gigas (fishing quota and/or closed season) must be followed to attain a rapid recovery of queen conch populations. This study represents a fundamental step in the understanding of the dynamic population structure of S. gigas in the

  17. Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

    OpenAIRE

    Hajirostamloo, Mahbobeh

    2005-01-01

    Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

  18. Population genetic structure of savannah elephants in Kenya: conservation and management implications

    DEFF Research Database (Denmark)

    Okello, John B A; Masembe, Charles; Rasmussen, Henrik B

    2008-01-01

    We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of allele...... through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations....

  19. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    OpenAIRE

    Vangestel, C; Mergeay, Joachim; Dawson, D. A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierar...

  20. Clonal diversity and fine-scale genetic structure in a high andean treeline population

    Czech Academy of Sciences Publication Activity Database

    Peng, Y.; Macek, P.; Macková, Jana; Romoleroux, K.; Hensen, I.

    2015-01-01

    Roč. 47, č. 1 (2015), s. 59-65 ISSN 0006-3606 Grant - others:GA AV ČR(CZ) IAA601110702; GA MŠk(CZ) LM2010009 Program:IA Institutional support: RVO:60077344 Keywords : AFLP * clonal diversity * clonal propagation * fine-scale genetic structure * Polylepis reticulata * treeline Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.944, year: 2015

  1. Genetic Dissection of Trabecular Bone Structure with Mouse Intersubspecific Consomic Strains

    Directory of Open Access Journals (Sweden)

    Taro Kataoka

    2017-10-01

    Full Text Available Trabecular bone structure has an important influence on bone strength, but little is known about its genetic regulation. To elucidate the genetic factor(s regulating trabecular bone structure, we compared the trabecular bone structures of two genetically remote mouse strains, C57BL/6J and Japanese wild mouse-derived MSM/Ms. Phenotyping by X-ray micro-CT revealed that MSM/Ms has structurally more fragile trabecular bone than C57BL/6J. Toward identification of genetic determinants for the difference in fragility of trabecular bone between the two mouse strains, we employed phenotype screening of consomic mouse strains in which each C57BL/6J chromosome is substituted by its counterpart from MSM/Ms. The results showed that many chromosomes affect trabecular bone structure, and that the consomic strain B6-Chr15MSM, carrying MSM/Ms-derived chromosome 15 (Chr15, has the lowest values for the parameters BV/TV, Tb.N, and Conn.D, and the highest values for the parameters Tb.Sp and SMI. Subsequent phenotyping of subconsomic strains for Chr15 mapped four novel trabecular bone structure-related QTL (Tbsq1-4 on mouse Chr15. These results collectively indicate that genetic regulation of trabecular bone structure is highly complex, and that even in the single Chr15, the combined action of the four Tbsqs controls the fragility of trabecular bone. Given that Tbsq4 is syntenic to human Chr 12q12-13.3, where several bone-related SNPs are assigned, further study of Tbsq4 should facilitate our understanding of the genetic regulation of bone formation in humans.

  2. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    Ayala, F.J.

    1987-01-01

    We determined the LD 50 for individuals with any one of four genetic constitutions. The LD 50 was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs

  3. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The STRUCTURE result was confirmed by Principal Coordinate analysis (PCoA) which also clustered beans in three groups. Most Andean genotypes were included in K3.1 and Mesoamerican genotypes belonged to the K3.2 and K3.3 subgroups. This study sets the stage for further analyses for agronomic traits such as ...

  4. Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus

    DEFF Research Database (Denmark)

    Mayoral, Elsa Garcia; Olsen, M.; Hedeholm, R.

    2016-01-01

    In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identifica...

  5. Triplet repeat DNA structures and human genetic disease: dynamic ...

    Indian Academy of Sciences (India)

    Unknown

    formed at the loop-outs. [Sinden R R, Potaman V N, Oussatcheva E A, Pearson C E, Lyubchenko Y L and Shlyakhtenko L S 2002 Triplet repeat DNA structures .... 36–39. 40–121 Huntingtin/polyglutamine expansion. Spinocerebellar ataxia 1. SCA1. 6p23. (CAG)n. 6–44. –. 39–82 (pure) Ataxin-1/polyglutamine expansion.

  6. Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India).

    Science.gov (United States)

    Singh, Gagandeep; Talwar, Indu; Sharma, Rubina; Matharoo, Kawaljit; Bhanwer, A J S

    2016-12-01

    The state of Punjab in the North-West part of India has acted as the main passage for all the major human invasions into the Indian subcontinent. It has resulted in the mixing of foreign gene pool into the local populations, which led to an extensive range of genetic diversity and has influenced the genetic structure of populations in Punjab, North-West India. The present study was conducted to examine the genetic structure, relationships, and extent of genetic differentiation in five Indo-European speaking ethnic groups of Punjab. A total of 1021 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris, and Scheduled castes were analyzed for four human-specific Ins/Del polymorphic loci (ACE, APO, PLAT, and D1) and three restriction fragment length polymorphisms ESR (PvuII), LPL (PvuII), and T2 (MspI) using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of the Alu insertion at APO locus was observed to exhibit the highest value (82.6-96.3 %), whereas D1 exhibited the lowest (26.5-45.6 %) among all the ethnic groups. The average heterozygosity among the studied populations ranged from 0.3816 in Banias to 0.4163 in Khatris. The F ST values ranged from 0.0418 to 0.0033 for the PLAT and LPL loci, respectively, with an average value being 0.0166. Phylogenetic analysis revealed that Banias and Khatris are genetically closest to each other. The Jat Sikhs are genetically close to Brahmins and are distant from the Banias. The Jat Sikhs, Banias, Brahmins, and Khatris are genetically very distant from the Scheduled castes. Overall, Uniform allele frequency distribution patterns, high average heterozygosity values, and a small degree of genetic differentiation in this study suggest a genetic proximity among the selected populations. A low level of genetic differentiation was observed in the studied population groups indicating that genetic drift might have been small or negligible in shaping

  7. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

  8. Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes.

    Science.gov (United States)

    Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

    2014-05-01

    Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco - the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.

  9. Microsatellite markers to determine population genetic structure in the golden anchovy, Coilia dussumieri.

    Science.gov (United States)

    Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

    2014-06-01

    Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

  10. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    Science.gov (United States)

    Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B J; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

    2013-01-01

    Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood

  11. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    Directory of Open Access Journals (Sweden)

    Valentina Coia

    Full Text Available Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet

  12. Genetic structure of Europeans: a view from the North-East.

    Directory of Open Access Journals (Sweden)

    Mari Nelis

    Full Text Available Using principal component (PC analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a Finland, b the Baltic region, Poland and Western Russia, and c Italy as its vertexes, and with d Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (lambda (ranging from 1.00 to 4.21, fixation index (F(st (ranging from 0.000 to 0.023, and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population, a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS.

  13. Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

    Science.gov (United States)

    Hruschka, Daniel J; Hadley, Craig; Brewis, Alexandra A; Stojanowski, Christopher M

    2015-01-01

    Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

  14. Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

    Directory of Open Access Journals (Sweden)

    Daniel J Hruschka

    Full Text Available Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28. However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74. Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

  15. Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

    Science.gov (United States)

    Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

    2018-01-01

    Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

  16. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

    Directory of Open Access Journals (Sweden)

    Małgorzata Pilot

    Full Text Available Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13C and δ(15N values for Eastern European wolves (Canis lupus as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure, to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.

  17. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Directory of Open Access Journals (Sweden)

    Federica Costantini

    Full Text Available While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  18. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Science.gov (United States)

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  19. Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us.

    Science.gov (United States)

    El Baidouri, Fouad; Diancourt, Laure; Berry, Vincent; Chevenet, François; Pratlong, Francine; Marty, Pierre; Ravel, Christophe

    2013-01-01

    Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease.

  20. Genetic Structure and Evolution of the Leishmania Genus in Africa and Eurasia: What Does MLSA Tell Us

    Science.gov (United States)

    El Baidouri, Fouad; Diancourt, Laure; Berry, Vincent; Chevenet, François; Pratlong, Francine; Marty, Pierre; Ravel, Christophe

    2013-01-01

    Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease. PMID:23785530

  1. Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

    Science.gov (United States)

    Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

    2018-01-01

    The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

  2. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

    Science.gov (United States)

    Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

    2017-04-01

    The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits

  3. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  4. Microsatellite based genetic structure of regional transboundary Istrian sheep breed populations in Croatia and Slovenia

    Directory of Open Access Journals (Sweden)

    Beatriz Gutierrez-Gil

    2015-02-01

    Full Text Available Istrian dairy sheep is a local breed essential for the identity and development of the Northern- Adriatic karstic region through high-quality products, primarily the hard sheep artisanal cheese. Border changes fragmented the initial Istrian dairy sheep population in three genetically isolated sub-populations in Italy (1000 animals, Slovenia (1150 animals and Croatia (2500 animals. Due to the drastic reduction of their population sizes and fragmentation, the populations in Croatia and Slovenia are included in governmentally supported conservation programs. The initial subpopulation in Italy was restored after near extinction with stock from Slovenia, and is used today in meat production. The aim of this study was to provide an initial understanding of the current genetic structure and distribution of the genetic variability that exists in Istrian sheep by analysing individuals sampled in two regional groups of Istrian sheep from Croatia and Slovenia. Cres island sheep and Lika pramenka sheep were used as out-groups for comparison. Genetic differentiation was analysed using factorial correspondence analysis and structure clustering over 26 microsatellite loci for a total of 104 sheep belonging to three breeds from Croatia and Slovenia. Factorial correspondence analysis and clustering-based structure analysis both showed three distinct populations: Lika pramenka sheep, Cres island sheep and Istrian sheep. We did not find a marked genetic divergence of the regional groups of Istrian sheep. Istrian sheep regional group from Slovenia showed lower genetic variability compared to the one from Croatia. Variability and structure information obtained in this study considered alongside with socio-cultural-contexts and economic goals for the Istrian sheep reared in Croatia and Slovenia indicate that the cross-border exchange of genetic material of animals carrying private alleles among populations would maintain these alleles at low frequencies and minimize

  5. Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa.

    Science.gov (United States)

    Muzhinji, Norman; Woodhall, James W; Truter, Mariette; van der Waals, Jacquie E

    2016-05-01

    Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic<