Science.gov

Sample records for landscape separating divergent

  1. Diverging vortex separator description and operation

    SciTech Connect

    Schilling, J.R.

    1981-10-01

    Geothermal field test results of the diverging vortex separator have shown operating efficiencies of 99.998% liquid removal at well head conditions in the Salton Sea Geothermal Field. These results indicate this separator concept to be a viable process alternative.

  2. Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence.

    PubMed

    Zellmer, A J; Knowles, L L

    2009-09-01

    Increasing habitat fragmentation poses an immediate threat to population viability, as gene flow patterns are changed in these altered landscapes. Patterns of genetic divergence can potentially reveal the impact of these shifts in landscape connectivity. However, divergence patterns not only carry the signature of altered contemporary landscapes, but also historical ones. When considered separately, both recent and historical landscape structure appear to significantly affect connectivity among 51 wood frog (Rana sylvatica) populations. However, by controlling for correlations among landscape structure from multiple time periods, we show that patterns of genetic divergence reflect recent landscape structure as opposed to landscape structure prior to European settlement of the region (before 1850s). At the same time, within-population genetic diversities remain high and a genetic signature of population bottlenecks is lacking. Together, these results suggest that metapopulation processes - not drift-induced divergence associated with strong demographic bottlenecks following habitat loss - underlie the strikingly rapid consequences of temporally shifting landscape structure on these amphibians. We discuss the implications of these results in the context of understanding the role of population demography in the adaptive variation observed in wood frog populations.

  3. The genomic landscape of species divergence in Ficedula flycatchers.

    PubMed

    Ellegren, Hans; Smeds, Linnéa; Burri, Reto; Olason, Pall I; Backström, Niclas; Kawakami, Takeshi; Künstner, Axel; Mäkinen, Hannu; Nadachowska-Brzyska, Krystyna; Qvarnström, Anna; Uebbing, Severin; Wolf, Jochen B W

    2012-11-29

    Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics. PMID:23103876

  4. Comparative landscape genetics of three closely related sympatric Hesperid butterflies with diverging ecological traits.

    PubMed

    Engler, Jan O; Balkenhol, Niko; Filz, Katharina J; Habel, Jan C; Rödder, Dennis

    2014-01-01

    To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to

  5. Comparative Landscape Genetics of Three Closely Related Sympatric Hesperid Butterflies with Diverging Ecological Traits

    PubMed Central

    Engler, Jan O.; Balkenhol, Niko; Filz, Katharina J.; Habel, Jan C.; Rödder, Dennis

    2014-01-01

    To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to

  6. Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers.

    PubMed

    Renaut, Sebastien; Owens, Gregory L; Rieseberg, Loren H

    2014-02-01

    The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterized. Here, through the use of transcriptome sequencing, we examined genomic divergence for three pairs of sister species of sunflowers. Two of the pairs (Helianthus petiolaris - H. debilis and H. annuus - H. argophyllus) have diverged along a similar latitudinal gradient and presumably experienced similar selective pressure. In contrast, a third species pair (H. exilis - H. bolanderi) diverged along a longitudinal gradient. Analyses of divergence, as measured in terms of FST, indicated little repeatability across the three pairs of species for individual genetic markers (SNPs), modest repeatability at the level of individual genes and the highest repeatability when large regions of the genome were compared. As expected, higher repeatability was observed for the two species pairs that have diverged along a similar latitudinal gradient, with genes involved in flowering time among the most divergent genes. Genes showing extreme low or high differentiation were more similar than genes showing medium levels of divergence, implying that both purifying and divergent selection contributed to repeatable patterns of divergence. The location of a gene along the chromosome also predicted divergence levels, presumably because of shared heterogeneity in both recombination and mutation rates. In conclusion, repeated genome evolution appeared to result from both similar selective pressures and shared local genomic landscapes.

  7. Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonids.

    PubMed

    Gomez-Uchida, Daniel; Knight, Thomas W; Ruzzante, Daniel E

    2009-12-01

    Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (theta) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies.

  8. Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs

    PubMed Central

    Wollenberg Valero, Katharina C.

    2015-01-01

    The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this biodiversity hotspot. Both extrinsic and intrinsic factors have been studied in a comparative framework, with extrinsic factors usually being related to the physical environment (landscape, climate, river catchments, mountain chains), and intrinsic factors being clade-specific traits or constraints (reproduction, ecology, morphology, physiology). Despite some general patterns emerging from such large-scale comparative analyses, it became clear that the mechanism of diversification in Madagascar may vary among clades, and may be a multifactorial process. In this contribution, I test for intrinsic factors promoting population-level divergence within a clade of terrestrial, diurnal leaf-litter frogs (genus Gephyromantis) that has previously been shown to diversify according to extrinsic factors. Landscape genetic analyses of the microendemic species Gephyromantis enki and its widely distributed, larger sister species Gephyromantis boulengeri over a rugged landscape in the Ranomafana area shows that genetic variance of the smaller species cannot be explained by landscape resistance alone. Both topographic and riverine barriers are found to be important in generating this divergence. This case study yields additional evidence for the probable importance of body size in lineage diversification. PMID:26136766

  9. Parental Separation Effects on Children's Divergent Thinking Abilities and Creativity Potential.

    ERIC Educational Resources Information Center

    Jenkins, Jeanne E.; And Others

    1988-01-01

    Investigates the effect of parental separation on the divergent thinking abilities and creativity potential of 116 single- and two-parent family children in grades three through five. Findings indicate a comparable level of divergent thinking between both groups; single-parent children scored significantly higher on creativity potential.…

  10. Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonids.

    PubMed

    Gomez-Uchida, Daniel; Knight, Thomas W; Ruzzante, Daniel E

    2009-12-01

    Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (theta) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies. PMID:19878451

  11. Splitting supersonic nozzle flow into separate jets by overexpansion into a multilobed divergent nozzle

    NASA Technical Reports Server (NTRS)

    Huff, R. G.; Groesbeck, D. E.

    1972-01-01

    Air flowing from a convergent nozzle at pressure ratios greater than 2.5 has been split into eight separate jets by overexpansion of the flow into a divergent, eight-lobed passage. The splitting of the flow is accompanied by a decrease in the nozzle axial centerline Mach number. This in part is due to the radial inflow of secondary air between the lobes toward the nozzle centerline. Each of the smaller jets is partially split after it leaves the end of the divergent lobed section of the nozzle, thus creating a velocity profile having 16 peaks. At a pressure ratio of 3.5 the flow decelerates to Mach 1 in three convergent nozzle throat diameters. Convergent nozzle flow normally requires 12 diameters to reach Mach 1. The nozzle has a sound attenuation of 12 decibels with a thrust loss of 9 percent for the best configuration tested.

  12. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    USGS Publications Warehouse

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  13. Preparative divergent flow IEF without carrier ampholytes for separation of complex biological samples.

    PubMed

    Stastna, Miroslava; Slais, Karel

    2010-01-01

    Efficient separation method is a crucial part of the process in which components of highly complex biological sample are identified and characterized. Based on the principles of recently newly established electrophoretic method called divergent flow IEF (DF IEF), we have tested the DF IEF instrument which is able to operate without the use of background carrier ampholytes. We have verified that during separation and focusing of sample consisting of high numbers of proteins (yeast lysate and wheat flour extract), the pH gradient of preparative DF IEF can be created by autofocusing of the sample components themselves without any addition of carrier ampholytes. In DF IEF, the proteins are separated, desalted and concentrated in one step. The fractions of yeast lysate sample, collected at the DF IEF output and subjected to gel IEF, contained the zones of proteins gradually covering the pI values from 3.7 to 8.5. In our experimental arrangement, the highest number of proteins has been found in fractions with pI values around 5.3 as detected by polyacrylamide gel IEF with CBB staining. During DF IEF, the selected protein bands have been concentrated up to 16.8-fold.

  14. Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation

    PubMed Central

    Ulirsch, Jacob C.; Lacy, Jessica N.; An, Xiuli; Mohandas, Narla; Mikkelsen, Tarjei S.; Sankaran, Vijay G.

    2014-01-01

    Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary proerythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (∼25% for GATA1, TAL1, and NFE2) but were more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression that is sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites associates with changes in the underlying chromatin structure, driving transcriptional divergence. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the β-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis. PMID:25521328

  15. Twins and Kindergarten Separation: Divergent Beliefs of Principals, Teachers, Parents, and Twins

    ERIC Educational Resources Information Center

    Gordon, Lynn Melby

    2015-01-01

    Should principals enforce mandatory separation of twins in kindergarten? Do school separation beliefs of principals differ from those of teachers, parents of twins, and twins themselves? This survey questioned 131 elementary principals, 54 kindergarten teachers, 201 parents of twins, and 112 twins. A majority of principals (71%) believed that…

  16. Quaternary origin and genetic divergence of the endemic cactus Mammillaria pectinifera in a changing landscape in the Tehuacán Valley, Mexico.

    PubMed

    Cornejo-Romero, A; Medina-Sánchez, J; Hernández-Hernández, T; Rendón-Aguilar, B; Valverde, P L; Zavala-Hurtado, A; Rivas-Arancibia, S P; Pérez-Hernández, M A; López-Ortega, G; Jiménez-Sierra, C; Vargas-Mendoza, C F

    2014-01-08

    The endemic Mexican cactus, Mammillaria pectinifera, shows low dispersal capabilities and isolated populations within the highly dissected landscape of Tehuacán Valley. These characteristics can restrict gene flow and act upon the genetic divergence and speciation in arid plants. We conducted a phylogeographic study to determine if the origin, current distribution, and genetic structure of M. pectinifera were driven by Quaternary geomorphic processes. Sequences of the plastids psbA-trnH and trnT-trnL obtained from 66 individuals from seven populations were used to estimate genetic diversity. Population differentiation was assessed by an analysis of molecular variance. We applied a stepwise phylogenetic calibration test to determine whether species origin and genetic divergence among haplotypes were temporally concordant with recognizable episodes of geomorphic evolution. The combination of plastid markers yielded six haplotypes, with high levels of haplotype diversity (h = 0.622) and low nucleotide diversity (π = 0.00085). The populations were found to be genetically structured (F(ST) = 0.682; P < 0.00001), indicating that geographic isolation and limited dispersal were the primary causes of genetic population differentiation. The estimated origin and divergence time among haplotypes were 0.017-2.39 and 0.019-1.237 mya, respectively, which correlates with Pleistocene tectonics and erosion events, supporting a hypothesis of geomorphically-driven geographical isolation. Based on a Bayesian skyline plot, these populations showed long term demographic stability, indicating that persistence in confined habitats has been the main response of this species to landscape changes. We conclude that the origin and haplotype divergence of M. pectinifera were a response to local Quaternary geomorphic evolution.

  17. To Segregate or to Separate? Special Education Expansion and Divergence in the United States and Germany

    ERIC Educational Resources Information Center

    Powell, Justin J. W.

    2009-01-01

    Over the past two hundred years in the United States and Germany, special educational systems have been institutionalized to facilitate access to learning opportunities for children with disabilities, difficulties, and disadvantages. Originally heralded as innovative, the positive views of these mainly segregating and separating educational…

  18. Habitat Discontinuities Separate Genetically Divergent Populations of a Rocky Shore Marine Fish

    PubMed Central

    Knutsen, Halvor; Jorde, Per Erik

    2016-01-01

    Habitat fragmentation has been suggested to be responsible for major genetic differentiations in a range of marine organisms. In this study, we combined genetic data and environmental information to unravel the relative role of geography and habitat heterogeneity on patterns of genetic population structure of corkwing wrasse (Symphodus melops), a rocky shore species at the northern limit of its distribution range in Scandinavia. Our results revealed a major genetic break separating populations inhabiting the western and southern coasts of Norway. This genetic break coincides with the longest stretch of sand in the whole study area, suggesting habitat fragmentation as a major driver of genetic differentiation of this obligate rocky shore benthic fish in Scandinavia. The complex fjords systems extending along the western coast of Norway appeared responsible for further regional genetic structuring. Our findings indicate that habitat discontinuities may lead to significant genetic fragmentation over short geographical distances, even for marine species with a pelagic larval phase, as for this rocky shore fish. PMID:27706178

  19. Species-specific separation of lake plankton reveals divergent food assimilation patterns in rotifers

    PubMed Central

    Burian, Alfred; Kainz, Martin J; Schagerl, Michael; Yasindi, Andrew

    2014-01-01

    1. The analysis of functional groups with a resolution to the individual species level is a basic requirement to better understand complex interactions in aquatic food webs. Species-specific stable isotope analyses are currently applied to analyse the trophic role of large zooplankton or fish species, but technical constraints complicate their application to smaller-sized plankton. 2. We investigated rotifer food assimilation during a short-term microzooplankton bloom in the East African soda lake Nakuru by developing a method for species-specific sampling of rotifers. 3. The two dominant rotifers, Brachionus plicatilis and Brachionus dimidiatus, were separated to single-species samples (purity >95%) and significantly differed in their isotopic values (4.1‰ in δ13C and 1.5‰ in δ15N). Bayesian mixing models indicated that isotopic differences were caused by different assimilation of filamentous cyanobacteria and particles <2 μm and underlined the importance of species-specific sampling of smaller plankton compartments. 4. A main difference was that the filamentous cyanobacterium Arthrospira fusiformis, which frequently forms blooms in African soda lakes, was an important food source for the larger-sized B. plicatilis (48%), whereas it was hardly ingested by B. dimidiatus. Overall, A. fusiformis was, relative to its biomass, assimilated to small extents, demonstrating a high grazing resistance of this species. 5. In combination with high population densities, these results demonstrate a strong potential of rotifer blooms to shape phytoplankton communities and are the first in situ demonstration of a quantitatively important direct trophic link between rotifers and filamentous cyanobacteria. PMID:25866422

  20. Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families.

    PubMed

    Mark Welch, David B; Cummings, Michael P; Hillis, David M; Meselson, Matthew

    2004-02-10

    Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids.

  1. Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps.

    PubMed

    Roschanski, Anna M; Csilléry, Katalin; Liepelt, Sascha; Oddou-Muratorio, Sylvie; Ziegenhagen, Birgit; Huard, Frédéric; Ullrich, Kristian K; Postolache, Dragos; Vendramin, Giovanni G; Fady, Bruno

    2016-02-01

    Understanding local adaptation in forest trees is currently a key research and societal priority. Geographically and ecologically marginal populations provide ideal case studies, because environmental stress along with reduced gene flow can facilitate the establishment of locally adapted populations. We sampled European silver fir (Abies alba Mill.) trees in the French Mediterranean Alps, along the margin of its distribution range, from pairs of high- and low-elevation plots on four different mountains situated along a 170-km east-west transect. The analysis of 267 SNP loci from 175 candidate genes suggested a neutral pattern of east-west isolation by distance among mountain sites. F(ST) outlier tests revealed 16 SNPs that showed patterns of divergent selection. Plot climate was characterized using both in situ measurements and gridded data that revealed marked differences between and within mountains with different trends depending on the season. Association between allelic frequencies and bioclimatic variables revealed eight genes that contained candidate SNPs, of which two were also detected using F(ST) outlier methods. All SNPs were associated with winter drought, and one of them showed strong evidence of selection with respect to elevation. Q(ST)-F(ST) tests for fitness-related traits measured in a common garden suggested adaptive divergence for the date of bud flush and for growth rate. Overall, our results suggest a complex adaptive picture for A. alba in the southern French Alps where, during the east-to-west Holocene recolonization, locally advantageous genetic variants established at both the landscape and local scales. PMID:26676992

  2. Algae separation from urban landscape water using a high density microbubble layer enhanced by micro-flocculation.

    PubMed

    Chen, Shuwen; Xu, Jingcheng; Liu, Jia; Wei, Qiaoling; Li, Guangming; Huang, Xiangfeng

    2014-01-01

    Eutrophication of raw water results in outbreaks of algae, which hinders conventional water treatment. In this study, high density microbubble layers combined with micro-flocculation was adopted to remove algae from urban landscape water, and the effects of pressure, hydraulic loading, microbubble layer height and flocculation dosage on the removal efficiency for algae were studied. The greatest removal efficiency for algae, chemical oxygen demand, nitrogen and phosphorus was obtained at 0.42 MPa with hydraulic loading at 5 m/h and a flocculation dosage of 4 mg/L using a microbubble layer with a height of 130 cm. Moreover, the size, clearance distance and concentration of microbubbles were found to be affected by pressure and the height of the microbubble layer. Based on the study, this method was an alternative for algae separation from urban landscape water and water purification.

  3. Divergent effects of the ‘biased’ 5-HT1A receptor agonists F15599 and F13714 in a novel object pattern separation task

    PubMed Central

    van Goethem, N P; Schreiber, R; Newman-Tancredi, A; Varney, M; Prickaerts, J

    2015-01-01

    Background and Purpose Pattern separation, that is, the formation of distinct representations from similar inputs, is an important hippocampal process implicated in cognitive domains like episodic memory. A deficit in pattern separation could lead to memory impairments in several psychiatric and neurological disorders. Hence, mechanisms by which pattern separation can be increased are of potential therapeutic interest. Experimental approach 5-HT1A receptors are involved in spatial memory. Herein we tested the ‘biased’ 5-HT1A receptor agonists F15599, which preferentially activates post-synaptic heteroreceptors, and F13714, which preferentially activates raphe-located autoreceptors, in rats in a novel spatial task assessing pattern separation, the object pattern separation (OPS) task. Key Results The acetylcholinesterase inhibitor donepezil, which served as a positive control, significantly improved spatial pattern separation at a dose of 1 mg·kg−1, p.o. F15599 increased pattern separation at 0.04 mg·kg−1, i.p., while F13714 decreased pattern separation at 0.0025 mg·kg−1, i.p. The selective 5-HT1A receptor antagonist WAY-100635 (0.63 mg·kg−1, s.c.) counteracted the effects of both agonists. These data suggest that acute preferential activation of post-synaptic 5-HT1A heteroreceptors improves spatial pattern separation, whereas acute preferential activation of raphe-located 5-HT1A autoreceptors impairs performance. Conclusions and Implications We successfully established and validated a novel, simple and robust OPS task and observed a diverging profile of response with ‘biased’ 5-HT1A receptor agonists based on their targeting of receptors in distinct brain regions. Our data suggest that the post-synaptic 5-HT1A receptor consists of a potential novel molecular target to improve pattern separation performance. PMID:25572672

  4. Using landscape history to predict biodiversity patterns in fragmented landscapes

    PubMed Central

    Ewers, Robert M; Didham, Raphael K; Pearse, William D; Lefebvre, Véronique; Rosa, Isabel M D; Carreiras, João M B; Lucas, Richard M; Reuman, Daniel C

    2013-01-01

    Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape ‘terrageny’, which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscapes. PMID:23931035

  5. Male competition fitness landscapes predict both forward and reverse speciation.

    PubMed

    Keagy, Jason; Lettieri, Liliana; Boughman, Janette W

    2016-01-01

    Speciation is facilitated when selection generates a rugged fitness landscape such that populations occupy different peaks separated by valleys. Competition for food resources is a strong ecological force that can generate such divergent selection. However, it is unclear whether intrasexual competition over resources that provide mating opportunities can generate rugged fitness landscapes that foster speciation. Here we use highly variable male F2 hybrids of benthic and limnetic threespine sticklebacks, Gasterosteus aculeatus Linnaeus, 1758, to quantify the male competition fitness landscape. We find that disruptive sexual selection generates two fitness peaks corresponding closely to the male phenotypes of the two parental species, favouring divergence. Most surprisingly, an additional region of high fitness favours novel hybrid phenotypes that correspond to those observed in a recent case of reverse speciation after anthropogenic disturbance. Our results reveal that sexual selection through male competition plays an integral role in both forward and reverse speciation.

  6. Climate oscillation during the Quaternary associated with landscape heterogeneity promoted allopatric lineage divergence of a temperate tree Kalopanax septemlobus (Araliaceae) in East Asia.

    PubMed

    Sakaguchi, Shota; Qiu, Ying-Xiong; Liu, Yi-Hui; Qi, Xin-Shuai; Kim, Sea-Hyun; Han, Jingyu; Takeuchi, Yayoi; Worth, James R P; Yamasaki, Michimasa; Sakurai, Shogo; Isagi, Yuji

    2012-08-01

    We investigated the biogeographic history of Kalopanax septemlobus, one of the most widespread temperate tree species in East Asia, using a combined phylogeographic and palaeodistribution modelling approach. Range-wide genetic differentiation at nuclear microsatellites (G'(ST) = 0.709; 2205 samples genotyped at five loci) and chloroplast DNA (G(ST) = 0.697; 576 samples sequenced for 2055 bp at three fragments) was high. A major phylogeographic break in Central China corresponded with those of other temperate species and the spatial delineation of the two temperate forest subkingdoms of East Asia, consistent with the forests having been isolated within both East and West China for multiple glacial-interglacial cycles. Evidence for multiple glacial refugia was found in most of its current range in China, South Japan and the southernmost part of the Korean Peninsula. In contrast, lineage admixture and absence of private alleles and haplotypes in Hokkaido and the northern Korean Peninsula support a postglacial origin of northernmost populations. Although palaeodistribution modelling predicted suitable climate across a land-bridge extending from South Japan to East China during the Last Glacial Maximum, the genetic differentiation of regional populations indicated a limited role of the exposed sea floor as a dispersal corridor at that time. Overall, this study provides evidence that differential impacts of Quaternary climate oscillation associated with landscape heterogeneity have shaped the genetic structure of a wide-ranging temperate tree in East Asia.

  7. Predictability of evolutionary trajectories in fitness landscapes.

    PubMed

    Lobkovsky, Alexander E; Wolf, Yuri I; Koonin, Eugene V

    2011-12-01

    Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.

  8. The Natural Product Resveratrol Inhibits Yeast Cell Separation by Extensively Modulating the Transcriptional Landscape and Reprogramming the Intracellular Metabolome

    PubMed Central

    Shen, Yan; Wang, Yang; Li, Jing; Lv, Hong; Huo, Keke

    2016-01-01

    An increasing number of studies have shown that the promising compound resveratrol treats multiple diseases, such as cancer and aging; however, the resveratrol mode-of-action (MoA) remains largely unknown. Here, by virtue of multiple omics approaches, we adopted fission yeast as a model system with the goal of dissecting the common MoA of the anti-proliferative activity of resveratrol. We found that the anti-proliferative activity of resveratrol is mainly due to its unique role of inhibiting the separation of sister cells, similar phenotype with the C2H2 zinc finger transcription factor Ace2 knock-out strain. Microarray analysis shown that resveratrol has extensive impact on the fission yeast transcription levels. Among the changed gene’s list, 40% of up-regulated genes are Core Environmental Stress Responses genes, and 57% of the down-regulated genes are periodically expressed. Moreover, resveratrol leverages the metabolome, which unbalances the intracellular pool sizes of several classes of amino acids, nucleosides, sugars and lipids, thus reflecting the remodulated metabolic networks. The complexity of the resveratrol MoA displayed in previous reports and our work demonstrates that multiple omics approaches must be applied together to obtain a complete picture of resveratrol’s anti-proliferative function. PMID:26950930

  9. Luminous Landscapes.

    ERIC Educational Resources Information Center

    Okrent, Inez

    2000-01-01

    Describes an activity for third-grade students in which they learn about early American landscape painters, specifically Frederick Church, Thomas Moran, and Albert Bierstadt. Students create natural landscapes, using the basic elements of landscape compositions. Discusses the process. (CMK)

  10. A Note on Divergences.

    PubMed

    Liang, Xiao

    2016-10-01

    In many areas of neural computation, like learning, optimization, estimation, and inference, suitable divergences play a key role. In this note, we study the conjecture presented by Amari ( 2009 ) and find a counterexample to show that the conjecture does not hold generally. Moreover, we investigate two classes of [Formula: see text]-divergence (Zhang, 2004 ), weighted f-divergence and weighted [Formula: see text]-divergence, and prove that if a divergence is a weighted f-divergence, as well as a Bregman divergence, then it is a weighted [Formula: see text]-divergence. This result reduces in form to the main theorem established by Amari ( 2009 ) when [Formula: see text] [Formula: see text].

  11. [Landscape and ecological genomics].

    PubMed

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25508669

  12. [Landscape and ecological genomics].

    PubMed

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25474890

  13. Sharing a Disparate Landscape

    ERIC Educational Resources Information Center

    Ali-Khan, Carolyne

    2010-01-01

    Working across boundaries of power, identity, and political geography is fraught with difficulties and contradictions. In Tali Tal and Iris Alkaher's, "Collaborative environmental projects in a multicultural society: Working from within separate or mutual landscapes?" the authors describe their efforts to do this in the highly charged atmosphere…

  14. Quantum skew divergence

    SciTech Connect

    Audenaert, Koenraad M. R.

    2014-11-15

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

  15. The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape.

    PubMed

    Farrington, Heather L; Lawson, Lucinda P; Clark, Courtney M; Petren, Kenneth

    2014-10-01

    Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species-trees recovered seven major finch clades: ground, tree, vegetarian, Cocos Island, grey and green warbler finches, and a distinct clade of sharp-beaked ground finches (Geospiza cf. difficilis) basal to all ground and tree finches. The ground and tree finch clades lack species-level phylogenetic structure. Interisland gene flow and interspecies introgression vary geographically in predictable ways. First, several species exhibit concordant patterns of population divergence across the channel separating the Galápagos platform islands from the separate volcanic province of northern islands. Second, peripheral islands have more admixed populations while central islands maintain more distinct species boundaries. This landscape perspective highlights a likely role for isolation of peripheral populations in initial divergence, and demonstrates that peripheral populations may maintain genetic diversity through outbreeding during the initial stages of speciation.

  16. The concept of hydrologic landscapes

    USGS Publications Warehouse

    Winter, T.C.

    2001-01-01

    Hydrologic landscapes are multiples or variations of fundamental hydrologic landscape units. A fundamental hydrologic landscape unit is defined on the basis of land-surface form, geology, and climate. The basic land-surface form of a fundamental hydrologic landscape unit is an upland separated from a lowland by an intervening steeper slope. Fundamental hydrologic landscape units have a complete hydrologic system consisting of surface runoff, ground-water flow, and interaction with atmospheric water. By describing actual landscapes in terms of land-surface slope, hydraulic properties of soils and geologic framework, and the difference between precipitation and evapotranspiration, the hydrologic system of actual landscapes can be conceptualized in a uniform way. This conceptual framework can then be the foundation for design of studies and data networks, syntheses of information on local to national scales, and comparison of process research across small study units in a variety of settings. The Crow Wing River watershed in central Minnesota is used as an example of evaluating stream discharge in the context of hydrologic landscapes. Lake-research watersheds in Wisconsin, Minnesota, North Dakota, and Nebraska are used as an example of using the hydrologic-landscapes concept to evaluate the effect of ground water on the degree of mineralization and major-ion chemistry of lakes that lie within ground-water flow systems.

  17. Landscape Architecture.

    ERIC Educational Resources Information Center

    American School and University, 1985

    1985-01-01

    Members of the American Society of Landscape Architects shape open spaces on the campuses of Georgetown University, District of Columbia; the University of Missouri; Auraria Higher Education Center, Colorado; and the University of Michigan. (MLF)

  18. Mars Landscapes

    NASA Video Gallery

    Spacecraft have studied the Martian surface for decades, giving Earthlings insights into the history, climate and geology of our nearest neighbor, Mars. These images are from "Mars Landscapes," a v...

  19. Mitochondrial DNA Detects a Complex Evolutionary History with Pleistocene Epoch Divergence for the Neotropical Malaria Vector Anopheles nuneztovari Sensu Lato

    PubMed Central

    Scarpassa, Vera Margarete; Conn, Jan E.

    2011-01-01

    Cryptic species and lineages characterize Anopheles nuneztovari s.l. Gabaldón, an important malaria vector in South America. We investigated the phylogeographic structure across the range of this species with cytochrome oxidase subunit I (COI) mitochondrial DNA sequences to estimate the number of clades and levels of divergence. Bayesian and maximum-likelihood phylogenetic analyses detected four groups distributed in two major monophyletic clades (I and II). Samples from the Amazon Basin were clustered in clade I, as were subclades II-A and II-B, whereas those from Bolivia/Colombia/Venezuela were restricted to one basal subclade (II-C). These data, together with a statistical parsimony network, confirm results of previous studies that An. nuneztovari is a species complex consisting of at least two cryptic taxa, one occurring in Colombia and Venezuela and the another occurring in the Amazon Basin. These data also suggest that additional incipient species may exist in the Amazon Basin. Divergence time and expansion tests suggested that these groups separated and expanded in the Pleistocene Epoch. In addition, the COI sequences clearly separated An. nuneztovari s.l. from the closely related species An. dunhami Causey, and three new records are reported for An. dunhami in Amazonian Brazil. These findings are relevant for vector control programs in areas where both species occur. Our analyses support dynamic geologic and landscape changes in northern South America, and infer particularly active divergence during the Pleistocene Epoch for New World anophelines. PMID:22049039

  20. Learning Landscapes

    ERIC Educational Resources Information Center

    Noyes, Andrew

    2004-01-01

    This article explores the metaphor of learning landscapes, a tool developed in order to map children's experiences of, and attitudes to, learning (mathematics) before and after the transfer from primary to secondary school. Firstly, the continuing problems surrounding school transfer and why a re-examination of this is required are considered.…

  1. Parallels and Divergences?

    ERIC Educational Resources Information Center

    Spray, Martin

    1985-01-01

    Discusses the varying philosophical viewpoints and program orientations associated with the conservation movement, assessing the implications of these divergences on the objectives and instructional methods of environmental education. Also identifies and explains the range of differences existing in environmental education programs. (ML)

  2. Converging or Diverging Lens?

    ERIC Educational Resources Information Center

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  3. Statistics of divergence times.

    PubMed

    Haubold, B; Wiehe, T

    2001-07-01

    Given the number of nucleotide substitutions between two species (K) and the substitution rate nu, the expectation of the corresponding divergence time is usually calculated as K/(2 nu). This is strictly true only if nu is regarded as a constant because the ratio of two random variables, such as K/(2 nu), has distributional properties different from those of the distribution of K. Therefore, both the mean and any confidence interval for divergence times are unknown in this situation. We model the distribution of K and nu using the Gamma distribution and calculate the mean and 95% confidence interval for the corresponding divergence time. These calculations are compared with results obtained by bootstrapping sequence data from the model plant Arabidopsis thaliana and its relatives. We show that for nonoverlapping pairs of phylogenetic distances, our method approaches the bootstrap results very closely. In contrast, regarding the mutation rate as a constant leads to strong underestimation of the confidence interval. An implementation of our method of computing divergence times is accessible through a web interface at http://www.soft.ice.mpg.de/cite.

  4. Self-organization in irregular landscapes: Detecting autogenic interactions from field data using descriptive statistics and dynamical systems theory

    NASA Astrophysics Data System (ADS)

    Larsen, L.; Watts, D.; Khurana, A.; Anderson, J. L.; Xu, C.; Merritts, D. J.

    2015-12-01

    The classic signal of self-organization in nature is pattern formation. However, the interactions and feedbacks that organize depositional landscapes do not always result in regular or fractal patterns. How might we detect their existence and effects in these "irregular" landscapes? Emergent landscapes such as newly forming deltaic marshes or some restoration sites provide opportunities to study the autogenic processes that organize landscapes and their physical signatures. Here we describe a quest to understand autogenic vs. allogenic controls on landscape evolution in Big Spring Run, PA, a landscape undergoing restoration from bare-soil conditions to a target wet meadow landscape. The contemporary motivation for asking questions about autogenic vs. allogenic controls is to evaluate how important initial conditions or environmental controls may be for the attainment of management objectives. However, these questions can also inform interpretation of the sedimentary record by enabling researchers to separate signals that may have arisen through self-organization processes from those resulting from environmental perturbations. Over three years at Big Spring Run, we mapped the dynamic evolution of floodplain vegetation communities and distributions of abiotic variables and topography. We used principal component analysis and transition probability analysis to detect associative interactions between vegetation and geomorphic variables and convergent cross-mapping on lidar data to detect causal interactions between biomass and topography. Exploratory statistics revealed that plant communities with distinct morphologies exerted control on landscape evolution through stress divergence (i.e., channel initiation) and promoting the accumulation of fine sediment in channels. Together, these communities participated in a negative feedback that maintains low energy and multiple channels. Because of the spatially explicit nature of this feedback, causal interactions could not

  5. Sharing a disparate landscape

    NASA Astrophysics Data System (ADS)

    Ali-Khan, Carolyne

    2010-06-01

    Working across boundaries of power, identity, and political geography is fraught with difficulties and contradictions. In Tali Tal and Iris Alkaher's, " Collaborative environmental projects in a multicultural society: Working from within separate or mutual landscapes?" the authors describe their efforts to do this in the highly charged atmosphere of Israel. This forum article offers a response to their efforts. Writing from a framework of critical pedagogy, I use the concepts of space and time to anchor my analysis, as I examine the issue of power in this Jew/Arab collaborative environmental project. This response problematizes "sharing" in a landscape fraught with disparities. It also looks to further Tal and Alkaher's work by geographically and politically grounding it in the broader current conflict and by juxtaposing sustainability with equity.

  6. Gene duplication and divergence produce divergent MHC genotypes without disassortative mating.

    PubMed

    Dearborn, Donald C; Gager, Andrea B; McArthur, Andrew G; Gilmour, Morgan E; Mandzhukova, Elena; Mauck, Robert A

    2016-09-01

    Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class II B genes in Leach's storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good statistical power, we consistently found random assortment of mates at MHC. Despite random mating, birds had MHC genotypes with functionally diverged alleles, averaging 13 amino acid differences in pairwise comparisons of exon 2 alleles within individuals. To test whether this high MHC diversity in individuals is driven by evolutionary divergence of the two duplicated genes, we built a phylogenetic permutation model. The model showed that genotypic diversity was strongly impacted by sequence divergence between the most common allele of each gene, with a smaller additional impact of monophyly of the two genes. Divergence of allele sequences between genes may have reduced the benefits of actively seeking MHC-dissimilar mates, in which case the evolutionary history of duplicated genes is shaping the adaptive landscape of sexual selection. PMID:27376487

  7. Divergence Boundary Conditions for Vector Helmholtz Equations with Divergence Constraints

    NASA Technical Reports Server (NTRS)

    Kangro, Urve; Nicolaides, Roy

    1997-01-01

    The idea of replacing a divergence constraint by a divergence boundary condition is investigated. The connections between the formulations are considered in detail. It is shown that the most common methods of using divergence boundary conditions do not always work properly. Necessary and sufficient conditions for the equivalence of the formulations are given.

  8. Divergent evolution in fluviokarst landscapes of central Kentucky

    USGS Publications Warehouse

    Phillips, J.D.; Martin, L.L.; Nordberg, V.G.; Andrews, W.A., Jr.

    2004-01-01

    Central Kentucky is characterized by a mixture of karst and fluvial features, typically manifested as mosaic of karst-rich/ channel-poor (KRCP) and channel-rich/karst-poor (CRKP) environments. At the regional scale the location and distribution of KRCP and CRKP areas are not always systematically related to structural, lithological, topographic, or other controls. This study examines the relationship of KRCP and CRKP zones along the Kentucky River gorge area, where rapid incision in the last 1??5 million years has lowered local base levels and modified slopes on the edge of the inner bluegrass plateau. At the scale of detailed field mapping on foot within a 4 km2 area, the development of karst and fluvial features is controlled by highly localized structural and topographic constraints, and can be related to slope changes associated with retreat of the Kentucky River gorge escarpment. A conceptual model of karst/fluvial transitions is presented, which suggests that minor, localized variations are sufficient to trigger a karst-fluvial or fluvial-karst switch when critical slope thresholds are crossed. ?? 2004 John Wiley and Sons, Ltd.

  9. Genetic structure and divergence in populations of Lutzomyia cruciata, a phlebotomine sand fly (Diptera: Psychodidae) vector of Leishmania mexicana in southeastern Mexico.

    PubMed

    Pech-May, Angélica; Marina, Carlos F; Vázquez-Domínguez, Ella; Berzunza-Cruz, Miriam; Rebollar-Téllez, Eduardo A; Narváez-Zapata, José A; Moo-Llanes, David; Ibáñez-Bernal, Sergio; Ramsey, Janine M; Becker, Ingeborg

    2013-06-01

    The low dispersal capacity of sand flies could lead to population isolation due to geographic barriers, climate variation, or to population fragmentation associated with specific local habitats due to landscape modification. The phlebotomine sand fly Lutzomyia cruciata has a wide distribution throughout Mexico and is a vector of Leishmania mexicana in the southeast. The aim of this study was to evaluate the genetic diversity, structure, and divergence within and among populations of Lu. cruciata in the state of Chiapas, and to infer the intra-specific phylogeny using the 3' end of the mitochondrial cytochrome b gene. We analyzed 62 sequences from four Lu. cruciata populations and found 26 haplotypes, high genetic differentiation and restricted gene flow among populations (Fst=0.416, Nm=0.701, p<0.001). The highest diversity values were recorded in populations from Loma Bonita and Guadalupe Miramar. Three lineages (100% bootstrap and 7% overall divergence) were identified using a maximum likelihood phylogenetic analysis which showed high genetic divergence (17.2-22.7%). A minimum spanning haplotype network also supported separation into three lineages. Genetic structure and divergence within and among Lu. cruciata populations are hence affected by geographic heterogeneity and evolutionary background. Data obtained in the present study suggest that Lu. cruciata in the state of Chiapas consists of at least three lineages. Such findings may have implications for vector capacity and hence for vector control strategies.

  10. Common Garden Experiment Reveals Genetic Control of Phenotypic Divergence between Swamp Sparrow Subspecies That Lack Divergence in Neutral Genotypes

    PubMed Central

    Ballentine, Barbara; Greenberg, Russell

    2010-01-01

    Background Adaptive divergence between populations in the face of strong selection on key traits can lead to morphological divergence between populations without concomitant divergence in neutral DNA. Thus, the practice of identifying genetically distinct populations based on divergence in neutral DNA may lead to a taxonomy that ignores evolutionarily important, rapidly evolving, locally-adapted populations. Providing evidence for a genetic basis of morphological divergence between rapidly evolving populations that lack divergence in selectively neutral DNA will not only inform conservation efforts but also provide insight into the mechanisms of the early processes of speciation. The coastal plain swamp sparrow, a recent colonist of tidal marsh habitat, differs from conspecific populations in a variety of phenotypic traits yet remains undifferentiated in neutral DNA. Methods and Principal Findings Here we use an experimental approach to demonstrate that phenotypic divergence between ecologically separated populations of swamp sparrows is the result of local adaptation despite the lack of divergence in neutral DNA. We find that morphological (bill size and plumage coloration) and life history (reproductive effort) differences observed between wild populations were maintained in laboratory raised individuals suggesting genetic divergence of fitness related traits. Conclusions and Significance Our results support the hypothesis that phenotypic divergence in swamps sparrows is the result of genetic differentiation, and demonstrate that adaptive traits have evolved more rapidly than neutral DNA in these ecologically divergent populations that may be in the early stages of speciation. Thus, identifying evolutionarily important populations based on divergence in selectively neutral DNA could miss an important level of biodiversity and mislead conservation efforts. PMID:20419104

  11. Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni

    PubMed Central

    Elmer, Kathryn R; Dávila, José A; Lougheed, Stephen C

    2007-01-01

    Background The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the wide-spread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae) from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs). We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five species-specific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador. Results We identified three distinct and well-supported clades within the Ecuadorean range of E. ockendeni: an uplands clade spanning north to south, a northeastern and central lowlands clade, and a central and southeastern clade, which is basal. Clades are separated by 12% to 15% net corrected p-distance for cytochrome b, with comparatively low sequence divergence within clades. Clades marginally overlap in some geographic areas (e.g., Napo River basin) but are reproductively isolated, evidenced by diagnostic differences in microsatellite PCR amplification profiles or DNA repeat number and coalescent analyses (in MDIV) best modelled without migration. Using Bayesian (BEAST) and net phylogenetic estimates, the Southeastern Clade diverged from the Upland/Lowland clades in the mid-Miocene or late Oligocene. Lowland and Upland clades speciated more recently, in the early or late Miocene. Conclusion Our findings uncover previously unsuspected cryptic species

  12. Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae).

    PubMed

    Lexer, C; Wüest, R O; Mangili, S; Heuertz, M; Stölting, K N; Pearman, P B; Forest, F; Salamin, N; Zimmermann, N E; Bossolini, E

    2014-09-01

    Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.

  13. Genetics of ecological divergence during speciation

    PubMed Central

    Arnegard, Matthew E.; McGee, Matthew D.; Matthews, Blake; Marchinko, Kerry B.; Conte, Gina L.; Kabir, Sahriar; Bedford, Nicole; Bergek, Sara; Chan, Yingguang Frank; Jones, Felicity C.; Kingsley, David M.; Peichel, Catherine L.; Schluter, Dolph

    2014-01-01

    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Though this process is a major generator of biodiversity, its genetic basis remains poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but that depend on the ecological context. PMID:24909991

  14. Weathering instability and landscape evolution

    NASA Astrophysics Data System (ADS)

    Phillips, Jonathan D.

    2005-04-01

    likely; although stability may be present at intermediate temporal scales if weathering-erosion feedbacks are weak. The distinction is important because stability is associated with convergent evolution whereby the effects of initial variations or disturbances are reduced over time as the landscape converges toward a stable equilibrium state. Instability, by contrast, indicates divergent evolution, increasing differentiation over time, and the persistence and growth of disturbance effects and initial variations.

  15. Landscaping for energy efficiency

    SciTech Connect

    1995-04-01

    This publication by the National Renewable Energy Laboratory addresses the use of landscaping for energy efficiency. The topics of the publication include minimizing energy expenses; landscaping for a cleaner environment; climate, site, and design considerations; planning landscape; and selecting and planting trees and shrubs. A source list for more information on landscaping for energy efficiency and a reading list are included.

  16. Landscape Heterogeneity Modulates Forest Sensitivity to Climate

    NASA Astrophysics Data System (ADS)

    Hoylman, Z. H.; Jencso, K. G.; Hu, J.; Martin, J. T.

    2015-12-01

    Elevation dependent snowmelt magnitude and timing strongly influences net ecosystem productivity in forested mountain watersheds. However, previous work has provided little insight into how internal watershed topography may modulate plant available water, microclimate and therefore forest growth. We analyzed 331 tree cores from three coniferous tree species across a range of elevation, landscape positions and aspects in the Lubrecht Experimental Forest, Montana, USA. We compared the annual basal area increment (BAI) to measures of the annual climatic water deficit, hydro-meteorological data in sideslope and hollow positions, and topographic indices derived from a LiDAR digital elevation models. Results indicate strong relationships between measures of BAI and the topographic wetness index, with differing slopes dependent on tree species. Generally, trees located in wetter landscape positions (hollows) exhibited greater annual basal growth relative to trees located in drier landscape positions (sideslopes). At the watershed scale, we evaluated the relationships between convergence and divergence, LiDAR derived estimates of basal area and seasonal patterns of the Landsat derived Normalized Difference Vegetation Index (NDVI; 1984-2012).These indicated differential growth response due to elevation gradients, irradiance and local convergence and divergence. Wetter landscape positions have higher values of greenness and basal area than drier positions. These observations suggest that the topography of semi-arid watersheds is a necessary consideration for quantifying conifer productivity and resiliency, due to its potential to mediate local microclimate and subsurface water redistribution.

  17. Degree landscapes in scale-free networks

    NASA Astrophysics Data System (ADS)

    Axelsen, Jacob Bock; Bernhardsson, Sebastian; Rosvall, Martin; Sneppen, Kim; Trusina, Ala

    2006-09-01

    We generalize the degree-organizational view of real-world networks with broad degree distributions in a landscape analog with mountains (high-degree nodes) and valleys (low-degree nodes). For example, correlated degrees between adjacent nodes correspond to smooth landscapes (social networks), hierarchical networks to one-mountain landscapes (the Internet), and degree-disassortative networks without hierarchical features to rough landscapes with several mountains. To quantify the topology, we here measure the widths of the mountains and the separation between different mountains. We also generate ridge landscapes to model networks organized under constraints imposed by the space the networks are embedded in, associated to spatial or in molecular networks to functional localization.

  18. Rapid shape divergences between natural and introduced populations of a horned beetle partly mirror divergences between species.

    PubMed

    Pizzo, Astrid; Roggero, Angela; Palestrini, Claudia; Moczek, Armin P; Rolando, Antonio

    2008-01-01

    Onthophagus taurus is a polyphenic beetle in which males express alternative major (horned) and minor (hornless) morphologies largely dependent on larval nutrition. O. taurus was originally limited to a Turanic-European-Mediterranean distribution, but became introduced to several exotic regions in the late 1960s. Using geometric morphometrics, we investigate the present-day morphological shape differentiation patterns among native (Italian) and introduced (Western Australian and Eastern US) populations. We then contrast these divergences to those observed between native O. taurus and its sympatric sister species O. illyricus. Our analysis failed to find significant divergences between O. taurus populations in external morphological traits (head, pronotum) when analyses were conducted separately for each sex. However, when sexes and male morphs were analyzed together, three important differences among populations emerged. First, relative warp analyses showed that native and introduced populations diverged in certain shape components that normally distinguish major and minor male morphs. Second, comparison of covariation of body regions (head vs. pronotum) in the three populations showed that populations diverged in the nature of this covariation, suggesting that different body regions are not totally constrained to evolve in concert. Lastly, and most importantly, the analysis of genitalic shape revealed little to no divergence of female genitalia, but unexpected substantial differentiation of male genitalia among the three O. taurus populations. This suggests that genitalic shape divergence can occur extremely rapidly even in the absence of sympatry and possible reinforcement, and that the genitalia of males and females may diverge independent of one another, at least during the early stage of interpopulational divergence. Interpopulation divergences in O. taurus mirrored aspects of interspecific divergences between O. taurus and O. illyricus in some cases but not

  19. Divergence in Dialogue

    PubMed Central

    Healey, Patrick G. T.; Purver, Matthew; Howes, Christine

    2014-01-01

    One of the best known claims about human communication is that people's behaviour and language use converge during conversation. It has been proposed that these patterns can be explained by automatic, cross-person priming. A key test case is structural priming: does exposure to one syntactic structure, in production or comprehension, make reuse of that structure (by the same or another speaker) more likely? It has been claimed that syntactic repetition caused by structural priming is ubiquitous in conversation. However, previous work has not tested for general syntactic repetition effects in ordinary conversation independently of lexical repetition. Here we analyse patterns of syntactic repetition in two large corpora of unscripted everyday conversations. Our results show that when lexical repetition is taken into account there is no general tendency for people to repeat their own syntactic constructions. More importantly, people repeat each other's syntactic constructions less than would be expected by chance; i.e., people systematically diverge from one another in their use of syntactic constructions. We conclude that in ordinary conversation the structural priming effects described in the literature are overwhelmed by the need to actively engage with our conversational partners and respond productively to what they say. PMID:24919186

  20. The Sahara's Diverse Landscape

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Vast stretches of uninterrupted sand are only one kind of Saharan landscape. This true-color MODIS image from November 9, 2001, reveals a diversity of land surface features, including ancient lava flows and volcanoes. Beginning at upper left and moving clockwise are the countries of Algeria, Tunisia, Libya, Chad, and Niger. Evidence of previous volcanic activity in the Sahara can be found in northeastern Chad, in particular, in a region known as Tibesti. Reaching up out of the surrounding desert, the dark rock of the Tibesti Plateau stands out in dark brown against the sand. Scattered throughout the region are the circular cones and calderas of several volcanoes. The dark remains of a lava flow mark the location of the Tousside volcano. North of Tibesti, in Libya, more dark-colored lava beds leave their mark on the landscape. Variety exists in Algeria, where the Grand Erg Oriental desert (far upper left) is hemmed in to the south by the Tinrhert Plateau. South of the Plateau, desert resumes briefly, only to give way to a mountainous region traced with impermanent rivers. In northern Niger, a sinuous gray-green line marks the edge of an escarpment that separates the Mangueni Plateau to the north from the rock deserts to the south. Image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC

  1. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence

    PubMed Central

    Kellom, Matthew; Raymond, Jason

    2016-01-01

    The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive “top-down” centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance. PMID:27536963

  2. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    PubMed

    Kellom, Matthew; Raymond, Jason

    2016-01-01

    The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance. PMID:27536963

  3. Segmenting the human genome based on states of neutral genetic divergence.

    PubMed

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-01

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  4. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

    PubMed Central

    Via, Sara

    2012-01-01

    In allopatric populations, geographical separation simultaneously isolates the entire genome, allowing genetic divergence to accumulate virtually anywhere in the genome. In sympatric populations, however, the strong divergent selection required to overcome migration produces a genetic mosaic of divergent and non-divergent genomic regions. In some recent genome scans, each divergent genomic region has been interpreted as an independent incidence of migration/selection balance, such that the reduction of gene exchange is restricted to a few kilobases around each divergently selected gene. I propose an alternative mechanism, ‘divergence hitchhiking’ (DH), in which divergent selection can reduce gene exchange for several megabases around a gene under strong divergent selection. Not all genes/markers within a DH region are divergently selected, yet the entire region is protected to some degree from gene exchange, permitting genetic divergence from mechanisms other than divergent selection to accumulate secondarily. After contrasting DH and multilocus migration/selection balance (MM/SB), I outline a model in which genomic isolation at a given genomic location is jointly determined by DH and genome-wide effects of the progressive reduction in realized migration, then illustrate DH using data from several pairs of incipient species in the wild. PMID:22201174

  5. Infrared divergences in de Sitter space

    SciTech Connect

    Polarski, D. Service d'Astrophysique, CEN Saclay, 91191 Gif-sur-Yvette CEDEX, France)

    1991-03-15

    Infrared divergences in de Sitter space are considered. It is shown that symmetry breaking is unavoidable only when the infrared divergence is strong enough. The static vacuum has no symmetry breaking despite the presence of an infrared divergence.

  6. Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes.

    PubMed

    Lobkovsky, Alexander E; Wolf, Yuri I; Koonin, Eugene V

    2013-07-01

    When selection is strong and mutations are rare, evolution can be thought of as an uphill trajectory in a rugged fitness landscape. In this context the fitness landscape is a directed acyclic graph in which nodes are genotypes and edges lead from lower to higher fitness genotypes that differ by a single mutation. Because the space of genotypes is vastly multi-dimensional, classification of fitness landscapes is challenging. Many proposed summary characteristics of fitness landscapes attempt to quantify biologically relevant and intuitive notions such as roughness or peak accessibility in alternative ways. Here we explore, in different types of landscapes, the behavior of the recently introduced mean path divergence which quantifies the degree of similarity among evolutionary trajectories with the same endpoints. We find that monotonic trajectories in empirical and model fitness landscapes are significantly more constrained, with low median path divergence, than those in purely additive landscapes. By contrast, transcription factor sequence specificity (aptamer binding affinity) landscapes are markedly smoother and allow substantial variability in monotonic paths that can be greater than that in fully additive landscapes. We propose that the smoothness of the specificity landscapes is a consequence of the simple dependence of the transcription factor binding affinity on the aptamer sequence in contrast to the complex sequence-fitness mapping in folding landscapes.

  7. Effective potential and quadratic divergences

    SciTech Connect

    Einhorn, M.B. ); Jones, D.R.T. )

    1992-12-01

    We use the effective potential to give a simple derivation of Veltman's formula for the quadratic divergence in the Higgs self-energy. We also comment on the effect of going beyond the one-loop approximation.

  8. Ultraviolet divergences in cosmological correlations

    SciTech Connect

    Weinberg, Steven

    2011-03-15

    A method is developed for dealing with ultraviolet divergences in calculations of cosmological correlations, which does not depend on dimensional regularization. An extended version of the WKB approximation is used to analyze the divergences in these calculations, and these divergences are controlled by the introduction of Pauli-Villars regulator fields. This approach is illustrated in the theory of a scalar field with arbitrary self-interactions in a fixed flat-space Robertson-Walker metric with arbitrary scale factor a(t). Explicit formulas are given for the counterterms needed to cancel all dependence on the regulator properties, and an explicit prescription is given for calculating finite regulator-independent correlation functions. The possibility of infrared divergences in this theory is briefly considered.

  9. Union of phylogeography and landscape genetics.

    PubMed

    Rissler, Leslie J

    2016-07-19

    Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the "microgeographic races" of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography. PMID:27432989

  10. Union of phylogeography and landscape genetics

    PubMed Central

    Rissler, Leslie J.

    2016-01-01

    Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the “microgeographic races” of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography. PMID:27432989

  11. Union of phylogeography and landscape genetics.

    PubMed

    Rissler, Leslie J

    2016-07-19

    Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the "microgeographic races" of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.

  12. The Campus Landscape.

    ERIC Educational Resources Information Center

    du Von, Jay

    1966-01-01

    All across the country, landscaping and site development are coming to the fore as essential and integral parts of university planning and development. This reprint concentrates on the function of landscape architecture, and briefly examines some of the major responsibilities of the landscape architect in planning a campus. Included are--(1)…

  13. Gardener and Landscape Worker. Student Material. Competency Based Education Curriculum.

    ERIC Educational Resources Information Center

    Long, Diana

    This secondary-level, competency-based curriculum contains modules for Gardener and Landscape Worker. A companion teacher's guide is available separately--see note. Each module contains a number of West Virginia-validated Gardener and Landscape Worker tasks/competencies with a performance guide listing the steps needed to perform each task,…

  14. Graybody Factors and Infrared Divergences

    NASA Astrophysics Data System (ADS)

    Anderson, Paul; Fabbri, Alessandro; Balbinot, Roberto; Parentani, Renaud

    2015-04-01

    A method of computing the gray-body factors for static spherically symmetric and BEC acoustic black holes using a Volterra integral equation is given. The results are used to investigate infrared divergences in the particle number, two-point function, point-split stress-energy tensor and density-density correlation function. Infrared divergences in the particle number and two-point function occur if the gray-body factor approaches a nonzero constant in the zero frequency limit, as happens for Schwarzschild-de Sitter black holes and BEC acoustic black holes. However, no infrared divergences occur in the point-split stress-energy tensor or the density-density correlation function. Supported in part by the National Science Foundation under Grant Nos. PHY-0856050 and PHY-1308325.

  15. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  16. Aeroacoustic Resonance with Convergent-Divergent Nozzles

    NASA Technical Reports Server (NTRS)

    Zaman, K. B. M. Q.; Dahl, M. D.

    1999-01-01

    Convergent-divergent nozzles, when run at off-design conditions, often undergo flow resonance accompanied by the emission of a tone. Apart from screech occurring at higher operating pressures, resonance is also common at lower Mach numbers near transonic as well as subsonic conditions. With data from six nozzles of different size and design Mach number, the present paper documents the characteristics of the latter phenomenon that is morphologically quite different from conventional screech. The resonance is due to a feedback loop internal to the nozzle and is apparently driven by unsteady laminar boundary layer separation near the throat of the nozzle. Appropriate boundary layer tripping prior to the throat is found to eliminate or alter most of the tones. The Helmholtz number of the resonance, based on the throat-to-exit length, is found to attain a value of approximately 0.15 at M(sub j)=1 for all nozzles. However, its variation with M(sub j) may be different and depend on the nozzle geometry. With nozzles having larger throat-to-exit angle of divergence, the frequency is found to increase, in some cases having stage jumps to lower frequencies, with increasing operating pressure. With nozzles having smaller angle of divergence, the frequency variation exhibits an increase followed by a decrease involving one prominent stage occurring around transonic (M(sub j)= 1) condition. While the mechanisms remain far from completely clear, a model involving downstream propagating aerodynamic disturbance together with acoustic feedback explains the overall frequency characteristics for most cases.

  17. Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

    PubMed

    Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

    2013-08-01

    Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure.

  18. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

    PubMed

    Gómez-Marín, Carlos; Tena, Juan J; Acemel, Rafael D; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-06-16

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  19. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

    PubMed Central

    Gómez-Marín, Carlos; Tena, Juan J.; Acemel, Rafael D.; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A.; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-01-01

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  20. Equivalence theorem and infrared divergences

    SciTech Connect

    Torma, T.

    1996-08-01

    We look at the equivalence theorem as a statement about the absence of polynomial infrared divergences when {ital m}{sub {ital W}}{r_arrow}0. We prove their absence in a truncated toy model and conjecture that, if they exist at all, they are due to couplings between light particles. {copyright} {ital 1996 The American Physical Society.}

  1. Divergent Thinking and Interview Ratings

    ERIC Educational Resources Information Center

    Batey, Mark; Rawles, Richard; Furnham, Adrian

    2009-01-01

    This study examined divergent thinking (DT) test scores of applicants taking part in a selection procedure for an undergraduate psychology degree (N = 370). Interviewers made six specific (creative intelligence, motivation, work habits, emotional stability, sociability, and social responsibility) and one overall recommendation rating on each…

  2. Another Paper Landscape?

    ERIC Educational Resources Information Center

    Radlak, Ted

    2001-01-01

    Describes the University of Toronto's extensive central campus revitalization plan to create lush landscapes that add to the school's image and attractiveness. Drawings and photographs are included. (GR)

  3. Landscape epidemiology of plant diseases.

    PubMed

    Plantegenest, Manuel; Le May, Christophe; Fabre, Frédéric

    2007-10-22

    Many agricultural landscapes are characterized by a high degree of heterogeneity and fragmentation. Landscape ecology focuses on the influence of habitat heterogeneity in space and time on ecological processes. Landscape epidemiology aims at applying concepts and approaches originating from landscape ecology to the study of pathogen dynamics at the landscape scale. However, despite the strong influence that the landscape properties may have on the spread of plant diseases, landscape epidemiology has still received little attention from plant pathologists. Some recent methodological and technological progress provides new and powerful tools to describe and analyse the spatial patterns of host-pathogen interactions. Here, we review some important topics in plant pathology that may benefit from a landscape perspective. These include the influence of: landscape composition on the global inoculum pressure; landscape heterogeneity on pathogen dynamics; landscape structure on pathogen dispersal; and landscape properties on the emergence of pathogens and on their evolution.

  4. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  5. The complete local genotype–phenotype landscape for the alternative splicing of a human exon

    PubMed Central

    Julien, Philippe; Miñana, Belén; Baeza-Centurion, Pablo; Valcárcel, Juan; Lehner, Ben

    2016-01-01

    The properties of genotype–phenotype landscapes are crucial for understanding evolution but are not characterized for most traits. Here, we present a >95% complete local landscape for a defined molecular function—the alternative splicing of a human exon (FAS/CD95 exon 6, involved in the control of apoptosis). The landscape provides important mechanistic insights, revealing that regulatory information is dispersed throughout nearly every nucleotide in an exon, that the exon is more robust to the effects of mutations than its immediate neighbours in genotype space, and that high mutation sensitivity (evolvability) will drive the rapid divergence of alternative splicing between species unless it is constrained by selection. Moreover, the extensive epistasis in the landscape predicts that exonic regulatory sequences may diverge between species even when exon inclusion levels are functionally important and conserved by selection. PMID:27161764

  6. Planetary Landscape Geography

    NASA Astrophysics Data System (ADS)

    Hargitai, H.

    INTRODUCTION Landscape is one of the most often used category in physical ge- ography. The term "landshap" was introduced by Dutch painters in the 15-16th cen- tury. [1] The elements that build up a landscape (or environment) on Earth consists of natural (biogenic and abiogenic - lithologic, atmospheric, hydrologic) and artificial (antropogenic) factors. Landscape is a complex system of these different elements. The same lithology makes different landscapes under different climatic conditions. If the same conditions are present, the same landscape type will appear. Landscapes build up a hierarchic system and cover the whole surface. On Earth, landscapes can be classified and qualified according to their characteristics: relief forms (morphology), and its potential economic value. Aesthetic and subjective parameters can also be considered. Using the data from landers and data from orbiters we can now classify planetary landscapes (these can be used as geologic mapping units as well). By looking at a unknown landscape, we can determine the processes that created it and its development history. This was the case in the Pathfinder/Sojourner panoramas. [2]. DISCUSSION Planetary landscape evolution. We can draw a raw landscape develop- ment history by adding the different landscape building elements to each other. This has a strong connection with the planet's thermal evolution (age of the planet or the present surface materials) and with orbital parameters (distance from the central star, orbit excentricity etc). This way we can build a complex system in which we use differ- ent evolutional stages of lithologic, atmospheric, hydrologic and biogenic conditions which determine the given - Solar System or exoplanetary - landscape. Landscape elements. "Simple" landscapes can be found on asteroids: no linear horizon is present (not differentiated body, only impact structures), no atmosphere (therefore no atmospheric scattering - black sky as part of the landscape) and no

  7. Rationalizing three-dimensional activity landscapes and the influence of molecular representations on landscape topology and the formation of activity cliffs.

    PubMed

    Peltason, Lisa; Iyer, Preeti; Bajorath, Jürgen

    2010-06-28

    Activity landscapes are defined by potency and similarity distributions of active compounds and reflect the nature of structure-activity relationships (SARs). Three-dimensional (3D) activity landscapes are reminiscent of topographical maps and particularly intuitive representations of compound similarity and potency distributions. From their topologies, SAR characteristics can be deduced. Accordingly, idealized theoretical landscape models have been utilized to rationalize SAR features, but "true" 3D activity landscapes have not yet been described in detail. Herein we present a computational approach to derive approximate 3D activity landscapes for actual compound data sets and to analyze exemplary landscape representations. These activity landscapes are generated within a consistent reference frame so that they can be compared across different activity classes. We show that SAR features of compound data sets can be derived from the topology of landscape models. A notable correlation is observed between global SAR phenotypes, assigned on the basis of SAR discontinuity scoring, and characteristic landscape topologies. We also show that different molecular representations can substantially alter the topology of activity landscapes for a given data set and modulate the formation of activity cliffs, which represent the most prominent landscape features. Depending on the choice of molecular representations, compounds forming a steep activity cliff in a given landscape might be separated in another and no longer form a cliff. However, comparison of alternative activity landscapes makes it possible to focus on compound subsets having high SAR information content.

  8. Estimating a geographically explicit model of population divergence.

    PubMed

    Knowles, L Lacey; Carstens, Bryan C

    2007-03-01

    consider the pattern of coalescence in the gene genealogies, the population-divergence model that best fits the data was estimated by considering the pattern of gene lineage coalescence across multiple individuals, as well as loci. These results indicate that sampling of multiple individuals per population is critical to obtaining an accurate estimate of the history of divergence so that the signal of common ancestry can be separated from the confounding influence of gene flow-even though estimates suggest that gene flow is not a predominant factor structuring patterns of genetic variation across these sky island populations. They also suggest that the gene genealogies contain information about population relationships, despite the lack of complete sorting of gene lineages. What emerges from the analyses is a model of population divergence that incorporates both contemporary distributions and historical associations, and shows a latitudinal and regional structuring of populations reminiscent of population displacements into multiple glacial refugia. Because the population-divergence model itself is built upon the specific events shaping the history of M. oregonensis, it provides a framework for estimating additional population-genetic parameters relevant to understanding the processes governing differentiation in geographically structured species and avoids the problems of relying on overly simplified and inaccurate divergence models. The utility of these approaches, as well as the caveats and future improvements, for estimating population relationships and historical associations relevant to genetic analyses of geographically structured species are discussed. PMID:17348914

  9. Fractal free energy landscapes in structural glasses.

    PubMed

    Charbonneau, Patrick; Kurchan, Jorge; Parisi, Giorgio; Urbani, Pierfrancesco; Zamponi, Francesco

    2014-01-01

    Glasses are amorphous solids whose constituent particles are caged by their neighbours and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers. Here we show, using theory and numerical simulation, that the landscape is much rougher than is classically assumed. Deep in the glass, it undergoes a 'roughness transition' to fractal basins, which brings about isostaticity and marginal stability on approaching jamming. Critical exponents for the basin width, the weak force distribution and the spatial spread of quasi-contacts near jamming can be analytically determined. Their value is found to be compatible with numerical observations. This advance incorporates the jamming transition of granular materials into the framework of glass theory. Because temperature and pressure control what features of the landscape are experienced, glass mechanics and transport are expected to reflect the features of the topology we discuss here. PMID:24759041

  10. Quasispecies on Fitness Landscapes.

    PubMed

    Schuster, Peter

    2016-01-01

    Selection-mutation dynamics is studied as adaptation and neutral drift on abstract fitness landscapes. Various models of fitness landscapes are introduced and analyzed with respect to the stationary mutant distributions adopted by populations upon them. The concept of quasispecies is introduced, and the error threshold phenomenon is analyzed. Complex fitness landscapes with large scatter of fitness values are shown to sustain error thresholds. The phenomenological theory of the quasispecies introduced in 1971 by Eigen is compared to approximation-free numerical computations. The concept of strong quasispecies understood as mutant distributions, which are especially stable against changes in mutations rates, is presented. The role of fitness neutral genotypes in quasispecies is discussed.

  11. Geomorphic control of landscape carbon accumulation

    USGS Publications Warehouse

    Rosenbloom, N.A.; Harden, J.W.; Neff, J.C.; Schimel, D.S.

    2006-01-01

    We use the CREEP process-response model to simulate soil organic carbon accumulation in an undisturbed prairie site in Iowa. Our primary objectives are to identify spatial patterns of carbon accumulation, and explore the effect of erosion on basin-scale C accumulation. Our results point to two general findings. First, redistribution of soil carbon by erosion results in a net increase in basin-wide carbon storage relative to a noneroding environment. Landscape-average mean residence times are increased in an eroding landscape owing to the burial/preservation of otherwise labile C. Second, field observations taken along a slope transect may overlook significant intraslope variations in carbon accumulation. Spatial patterns of modeled deep C accumulation are complex. While surface carbon with its relatively short equilibration time is predictable from surface properties, deep carbon is strongly influenced by the landscape's geomorphic and climatic history, resulting in wide spatial variability. Convergence and divergence associated with upland swales and interfluves result in bimodal carbon distributions in upper and mid slopes; variability in carbon storage within modeled mid slopes was as high as simulated differences between erosional shoulders and depositional valley bottoms. The bimodality of mid-slope C variability in the model suggests that a three-dimensional sampling strategy is preferable over the traditional two-dimensional analog or "catena" approach. Copyright 2006 by the American Geophysical Union.

  12. Landscape and Flux Framework for Networks

    NASA Astrophysics Data System (ADS)

    Wang, Jin

    2010-03-01

    We developed a global framework to robustness of networks applied to biological oscillation by directly exploring the probabilistic distribution in the whole protein concentration space (therefore global) for oscillations with a stochastic approach. We uncovered two distinct natures essential for characterizing the global probabilistic dynamics of biological oscillations: the underlying potential landscape directly (logarithmically) related to the steady state probability distribution and the corresponding flux related to the speed of the protein concentration changes. We found that the underlying potential landscape for the oscillation has a distinct closed ring valley shape when the fluctuations are small. This global landscape structure leads to attractions of the system to the ring valley. On the ring, we found that the non-equilibrium flux is the driving force for oscillations. Therefore, both structured landscape and flux are needed to guarantee a global robust oscillation. The barrier height separating the oscillation ring and other areas derived from the landscape topography, is shown to be correlated with the escaping time from the limit cycle attractor, and therefore provides a quantitative measure of the robustness for the network. The landscape becomes shallower and the closed ring valley shape structure becomes weaker (lower barrier height) with larger fluctuations. We observe that the period and the amplitude of the oscillations are more dispersed and oscillations become less coherent when the fluctuations increase. When the fluctuations become very large, the landscape is flattened out and coherence of the oscillations is destroyed. Robustness decreases. When the fluctuations are small, changing the inherent parameters of the system such as chemical rates, equilibrium constants and concentrations can lead to different robust behaviors such as multi-stability. By exploring the sensitivity of barrier height on the parameters of the system, we can

  13. Ultraviolet divergences and supersymmetric theories

    SciTech Connect

    Sagnotti, A.

    1984-09-01

    This article is closely related to the one by Ferrara in these same Proceedings. It deals with what is perhaps the most fascinating property of supersymmetric theories, their improved ultraviolet behavior. My aim here is to present a survey of the state of the art as of August, 1984, and a somewhat more detailed discussion of the breakdown of the superspace power-counting beyond N = 2 superfields. A method is also described for simplifying divergence calculations that uses the locality of subtracted Feynman integrals. 74 references.

  14. Ultracapacitor separator

    DOEpatents

    Wei, Chang; Jerabek, Elihu Calvin; LeBlanc, Jr., Oliver Harris

    2001-03-06

    An ultracapacitor includes two solid, nonporous current collectors, two porous electrodes separating the collectors, a porous separator between the electrodes and an electrolyte occupying the pores in the electrodes and separator. The electrolyte is a polar aprotic organic solvent and a salt. The porous separator comprises a wet laid cellulosic material.

  15. Urban thermal landscape characterization and analysis

    NASA Astrophysics Data System (ADS)

    Xue, Y.; Fung, T.; Tsou, J.

    2014-03-01

    Urban warming is sensitive to the nature (thermal properties, including albedo, water content, heat capacity and thermal conductivity) and the placement (surface geometry or urban topography) of urban surface. In this research, the pattern and variation of urban surface temperature is regarded as one kind of landscape, urban thermal landscape, which is assumed as the presentation of local surface heating process upon urban landscape. The goal of this research is to develop a research framework incorporating geospatial statistics, thermal infrared remote sensing and landscape ecology to study the urban effect on local surface thermal landscape regarding both the pattern and process. This research chose Hong Kong as the case study. Within the study area, urban and rural area coexists upon a hilly topography. In order to probe the possibility of local surface warming mechanism discrepancy between urban and rural area, the sample points are grouped into urban and rural categories in according with the land use map taken into a linear regression model separately to examine the possible difference in local warming mechanism. Global regression analysis confirmed the relationship between environmental factors and surface temperature and the urban-rural distinctive mechanism of dominating diurnal surface warming is uncovered.

  16. Agri-environmental collaboratives as bridging organisations in landscape management.

    PubMed

    Prager, Katrin

    2015-09-15

    In recent years, landscape and its management has become a focus of policies and academic conceptualisation. Landscape is understood as a concept of interconnected natural and human systems. Its management must take into account the dynamic interdependencies and diverging interests of various stakeholders at different levels. Bridging organisations can provide an arena for trust-building, conflict resolution, learning and collaboration between relevant stakeholders. This paper draws on two strands of literature - landscape governance and co-management of social-ecological systems - to investigate the contributions of agri-environmental collaboratives (AEC) to sustainable landscape management. Based on data from 41 interviews with key informants and AEC members in Germany and the Netherlands, six fields of contributions were identified: policy implementation and service provision; coordination and mediation; awareness raising and behaviour change; care for 'everyday' landscapes; maintenance and protection of landscapes (including species and habitats); and income generation and economic benefits. Some of the contributions evolve around the specific role of AEC as bridging organisations, but other contributions such as economic benefits emerge beyond this analytical lens. The paper therefore emphasises holistic, bottom up assessment of AEC contributions and argues that governments should support such organisations through i) funding for facilitators and ii) funding for impact monitoring and data management.

  17. Agri-environmental collaboratives as bridging organisations in landscape management.

    PubMed

    Prager, Katrin

    2015-09-15

    In recent years, landscape and its management has become a focus of policies and academic conceptualisation. Landscape is understood as a concept of interconnected natural and human systems. Its management must take into account the dynamic interdependencies and diverging interests of various stakeholders at different levels. Bridging organisations can provide an arena for trust-building, conflict resolution, learning and collaboration between relevant stakeholders. This paper draws on two strands of literature - landscape governance and co-management of social-ecological systems - to investigate the contributions of agri-environmental collaboratives (AEC) to sustainable landscape management. Based on data from 41 interviews with key informants and AEC members in Germany and the Netherlands, six fields of contributions were identified: policy implementation and service provision; coordination and mediation; awareness raising and behaviour change; care for 'everyday' landscapes; maintenance and protection of landscapes (including species and habitats); and income generation and economic benefits. Some of the contributions evolve around the specific role of AEC as bridging organisations, but other contributions such as economic benefits emerge beyond this analytical lens. The paper therefore emphasises holistic, bottom up assessment of AEC contributions and argues that governments should support such organisations through i) funding for facilitators and ii) funding for impact monitoring and data management. PMID:26203877

  18. Two-time-scale population evolution on a singular landscape

    NASA Astrophysics Data System (ADS)

    Xu, Song; Jiao, Shuyun; Jiang, Pengyao; Ao, Ping

    2014-01-01

    Under the effect of strong genetic drift, it is highly probable to observe gene fixation or gene loss in a population, shown by singular peaks on a potential landscape. The genetic drift-induced noise gives rise to two-time-scale diffusion dynamics on the bipeaked landscape. We find that the logarithmically divergent (singular) peaks do not necessarily imply infinite escape times or biological fixations by iterating the Wright-Fisher model and approximating the average escape time. Our analytical results under weak mutation and weak selection extend Kramers's escape time formula to models with B (Beta) function-like equilibrium distributions and overcome constraints in previous methods. The constructed landscape provides a coherent description for the bistable system, supports the quantitative analysis of bipeaked dynamics, and generates mathematical insights for understanding the boundary behaviors of the diffusion model.

  19. Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species.

    PubMed

    McGovern, Tamara M; Keever, Carson C; Saski, Christopher A; Hart, Michael W; Marko, Peter B

    2010-11-01

    Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation. PMID:21040048

  20. Landscape evolution (A Review)

    PubMed Central

    Sharp, Robert P.

    1982-01-01

    Landscapes are created by exogenic and endogenic processes acting along the interface between the lithosphere and the atmosphere and hydrosphere. Various landforms result from the attack of weathering and erosion upon the highly heterogeneous lithospheric surface. Landscapes are dynamic, acutely sensitive to natural and artificial perturbation. Undisturbed, they can evolve through a succession of stages to a plain of low relief. Often, the progression of an erosion cycle is interrupted by tectonic or environmental changes; thus, many landscapes preserve vestiges of earlier cycles useful in reconstructing the recent history of Earth's surface. Landforms are bounded by slopes, so their evolution is best understood through study of slopes and the complex of factors controlling slope character and development. The substrate, biosphere, climatic environment, and erosive processes are principal factors. Creep of the disintegrated substrate and surface wash by water are preeminent. Some slopes attain a quasisteady form and recede parallel to themselves (backwearing); others become ever gentler with time (downwearing). The lovely convex/rectilinear/concave profile of many debris-mantled slopes reflects an interplay between creep and surface wash. Landscapes of greatest scenic attraction are usually those in which one or two genetic factors have strongly dominated or those perturbed by special events. Nature has been perturbing landscapes for billions of years, so mankind can learn about landscape perturbation from natural examples. Images

  1. DISSIPATIVE DIVERGENCE OF RESONANT ORBITS

    SciTech Connect

    Batygin, Konstantin; Morbidelli, Alessandro

    2013-01-01

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

  2. Precision cosmology and the landscape

    SciTech Connect

    Bousso, Raphael; Bousso, Raphael

    2006-10-01

    After reviewing the cosmological constant problem -- why is Lambda not huge? -- I outline the two basic approaches that had emerged by the late 1980s, and note that each made a clear prediction. Precision cosmological experiments now indicate that the cosmological constant is nonzero. This result strongly favors the environmental approach, in which vacuum energy can vary discretely among widely separated regions in the universe. The need to explain this variation from first principles constitutes an observational constraint on fundamental theory. I review arguments that string theory satisfies this constraint, as it contains a dense discretuum of metastable vacua. The enormous landscape of vacua calls for novel, statistical methods of deriving predictions, and it prompts us to reexamine our description of spacetime on the largest scales. I discuss the effects of cosmological dynamics, and I speculate that weighting vacua by their entropy production may allow for prior-free predictions that do not resort to explicitly anthropic arguments.

  3. Guises and disguises of quadratic divergences

    SciTech Connect

    Cherchiglia, A.L.; Vieira, A.R.; Hiller, Brigitte; Baêta Scarpelli, A.P.; Sampaio, Marcos

    2014-12-15

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

  4. Geomorpho-Landscapes

    NASA Astrophysics Data System (ADS)

    Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

    2014-05-01

    Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

  5. From landscape to domain: Soils role in landscape classifications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil landscape classifications are designed to divide landscapes into units with significance for the provisioning and regulating of ecosystem services and the development of conservation plans for natural resources. More specifically, such classifications serve as the basis for stratifying manageme...

  6. Modeling animal landscapes.

    PubMed

    Porter, W P; Ostrowski, S; Williams, J B

    2010-01-01

    There is an increasing need to assess the effects of climate and land-use change on habitat quality, ideally from a mechanistic basis. The symposium "Molecules to Migration: Pressures of Life" at the Fourth International Conference in Africa for Comparative Physiology and Biochemistry, Maasai Mara National Reserve, Kenya, 2008, illustrated how the principles of biophysical ecology can capture the mechanistic links between organisms, climate, and other habitat features. These principles provide spatially explicit assessments of habitat quality from a physiological perspective (i.e., "animal landscapes") that can be validated independently of the data used to derive and parameterize them. The contents of this symposium showcased how the modeling of animal landscapes can be used to assess key issues in applied and theoretical ecology. The presentations included applications to amphibians, reptiles, birds, and mammals. The rare Arabian oryx on the Arabian Peninsula is used as an example for energetic calculations and their implications for behavior on the landscape. PMID:20670170

  7. Divergent Thinking and Age-Related Changes

    ERIC Educational Resources Information Center

    Palmiero, Massimiliano; Di Giacomo, Dina; Passafiume, Domenico

    2014-01-01

    Aging can affect cognition in different ways. The extent to which aging affects divergent thinking is unclear. In this study, younger and older adults were compared at the performance on the Torrance Test of Creative Thinking in visual and verbal form. Results showed that older adults can think divergently as younger participants, although they…

  8. Sampling in landscape genomics.

    PubMed

    Manel, Stéphanie; Albert, Cécile H; Yoccoz, Nigel G

    2012-01-01

    Landscape genomics, based on the sampling of individuals genotyped for a large number of markers, may lead to the identification of regions of the genome correlated to selection pressures caused by the environment. In this chapter, we discuss sampling strategies to be used in a landscape genomics approach. We suggest that designs based on model-based stratification using the climatic and/or biological spaces are in general more efficient than designs based on the geographic space. More work is needed to identify designs that allow disentangling environmental selection pressures versus other processes such as range expansions or hierarchical population structure.

  9. Labyrinthine granular landscapes.

    PubMed

    Caps, H; Vandewalle, N

    2001-11-01

    We have numerically studied a model of granular landscape eroded by wind. We show the appearance of labyrinthic patterns when the wind orientation turns by 90 degrees. The occurrence of such structures is discussed. Moreover, we introduce the density n(k) of "defects" as the dynamic parameter governing the landscape evolution. A power-law behavior of n(k) is found as a function of time. In the case of wind variations, the exponent (drastically) shifts from two to one. The presence of two asymptotic values of n(k) implies the irreversibility of the labyrinthic formation process.

  10. MHD simple waves and the divergence wave

    SciTech Connect

    Webb, G. M.; Pogorelov, N. V.; Zank, G. P.

    2010-03-25

    In this paper we investigate magnetohydrodynamic (MHD) simple divergence waves in MHD, for models in which nablacentre dotBnot =0. These models are related to the eight wave Riemann solvers in numerical MHD, in which the eighth wave is the divergence wave associated with nablacentre dotBnot =0. For simple wave solutions, all physical variables (the gas density, pressure, fluid velocity, entropy, and magnetic field induction in the MHD case) depend on a single phase function phi. We consider the form of the MHD equations used by both Powell et al. and Janhunen. It is shown that the Janhunen version of the equations possesses fully nonlinear, exact simple wave solutions for the divergence wave, but no physically meaningful simple divergence wave solution exists for the Powell et al. system. We suggest that the 1D simple, divergence wave solution for the Janhunen system, may be useful for the testing and validation of numerical MHD codes.

  11. Vorticity and Divergence in the Solar Photosphere

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Noyes, Robert W.; Tarbell, Theodore D.; Title, Alan M.

    1995-07-01

    We have studied an outstanding sequence of continuum images of the solar granulation from Pic du Midi Observatory. We have calculated the horizontal vector flow field using a correlation tracking algorithm, and from this determined three scalar fields: the vertical component of the curl, the horizontal divergence, and the horizontal flow speed. The divergence field has substantially longer coherence time and more power than does the curl field. Statistically, curl is better correlated with regions of negative divergence that is, the vertical vorticity is higher in downflow regions, suggesting excess vorticity in intergranular lanes. The average value of the divergence is largest (i.e., outflow is largest) where the horizontal speed is large; we associate these regions with exploding granules. A numerical simulation of general convection also shows similar statistical differences between curl and divergence. Some individual small bright points in the granulation pattern show large local vorticities.

  12. Vorticity and divergence in the solar photosphere

    NASA Technical Reports Server (NTRS)

    Wang, YI; Noyes, Robert W.; Tarbell, Theodore D.; Title, Alan M.

    1995-01-01

    We have studied an outstanding sequence of continuum images of the solar granulation from Pic du Midi Observatory. We have calculated the horizontal vector flow field using a correlation tracking algorithm, and from this determined three scalar field: the vertical component of the curl; the horizontal divergence; and the horizontal flow speed. The divergence field has substantially longer coherence time and more power than does the curl field. Statistically, curl is better correlated with regions of negative divergence - that is, the vertical vorticity is higher in downflow regions, suggesting excess vorticity in intergranular lanes. The average value of the divergence is largest (i.e., outflow is largest) where the horizontal speed is large; we associate these regions with exploding granules. A numerical simulation of general convection also shows similar statistical differences between curl and divergence. Some individual small bright points in the granulation pattern show large local vorticities.

  13. Divergent thermopower without a quantum phase transition.

    PubMed

    Limtragool, Kridsanaphong; Phillips, Philip W

    2014-08-22

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

  14. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

    PubMed

    Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

    2015-09-22

    Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an

  15. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

    PubMed

    Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

    2015-09-22

    Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an

  16. Adaptive genetic divergence along narrow environmental gradients in four stream insects.

    PubMed

    Watanabe, Kozo; Kazama, So; Omura, Tatsuo; Monaghan, Michael T

    2014-01-01

    A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified the environmental characteristics contributing to divergence by comparing genetic distances at non-neutral loci between sites with Euclidean distances for each of 15 environmental variables. Comparisons were made using partial Mantel tests to control for geographic distance. In all four species, we found strong evidence for non-neutral divergence along environmental gradients at between 6 and 21 loci per species. The relative contribution of these environmental variables to each species' ecological niche was quantified as the specialization index, S, based on ecological data. In each species, the variable most significantly correlated with genetic distance at non-neutral loci was the same variable along which each species was most narrowly distributed (i.e., highest S). These were gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen. This adaptive divergence occurred in the face of ongoing gene flow (Fst = 0.01-0.04), indicating that selection was strong enough to overcome homogenization at the landscape scale. Our results suggest that adaptive divergence is pronounced, occurs along different environmental gradients for different species, and may consistently occur along the narrowest components of species' niche.

  17. Adaptive Genetic Divergence along Narrow Environmental Gradients in Four Stream Insects

    PubMed Central

    Watanabe, Kozo; Kazama, So; Omura, Tatsuo; Monaghan, Michael T.

    2014-01-01

    A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified the environmental characteristics contributing to divergence by comparing genetic distances at non-neutral loci between sites with Euclidean distances for each of 15 environmental variables. Comparisons were made using partial Mantel tests to control for geographic distance. In all four species, we found strong evidence for non-neutral divergence along environmental gradients at between 6 and 21 loci per species. The relative contribution of these environmental variables to each species' ecological niche was quantified as the specialization index, S, based on ecological data. In each species, the variable most significantly correlated with genetic distance at non-neutral loci was the same variable along which each species was most narrowly distributed (i.e., highest S). These were gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen. This adaptive divergence occurred in the face of ongoing gene flow (Fst = 0.01–0.04), indicating that selection was strong enough to overcome homogenization at the landscape scale. Our results suggest that adaptive divergence is pronounced, occurs along different environmental gradients for different species, and may consistently occur along the narrowest components of species' niche. PMID:24681871

  18. Mandibular shape and skeletal divergency.

    PubMed

    Ferrario, V F; Sforza, C; De Franco, D J

    1999-04-01

    Pre-treatment lateral cephalograms of 41 skeletal Class I girls aged 11 to 15 were divided according to MP-SN angle: lower than 28 degrees (hypodivergent, 10 girls), between 31 and 34 degrees (normodivergent, 18 girls), or larger than 37 degrees (hyperdivergent, 13 girls). The mandibular outlines were traced and digitized, and differences in shape were quantified using the elliptic Fourier series. Size differences were measured from the areas enclosed by the mandibular outlines. Shape differences were assessed by calculating a morphological distance (MD) between the size-independent mean mathematical reconstructions of the mandibular outlines of the three divergency classes. Mandibular shape was different in the three classes: large variations were found in hyperdivergent girls versus normodivergent girls (MD = 4.61), while smaller differences were observed in hypodivergent girls (MD versus normodivergent 2.91). Mean size-independent mandibular shapes were superimposed on an axis passing through the centres of gravity of the condyle and of the chin. Normodivergent and hyperdivergent mandibles differed mostly at gonion, the coronoid process, sigmoid notch, alveolar process, posterior border of the ramus, and along the mandibular plane. A significant size effect was also found, with smaller mandibles in the hyperdivergent girls.

  19. Genetic Variability and Divergence in Grayling, THYMALLUS ARCTICUS

    PubMed Central

    Lynch, J. C.; Vyse, E. R.

    1979-01-01

    In North America there are two disjunct forms of grayling, Montana and arctic, which have been separated for approximately 75,000 to 100,000 years. Electrophoretic analysis of thirty-six protein loci in these forms has revealed: (1) levels of gene duplication comparable to other salmonids, (2) a level of heterozygosity similar to other salmonids, (3) a fast and a slow evolving set of proteins, and (4) no obvious relationship between genetic variability and enzyme function. The genetic divergence between these populations may warrant subspecific designations for these two forms. PMID:499766

  20. An update of DIVERGE software for functional divergence analysis of protein family.

    PubMed

    Gu, Xun; Zou, Yangyun; Su, Zhixi; Huang, Wei; Zhou, Zhan; Arendsee, Zebulun; Zeng, Yanwu

    2013-07-01

    DIVERGE is a software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides a suite of statistical tools for selection and prioritization of the amino acid sites that are responsible for the functional divergence of a gene family. The synergistic efforts of DIVERGE and other methods have convincingly demonstrated that the pattern of rate change at a particular amino acid site may contain insightful information about the underlying functional divergence following gene duplication. These predicted sites may be used as candidates for further experiments. We are now releasing an updated version of DIVERGE with the following improvements: 1) a feasible approach to examining functional divergence in nearly complete sequences by including deletions and insertions (indels); 2) the calculation of the false discovery rate of functionally diverging sites; 3) estimation of the effective number of functional divergence-related sites that is reliable and insensitive to cutoffs; 4) a statistical test for asymmetric functional divergence; and 5) a new method to infer functional divergence specific to a given duplicate cluster. In addition, we have made efforts to improve software design and produce a well-written software manual for the general user.

  1. Landscape Management: Field Specialist.

    ERIC Educational Resources Information Center

    Newton, Deborah; Newton, Steve

    This module is the second volume in a series of three publications on landscape management. The module contains five instructional units that cover the following topics: orientation; equipment; irrigation systems and maintenance; plant material identification and pests; and turf identification and pests. Each instructional unit follows a standard…

  2. Biofuels from urban landscapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biomass from urban landscapes is an untapped resource. Lawn thatch and clippings, fallen leaves and tree limbs are all potential sources of biofuels. Most cities already collect and transport these materials to disposal sites; but, alternatively could collect and transport these materials to a loc...

  3. Moving into Landscapes

    ERIC Educational Resources Information Center

    Nelson, Cindy

    2008-01-01

    This article describes a lesson, designed for second graders, that begins with the teacher showing and talking about a few landscape fundamentals: horizon line, depth, and the mood or feeling that a work of art inspires. A class discussion ensues about how an artist's images can make one feel, how they can convey calmness, warmth, anxiety, or a…

  4. LANDSCAPE MANAGEMENT PRACTICES

    EPA Science Inventory

    USDA Conservation Practices are applied at various scales ranging from a portion of a field or a specific farm operation to the watershed or landscape scale. The Conservation Effects Assessment Project is a joint effort of USDA Conservation and Research agencies to determine the...

  5. Shaping the Landscape.

    ERIC Educational Resources Information Center

    Naturescope, 1987

    1987-01-01

    Provides background information on various agents that change the landscape. Includes teaching activities on weathering, water, wind and ice erosion, plate tectonics, sedimentation, deposition, mountain building, and determining contour lines. Contains reproducible handouts and worksheets for two of the activities. (TW)

  6. A Curious Landscape

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 'postcard' from the panoramic camera on the Mars Exploration Rover Opportunity shows the view of the martian landscape southwest of the rover. The image was taken in the late martian afternoon at Meridiani Planum on Mars, where Opportunity landed at approximately 9:05 p.m. PST on Saturday, Jan. 24.

  7. Landscapes. Artists' Workshop Series.

    ERIC Educational Resources Information Center

    King, Penny; Roundhill, Clare

    This instructional resource, designed to be used by and with elementary level students, provides inspiration for landscape painting by presenting the work of six different artists. These include: "Fuji in Clear Weather" (Katsushika Hokusai, 1823-29); "The Tree of Life" (Gustav Klimt, c. 1905-1909); "The Waterlily Pond" (Claude Monet, 1899);…

  8. Desert landscape irrigation

    SciTech Connect

    Quinones, R.

    1995-06-01

    Industrialization can take place in an arid environment if a long term, overall water management program is developed. The general rule to follow is that recharge must equal or exceed use. The main problem encountered in landscape projects is that everyone wants a lush jungle setting, tall shade trees, ferns, with a variety of floral arrangements mixed in. What we want, what we can afford, and what we get are not always the same. Vegetation that requires large quantities of water are not native to any desert. Surprisingly; there are various types of fruit trees, and vegetables that will thrive in the desert. Peaches, plums, nut trees, do well with drip irrigation as well as tomatoes. Shaded berry plans will also do well, the strawberry being one. In summary; if we match our landscape to our area, we can then design our irrigation system to maintain our landscape and grow a variety of vegetation in any arid or semiarid environment. The application of science and economics to landscaping has now come of age.

  9. Rivers and landscape

    SciTech Connect

    Petts, G.; Foster, I.

    1985-01-01

    This book provides readers with a knowledge of river systems, emphasising functional relationships between forms and processes, and the historical change of fluvial landscapes including evidence from valley fills and lake sediments. In explaining the properties and dynamics of river systems, the authors focus on new approaches, ideas and interpretations.

  10. Divergent sexual selection via male competition: ecology is key.

    PubMed

    Lackey, A C R; Boughman, J W

    2013-08-01

    Sexual selection and ecological differences are important drivers of speciation. Much research has focused on female choice, yet the role of male competition in ecological speciation has been understudied. Here, we test how mating habitats impact sexual selection and speciation through male competition. Using limnetic and benthic species of threespine stickleback fish, we find that different mating habitats select differently on male traits through male competition. In mixed habitat with both vegetated and open areas, selection favours two trait combinations of male body size and nuptial colour: large with little colour and small with lots of colour. This matches what we see in reproductively isolated stickleback species, suggesting male competition could promote trait divergence and reproductive isolation. In contrast, when only open habitat exists, selection favours one trait combination, large with lots of colour, which would hinder trait divergence and reproductive isolation. Other behavioural mechanisms in male competition that might promote divergence, such as avoiding aggression with heterospecifics, are insufficient to maintain separate species. This work highlights the importance of mating habitats in male competition for both sexual selection and speciation.

  11. Velocity field measurements in oblique static divergent vocal fold models

    NASA Astrophysics Data System (ADS)

    Erath, Byron

    2005-11-01

    During normal phonation, the vocal fold cycle is characterized by the glottal opening transitioning from a convergent to a divergent passage and then closing before the cycle is repeated. Under ordinary phonatory conditions, both vocal folds, which form the glottal passage, move in phase with each other, creating a time-varying symmetric opening. However, abnormal pathological conditions, such as unilateral paralysis, and polyps, can result in geometrical asymmetries between the vocal folds throughout the phonatory cycle. This study investigates pulsatile flow fields through 7.5 times life-size vocal fold models with included divergence angles of 5 to 30 degrees, and obliquities between the vocal folds of up to 15 degrees. Flow conditions were scaled to match physiological parameters. Data were taken at the anterior posterior mid-plane using phase-averaged Particle Image Velocimetry (PIV). Viscous flow phenomena including the Coanda effect, flow separation points, and jet "flapping" were investigated. The results are compared to previously reported work of flow through symmetric divergent vocal fold models.

  12. Campus Landscape: Functions, Forms, Features.

    ERIC Educational Resources Information Center

    Dober, Richard P.

    This guide provides information, instruction, and ideas on planning and designing every aspect of the campus landscape, from parking lots to playing fields. Using real-world examples of classic and contemporary campus landscapes, it features coverage of landscape restoration and regeneration; provides an assessment matrix for consistent, effective…

  13. Geomorphology of anthropogenic landscapes

    NASA Astrophysics Data System (ADS)

    Sofia, Giulia; Tarolli, Paolo

    2015-04-01

    The construction of urban areas and the development of road networks leave a significant signature on the Earth surface, providing a geomorphological evidence to support the idea that humans are nowadays a geomorphic agent having deep effects on the morphological organization of the landscape. The reconstruction or identification of anthropogenic topographies, therefore, provides a mechanism for quantifying anthropogenic changes to the landscape systems in the Anthropocene. Following this research line, the present study tests the effectiveness of a recently published topographic index, the Slope Local Length of Autocorrelation (SLLAC, Sofia et al. 2014) to portrait anthropogenic geomorphology, focusing in particular on road network density, and urban complexity (UCI). At first, the research considers the increasing of anthropic structures and the resulting changes in the SLLAC and in two derived parameters (mean SLLAC per km2 and SLLAC roughness, or Surface Peak Curvature -Spc). As a second step, considering the SLLAC derived indices, the anthropogenic geomorphology is automatically depicted using a k-means clustering algorithm. In general, the increasing of road network density or of the UCI is positively correlated to the mean SLLAC per km2, while the Spc is negatively correlated to the increasing of the anthropic structures. Areas presenting different road network organization are effectively captured considering multiple combinations of the defined parameters. Landscapes with small scattered towns, and a network with long roads in a dendritic shape (with hierarchical branching) are characterized simultaneously by high mean SLLAC and low Spc. Large and complex urban areas served by rectilinear networks with numerous short straight lines and right angles, have either a maximized mean SLLAC or a minimized Spc or both. In all cases, the anthropogenic landscape identified by the procedure is comparable to the ones identified manually from orthophoto, with the

  14. How old is the Hawaiian biota? Geology and phylogeny suggest recent divergence.

    PubMed

    Price, Jonathan P; Clague, David A

    2002-12-01

    This study quantifies long-term landscape changes in the Hawaiian archipelago relating to dispersal, speciation and extinction. Accounting for volcano growth, subsidence and erosion, we modelled the elevations of islands at time intervals of 0.5 Myr for the last 32 Myr; we also assessed the variation in the spacing of volcanoes during this period. The size, spacing and total number of volcanic islands have varied greatly over time, with the current landscape of large, closely spaced islands preceded by a period with smaller, more distantly spaced islands. Considering associated changes in rates of dispersal and speciation, much of the present species pool is probably the result of recent colonization from outside the archipelago and divergence within contemporary islands, with limited dispersal from older islands. This view is in accordance with abundant phylogenetic studies of Hawaiian organisms that estimate the timing of colonization and divergence within the archipelago. Twelve out of 15 multi-species lineages have diverged within the lifetime of the current high islands (last 5 Myr). Three of these, and an additional seven (mostly single-species) lineages, have colonized the archipelago within this period. The timing of colonization of other lineages remains uncertain.

  15. Divergent and convergent evolution in metastases suggest treatment strategies based on specific metastatic sites

    PubMed Central

    Cunningham, Jessica J.; Brown, Joel S.; Vincent, Thomas L.

    2015-01-01

    Background and objective: Systemic therapy for metastatic cancer is currently determined exclusively by the site of tumor origin. Yet, there is increasing evidence that the molecular characteristics of metastases significantly differ from the primary tumor. We define the evolutionary dynamics of metastases that govern this molecular divergence and examine their potential contribution to variations in response to targeted therapies. Methodology: Darwinian interactions of transformed cells with the tissue microenvironments at primary and metastatic sites are analyzed using evolutionary game theory. Computational models simulate responses to targeted therapies in different organs within the same patient. Results: Tumor cells, although maximally fit at their primary site, typically have lower fitness on the adaptive landscapes offered by the metastatic sites due to organ-specific variations in mesenchymal properties and signaling pathways. Clinically evident metastases usually exhibit time-dependent divergence from the phenotypic mean of the primary population as the tumor cells evolve and adapt to their new circumstances. In contrast, tumors from different primary sites evolving on identical metastatic adaptive landscapes exhibit phenotypic convergence. Thus, metastases in the liver from different primary tumors and even in different hosts will evolve toward similar adaptive phenotypes. The combination of evolutionary divergence from the primary cancer phenotype and convergence towards similar adaptive strategies in the same tissue cause significant variations in treatment responses particularly for highly targeted therapies. Conclusion and implications: The results suggest that optimal therapies for disseminated cancer must take into account the site(s) of metastatic growth as well as the primary organ. PMID:25794501

  16. Tigers of Sundarbans in India: is the population a separate conservation unit?

    PubMed

    Singh, Sujeet Kumar; Mishra, Sudhanshu; Aspi, Jouni; Kvist, Laura; Nigam, Parag; Pandey, Puneet; Sharma, Reeta; Goyal, Surendra Prakash

    2014-01-01

    The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate "evolutionarily significant unit" (ESU) following the adaptive evolutionary conservation (AEC) concept.

  17. Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

    PubMed Central

    Singh, Sujeet Kumar; Mishra, Sudhanshu; Aspi, Jouni; Kvist, Laura; Nigam, Parag; Pandey, Puneet; Sharma, Reeta; Goyal, Surendra Prakash

    2015-01-01

    The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate “evolutionarily significant unit” (ESU) following the adaptive evolutionary conservation (AEC) concept. PMID:25919139

  18. Tigers of Sundarbans in India: is the population a separate conservation unit?

    PubMed

    Singh, Sujeet Kumar; Mishra, Sudhanshu; Aspi, Jouni; Kvist, Laura; Nigam, Parag; Pandey, Puneet; Sharma, Reeta; Goyal, Surendra Prakash

    2014-01-01

    The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate "evolutionarily significant unit" (ESU) following the adaptive evolutionary conservation (AEC) concept. PMID:25919139

  19. Competition asymmetry with taxon divergence.

    PubMed

    Barnes, David K A

    2003-03-22

    Most organisms experience competition for resources, probably most of the time. As the structure and requirements of closely related species are generally liable to be more similar than in distantly linked species, Darwin suggested that the potential for competition was greater in the former. Since that time, studies have concentrated on interactions of either conspecifics or congeneric species. Shared critical resources, which organisms compete for, are generally mates, food and space (for access to the former). Whilst mates are valued only within species, in that the definition of a species requires it so, both food and space have the potential to be shared by very different organisms. It is now clear that vertebrates may compete with remotely related species: e.g. with squid for krill and with insects for nectar or seeds. Diamond suggested that (i) mutual aggression, (ii) displacement and (iii) evolutionary change in morphology would be increasingly asymmetric with competitor dissimilarity. Thus, with increasing taxonomic distance between two competitors (A and B), increasing aggression is exhibited between them and, increasingly, one consistently displaces the other. Here, Darwin's suggestion and Diamond's first two theories are tested across a taxonomic spectrum for the first time to the best of the author's knowledge. The proportion of spatial competitors in two different marine invertebrate groups demonstrating mutual aggression and displacement increases with taxon divergence (Nei's genetic identity). Congenerics were twice as likely to fight as conspecifics, and confamilial competitors were three times as likely to fight as conspecifics. This relationship seems robust to taxonomic and environmental variability. Competitors do not need to be as distant as birds and bees for complete asymmetry, a different family seems sufficient.

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

    PubMed

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

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax. PMID:25406249

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

    PubMed

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

    2014-10-01

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

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

    PubMed Central

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

    2013-01-01

    Background and Aims Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes. PMID:24205167

  3. Exploring the conformational energy landscape of proteins

    SciTech Connect

    Nienhaus, G.U. |; Mueller, J.D.; McMahon, B.H.

    1997-04-01

    Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.

  4. Landscape genetics and the spatial distribution of chronic wasting disease

    USGS Publications Warehouse

    Blanchong, Julie A.; Samuel, M.D.; Scribner, K.T.; Weckworth, B.V.; Langenberg, J.A.; Filcek, K.B.

    2008-01-01

    Predicting the spread of wildlife disease is critical for identifying populations at risk, targeting surveillance and designing proactive management programmes. We used a landscape genetics approach to identify landscape features that influenced gene flow and the distribution of chronic wasting disease (CWD) in Wisconsin white-tailed deer. CWD prevalence was negatively correlated with genetic differentiation of study area deer from deer in the area of disease origin (core-area). Genetic differentiation was greatest, and CWD prevalence lowest, in areas separated from the core-area by the Wisconsin River, indicating that this river reduced deer gene flow and probably disease spread. Features of the landscape that influence host dispersal and spatial patterns of disease can be identified based on host spatial genetic structure. Landscape genetics may be used to predict high-risk populations based on their genetic connection to infected populations and to target disease surveillance, control and preventative activities. ?? 2007 The Royal Society.

  5. Landscape genetics and the spatial distribution of chronic wasting disease.

    PubMed

    Blanchong, Julie A; Samuel, Michael D; Scribner, Kim T; Weckworth, Byron V; Langenberg, Julia A; Filcek, Kristine B

    2008-02-23

    Predicting the spread of wildlife disease is critical for identifying populations at risk, targeting surveillance and designing proactive management programmes. We used a landscape genetics approach to identify landscape features that influenced gene flow and the distribution of chronic wasting disease (CWD) in Wisconsin white-tailed deer. CWD prevalence was negatively correlated with genetic differentiation of study area deer from deer in the area of disease origin (core-area). Genetic differentiation was greatest, and CWD prevalence lowest, in areas separated from the core-area by the Wisconsin River, indicating that this river reduced deer gene flow and probably disease spread. Features of the landscape that influence host dispersal and spatial patterns of disease can be identified based on host spatial genetic structure. Landscape genetics may be used to predict high-risk populations based on their genetic connection to infected populations and to target disease surveillance, control and preventative activities.

  6. Char separator

    DOEpatents

    Matthews, Francis T.

    1979-01-01

    Particulates removed from the flue gases produced in a fluidized-bed furnace are separated into high-and low-density portions. The low-density portion is predominantly char, and it is returned to the furnace or burned in a separate carbon burnup cell. The high-density portion, which is predominantly limestone products and ash, is discarded or reprocessed. According to another version, the material drained from the bed is separated, the resulting high-and low-density portions being treated in a manner similar to that in which the flue-gas particulates are treated.

  7. CENTRIFUGAL SEPARATORS

    DOEpatents

    Skarstrom, C.

    1959-03-10

    A centrifugal separator is described for separating gaseous mixtures where the temperature gradients both longitudinally and radially of the centrifuge may be controlled effectively to produce a maximum separation of the process gases flowing through. Tbe invention provides for the balancing of increases and decreases in temperature in various zones of the centrifuge chamber as the result of compression and expansions respectively, of process gases and may be employed effectively both to neutralize harmful temperature gradients and to utilize beneficial temperaturc gradients within the centrifuge.

  8. Stereoisomers Separation

    NASA Astrophysics Data System (ADS)

    Wieczorek, Piotr

    The use of capillary electrophoresis for enantiomer separation and optical purity determination is presented. The contents start with basic information about the nature of stereoizomers and the mechanism of enantioseparation using capillary electrophoresis techniques. The molecules to be separated show identical chemical structure and electrochemical behavior. Therefore, the chiral recognition of enantiomers is possible only by bonding to chiral selector and the separation based on very small differences in complexation energies of diastereomer complexes formed. This method is useful for this purpose due to the fact that different compounds can be used as chiral selectors. The mostly used chiral selectors like cyclodextrins, crown ethers, chiral surfactants, macrocyclic antibiotics, transition metal complexes, natural, and synthetic polymers and their application for this purpose is also discussed. Finally, examples of practical applications of electromigration techniques for enantiomers separation and determination are presented.

  9. Cognitive attributes and aesthetic preferences in assessment and differentiation of landscapes.

    PubMed

    Sevenant, Marjanne; Antrop, Marc

    2009-07-01

    The increasing pace and scale of landscape changes involve objective measurements in order to estimate the effects of changes on people's landscape preferences in a meaningful way. In the literature, some attempts have been made to provide a more conceptual base related to landscape preferences. These concepts and their indicators need to be tested empirically in different contexts and landscape types. In the present study, different items related to theoretical concepts of both aesthetic preference and cognitive rating were examined. They were combined in an in situ questionnaire, which was conducted among undergraduate students in geography during two different field excursions. Stimuli consisted of 11 landscape vistas selected during the excursions. All vistas represent rather rural landscapes but they vary with regard to relief, degree of urbanisation, and degree of agricultural land use. Statistical analysis of all data yielded significant correlations between aesthetic and cognitive ratings. However, these correlations did not appear to be very strong. When considering landscape vistas separately, the relations between all cognitive ratings seemed to vary. Further, not all cognitive aspects had an equal predicting value for aesthetic preference. Moreover, this predicting value appeared to vary between different landscape vistas. The groups of interrelated cognitive aspects could not be associated consistently with theoretical concepts. The results demonstrated the inconsistencies existing between the contents of the theoretical concepts and the indicators found within the landscape. The findings argued for the necessity to distinguish between different ratings and landscape types instead of using unitary preference measures and generalized data when studying landscape preference.

  10. Product separator

    DOEpatents

    Welsh, Robert A.; Deurbrouck, Albert W.

    1976-01-20

    A secondary light sensitive photoelectric product separator for use with a primary product separator that concentrates a material so that it is visually distinguishable from adjacent materials. The concentrate separation is accomplished first by feeding the material onto a vibratory inclined surface with a liquid flow, such as a wet concentrating table. Vibrations generally perpendicular to the stream direction of flow cause the concentrate to separate from its mixture according to its color. When the concentrate and its surrounding stream reach the recovery end of the table, a detecting device notes the line of color demarcation and triggers a signal if it differs from a normal condition. If no difference is noted nothing moves on the second separator. However, if a difference is detected in the constant monitoring of the color line's location, a product splitter and recovery unit normally positioned near the color line at the recovery end, moves to a new position. In this manner the selected separated concentrate is recovered at a maximum rate regardless of variations in the flow stream or other conditions present.

  11. Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea.

    PubMed

    Jørgensen, Hanne B H; Hansen, Michael M; Bekkevold, Dorte; Ruzzante, Daniel E; Loeschcke, Volker

    2005-09-01

    Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.

  12. Simulations of Fluvial Landscapes

    NASA Astrophysics Data System (ADS)

    Cattan, D.; Birnir, B.

    2013-12-01

    The Smith-Bretherton-Birnir (SBB) model for fluvial landsurfaces consists of a pair of partial differential equations, one governing water flow and one governing the sediment flow. Numerical solutions of these equations have been shown to provide realistic models in the evolution of fluvial landscapes. Further analysis of these equations shows that they possess scaling laws (Hack's Law) that are known to exist in nature. However, the simulations are highly dependent on the numerical methods used; with implicit methods exhibiting the correct scaling laws, but the explicit methods fail to do so. These equations, and the resulting models, help to bridge the gap between the deterministic and the stochastic theories of landscape evolution. Slight modifications of the SBB equations make the results of the model more realistic. By modifying the sediment flow equation, the model obtains more pronounced meandering rivers. Typical landsurface with rivers.

  13. Wildfire and landscape change

    USGS Publications Warehouse

    Santi, P.; Cannon, S.; DeGraff, J.

    2013-01-01

    Wildfire is a worldwide phenomenon that is expected to increase in extent and severity in the future, due to fuel accumulations, shifting land management practices, and climate change. It immediately affects the landscape by removing vegetation, depositing ash, influencing water-repellent soil formation, and physically weathering boulders and bedrock. These changes typically lead to increased erosion through sheetwash, rilling, dry ravel, and increased mass movement in the form of floods, debris flow, rockfall, and landslides. These process changes bring about landform changes as hillslopes are lowered and stream channels aggrade or incise at increased rates. Furthermore, development of alluvial fans, debris fans, and talus cones are enhanced. The window of disturbance to the landscape caused by wildfire is typically on the order of three to four years, with some effects persisting up to 30 years.

  14. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).

    PubMed

    Berg, Paul R; Jentoft, Sissel; Star, Bastiaan; Ring, Kristoffer H; Knutsen, Halvor; Lien, Sigbjørn; Jakobsen, Kjetill S; André, Carl

    2015-06-01

    How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.

  15. Environmental versus Anthropogenic Effects on Population Adaptive Divergence in the Freshwater Snail Lymnaea stagnalis

    PubMed Central

    Bouétard, Anthony; Côte, Jessica; Besnard, Anne-Laure; Collinet, Marc; Coutellec, Marie-Agnès

    2014-01-01

    Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using QST -FST comparisons. Despite strong neutral differentiation (mean FST = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment. PMID:25207985

  16. Local fitness landscape of the green fluorescent protein.

    PubMed

    Sarkisyan, Karen S; Bolotin, Dmitry A; Meer, Margarita V; Usmanova, Dinara R; Mishin, Alexander S; Sharonov, George V; Ivankov, Dmitry N; Bozhanova, Nina G; Baranov, Mikhail S; Soylemez, Onuralp; Bogatyreva, Natalya S; Vlasov, Peter K; Egorov, Evgeny S; Logacheva, Maria D; Kondrashov, Alexey S; Chudakov, Dmitry M; Putintseva, Ekaterina V; Mamedov, Ilgar Z; Tawfik, Dan S; Lukyanov, Konstantin A; Kondrashov, Fyodor A

    2016-05-19

    Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.

  17. Local fitness landscape of the green fluorescent protein.

    PubMed

    Sarkisyan, Karen S; Bolotin, Dmitry A; Meer, Margarita V; Usmanova, Dinara R; Mishin, Alexander S; Sharonov, George V; Ivankov, Dmitry N; Bozhanova, Nina G; Baranov, Mikhail S; Soylemez, Onuralp; Bogatyreva, Natalya S; Vlasov, Peter K; Egorov, Evgeny S; Logacheva, Maria D; Kondrashov, Alexey S; Chudakov, Dmitry M; Putintseva, Ekaterina V; Mamedov, Ilgar Z; Tawfik, Dan S; Lukyanov, Konstantin A; Kondrashov, Fyodor A

    2016-05-19

    Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design. PMID:27193686

  18. Topological microstructure analysis using persistence landscapes

    NASA Astrophysics Data System (ADS)

    Dłotko, Paweł; Wanner, Thomas

    2016-11-01

    Phase separation mechanisms can produce a variety of complicated and intricate microstructures, which often can be difficult to characterize in a quantitative way. In recent years, a number of novel topological metrics for microstructures have been proposed, which measure essential connectivity information and are based on techniques from algebraic topology. Such metrics are inherently computable using computational homology, provided the microstructures are discretized using a thresholding process. However, while in many cases the thresholding is straightforward, noise and measurement errors can lead to misleading metric values. In such situations, persistence landscapes have been proposed as a natural topology metric. Common to all of these approaches is the enormous data reduction, which passes from complicated patterns to discrete information. It is therefore natural to wonder what type of information is actually retained by the topology. In the present paper, we demonstrate that averaged persistence landscapes can be used to recover central system information in the Cahn-Hilliard theory of phase separation. More precisely, we show that topological information of evolving microstructures alone suffices to accurately detect both concentration information and the actual decomposition stage of a data snapshot. Considering that persistent homology only measures discrete connectivity information, regardless of the size of the topological features, these results indicate that the system parameters in a phase separation process affect the topology considerably more than anticipated. We believe that the methods discussed in this paper could provide a valuable tool for relating experimental data to model simulations.

  19. Map Separates

    USGS Publications Warehouse

    ,

    2001-01-01

    U.S. Geological Survey (USGS) topographic maps are printed using up to six colors (black, blue, green, red, brown, and purple). To prepare your own maps or artwork based on maps, you can order separate black-and-white film positives or negatives for any color printed on a USGS topographic map, or for one or more of the groups of related features printed in the same color on the map (such as drainage and drainage names from the blue plate.) In this document, examples are shown with appropriate ink color to illustrate the various separates. When purchased, separates are black-and-white film negatives or positives. After you receive a film separate or composite from the USGS, you can crop, enlarge or reduce, and edit to add or remove details to suit your special needs. For example, you can adapt the separates for making regional and local planning maps or for doing many kinds of studies or promotions by using the features you select and then printing them in colors of your choice.

  20. Incorporating Bioenergy in Sustainable Landscape Designs Workshop Two: Agricultural Landscapes

    SciTech Connect

    Negri, M. Cristina; Ssegane, H.

    2015-08-01

    The Bioenergy Technologies Office hosted two workshops on Incorporating Bioenergy in Sustainable Landscape Designs with Oak Ridge and Argonne National Laboratories in 2014. The second workshop focused on agricultural landscapes and took place in Argonne, IL from June 24—26, 2014. The workshop brought together experts to discuss how landscape design can contribute to the deployment and assessment of sustainable bioenergy. This report summarizes the discussions that occurred at this particular workshop.

  1. Appendix E: Research papers. Use of remote sensing in landscape stratification for environmental impact assessment

    NASA Technical Reports Server (NTRS)

    Stanturf, J. A.; Heimbuch, D. G.

    1980-01-01

    A refinement to the matrix approach to environmental impact assessment is to use landscape units in place of separate environmental elements in the analysis. Landscape units can be delineated by integrating remotely sensed data and available single-factor data. A remote sensing approach to landscape stratification is described and the conditions under which it is superior to other approaches that require single-factor maps are indicated. Flowcharts show the steps necessary to develop classification criteria, delineate units and a map legend, and use the landscape units in impact assessment. Application of the approach to assessing impacts of a transmission line in Montana is presented to illustrate the method.

  2. Phylogeny and dating of divergences within the genus Thymallus (Salmonidae: Thymallinae) using complete mitochondrial genomes.

    PubMed

    Ma, Bo; Jiang, Haiying; Sun, Peng; Chen, Jinping; Li, Linmiao; Zhang, Xiujuan; Yuan, Lihong

    2016-09-01

    The genus Thymallus has attracted increasing attention in recent years because of its sharp demographic decline. In this study, we reported four complete mitochondrial genomes in the Thymallus genus: Baikal-Lena grayling (T. arcticus baicalolenensis), lower Amur grayling (T. tugarinae), Yalu grayling (T. a. yaluensis), and Mongolian grayling (T. brevirostris). The total length of the four new grayling mtDNAs ranged from 16 658 to 16 663 bp, all of which contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny within Thymallinae. Our study validated that the Yalu grayling should be a synonym of the Amur grayling (T. grubii) at the whole mitogenome level. The phylogenetic and dating analyses placed the Amur grayling at the deepest divergence node within Thymallus, diverging at ∼14.95 Ma. The lower Amur grayling diverged at the next deepest node (∼12.14 Ma). This was followed by T. thymallus, which diverged at ∼9.27 Ma. The Mongolian grayling and the ancestor of the sister species, T. arcticus and T. arcticus baicalolenensis, diverged at ∼7.79 Ma, with T. arcticus and T. arcticus baicalolenensis separating at ∼6.64 Ma. Our study provides far better resolution of the phylogenetic relationships and divergence dates of graylings than previous studies.

  3. "Islands of Divergence" in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements.

    PubMed

    Sodeland, Marte; Jorde, Per Erik; Lien, Sigbjørn; Jentoft, Sissel; Berg, Paul R; Grove, Harald; Kent, Matthew P; Arnyasi, Mariann; Olsen, Esben Moland; Knutsen, Halvor

    2016-01-01

    In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at "genomic islands of divergence," resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod (Gadus morhua) within geographically fine-scaled coastal areas. The "genomic islands" extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were identified, with little or no gene exchange between them. These patterns of recombination and divergence mirror genomic signatures previously described for large polymorphic inversions, which have been shown to repress recombination across extensive chromosomal segments. The lack of genetic exchange permits divergence between noninverted and inverted chromosomes in spite of gene flow. For the rearrangements on linkage groups 2 and 12, allelic frequency shifts between coastal and oceanic environments suggest a role in ecological adaptation, in agreement with recently reported associations between molecular variation within these genomic regions and temperature, oxygen, and salinity levels. Elevated genetic differentiation in these genomic regions has previously been described on both sides of the Atlantic Ocean, and we therefore suggest that these polymorphisms are involved in adaptive divergence across the species distributional range. PMID:26983822

  4. Antagonistic selection factors induce a continuous population divergence in a polymorphism.

    PubMed

    Takahashi, Y; Nagata, N; Kawata, M

    2014-04-01

    Understanding the relative importance of selection and stochastic factors in population divergence of adaptive traits is a classical topic in evolutionary biology. However, it is difficult to separate these factors and detect the effects of selection when two or more contrasting selective factors are simultaneously acting on a single locus. In the damselfly Ischnura senegalensis, females exhibit color dimorphism and morph frequencies change geographically. We here evaluated the role of selection and stochastic factors in population divergence of morph frequencies by comparing the divergences in color locus and neutral loci. Comparisons between population pairwise FST for neutral loci and for the color locus did not detect any stochastic factors affecting color locus. Although comparison between population divergence in color and neutral loci using all populations detected only divergent selection, we detected two antagonistic selective factors acting on the color locus, that is, balancing and divergent selection, when considering geographical distance between populations. Our results suggest that a combination of two antagonistic selective factors, rather than stochastic factors, establishes the geographic cline in morph frequency in this system. PMID:24281546

  5. Inflation, dark matter, and dark energy in the string landscape.

    PubMed

    Liddle, Andrew R; Ureña-López, L Arturo

    2006-10-20

    We consider the conditions needed to unify the description of dark matter, dark energy, and inflation in the context of the string landscape. We find that incomplete decay of the inflaton field gives the possibility that a single field is responsible for all three phenomena. By contrast, unifying dark matter and dark energy into a single field, separate from the inflaton, appears rather difficult.

  6. Classical Chinese Landscape Painting and the Aesthetic Appreciation of Nature

    ERIC Educational Resources Information Center

    Turner, Matthew

    2009-01-01

    Recent theories of the aesthetic appreciation of nature or natural environments have done much to clarify what might be essential to such appreciation. Such accounts are incomplete, however, as they depend on a strict separation between works of art and nature itself. This paper shows how classical Chinese landscape painting offers a way to…

  7. Understanding Patchy Landscape Dynamics: Towards a Landscape Language

    PubMed Central

    Gaucherel, Cédric; Boudon, Frédéric; Houet, Thomas; Castets, Mathieu; Godin, Christophe

    2012-01-01

    Patchy landscapes driven by human decisions and/or natural forces are still a challenge to be understood and modelled. No attempt has been made up to now to describe them by a coherent framework and to formalize landscape changing rules. Overcoming this lacuna was our first objective here, and this was largely based on the notion of Rewriting Systems, also called Formal Grammars. We used complicated scenarios of agricultural dynamics to model landscapes and to write their corresponding driving rule equations. Our second objective was to illustrate the relevance of this landscape language concept for landscape modelling through various grassland managements, with the final aim to assess their respective impacts on biological conservation. For this purpose, we made the assumptions that a higher grassland appearance frequency and higher land cover connectivity are favourable to species conservation. Ecological results revealed that dairy and beef livestock production systems are more favourable to wild species than is hog farming, although in different ways. Methodological results allowed us to efficiently model and formalize these landscape dynamics. This study demonstrates the applicability of the Rewriting System framework to the modelling of agricultural landscapes and, hopefully, to other patchy landscapes. The newly defined grammar is able to explain changes that are neither necessarily local nor Markovian, and opens a way to analytical modelling of landscape dynamics. PMID:23049935

  8. Isotope separation

    DOEpatents

    Bartlett, Rodney J.; Morrey, John R.

    1978-01-01

    A method and apparatus is described for separating gas molecules containing one isotope of an element from gas molecules containing other isotopes of the same element in which all of the molecules of the gas are at the same electronic state in their ground state. Gas molecules in a gas stream containing one of the isotopes are selectively excited to a different electronic state while leaving the other gas molecules in their original ground state. Gas molecules containing one of the isotopes are then deflected from the other gas molecules in the stream and thus physically separated.

  9. ISOTOPE SEPARATORS

    DOEpatents

    Bacon, C.G.

    1958-08-26

    An improvement is presented in the structure of an isotope separation apparatus and, in particular, is concerned with a magnetically operated shutter associated with a window which is provided for the purpose of enabling the operator to view the processes going on within the interior of the apparatus. The shutier is mounted to close under the force of gravity in the absence of any other force. By closing an electrical circuit to a coil mouated on the shutter the magnetic field of the isotope separating apparatus coacts with the magnetic field of the coil to force the shutter to the open position.

  10. Economic linkages to changing landscapes.

    PubMed

    Peterson, Jeffrey M; Caldas, Marcellus M; Bergtold, Jason S; Sturm, Belinda S; Graves, Russell W; Earnhart, Dietrich; Hanley, Eric A; Brown, J Christopher

    2014-01-01

    Many economic processes are intertwined with landscape change. A large number of individual economic decisions shape the landscape, and in turn the changes in the landscape shape economic decisions. This article describes key research questions about the economics of landscape change and reviews the state of research knowledge. The rich and varied economic-landscape interactions are an active area of research by economists, geographers, and others. Because the interactions are numerous and complex, disentangling the causal relationships in any given landscape system is a formidable research challenge. Limited data with mismatched temporal and spatial scales present further obstacles. Nevertheless, the growing body of economic research on these topics is advancing and shares fundamental challenges, as well as data and methods, with work in other disciplines.

  11. Habitat selection in a rocky landscape: experimentally decoupling the influence of retreat site attributes from that of landscape features.

    PubMed

    Croak, Benjamin M; Pike, David A; Webb, Jonathan K; Shine, Richard

    2012-01-01

    Organisms selecting retreat sites may evaluate not only the quality of the specific shelter, but also the proximity of that site to resources in the surrounding area. Distinguishing between habitat selection at these two spatial scales is complicated by co-variation among microhabitat factors (i.e., the attributes of individual retreat sites often correlate with their proximity to landscape features). Disentangling this co-variation may facilitate the restoration or conservation of threatened systems. To experimentally examine the role of landscape attributes in determining retreat-site quality for saxicolous ectotherms, we deployed 198 identical artificial rocks in open (sun-exposed) sites on sandstone outcrops in southeastern Australia, and recorded faunal usage of those retreat sites over the next 29 months. Several landscape-scale attributes were associated with occupancy of experimental rocks, but different features were important for different species. For example, endangered broad-headed snakes (Hoplocephalus bungaroides) preferred retreat sites close to cliff edges, flat rock spiders (Hemicloea major) preferred small outcrops, and velvet geckos (Oedura lesueurii) preferred rocks close to the cliff edge with higher-than-average sun exposure. Standardized retreat sites can provide robust experimental data on the effects of landscape-scale attributes on retreat site selection, revealing interspecific divergences among sympatric taxa that use similar habitats.

  12. Habitat Selection in a Rocky Landscape: Experimentally Decoupling the Influence of Retreat Site Attributes from That of Landscape Features

    PubMed Central

    Croak, Benjamin M.; Pike, David A.; Webb, Jonathan K.; Shine, Richard

    2012-01-01

    Organisms selecting retreat sites may evaluate not only the quality of the specific shelter, but also the proximity of that site to resources in the surrounding area. Distinguishing between habitat selection at these two spatial scales is complicated by co-variation among microhabitat factors (i.e., the attributes of individual retreat sites often correlate with their proximity to landscape features). Disentangling this co-variation may facilitate the restoration or conservation of threatened systems. To experimentally examine the role of landscape attributes in determining retreat-site quality for saxicolous ectotherms, we deployed 198 identical artificial rocks in open (sun-exposed) sites on sandstone outcrops in southeastern Australia, and recorded faunal usage of those retreat sites over the next 29 months. Several landscape-scale attributes were associated with occupancy of experimental rocks, but different features were important for different species. For example, endangered broad-headed snakes (Hoplocephalus bungaroides) preferred retreat sites close to cliff edges, flat rock spiders (Hemicloea major) preferred small outcrops, and velvet geckos (Oedura lesueurii) preferred rocks close to the cliff edge with higher-than-average sun exposure. Standardized retreat sites can provide robust experimental data on the effects of landscape-scale attributes on retreat site selection, revealing interspecific divergences among sympatric taxa that use similar habitats. PMID:22701592

  13. Rapid Diversity Loss of Competing Animal Species in Well-Connected Landscapes.

    PubMed

    Schippers, Peter; Hemerik, Lia; Baveco, Johannes M; Verboom, Jana

    2015-01-01

    Population viability of a single species, when evaluated with metapopulation based landscape evaluation tools, always increases when the connectivity of the landscape increases. However, when interactions between species are taken into account, results can differ. We explore this issue using a stochastic spatially explicit meta-community model with 21 competing species in five different competitive settings: (1) weak, coexisting competition, (2) neutral competition, (3) strong, excluding competition, (4) hierarchical competition and (5) random species competition. The species compete in randomly generated landscapes with various fragmentation levels. With this model we study species loss over time. Simulation results show that overall diversity, the species richness in the entire landscape, decreases slowly in fragmented landscapes whereas in well-connected landscapes rapid species losses occur. These results are robust with respect to changing competitive settings, species parameters and spatial configurations. They indicate that optimal landscape configuration for species conservation differs between metapopulation approaches, modelling species separately and meta-community approaches allowing species interactions. The mechanism behind this is that species in well-connected landscapes rapidly outcompete each other. Species that become abundant, by chance or by their completive strength, send out large amounts of dispersers that colonize and take over other patches that are occupied by species that are less abundant. This mechanism causes rapid species loss. In fragmented landscapes the colonization rate is lower, and it is difficult for a new species to establish in an already occupied patch. So, here dominant species cannot easily take over patches occupied by other species and higher diversity is maintained for a longer time. These results suggest that fragmented landscapes have benefits for species conservation previously unrecognized by the landscape ecology

  14. SEPARATION PROCESS

    DOEpatents

    Stoughton, R.W.

    1961-10-24

    A process for separating tetravalent plutonium from aqueous solutions and from niobium and zirconium by precipitation on lanthanum oxalate is described. The oxalate ions of the precipitate may be decomposed by heating in the presence of an oxidizing agent, forming a plutonium compound readily soluble in acid. (AEC)

  15. Plasma separation

    NASA Technical Reports Server (NTRS)

    Steurer, Wolfgang

    1992-01-01

    This process employs a thermal plasma for the separation and production of oxygen and metals. It is a continuous process that requires no consumables and relies entirely on space resources. The almost complete absence of waste renders it relatively clean. It can be turned on or off without any undesirable side effects or residues. The prime disadvantage is its high power consumption.

  16. Landscape Construction in Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Tang, Ying; Yuan, Ruoshi; Wang, Gaowei; Ao, Ping

    The idea of landscape has been recently applied to study various of biological problems. We demonstrate that a dynamical structure built into nonlinear dynamical systems allows us to construct such a global optimization landscape, which serves as the Lyapunov function for the ordinary differential equation. We find exact constructions on the landscape for a class of dynamical systems, including a van der Pol type oscillator, competitive Lotka-Volterra systems, and a chaotic system. The landscape constructed provides a new angle for understanding and modelling biological network dynamics.

  17. Ion divergence in magnetically insulated diodes

    SciTech Connect

    Slutz, S.A.; Lemke, R.W.; Pointon, T.D.; Desjarlais, M.P.; Johnson, D.J.; Mehlhorn, T.A.; Filuk, A.; Bailey, J.

    1995-12-01

    Magnetically insulated ion diodes are being developed to drive inertial confinement fusion. Ion beam microdivergence must be reduced to achieve the very high beam intensities required to achieve this goal. Three-dimensional particle-in-cell simulations indicate that instability induced fluctuations can produce significant ion divergence during acceleration. These simulations exhibit a fast growing mode early in time, which has been identified as the diocotron instability. The divergence generated by this mode is modest due to the relatively high frequency (>1GHz). Later, a low-frequency low-phase-velocity instability develops. This instability couples effectively to the ions, since the frequency is approximately the reciprocal of the ion transit time, and can generate unacceptably large ion divergences (>30 mrad). Linear stability theory reveals that this mode requires perturbations parallel to the applied magnetic field and is related to the modified two stream instability. Measurements of ion density fluctuations and energy-momentum correlations have confirmed that instabilities develop in ion diodes and contribute to the ion divergence. In addition, spectroscopic measurements indicate that the ions have a significant transverse temperature very close to the emission surface. Passive lithium fluoride (LiF) anodes have larger transverse beam temperatures than laser irradiated active sources. Calculations of source divergence expected from the roughness of LiF surfaces and the possible removal of this layer is presented.

  18. High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

    PubMed Central

    2014-01-01

    Background Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe. PMID:24998243

  19. Stonehenge and its Landscape

    NASA Astrophysics Data System (ADS)

    Ruggles, Clive L. N.

    In the 1960s and 1970s, Stonehenge polarized academic opinion between those (mainly astronomers) who claimed it demonstrated great astronomical sophistication and those (mainly archaeologists) who denied it had anything to do with astronomy apart from the solstitial alignment of its main axis. Now, several decades later, links to the annual passage of the sun are generally recognized as an essential part of the function and meaning not only of Stonehenge but also of several other nearby monuments, giving us important insights into beliefs and actions relating to the seasonal cycle by the prehistoric communities who populated this chalkland landscape in the third millennium BC Links to the moon remain more debatable.

  20. Climates, Landscapes, and Civilizations

    NASA Astrophysics Data System (ADS)

    Schultz, Colin

    2013-10-01

    Humans are now the dominant driver of global climate change. From ocean acidification to sea level rise, changes in precipitation patterns, and rising temperatures, global warming is presenting us with an uncertain future. However, this is not the first time human civilizations have faced a changing world. In the AGU monograph Climates, Landscapes, and Civilizations, editors Liviu Giosan, Dorian Q. Fuller, Kathleen Nicoll, Rowan K. Flad, and Peter C. Clift explore how some ancient peoples weathered the shifting storms while some faded away. In this interview, Eos speaks with Liviu Giosan about the decay of civilizations, ancient adaptation, and the surprisingly long history of humanity's effect on the Earth.

  1. Wind-Eroded Landscape

    NASA Technical Reports Server (NTRS)

    2005-01-01

    5 August 2005 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a dust-mantled, wind-eroded landscape in the Medusae Sulci region of Mars. Wind eroded the bedrock in this region, and then, later, windblown dust covered much of the terrain.

    Location near: 5.7oS, 160.2oW Image width: width: 3 km (1.9 mi) Illumination from: lower left Season: Southern Spring

  2. Probing the String Landscape

    ScienceCinema

    Keith Dienes

    2016-07-12

    We are currently in the throes of a potentially huge paradigm shift in physics. Motivated by recent developments in string theory and the discovery of the so-called "string landscape", physicists are beginning to question the uniqueness of fundamental theories of physics and the methods by which such theories might be understood and investigated. In this colloquium, I will give a non-technical introduction to the nature of this paradigm shift and how it developed. I will also discuss some of the questions to which it has led, and the nature of the controversies it has spawned.

  3. Probing the String Landscape

    SciTech Connect

    Keith Dienes

    2009-12-01

    We are currently in the throes of a potentially huge paradigm shift in physics. Motivated by recent developments in string theory and the discovery of the so-called "string landscape", physicists are beginning to question the uniqueness of fundamental theories of physics and the methods by which such theories might be understood and investigated. In this colloquium, I will give a non-technical introduction to the nature of this paradigm shift and how it developed. I will also discuss some of the questions to which it has led, and the nature of the controversies it has spawned.

  4. Phylogenetic position and subspecies divergence of the endangered New Zealand Dotterel (Charadrius obscurus).

    PubMed

    Barth, Julia M I; Matschiner, Michael; Robertson, Bruce C

    2013-01-01

    The New Zealand Dotterel (Charadrius obscurus), an endangered shorebird of the family Charadriidae, is endemic to New Zealand where two subspecies are recognized. These subspecies are not only separated geographically, with C. o. aquilonius being distributed in the New Zealand North Island and C. o. obscurus mostly restricted to Stewart Island, but also differ substantially in morphology and behavior. Despite these divergent traits, previous work has failed to detect genetic differentiation between the subspecies, and the question of when and where the two populations separated is still open. Here, we use mitochondrial and nuclear markers to address molecular divergence between the subspecies, and apply maximum likelihood and Bayesian methods to place C. obscurus within the non-monophyletic genus Charadrius. Despite very little overall differentiation, distinct haplotypes for the subspecies were detected, thus supporting molecular separation of the northern and southern populations. Phylogenetic analysis recovers a monophyletic clade combining the New Zealand Dotterel with two other New Zealand endemic shorebirds, the Wrybill and the Double-Banded Plover, thus suggesting a single dispersal event as the origin of this group. Divergence dates within Charadriidae were estimated with BEAST 2, and our results indicate a Middle Miocene origin of New Zealand endemic Charadriidae, a Late Miocene emergence of the lineage leading to the New Zealand Dotterel, and a Middle to Late Pleistocene divergence of the two New Zealand Dotterel subspecies.

  5. Performance of Several Conical Convergent-Divergent Rocket-Type Exhaust Nozzles

    NASA Technical Reports Server (NTRS)

    Campbell, C. E.; Farley, J. M.

    1960-01-01

    An investigation was conducted to obtain nozzle performance data with relatively large-scale models at pressure ratios as high as 120. Conical convergent-divergent nozzles with divergence angles alpha of 15, 25, and 29 deg. were each tested at area ratios of approximately 10, 25, and 40. Heated air (1200 F) was supplied at the nozzle inlet at pressures up to 145 pounds per square inch absolute and was exhausted into quiescent air at pressures as low as 1.2 pounds per square inch absolute. Thrust ratios for all nozzle configurations are presented over the range of pressure ratios attainable and were extrapolated when possible to design pressure ratio and beyond. Design thrust ratios decreased with increasing nozzle divergence angle according to the trend predicted by the (1 + cos alpha)/2 parameter. Decreasing the nozzle divergence angle resulted in sizable increases in thrust ratio for a given surface-area ratio (nozzle weight), particularly at low nozzle pressure ratios. Correlations of the nozzle static pressure at separation and of the average static pressure downstream of separation with various nozzle parameters permitted the calculation of thrust in the separated-flow region from unseparated static-pressure distributions. Thrust ratios calculated by this method agreed with measured values within about 1 percent.

  6. Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro.

    PubMed

    Zancolli, Giulia; Rödel, Mark-Oliver; Steffan-Dewenter, Ingolf; Storfer, Andrew

    2014-10-01

    Estimating population connectivity and species' abilities to disperse across the landscape is crucial for understanding the long-term persistence of species in changing environments. Surprisingly, few landscape genetic studies focused on tropical regions despite the alarming extinction rates within these ecosystems. Here, we compared the influence of landscape features on the distribution of genetic variation of an Afromontane frog, Amietia wittei, with that of its more broadly distributed lowland congener, Amietia angolensis, on Mt. Kilimanjaro, Tanzania. We predicted high gene flow in the montane species with movements enhanced through terrestrial habitats of the continuous rainforest. In contrast, dispersal might be restricted to aquatic corridors and reduced by anthropogenic disturbance in the lowland species. We found high gene flow in A. wittei relative to other montane amphibians. Nonetheless, gene flow was lower than in the lowland species which showed little population structure. Least-cost path analysis suggested that dispersal is facilitated by stream networks in both species, but different landscape features were identified to influence connectivity among populations. Contrary to a previous study, gene flow in the lowland species was negatively correlated with the presence of human settlements. Also, genetic subdivision in A. wittei did not coincide with specific physical barriers as in other landscape genetic studies, suggesting that factors other than topography may contribute to population divergence. Overall, these results highlight the importance of a comparative landscape genetic approach for assessing the influence of the landscape matrix on population connectivity, particularly because nonintuitive results can alter the course of conservation and management.

  7. Context Dependent Effect of Landscape on the Occurrence of an Apex Predator across Different Climate Regions

    PubMed Central

    Fujita, Go; Azuma, Atsuki; Nonaka, Jun; Sakai, Yoshiaki; Sakai, Hatsumi; Iseki, Fumitaka; Itaya, Hiroo; Fukasawa, Keita; Miyashita, Tadashi

    2016-01-01

    In studies of habitat suitability at landscape scales, transferability of species-landscape associations among sites are likely to be critical because it is often impractical to collect datasets across various regions. However, limiting factors, such as prey availability, are not likely to be constant across scales because of the differences in species pools. This is particularly true for top predators that are often the target for conservation concern. Here we focus on gray-faced buzzards, apex predators of farmland-dominated landscapes in East Asia. We investigated context dependency of “buzzard-landscape relationship”, using nest location datasets from five sites, each differing in landscape composition. Based on the similarities of prey items and landscape compositions across the sites, we determined several alternative ways of grouping the sites, and then examined whether buzzard-landscape relationship change among groups, which was conducted separately for each way of grouping. As a result, the model of study-sites grouping based on similarities in prey items showed the smallest ΔAICc. Because the terms of interaction between group IDs and areas of broad-leaved forests and grasslands were selected, buzzard-landscape relationship showed a context dependency, i.e., these two landscape elements strengthen the relationship in southern region. The difference in prey fauna, which is associated with the difference in climate, might generate regional differences in the buzzard-landscape associations. PMID:27123930

  8. Context Dependent Effect of Landscape on the Occurrence of an Apex Predator across Different Climate Regions.

    PubMed

    Fujita, Go; Azuma, Atsuki; Nonaka, Jun; Sakai, Yoshiaki; Sakai, Hatsumi; Iseki, Fumitaka; Itaya, Hiroo; Fukasawa, Keita; Miyashita, Tadashi

    2016-01-01

    In studies of habitat suitability at landscape scales, transferability of species-landscape associations among sites are likely to be critical because it is often impractical to collect datasets across various regions. However, limiting factors, such as prey availability, are not likely to be constant across scales because of the differences in species pools. This is particularly true for top predators that are often the target for conservation concern. Here we focus on gray-faced buzzards, apex predators of farmland-dominated landscapes in East Asia. We investigated context dependency of "buzzard-landscape relationship", using nest location datasets from five sites, each differing in landscape composition. Based on the similarities of prey items and landscape compositions across the sites, we determined several alternative ways of grouping the sites, and then examined whether buzzard-landscape relationship change among groups, which was conducted separately for each way of grouping. As a result, the model of study-sites grouping based on similarities in prey items showed the smallest ΔAICc. Because the terms of interaction between group IDs and areas of broad-leaved forests and grasslands were selected, buzzard-landscape relationship showed a context dependency, i.e., these two landscape elements strengthen the relationship in southern region. The difference in prey fauna, which is associated with the difference in climate, might generate regional differences in the buzzard-landscape associations.

  9. Context Dependent Effect of Landscape on the Occurrence of an Apex Predator across Different Climate Regions.

    PubMed

    Fujita, Go; Azuma, Atsuki; Nonaka, Jun; Sakai, Yoshiaki; Sakai, Hatsumi; Iseki, Fumitaka; Itaya, Hiroo; Fukasawa, Keita; Miyashita, Tadashi

    2016-01-01

    In studies of habitat suitability at landscape scales, transferability of species-landscape associations among sites are likely to be critical because it is often impractical to collect datasets across various regions. However, limiting factors, such as prey availability, are not likely to be constant across scales because of the differences in species pools. This is particularly true for top predators that are often the target for conservation concern. Here we focus on gray-faced buzzards, apex predators of farmland-dominated landscapes in East Asia. We investigated context dependency of "buzzard-landscape relationship", using nest location datasets from five sites, each differing in landscape composition. Based on the similarities of prey items and landscape compositions across the sites, we determined several alternative ways of grouping the sites, and then examined whether buzzard-landscape relationship change among groups, which was conducted separately for each way of grouping. As a result, the model of study-sites grouping based on similarities in prey items showed the smallest ΔAICc. Because the terms of interaction between group IDs and areas of broad-leaved forests and grasslands were selected, buzzard-landscape relationship showed a context dependency, i.e., these two landscape elements strengthen the relationship in southern region. The difference in prey fauna, which is associated with the difference in climate, might generate regional differences in the buzzard-landscape associations. PMID:27123930

  10. Bregman Clustering for Separable Instances

    NASA Astrophysics Data System (ADS)

    Ackermann, Marcel R.; Blömer, Johannes

    The Bregman k-median problem is defined as follows. Given a Bregman divergence D φ and a finite set P subseteq { R}^d of size n, our goal is to find a set C of size k such that the sum of errors cost(P,C) = ∑ p ∈ P min c ∈ C D φ (p,c) is minimized. The Bregman k-median problem plays an important role in many applications, e.g., information theory, statistics, text classification, and speech processing. We study a generalization of the kmeans++ seeding of Arthur and Vassilvitskii (SODA '07). We prove for an almost arbitrary Bregman divergence that if the input set consists of k well separated clusters, then with probability 2^{-{O}(k)} this seeding step alone finds an {O}(1)-approximate solution. Thereby, we generalize an earlier result of Ostrovsky et al. (FOCS '06) from the case of the Euclidean k-means problem to the Bregman k-median problem. Additionally, this result leads to a constant factor approximation algorithm for the Bregman k-median problem using at most 2^{{O}(k)}n arithmetic operations, including evaluations of Bregman divergence D φ .

  11. Evolutionary Divergence of Arabidopsis thaliana Classical Peroxidases.

    PubMed

    Kupriyanova, E V; Mamoshina, P O; Ezhova, T A

    2015-10-01

    Polymorphisms of 62 peroxidase genes derived from Arabidopsis thaliana were investigated to evaluate evolutionary dynamics and divergence of peroxidase proteins. By comparing divergence of duplicated genes AtPrx53-AtPrx54 and AtPrx36-AtPrx72 and their products, nucleotide and amino acid substitutions were identified that were apparently targets of positive selection. These substitutions were detected among paralogs of 461 ecotypes from Arabidopsis thaliana. Some of these substitutions are conservative and matched paralogous peroxidases in other Brassicaceae species. These results suggest that after duplication, peroxidase genes evolved under the pressure of positive selection, and amino acid substitutions identified during our study provided divergence of properties and physiological functions in peroxidases. Our predictions regarding functional significance for amino acid residues identified in variable sites of peroxidases may allow further experimental assessment of evolution of peroxidases after gene duplication.

  12. Optical rain gauge using a divergent beam.

    PubMed

    Wang, T I; Lawrence, R S; Tsay, M K

    1980-11-01

    We have shown that path-averaged rain rates can be obtained from the raindrop-induced amplitude scintillations of a divergent laser beam (spherical wave case). We found that the rain rate obtained from a divergent beam is less sensitive to drop-size distribution than that from a collimated beam. However, the path-weighting function is heavily weighted toward the receiving end in the spherical wave case, whereas in the plane wave case, it is almost uniformly weighted along the optical path. The theory was confirmed by observations on two optical paths, one using a collimated beam on a 200-m path, the other using a divergent beam on a 1000-m path. The results for the longer path show a saturation effect for rain rates higher than 12 mm/h.

  13. Divergence detectors for multitarget tracking algorithms

    NASA Astrophysics Data System (ADS)

    Mahler, Ronald

    2013-05-01

    Single-target tracking filters will typically diverge when their internal measurement or motion models deviate too much from the actual models. Niu, Varshney, Alford, Bubalo, Jones, and Scalzo have proposed a metric-- the normalized innovation squared (NIS)--that recursively estimates the degree of nonlinearity in a single-target tracking problem by detecting filter divergence. This paper establishes the following: (1) NIS can be extended to generalized NIS (GNIS), which addresses more general nonlinearities; (2) NIS and GNIS are actually anomaly detectors, rather than filter-divergence detectors; (3) NIS can be heuristically generalized to a multitarget NIS (MNIS) metric; (4) GNIS also can be rigorously extended to multitarget problems via the multitarget GNIS (MGNIS); (5) explicit, computationally tractable formulas for MGNIS can be derived for use with CPHD and PHD filters; and thus (6) these formulas can be employed as anomaly detectors for use with these filters.

  14. Conservation of species in dynamic landscapes: divergent fates of Silene tatarica populations in riparian habitats.

    PubMed

    Jäkäläniemi, Anne; Tuomi, Juha; Siikamäki, Pirkko

    2006-06-01

    In transient environments, where local extinctions occur as a result of destruction or deterioration of the local habitat, the long-term persistence of a species requires successful colonizations at new, suitable sites. This kind of habitat tracking should be associated with the asynchronous dynamics of local populations, and it can be especially important for the conservation of rare plant species in riparian habitats. We determined spatiotemporal variation in the demography of the perennial Silene tatarica (L.) Pers. in 15 populations (1998-2003) located in periodically disturbed riparian habitats. The habitats differed according to their morphology (flat shores, slopes) and the amount of bare ground (open, intermediate, closed) along a successional gradient. We used elasticity and life-table response analyses and stochastic simulations to study the variation in population demography. Finite population growth rate was higher in intermediate habitats than in open and closed habitats. In stochastic simulations population size increased in most cases, but four populations were projected to become extinct within 12-70 years. The viability of local populations depended most on the survival and growth of juvenile individuals and on the fecundity of large fertile individuals. On a regional scale, the persistence of this species will require a viable network of local populations as protection against local extinctions caused by natural disturbances and succession. Accordingly, the long-term persistence of riparian species may depend on habitat changes; thus, their conservation requires maintenance of natural disturbance dynamics. Along regulated rivers, management activities such as the creation of open habitats for new colonization should be implemented. Similarly, these activities can be rather general requirements for the conservation of endangered species dependent on transient habitats along successional gradients.

  15. Gas separating

    DOEpatents

    Gollan, Arye

    1988-01-01

    Feed gas is directed tangentially along the non-skin surface of gas separation membrane modules comprising a cylindrical bundle of parallel contiguous hollow fibers supported to allow feed gas to flow from an inlet at one end of a cylindrical housing through the bores of the bundled fibers to an outlet at the other end while a component of the feed gas permeates through the fibers, each having the skin side on the outside, through a permeate outlet in the cylindrical casing.

  16. Gas separating

    DOEpatents

    Gollan, Arye Z. [Newton, MA

    1990-12-25

    Feed gas is directed tangentially along the non-skin surface of gas separation membrane modules comprising a cylindrical bundle of parallel contiguous hollow fibers supported to allow feed gas to flow from an inlet at one end of a cylindrical housing through the bores of the bundled fibers to an outlet at the other end while a component of the feed gas permeates through the fibers, each having the skin side on the outside, through a permeate outlet in the cylindrical casing.

  17. Landscapes Impacted by Light

    NASA Astrophysics Data System (ADS)

    Arellano, B.; Roca, J.

    2016-06-01

    The gradual spread of urbanization, the phenomenon known under the term urban sprawl, has become one of the paradigms that have characterized the urban development since the second half of the twentieth century and early twenty-first century. However, there is no unanimous consensus about what means "urbanization". The plurality of forms of human settlement on the planet difficult to identify the urbanization processes. The arrival of electrification to nearly every corner of the planet is certainly the first and more meaningful indicator of artificialization of land. In this sense, the paper proposes a new methodology based on the analysis of the satellite image of nighttime lights designed to identify the highly impacted landscapes worldwide and to build an index of Land Impacted by Light per capita (LILpc) as an indicator of the level of urbanization. The used methodology allows the identification of different typologies of urbanized areas (villages, cities or metropolitan areas), as well as "rural", "rurban", "periurban" and "central" landscapes. The study identifies 186,134 illuminated contours (urbanized areas). In one hand, 404 of these contours could be consider as real "metropolitan areas"; and in the other hand, there are 161,821 contours with less than 5,000 inhabitants, which could be identify as "villages". Finally, the paper shows that 44.5 % live in rural areas, 15.5 % in rurban spaces, 26.2 % in suburban areas and only 18.4 % in central areas.

  18. Intrinsically Disordered Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

    2015-05-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.

  19. Landscape Evolution of Titan

    NASA Technical Reports Server (NTRS)

    Moore, Jeffrey

    2012-01-01

    Titan may have acquired its massive atmosphere relatively recently in solar system history. The warming sun may have been key to generating Titan's atmosphere over time, starting from a thin atmosphere with condensed surface volatiles like Triton, with increased luminosity releasing methane, and then large amounts of nitrogen (perhaps suddenly), into the atmosphere. This thick atmosphere, initially with much more methane than at present, resulted in global fluvial erosion that has over time retreated towards the poles with the removal of methane from the atmosphere. Basement rock, as manifested by bright, rough, ridges, scarps, crenulated blocks, or aligned massifs, mostly appears within 30 degrees of the equator. This landscape was intensely eroded by fluvial processes as evidenced by numerous valley systems, fan-like depositional features and regularly-spaced ridges (crenulated terrain). Much of this bedrock landscape, however, is mantled by dunes, suggesting that fluvial erosion no longer dominates in equatorial regions. High midlatitude regions on Titan exhibit dissected sedimentary plains at a number of localities, suggesting deposition (perhaps by sediment eroded from equatorial regions) followed by erosion. The polar regions are mainly dominated by deposits of fluvial and lacustrine sediment. Fluvial processes are active in polar areas as evidenced by alkane lakes and occasional cloud cover.

  20. Norwegian millstone quarry landscapes

    NASA Astrophysics Data System (ADS)

    Heldal, Tom; Meyer, Gurli; Grenne, Tor

    2013-04-01

    Rotary querns and millstones were used in Norway since just after the Roman Period until the last millstone was made in the 1930s. Throughout all this time millstone mining was fundamental for daily life: millstones were needed to grind grain, our most important food source. We can find millstone quarries in many places in the country from coast to mountain. Some of them cover many square kilometers and count hundreds of quarries as physical testimonies of a long and great production history. Other quarries are small and hardly visible. Some of this history is known through written and oral tradition, but most of it is hidden and must be reconstructed from the traces we can find in the landscape today. The Millstone project has put these quarry landscapes on the map, and conducted a range of case studies, including characterization of archaeological features connected to the quarrying, interpretation of quarrying techniques and evolution of such and establishing distribution and trade patterns by the aid of geological provenance. The project also turned out to be a successful cooperation between different disciplines, in particular geology and archaeology.

  1. Intrinsically disordered energy landscapes.

    PubMed

    Chebaro, Yassmine; Ballard, Andrew J; Chakraborty, Debayan; Wales, David J

    2015-01-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such 'intrinsically disordered' landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an α-helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

  2. Separation system

    DOEpatents

    Rubin, Leslie S.

    1986-01-01

    A separation system for dewatering radioactive waste materials includes a disposal container, drive structure for receiving the container, and means for releasably attaching the container to the drive structure. Separation structure disposed in the container adjacent the inner surface of the side wall structure retains solids while allowing passage of liquids. Inlet port structure in the container top wall is normally closed by first valve structure that is centrifugally actuated to open the inlet port and discharge port structure at the container periphery receives liquid that passes through the separation structure and is normally closed by second valve structure that is centrifugally actuated to open the discharge ports. The container also includes coupling structure for releasable engagement with the centrifugal drive structure. Centrifugal force produced when the container is driven in rotation by the drive structure opens the valve structures, and radioactive waste material introduced into the container through the open inlet port is dewatered, and the waste is compacted. The ports are automatically closed by the valves when the container drum is not subjected to centrifugal force such that containment effectiveness is enhanced and exposure of personnel to radioactive materials is minimized.

  3. Component separations.

    PubMed

    Heller, Lior; McNichols, Colton H; Ramirez, Oscar M

    2012-02-01

    Component separation is a technique used to provide adequate coverage for midline abdominal wall defects such as a large ventral hernia. This surgical technique is based on subcutaneous lateral dissection, fasciotomy lateral to the rectus abdominis muscle, and dissection on the plane between external and internal oblique muscles with medial advancement of the block that includes the rectus muscle and its fascia. This release allows for medial advancement of the fascia and closure of up to 20-cm wide defects in the midline area. Since its original description, components separation technique underwent multiple modifications with the ultimate goal to decrease the morbidity associated with the traditional procedure. The extensive subcutaneous lateral dissection had been associated with ischemia of the midline skin edges, wound dehiscence, infection, and seroma. Although the current trend is to proceed with minimally invasive component separation and to reinforce the fascia with mesh, the basic principles of the techniques as described by Ramirez et al in 1990 have not changed over the years. Surgeons who deal with the management of abdominal wall defects are highly encouraged to include this technique in their collection of treatment options.

  4. Temporary divergence paralysis in viral meningitis.

    PubMed

    Bakker, Stef L M; Gan, Ivan M

    2008-06-01

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

  5. Diverging Fluctuations of the Lyapunov Exponents

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  6. Fantasy Landscapes with a Message

    ERIC Educational Resources Information Center

    D'Amico, Elizabeth

    2005-01-01

    The author of this article describes using a Fantasy Landscapes lesson to get students expressing environmental issues through art. The Fantasy Landscapes lesson is an exploration of art elements and design principles through visual problem solving that links ideas, language, and theory to art. To get students thinking specifically about…

  7. Landscape in a Lacquer Box

    ERIC Educational Resources Information Center

    Savage, Martha

    2010-01-01

    A symbolic dry landscape garden of Eastern origin holds a special fascination for the author's middle-school students, which is why the author chose to create a project exploring this view of nature. A dry landscape garden, or "karesansui," is an arrangement of rocks, worn by nature and surrounded by a "sea" of sand, raked into patterns…

  8. Landscaping With Maintenance in Mind.

    ERIC Educational Resources Information Center

    Sorensen, Randy

    2000-01-01

    Examines school ground landscape design that enhances attractive of the school and provides for easier maintenance. Landscape design issues discussed include choice of grass, trees, and shrubs; irrigation; and safety and access. Other considerations for lessening maintenance problems for facility managers are also highlighted. (GR)

  9. Singularities of quantum control landscapes

    NASA Astrophysics Data System (ADS)

    Wu, Re-Bing; Long, Ruixing; Dominy, Jason; Ho, Tak-San; Rabitz, Herschel

    2012-07-01

    Quantum control landscape theory was formulated to assess the ease of finding optimal control fields in simulations and in the laboratory. The landscape is the observable as a function of the controls, and a primary goal of the theory is the analysis of landscape features. In what is referred to as the kinematic picture of the landscape, prior work showed that the landscapes are generally free of traps that could halt the search for an optimal control at a suboptimal observable value. The present paper considers the dynamical picture of the landscape, seeking the existence of singular controls, especially of a nonkinematic nature along with an assessment of whether they correspond to traps. We analyze the necessary and sufficient conditions for singular controls to be kinematic or nonkinematic critical solutions and the likelihood of their being encountered while maximizing an observable. An algorithm is introduced to seek singular controls on the landscape in simulations along with an associated Hessian landscape analysis. Simulations are performed for a large number of model finite-level quantum systems, showing that all the numerically identified kinematic and nonkinematic singular critical controls are not traps, in support of the prior empirical observations on the ease of finding high-quality optimal control fields.

  10. Complex Landscape Terms in Seri

    ERIC Educational Resources Information Center

    O'Meara, Carolyn; Bohnemeyer, Jurgen

    2008-01-01

    The nominal lexicon of Seri is characterized by a prevalence of analytical descriptive terms. We explore the consequences of this typological trait in the landscape domain. The complex landscape terms of Seri classify geographic entities in terms of their material make-up and spatial properties such as shape, orientation, and merological…

  11. Landscape heterogeneity modulates forest sensitivity to climate

    NASA Astrophysics Data System (ADS)

    Jencso, Kelsey; Hu, Jia; Hoylman, Zachary

    2015-04-01

    Elevation dependent snowmelt magnitude and timing strongly influences net ecosystem productivity in forested mountain watersheds. However, previous work has provided little insight into how internal watershed topography and organization may modulate plant available water and forest growth across elevation gradients. We collected 800 tree cores from four coniferous tree species across a range of elevation, topographic positions and aspects in the Lubrecht Experimental Forest, Montana, USA. We compared the annual basal area increment growth rate to precipitation and temperature from a 60-year SNOTEL data record, groundwater and soil moisture data in sideslope and hollow positions, and topographic indices derived from a LiDAR digital elevation model. At the watershed scale, we evaluated the relationships between topographic indices, LiDAR derived estimates of basal area and seasonal patterns of the Landsat derived Enhanced Vegetation Index. Preliminary results indicate strong relationships between the rates of annual basal growth and the topographic wetness index (TWI), with differing slopes dependent on tree species (P. menziesii R2 = 0.66-0.71, P. ponderosa R2 = 0.87, L. occidentalis R2 = 0.71) and elevation. Generally, trees located in wetter landscape positions (higher TWI) exhibited greater annual growth per unit of precipitation relative to trees located in drier landscape positions (lower TWI). Similarly, watershed scale analysis of LiDAR derived biomass and seasonal greenness indicates differential growth response due to local convergence and divergence across elevation and insolation gradients. These observations suggest that topographically driven water redistribution patterns may modulate the effects of large scale gradients in precipitation and temperature, thereby creating hotspots for conifer productivity in semiarid watersheds.

  12. An Alternative String Landscape Cosmology: Eliminating Bizarreness

    NASA Astrophysics Data System (ADS)

    Clavelli, L.; Goldstein, Gary R.

    2013-11-01

    In what has become a standard eternal inflation picture of the string landscape there are many problematic consequences and a difficulty defining probabilities for the occurrence of each type of universe. One feature in particular that might be philosophically disconcerting is the infinite cloning of each individual and each civilization in infinite numbers of separated regions of the multiverse. Even if this is not ruled out due to causal separation one should ask whether the infinite cloning is a universal prediction of string landscape models or whether there are scenarios in which it is avoided. If a viable alternative cosmology can be constructed one might search for predictions that might allow one to discriminate experimentally between the models. We present one such scenario although, in doing so, we are forced to give up several popular presuppositions including the absence of a preferred frame and the homogeneity of matter in the universe. The model also has several ancillary advantages. We also consider the future lifetime of the current universe before becoming a light trapping region.

  13. Wiring of Divergent Networks in the Central Auditory System

    PubMed Central

    Lee, Charles C.; Kishan, Amar U.; Winer, Jeffery A.

    2011-01-01

    Divergent axonal projections are found throughout the central auditory system. Here, we evaluate these branched projections in terms of their types, distribution, and putative physiological roles. In general, three patterns of axon collateralization are found: intricate local branching, long-distance collaterals, and branched axons (BAs) involved in feedback-control loops. Local collaterals in the auditory cortex may be involved in local processing and modulation of neuronal firing, while long-range collaterals are optimized for wide-dissemination of information. Rarely do axons branch to both ascending and descending targets. Branched projections to two or more widely separated nuclei or areas are numerically sparse but widespread. Finally, branching to contralateral targets is evident at multiple levels of the auditory pathway and may enhance binaural computations for sound localization. These patterns of axonal branching are comparable to those observed in other modalities. We conclude that the operations served by BAs are area- and nucleus-specific and may complement the divergent unbranched projections of local neuronal populations. PMID:21847372

  14. Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris).

    PubMed

    Lanier, Hayley C; Massatti, Rob; He, Qixin; Olson, Link E; Knowles, L Lacey

    2015-07-01

    Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate-sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site-associated DNA sequencing (RADSeq) data set containing 4156 single nucleotide polymorphisms with ecological niche models (ENMs) of present and past habitat suitability to characterize population composition and evaluate the effects of historical range shifts, contemporary climates and landscape factors on gene flow in Collared Pikas, which are found in Alaska and adjacent regions of northwestern Canada and are the lesser-studied of North America's two pika species. The results suggest that contemporary environmental factors contribute little to current population connectivity. Instead, genetic diversity is strongly shaped by the presence of three ancestral lineages isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and genetic data, populations originating from a northern refugium experienced longer-term stability, whereas both southern lineages underwent population expansion - contradicting the southern stability and northern expansion patterns seen in many other taxa. Current populations are comparable with respect to generally low diversity within populations and little-to-no recent admixture. The predominance of divergent histories structuring populations implies that if we are to understand and manage pika populations, we must specifically assess and accurately account for the forces underlying genetic similarity. PMID:26096099

  15. Parallelism and historical contingency during rapid ecotype divergence in an isopod.

    PubMed

    Eroukhmanoff, F; Hargeby, A; Arnberg, N N; Hellgren, O; Bensch, S; Svensson, E I

    2009-05-01

    Recent studies on parallel evolution have focused on the relative role of selection and historical contingency during adaptive divergence. Here, we study geographically separate and genetically independent lake populations of a freshwater isopod (Asellus aquaticus) in southern Sweden. In two of these lakes, a novel habitat was rapidly colonized by isopods from a source habitat. Rapid phenotypic changes in pigmentation, size and sexual behaviour have occurred, presumably in response to different predatory regimes. We partitioned the phenotypic variation arising from habitat ('selection': 81–94%), lake ('history': 0.1–6%) and lake × habitat interaction ('unique diversification': 0.4–13%) for several traits. There was a limited role for historical contingency but a strong signature of selection. We also found higher phenotypic variation in the source populations. Phenotype sorting during colonization and strong divergent selection might have contributed to these rapid changes. Consequently, phenotypic divergence was only weakly influenced by historical contingency. PMID:21462414

  16. Complete lack of mitochondrial divergence between two species of NE Atlantic marine intertidal gastropods.

    PubMed

    Kemppainen, P; Panova, M; Hollander, J; Johannesson, K

    2009-10-01

    Some mitochondrial introgression is common between closely related species, but distinct species rarely show substantial introgression in their entire distribution range. In this study, however, we report a complete lack of mitochondrial divergence between two sympatric species of flat periwinkles (Littorina fabalis and Littorina obtusata) which, based on previous allozyme studies, diverged approximately 1 Ma. We re-examined their species status using both morphology (morphometric analysis) and neutral genetic markers (microsatellites) and our results confirmed that these species are well separated. Despite this, the two species shared all common cytochrome-b haplotypes throughout their NE Atlantic distribution and no deep split between typical L. fabalis and L. obtusata haplotypes could be found. We suggest that incomplete lineage sorting explains most of the lack of mitochondrial divergence between these species. However, coalescent-based analyses and the sympatric sharing of unique haplotypes suggest that introgressive hybridization also has occurred. PMID:19678865

  17. Fitness Landscapes of Functional RNAs.

    PubMed

    Kun, Ádám; Szathmáry, Eörs

    2015-08-21

    The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.

  18. Fitness Landscapes of Functional RNAs

    PubMed Central

    Kun, Ádám; Szathmáry, Eörs

    2015-01-01

    The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world. PMID:26308059

  19. Gas separating

    DOEpatents

    Gollan, A.

    1988-03-29

    Feed gas is directed tangentially along the non-skin surface of gas separation membrane modules comprising a cylindrical bundle of parallel contiguous hollow fibers supported to allow feed gas to flow from an inlet at one end of a cylindrical housing through the bores of the bundled fibers to an outlet at the other end while a component of the feed gas permeates through the fibers, each having the skin side on the outside, through a permeate outlet in the cylindrical casing. 3 figs.

  20. Gas separating

    DOEpatents

    Gollan, A.Z.

    1990-12-25

    Feed gas is directed tangentially along the non-skin surface of gas separation membrane modules comprising a cylindrical bundle of parallel contiguous hollow fibers supported to allow feed gas to flow from an inlet at one end of a cylindrical housing through the bores of the bundled fibers to an outlet at the other end while a component of the feed gas permeates through the fibers, each having the skin side on the outside, through a permeate outlet in the cylindrical casing. 3 figs.

  1. Scholarly Groups' Choices Yield Diverging Fortunes

    ERIC Educational Resources Information Center

    Berrett, Dan

    2012-01-01

    Scholarly groups have long served as hubs of academic life and the embodiments of their disciplines, but they face uncertain and divergent futures. Some disciplinary associations are struggling to remain relevant and financially viable as demographic and technological changes threaten their traditional sources of revenue. The core of their…

  2. Controversial Issues Confronting Special Education: Divergent Perspectives.

    ERIC Educational Resources Information Center

    Stainback, William; Stainback, Susan

    This book of 24 papers presents divergent views on 12 issues in special education: organizational strategies, classroom service delivery approaches, maximizing the talents and gifts of students, classification and labeling, assessment, instructional strategies, classroom management, collaboration/consultation, research practices, higher education,…

  3. Geographically multifarious phenotypic divergence during speciation

    PubMed Central

    Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Alex Buerkle, C; Forister, Matthew L

    2013-01-01

    Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference). PMID:23532669

  4. Genomic divergence during speciation: causes and consequences

    PubMed Central

    Nosil, Patrik; Feder, Jeffrey L.

    2012-01-01

    Speciation is a fundamental process responsible for the diversity of life. Progress has been made in detecting individual ‘speciation genes’ that cause reproductive isolation. In contrast, until recently, less attention has been given to genome-wide patterns of divergence during speciation. Thus, major questions remain concerning how individual speciation genes are arrayed within the genome, and how this affects speciation. This theme issue is dedicated to exploring this genomic perspective of speciation. Given recent sequencing and computational advances that now allow genomic analyses in most organisms, the goal is to help move the field towards a more integrative approach. This issue draws upon empirical studies in plants and animals, and theoretical work, to review and further document patterns of genomic divergence. In turn, these studies begin to disentangle the role that different processes, such as natural selection, gene flow and recombination rate, play in generating observed patterns. These factors are considered in the context of how genomes diverge as speciation unfolds, from beginning to end. The collective results point to how experimental work is now required, in conjunction with theory and sequencing studies, to move the field from descriptive studies of patterns of divergence towards a predictive framework that tackles the causes and consequences of genome-wide patterns. PMID:22201163

  5. Reinforcement and divergence under assortative mating.

    PubMed

    Kirkpatrick, M

    2000-08-22

    Traits that cause assortative mating such as the flowering time in plants and body size in animals can produce reproductive isolation between hybridizing populations. Can selection against unfit hybrids cause two populations to diverge in their mean values for these kinds of traits? Here I present a haploid analytical model of one population that receives gene flow from another. The partial pre-zygotic isolation between the two populations is caused by assortative mating for a trait that is influenced by any number of genes with additive effects. The post-zygotic isolation is caused by selection against genetic incompatibilities that can involve any form of selection on individual genes and gene combinations (epistasis). The analysis assumes that the introgression rate and selection coefficients are small. The results show that the assortment trait mean will not diverge from the immigrants unless there is direct selection on the trait favouring it to do so or there are genes of very large effect. The amount of divergence at equilibrium is determined by a balance between direct selection on the assortment trait and introgression from the other population. Additional selection against hybrid genetic incompatibilities reduces the effective migration rate and allows greater divergence. The role of assortment in speciation is discussed in the light of these results.

  6. Taming infrared divergences in the effective potential

    NASA Astrophysics Data System (ADS)

    Elias-Miró, J.; Espinosa, J. R.; Konstandin, T.

    2014-08-01

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

  7. Neutral and Adaptive Drivers of Microgeographic Genetic Divergence within Continuous Populations: The Case of the Neotropical Tree Eperua falcata (Aubl.)

    PubMed Central

    Brousseau, Louise; Foll, Matthieu; Scotti-Saintagne, Caroline; Scotti, Ivan

    2015-01-01

    Background In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied. Methods We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree Eperua falcate Aubl. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers. Results Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of

  8. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.

    PubMed

    Gallone, Brigida; Steensels, Jan; Prahl, Troels; Soriaga, Leah; Saels, Veerle; Herrera-Malaver, Beatriz; Merlevede, Adriaan; Roncoroni, Miguel; Voordeckers, Karin; Miraglia, Loren; Teiling, Clotilde; Steffy, Brian; Taylor, Maryann; Schwartz, Ariel; Richardson, Toby; White, Christopher; Baele, Guy; Maere, Steven; Verstrepen, Kevin J

    2016-09-01

    Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP. PMID:27610566

  9. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.

    PubMed

    Gallone, Brigida; Steensels, Jan; Prahl, Troels; Soriaga, Leah; Saels, Veerle; Herrera-Malaver, Beatriz; Merlevede, Adriaan; Roncoroni, Miguel; Voordeckers, Karin; Miraglia, Loren; Teiling, Clotilde; Steffy, Brian; Taylor, Maryann; Schwartz, Ariel; Richardson, Toby; White, Christopher; Baele, Guy; Maere, Steven; Verstrepen, Kevin J

    2016-09-01

    Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP.

  10. Buildings Interoperability Landscape

    SciTech Connect

    Hardin, Dave; Stephan, Eric G.; Wang, Weimin; Corbin, Charles D.; Widergren, Steven E.

    2015-12-31

    Through its Building Technologies Office (BTO), the United States Department of Energy’s Office of Energy Efficiency and Renewable Energy (DOE-EERE) is sponsoring an effort to advance interoperability for the integration of intelligent buildings equipment and automation systems, understanding the importance of integration frameworks and product ecosystems to this cause. This is important to BTO’s mission to enhance energy efficiency and save energy for economic and environmental purposes. For connected buildings ecosystems of products and services from various manufacturers to flourish, the ICT aspects of the equipment need to integrate and operate simply and reliably. Within the concepts of interoperability lie the specification, development, and certification of equipment with standards-based interfaces that connect and work. Beyond this, a healthy community of stakeholders that contribute to and use interoperability work products must be developed. On May 1, 2014, the DOE convened a technical meeting to take stock of the current state of interoperability of connected equipment and systems in buildings. Several insights from that meeting helped facilitate a draft description of the landscape of interoperability for connected buildings, which focuses mainly on small and medium commercial buildings. This document revises the February 2015 landscape document to address reviewer comments, incorporate important insights from the Buildings Interoperability Vision technical meeting, and capture thoughts from that meeting about the topics to be addressed in a buildings interoperability vision. In particular, greater attention is paid to the state of information modeling in buildings and the great potential for near-term benefits in this area from progress and community alignment.

  11. A Novel Acetivibrio cellulolyticus Anchoring Scaffoldin That Bears Divergent Cohesins

    PubMed Central

    Xu, Qi; Barak, Yoav; Kenig, Rina; Shoham, Yuval; Bayer, Edward A.; Lamed, Raphael

    2004-01-01

    Sequencing of a cellulosome-integrating gene cluster in Acetivibrio cellulolyticus was completed. The cluster contains four tandem scaffoldin genes (scaA, scaB, scaC, and scaD) bounded upstream and downstream, respectively, by a presumed cellobiose phosphorylase and a nucleotide methylase. The sequences and properties of scaA, scaB, and scaC were reported previously, and those of scaD are reported here. The scaD gene encodes an 852-residue polypeptide that includes a signal peptide, three cohesins, and a C-terminal S-layer homology (SLH) module. The calculated molecular weight of the mature ScaD is 88,960; a 67-residue linker segment separates cohesins 1 and 2, and two ∼30-residue linkers separate cohesin 2 from 3 and cohesin 3 from the SLH module. The presence of an SLH module in ScaD indicates its role as an anchoring protein. The first two ScaD cohesins can be classified as type II, similar to the four cohesins of ScaB. Surprisingly, the third ScaD cohesin belongs to the type I cohesins, like the seven ScaA cohesins. ScaD is the first scaffoldin to be described that contains divergent types of cohesins as integral parts of the polypeptide chain. The recognition properties among selected recombinant cohesins and dockerins from the different scaffoldins of the gene cluster were investigated by affinity blotting. The results indicated that the divergent types of ScaD cohesins also differ in their preference of dockerins. ScaD thus plays a dual role, both as a primary scaffoldin, capable of direct incorporation of a single dockerin-borne enzyme, and as a secondary scaffoldin that anchors the major primary scaffoldin, ScaA and its complement of enzymes to the cell surface. PMID:15317783

  12. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: evolutionary shifts in chemical communication channels?

    PubMed

    Buellesbach, J; Gadau, J; Beukeboom, L W; Echinger, F; Raychoudhury, R; Werren, J H; Schmitt, T

    2013-11-01

    The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyse their chemical divergence and investigate their role as species-specific sexual signalling cues. Males and females of all four Nasonia species showed unique, nonoverlapping CHC profiles unambiguously separating them. Surprisingly, male and female phylogenies based on the chemical distances between their CHC profiles differed dramatically, where only male CHC divergence parallels the molecular phylogeny of Nasonia. In particular, N. giraulti female CHC profiles were the most divergent from all other species and very different from its most closely related sibling species N. oneida. Furthermore, although our behavioural assays indicate that female CHC profiles can generally be perceived as sexual cues attracting males in Nasonia, this function has apparently been lost in the highly divergent female N. giraulti CHC profiles. Curiously, N. giraulti males are still attracted to heterospecific, but not to conspecific female CHC profiles. We suggest that this striking discrepancy has been caused by an extensive evolutionary shift in female N. giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to.

  13. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: Evolutionary shifts in chemical communication channels?

    PubMed Central

    Buellesbach, Jan; Gadau, Jürgen; Beukeboom, Leo W.; Echinger, Felix; Raychoudhury, Rhitoban; Werren, John H.; Schmitt, Thomas

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitutes a key feature of chemical signaling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In the present study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyze their chemical divergence, and investigate their role as species-specific sexual signaling cues. Males and females of all four Nasonia species showed unique, non-overlapping CHC profiles unambiguously separating them. Surprisingly, male and female phylogenies based on the chemical distances between their CHC profiles differed dramatically, where only male CHC divergence parallels the molecular phylogeny of Nasonia. In particular, N. giraulti female CHC profiles were the most divergent from all other species and very different from its most closely related sibling species N. oneida. Furthermore, although our behavioural assays indicate that female CHC can generally be perceived as sexual cues attracting males in Nasonia, this function has apparently been lost in the highly divergent female N. giraulti CHC profiles. Curiously, N. giraulti males are still attracted to heterospecific, but not to conspecific female CHC profiles. We suggest that this striking discrepancy has been caused by an extensive evolutionary shift in female N. giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to. PMID:24118588

  14. Evolution of the SH3 Domain Specificity Landscape in Yeasts.

    PubMed

    Verschueren, Erik; Spiess, Matthias; Gkourtsa, Areti; Avula, Teja; Landgraf, Christiane; Mancilla, Victor Tapia; Huber, Aline; Volkmer, Rudolf; Winsor, Barbara; Serrano, Luis; Hochstenbach, Frans; Distel, Ben

    2015-01-01

    To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida albicans, and Schizosaccharomyces pombe, encompassing 400 million years of evolution. We first aligned and catalogued the families of SH3-containing proteins in these four species to determine the relationships between homologous domains. Then, we tagged and purified all soluble SH3 domains (82 in total) to perform a quantitative peptide assay (SPOT) for each SH3 domain. All SPOT readouts were hierarchically clustered and we observed that the organization of the SH3 specificity landscape in three distinct profile classes remains conserved across these four yeast species. We also produced a specificity profile for each SH3 domain from manually aligned top SPOT hits and compared the within-family binding motif consensus. This analysis revealed a striking example of binding motif divergence in a C. albicans Rvs167 paralog, which cannot be explained by overall SH3 sequence or interface residue divergence, and we validated this specificity change with a yeast two-hybrid (Y2H) assay. In addition, we show that position-weighted matrices (PWM) compiled from SPOT assays can be used for binding motif screening in potential binding partners and present cases where motifs are either conserved or lost among homologous SH3 interacting proteins. Finally, by comparing pairwise SH3 sequence identity to binding profile correlation we show that for ~75% of all analyzed families the SH3 specificity profile was remarkably conserved over a large evolutionary distance. Thus, a high sequence identity within an SH3 domain family predicts conserved binding specificity, whereas divergence in sequence identity often coincided with a change in binding specificity within this family. As such, our results are important for future studies aimed at unraveling complex specificity

  15. [Landscape classification: research progress and development trend].

    PubMed

    Liang, Fa-Chao; Liu, Li-Ming

    2011-06-01

    Landscape classification is the basis of the researches on landscape structure, process, and function, and also, the prerequisite for landscape evaluation, planning, protection, and management, directly affecting the precision and practicability of landscape research. This paper reviewed the research progress on the landscape classification system, theory, and methodology, and summarized the key problems and deficiencies of current researches. Some major landscape classification systems, e. g. , LANMAP and MUFIC, were introduced and discussed. It was suggested that a qualitative and quantitative comprehensive classification based on the ideology of functional structure shape and on the integral consideration of landscape classification utility, landscape function, landscape structure, physiogeographical factors, and human disturbance intensity should be the major research directions in the future. The integration of mapping, 3S technology, quantitative mathematics modeling, computer artificial intelligence, and professional knowledge to enhance the precision of landscape classification would be the key issues and the development trend in the researches of landscape classification.

  16. Particle separation

    NASA Technical Reports Server (NTRS)

    Moosmuller, Hans (Inventor); Chakrabarty, Rajan K. (Inventor); Arnott, W. Patrick (Inventor)

    2011-01-01

    Embodiments of a method for selecting particles, such as based on their morphology, is disclosed. In a particular example, the particles are charged and acquire different amounts of charge, or have different charge distributions, based on their morphology. The particles are then sorted based on their flow properties. In a specific example, the particles are sorted using a differential mobility analyzer, which sorts particles, at least in part, based on their electrical mobility. Given a population of particles with similar electrical mobilities, the disclosed process can be used to sort particles based on the net charge carried by the particle, and thus, given the relationship between charge and morphology, separate the particles based on their morphology.

  17. Particle separation

    DOEpatents

    Moosmuller, Hans; Chakrabarty, Rajan K.; Arnott, W. Patrick

    2011-04-26

    Embodiments of a method for selecting particles, such as based on their morphology, is disclosed. In a particular example, the particles are charged and acquire different amounts of charge, or have different charge distributions, based on their morphology. The particles are then sorted based on their flow properties. In a specific example, the particles are sorted using a differential mobility analyzer, which sorts particles, at least in part, based on their electrical mobility. Given a population of particles with similar electrical mobilities, the disclosed process can be used to sort particles based on the net charge carried by the particle, and thus, given the relationship between charge and morphology, separate the particles based on their morphology.

  18. Landscape characterization and biodiversity research

    SciTech Connect

    Dale, V.H.; Offerman, H.; Frohn, R.; Gardner, R.H.

    1995-03-01

    Rapid deforestation often produces landscape-level changes in forest characteristics and structure, including area, distribution, and forest habitat types. Changes in landscape pattern through fragmentation or aggregation of natural habitats can alter patterns of abundance for single species and entire communities. Examples of single-species effects include increased predation along the forest edge, the decline in the number of species with poor dispersal mechanisms, and the spread of exotic species that have deleterious effects (e.g., gypsy moth). A decrease in the size and number of natural habitat patches increases the probability of local extirpation and loss of diversity of native species, whereas a decline in connectivity between habitat patches can negatively affect species persistence. Thus, there is empirical justification for managing entire landscapes, not just individual habitat types, in order to insure that native plant and animal diversity is maintained. A landscape is defined as an area composed of a mosaic of interacting ecosystems, or patches, with the heterogeneity among the patches significantly affecting biotic and abiotic processes in the landscape. Patches comprising a landscape are usually composed of discrete areas of relatively homogeneous environmental conditions and must be defined in terms of the organisms of interest. A large body of theoretical work in landscape ecology has provided a wealth of methods for quantifying spatial characteristics of landscapes. Recent advances in remote sensing and geographic information systems allow these methods to be applied over large areas. The objectives of this paper are to present a brief overview of common measures of landscape characteristics, to explore the new technology available for their calculation, to provide examples of their application, and to call attention to the need for collection of spatially-explicit field data.

  19. An experimental investigation of velocity fields in divergent glottal models of the human vocal tract

    NASA Astrophysics Data System (ADS)

    Erath, Byron D.; Plesniak, Michael W.

    2005-09-01

    In speech, sound production arises from fluid-structure interactions within the larynx as well as viscous flow phenomena that is most likely to occur during the divergent orientation of the vocal folds. Of particular interest are the flow mechanisms that influence the location of flow separation points on the vocal folds walls. Physiologically scaled pulsatile flow fields in 7.5 times real size static divergent glottal models were investigated. Three divergence angles were investigated using phase-averaged particle image velocimetry (PIV). The pulsatile glottal jet exhibited a bi-modal stability toward both glottal walls, although there was a significant amount of variance in the angle the jet deflected from the midline. The attachment of the Coanda effect to the glottal model walls occurred when the pulsatile velocity was a maximum, and the acceleration of the waveform was zero. The location of the separation and reattachment points of the flow from the glottal models was a function of the velocity waveform and divergence angle. Acoustic analogies show that a dipole sound source contribution arising from the fluid interaction (Coanda jet) with the vocal fold walls is expected. [Work funded by NIH Grant RO1 DC03577.

  20. Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism

    PubMed Central

    Parsons, Kevin J.; Wang, Jason; Anderson, Graeme; Albertson, R. Craig

    2015-01-01

    Exemplary systems for adaptive divergence are often characterized by their large degrees of phenotypic variation. This variation represents the outcome of generations of diversifying selection. However, adaptive radiations can also contain a hierarchy of differentiation nested within them where species display only subtle phenotypic differences that still have substantial effects on ecology, function, and ultimately fitness. Sexual dimorphisms are also common in species displaying adaptive divergence and can be the result of differential selection between sexes that produce ecological differences between sexes. Understanding the genetic basis of subtle variation (between certain species or sexes) is therefore important for understanding the process of adaptive divergence. Using cichlids from the dramatic adaptive radiation of Lake Malawi, we focus on understanding the genetic basis of two aspects of relatively subtle phenotypic variation. This included a morphometric comparison of the patterns of craniofacial divergence between two ecologically similar species in relation to the larger adaptive radiation of Malawi, and male–female morphological divergence between their F2 hybrids. We then genetically map craniofacial traits within the context of sex and locate several regions of the genome that contribute to variation in craniofacial shape that is relevant to sexual dimorphism within species and subtle divergence between closely related species, and possibly to craniofacial divergence in the Malawi radiation as a whole. To enhance our search for candidate genes we take advantage of population genomic data and a genetic map that is anchored to the cichlid genome to determine which genes within our QTL regions are associated with SNPs that are alternatively fixed between species. This study provides a holistic understanding of the genetic underpinnings of adaptive divergence in craniofacial shape. PMID:26038365

  1. How soil shapes the landscape

    NASA Astrophysics Data System (ADS)

    Minasny, Budiman; Finke, Peter; Vanwalleghem, Tom Tom; Stockmann, Uta; McBratney, Alex

    2014-05-01

    There has been an increase in interest in quantitative modelling of soil genesis, which can provide prediction of environmental changes through numerical models. Modelling soil formation is a difficult task because soil itself is highly complex with interactions between water, inorganic materials and organic matter. This paper will provide a review on the research efforts of modelling soil genesis, their connection with landscape models and the inexorable genesis of the IUSS soil landscape modelling working group. Quantitative modelling soil formation using mechanistic models have begun in the 1980s such as the 'soil deficit' model by Kirkby (1985), Hoosbeek & Bryant's pedodynamic model (1992), and recently the SoilGen model by Finke (2008). These profile models considered the chemical reactions and physical processes in the soil at the horizon and pedon scale. The SoilGen model is an integration of sub-models, such as water and solute movement, heat transport, soil organic matter decomposition, mineral dissolution, ion exchange, adsorption, speciation, complexation and precipitation. The model can calculate with detail the chemical changes and materials fluxes in a profile and has been successfully applied. While they can simulate soil profile development in detail, there is still a gap how the processes act in the landscape. Meanwhile research in landscape formation in geomorphology is progressing steadily over time, slope development models model have been developed since 1970s (Ahnert, 1977). Soil was also introduced in a landscape, however soil processes are mainly modelled through weathering and transport processes (Minasny & McBratney 1999, 2001). Recently, Vanwalleghem et al. (2013) are able to combine selected physical, chemical and biological processes to simulate a full 3-D soil genesis in the landscape. Now there are research gaps between the 2 approaches: the landscape modellers increasingly recognise the importance of soil and need more detailed soil

  2. Connecting Brabant's cover sand landscapes through landscape history

    NASA Astrophysics Data System (ADS)

    Heskes, Erik; van den Ancker, Hanneke; Jungerius, Pieter Dirk; Harthoorn, Jaap; Maes, Bert; Leenders, Karel; de Jongh, Piet; Kluiving, Sjoerd; van den Oetelaar, Ger

    2015-04-01

    Noord-Brabant has the largest variety of cover sand landscapes in The Netherlands, and probably in Western Europe. During the Last Ice Age the area was not covered by land ice and a polar desert developed in which sand dunes buried the existing river landscapes. Some of these polar dune landscapes experienced a geomorphological and soil development that remained virtually untouched up to the present day, such as the low parabolic dunes of the Strabrechtse Heide or the later and higher dunes of the Oisterwijkse Vennen. As Noord-Brabant lies on the fringe of a tectonic basin, the thickness of cover sand deposits in the Centrale Slenk, part of a rift through Europe, amounts up to 20 metres. Cover sand deposits along the fault lines cause the special phenomenon of 'wijst' to develop, in which the higher grounds are wetter than the boarding lower grounds. Since 4000 BC humans settled in these cover sand landscapes and made use of its small-scale variety. An example are the prehistoric finds on the flanks and the historic towns on top of the 'donken' in northwest Noord-Brabant, where the cover sand landscapes are buried by river and marine deposits and only the peaks of the dunes protrude as donken. Or the church of Handel that is built beside a 'wijst' source and a site of pilgrimage since living memory. Or the 'essen' and plaggen agriculture that developed along the stream valleys of Noord-Brabant from 1300 AD onwards, giving rise to geomorphological features as 'randwallen' and plaggen soils of more than a metre thickness. Each region of Brabant each has its own approach in attracting tourists and has not yet used this common landscape history to connect, manage and promote their territories. We propose a landscape-historical approach to develop a national or European Geopark Brabants' cover sand landscapes, in which each region focuses on a specific part of the landscape history of Brabant, that stretches from the Late Weichselian polar desert when the dune

  3. Genetic divergence between subpopulations of the eastern Pacific goose barnacle Pollicipes elegans: mitochondrial cytochrome c subunit 1 nucleotide sequences.

    PubMed

    Van Syoc, R J

    1994-12-01

    Nucleotide sequence data derived from polymerase chain reaction products from the cytochrome oxidase subunit 1 gene of mitochondrial DNA provide evidence for interrupted gene flow and subsequent genetic divergence between geographically separate subpopulations of the edible goose barnacle, Pollicipes elegans, with a 4400-km latitudinal distribution in the eastern Pacific Ocean. The amphitropical subpopulations of Pollicipes elegans have a net nucleotide sequence divergence of about 1.2%. A range of mutation rates are applied to calculate estimates for the timing of this divergence. The earliest estimated time of divergence agrees with a Pliocene time of general warming in the eastern Pacific. The latest estimated times coincide with the Pleistocene epoch and periods of cooling and warming that could have allowed for a series of expansions and contractions of P. elegans populations in the eastern tropical Pacific. These expansions and contractions may, therefore, represent alternating periods of genetic exchange and isolation of the two populations.

  4. Megafans and Trumpeter Bird Biodiversity-Psophia Phylogeography and Landscape Evolution in Amazonia

    NASA Technical Reports Server (NTRS)

    Wilkinson, Justin

    2014-01-01

    Based on geomorphic character and mapped geology, geologists have interpreted the landscape surrounding the Andes Mountains as becoming progressively younger to the East. These sedimentary materials filled the late Miocene swampland that formerly occupied central and western Amazonia. Apart from the ancient landscapes of the Guiana Highlands (top right, figure 1a), Zone Ac is the oldest, followed by Zone Aw, within which megafan Jw is older than megafan Je (figure 1a). DNA-based paleogeography of the trumpeters shows that younger clades diverge from parent lineages with increasing distance from the Andes chain. Thus, Psophia napensis diverges from the P. crepitans parent, and P. ochroptera diverges from P. napensis. The P. ochroptera population is confined solely to the Je megafan (figure 1a). The same trend is seen on the south side of the Amazon depression. Since the timing of the events seems to be of exactly the same order [post-Miocene for the land surfaces and trumpeter divergence within the last 3 million years (figure 1d)], it seems reasonable to think that the megafans provided the substrate on which new bird lineages could speciate. Such physical controls of evolution are becoming more important in the understanding of biodiversity.

  5. Field dynamics and tunneling in a flux landscape

    SciTech Connect

    Johnson, Matthew C.; Larfors, Magdalena

    2008-10-15

    We investigate field dynamics and tunneling between metastable minima in a landscape of type IIB flux compactifications, utilizing monodromies of the complex structure moduli space to continuously connect flux vacua. After describing the generic features of a flux-induced potential for the complex structure and type IIB axiodilaton, we specialize to the mirror quintic Calabi-Yau to obtain an example landscape. Studying the cosmological dynamics of the complex structure moduli, we find that the potential generically does not support slow-roll inflation and that in general the landscape separates neatly into basins of attraction of the various minima. We then discuss tunneling, with the inclusion of gravitational effects, in many-dimensional field spaces. A set of constraints on the form of the Euclidean paths through field space are presented, and then applied to construct approximate instantons mediating the transition between de Sitter vacua in the flux landscape. We find that these instantons are generically thick wall and that the tunneling rate is suppressed in the large-volume limit. We also consider examples where supersymmetry is not broken by fluxes, in which case near-Bogomolnyi-Prasad-Sommerfeld thin-wall bubbles can be constructed. We calculate the bubble-wall tension, finding that it scales like a D- or NS-brane bubble, and comment on the implications of this correspondence. Finally, we present a brief discussion of eternal inflation in the flux landscape.

  6. Comparing the folding and misfolding energy landscapes of phosphoglycerate kinase.

    PubMed

    Agócs, Gergely; Szabó, Bence T; Köhler, Gottfried; Osváth, Szabolcs

    2012-06-20

    Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the properties of the energy landscape governing structure formation were reconstructed. A gradual transition of the energy landscape between folding and amyloid formation was observed. In the early steps of both folding and misfolding, the protein searches through a hierarchically structured energy landscape to form a molten globule in a few seconds. Depending on the conditions, this intermediate either folds to the native state in a few minutes, or forms amyloid fibers in several days. As conditions are changed from folding to misfolding, the barrier separating the molten globule and native states increases, although the barrier to the amyloid does not change. In the meantime, the native state also becomes more unstable and the amyloid more stable. We conclude that the lower region of the energy landscape determines the final protein structure. PMID:22735533

  7. 23 CFR 752.4 - Landscape development.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 23 Highways 1 2011-04-01 2011-04-01 false Landscape development. 752.4 Section 752.4 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RIGHT-OF-WAY AND ENVIRONMENT LANDSCAPE AND ROADSIDE DEVELOPMENT § 752.4 Landscape development. (a) Landscape development, which includes...

  8. 23 CFR 752.4 - Landscape development.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 23 Highways 1 2013-04-01 2013-04-01 false Landscape development. 752.4 Section 752.4 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RIGHT-OF-WAY AND ENVIRONMENT LANDSCAPE AND ROADSIDE DEVELOPMENT § 752.4 Landscape development. (a) Landscape development, which includes...

  9. 23 CFR 752.4 - Landscape development.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 23 Highways 1 2014-04-01 2014-04-01 false Landscape development. 752.4 Section 752.4 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RIGHT-OF-WAY AND ENVIRONMENT LANDSCAPE AND ROADSIDE DEVELOPMENT § 752.4 Landscape development. (a) Landscape development, which includes...

  10. 23 CFR 752.4 - Landscape development.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 23 Highways 1 2012-04-01 2012-04-01 false Landscape development. 752.4 Section 752.4 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RIGHT-OF-WAY AND ENVIRONMENT LANDSCAPE AND ROADSIDE DEVELOPMENT § 752.4 Landscape development. (a) Landscape development, which includes...

  11. Morphological and niche divergence of pinyon pines.

    PubMed

    Ortiz-Medrano, Alejandra; Scantlebury, Daniel Patrick; Vázquez-Lobo, Alejandra; Mastretta-Yanes, Alicia; Piñero, Daniel

    2016-05-01

    The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation. PMID:27092235

  12. Wall Pressure Measurements in a Convergent-Divergent Nozzle with Varying Inlet Asymmetry

    NASA Astrophysics Data System (ADS)

    Senthilkumar, C.; Elangovan, S.; Rathakrishnan, E.

    2016-06-01

    In this paper, flow separation of a convergent-divergent (C-D) nozzle is placed downstream of a supersonic flow delivered from Mach 2.0 nozzle is investigated. Static pressure measurements are conducted using pressure taps. The flow characteristics of straight and slanted entry C-D nozzle are investigated for various NPR of Mach 2.0 nozzle. The effect of asymmetry at inlet by providing 15°, 30°, 45° and 57° cut is analyzed. Particular attention is given to the location of the shock within the divergent section of the test nozzle. This location is examined as a function both NPR of Mach 2.0 nozzle and test nozzle inlet angle. Some of the measurements are favorably compared to previously developed theory. A Mach number ratio of 0.81 across the flow separation region was obtained.

  13. Accidental inflation in the landscape

    SciTech Connect

    Blanco-Pillado, Jose J.; Metallinos, Konstantinos; Gomez-Reino, Marta E-mail: marta.gomez-reino.perez@cern.ch

    2013-02-01

    We study some aspects of fine tuning in inflationary scenarios within string theory flux compactifications and, in particular, in models of accidental inflation. We investigate the possibility that the apparent fine-tuning of the low energy parameters of the theory needed to have inflation can be generically obtained by scanning the values of the fluxes over the landscape. Furthermore, we find that the existence of a landscape of eternal inflation in this model provides us with a natural theory of initial conditions for the inflationary period in our vacuum. We demonstrate how these two effects work in a small corner of the landscape associated with the complex structure of the Calabi-Yau manifold P{sup 4}{sub [1,1,1,6,9]} by numerically investigating the flux vacua of a reduced moduli space. This allows us to obtain the distribution of observable parameters for inflation in this mini-landscape directly from the fluxes.

  14. Studying Landforms through Landscape Painting.

    ERIC Educational Resources Information Center

    Glenn, William H.

    1981-01-01

    Using three specific works of art, the author demonstrates how a study of selected landscape paintings can be integrated into units on landforms in secondary school earth science and general science courses. (Author/SJL)

  15. Phenotypic plasticity and divergence in gene expression.

    PubMed

    Healy, Timothy M; Schulte, Patricia M

    2015-07-01

    The extent to which phenotypic plasticity, or the ability of a single genotype to produce different phenotypes in different environments, impedes or promotes genetic divergence has been a matter of debate within evolutionary biology for many decades (see, for example, Ghalambor et al. ; Pfennig et al. ). Similarly, the role of evolution in shaping phenotypic plasticity remains poorly understood (Pigliucci ). In this issue of Molecular Ecology, Dayan et al. () provide empirical data relevant to these questions by assessing the extent of plasticity and divergence in the expression levels of 2272 genes in muscle tissue from killifish (genus Fundulus) exposed to different temperatures. F. heteroclitus (Fig. A) and F. grandis are minnows that inhabit estuarine marshes (Fig. B) along the coasts of the Atlantic Ocean and Gulf of Mexico in North America. These habitats undergo large variations in temperature both daily and seasonally, and these fish are known to demonstrate substantial phenotypic plasticity in response to temperature change (e.g. Fangue et al. ). Furthermore, the range of F. heteroclitus spans a large latitudinal gradient of temperatures, such that northern populations experience temperatures that are on average ~10°C colder than do southern populations (Schulte ). By comparing gene expression patterns between populations of these fish from different thermal habitats held in the laboratory at three different temperatures, Dayan et al. () address two important questions regarding the interacting effects of plasticity and evolution: (i) How does phenotypic plasticity affect adaptive divergence? and (ii) How does adaptive divergence affect plasticity? PMID:26096949

  16. Automated leukocyte recognition using fuzzy divergence.

    PubMed

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

    2010-10-01

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

  17. Planetary landscape: a new synthesis

    NASA Astrophysics Data System (ADS)

    Hargitai, H.

    The elements that build up a landscape on Earth consists of natural (biogenic and abiogenic - lithologic, atmospheric, hydrologic) and artificial (antropogenic) factors. Landscape is a complex system of these different elements, which interact with one another. For example the same lithology makes different landscapes under different climatic conditions. If the same conditions are present, the same landscape type will appear. The mosaic of ecotopes (topical) units, which are the system of homogenous caharacteristic areas of various geotopes makes up different level geochores (chorical unit). Geochores build up a hierarchic system and cover the whole surface.On Earth, landscapes can be qualified according to their characteristics: relief forms (morphology), and its potential economic value. Aesthetic and subjective parameters can also be considered especially when speaking of a residental area. We now propose the determination of "planetary landscape sets" which can potentially occur on the solid surface of a planetary body during its lifetime. This naturally includes landscapes of the present state of planetary bodies and also paleolandscapes from the past of planets, including Earth. Landscapes occur in the boundary of the planets solid and not solid sphere that is on the solid-vacuum, the solid - gas and on the solid - liquid boundary. Thinking this way a landscape can occurs on the ocean floor as well. We found that for the determination of a planetary landscape system, we can use the experiences from the making of the terminology and nomenclature system of Earth undersea topography. [1] The nomenclature system and the terminology used by astrogeologists could be revised. Common names of features should be defined (nova, tessera, volcano, tholus, lobate ejecta crater etc) with a type example for each. A well defined hierarchy for landscape types should be defined. The Moon is the best example, since it uses many names that originates from the 17th century, mixed

  18. Protein evolution on rugged landscapes

    SciTech Connect

    Macken, C.A. ); Perelson, A.S. Sante Fe Institute, NM )

    1989-08-01

    The authors analyze a mathematical model of protein evolution in which the evolutionary process is viewed as hill-climbing on a random fitness landscape. In studying the structure of such landscapes, they note that a large number of local optima exist, and they calculate the time and number of mutational changes until a protein gets trapped at a local optimum. Such a hill-climbing process may underlie the evolution of antibody molecules by somatic hypermutation.

  19. Magnetohydrodynamic energy conversion by using convexly divergent channel

    SciTech Connect

    Murakami, Tomoyuki; Okuno, Yoshihiro

    2009-12-21

    We describe a magnetohydrodynamic (MHD) electrical power generator equipped with a convexly divergent channel, as determined through shock-tunnel-based experiments. The quality of MHD power-generating plasma and the energy conversion efficiency in the convexly divergent channel are compared with those from previous linearly divergent channel. The divergence enhancement in the channel upstream is effective for suppressing an excessive increase in static pressure, whereby notably high isentropic efficiency is achieved.

  20. Titan Polar Landscape Evolution

    NASA Technical Reports Server (NTRS)

    Moore, Jeffrey M.

    2016-01-01

    With the ongoing Cassini-era observations and studies of Titan it is clear that the intensity and distribution of surface processes (particularly fluvial erosion by methane and Aeolian transport) has changed through time. Currently however, alternate hypotheses substantially differ among specific scenarios with respect to the effects of atmospheric evolution, seasonal changes, and endogenic processes. We have studied the evolution of Titan's polar region through a combination of analysis of imaging, elevation data, and geomorphic mapping, spatially explicit simulations of landform evolution, and quantitative comparison of the simulated landscapes with corresponding Titan morphology. We have quantitatively evaluated alternate scenarios for the landform evolution of Titan's polar terrain. The investigations have been guided by recent geomorphic mapping and topographic characterization of the polar regions that are used to frame hypotheses of process interactions, which have been evaluated using simulation modeling. Topographic information about Titan's polar region is be based on SAR-Topography and altimetry archived on PDS, SAR-based stereo radar-grammetry, radar-sounding lake depth measurements, and superposition relationships between geomorphologic map units, which we will use to create a generalized topographic map.

  1. Nanofiber patent landscape.

    PubMed

    Ngiam, Michelle; Ramakrishna, Seeram; Raghunath, Michael; Chan, Casey K

    2007-01-01

    Despite the large number of publications in peer review literature in the field of nanofibers, there is still uncertainty as to what aspects of these research results have commercial applications. In an effort to better understand the technological progress made in the field of nanofibers, we surveyed the patents issued in the United States from 1976 up to end 2006. The present review will provide an overall view of the current patent landscape including trends and key applications. Key assignees and key inventors were identified and their contributions were discussed. Patents were identified using keywords such as nanofibers, ultrafine, and electrospinning. After patents were downloaded, we reviewed each patent for relevancy and identified 100 patents to be related to nanofibers. 75% of the current issued patents on nanofibers are directed at either fabrication methods or the use of nanofibers in filtration systems. The patent data indicates that medical applications and medical products using nanofibers appear to be the emerging application for nanofibers. We anticipate a growing number of patents on novel applications for nanofiber would originate from academic centers in the future.

  2. PSEUDO-CODEWORD LANDSCAPE

    SciTech Connect

    CHERTKOV, MICHAEL; STEPANOV, MIKHAIL

    2007-01-10

    The authors discuss performance of Low-Density-Parity-Check (LDPC) codes decoded by Linear Programming (LP) decoding at moderate and large Signal-to-Noise-Ratios (SNR). Frame-Error-Rate (FER) dependence on SNR and the noise space landscape of the coding/decoding scheme are analyzed by a combination of the previously introduced instanton/pseudo-codeword-search method and a new 'dendro' trick. To reduce complexity of the LP decoding for a code with high-degree checks, {ge} 5, they introduce its dendro-LDPC counterpart, that is the code performing identifically to the original one under Maximum-A-Posteriori (MAP) decoding but having reduced (down to three) check connectivity degree. Analyzing number of popular LDPC codes and their dendro versions performing over the Additive-White-Gaussian-Noise (AWGN) channel, they observed two qualitatively different regimes: (i) error-floor sets early, at relatively low SNR, and (ii) FER decays with SNR increase faster at moderate SNR than at the largest SNR. They explain these regimes in terms of the pseudo-codeword spectra of the codes.

  3. Sunitinib Possible Sex-Divergent Therapeutic Outcomes.

    PubMed

    Segarra, Ignacio; Modamio, Pilar; Fernández, Cecilia; Mariño, Eduardo L

    2016-10-01

    Sunitinib is a tyrosine kinase inhibitor used for the treatment of renal cell carcinoma and metastatic brain tumors. Preclinical pharmacokinetic studies have shown higher sunitinib hepatic and brain exposure in female mice and higher sunitinib kidney concentrations in male mice. We explored whether sex-divergent tissue pharmacokinetics may anticipate sex-divergent therapeutic and toxicology responses in male and female patients. The review of the available scientific literature identified case reports, case series reports, clinical trials, and other studies associating sex with sunitinib outcomes. The results suggest male patients may respond better to renal cell carcinoma treatment and female patients may have better brain tumor treatment outcomes but a higher incidence of adverse events. Although more high-quality evidence is needed, these results, as anticipated by the preclinical data, may indicate possible sunitinib sex-divergent therapeutic outcomes in patients. In addition, we propose the systematic analysis of sex-based outcomes in clinical trial reports and their inclusion and review in the ethics committees and review boards to prevent, amongst others, patient burden in upcoming clinical trials. PMID:27318944

  4. Restoration of divergent free-standing implants in the maxilla.

    PubMed

    Schneider, Allen L; Kurtzman, Gregori M

    2002-01-01

    Divergent implants in the maxilla can make restoration with removable prosthetics difficult when the implants will not be splinted with a superstructure. Attachments to be used with individual implants require that the implants be within 10 degrees of divergence. This article will address a new angled male designed to fit the locator attachment (female component) that can accommodate up to a 40 degrees divergence.

  5. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).

    PubMed

    Berg, Paul R; Jentoft, Sissel; Star, Bastiaan; Ring, Kristoffer H; Knutsen, Halvor; Lien, Sigbjørn; Jakobsen, Kjetill S; André, Carl

    2015-06-01

    How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation. PMID:25994933

  6. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.)

    PubMed Central

    Berg, Paul R.; Jentoft, Sissel; Star, Bastiaan; Ring, Kristoffer H.; Knutsen, Halvor; Lien, Sigbjørn; Jakobsen, Kjetill S.; André, Carl

    2015-01-01

    How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation. PMID:25994933

  7. Divergence in an obligate mutualism is not explained by divergent climatic factors

    USGS Publications Warehouse

    Godsoe, W.; Strand, Espen; Smith, C.I.; Yoder, J.B.; Esque, T.C.; Pellmyr, O.

    2009-01-01

    Adaptation to divergent environments creates and maintains biological diversity, but we know little about the importance of different agents of ecological divergence. Coevolution in obligate mutualisms has been hypothesized to drive divergence, but this contention has rarely been tested against alternative ecological explanations. Here, we use a well-established example of coevolution in an obligate pollination mutualism, Yucca brevifolia and its two pollinating yucca moths, to test the hypothesis that divergence in this system is the result of mutualists adapting to different abiotic environments as opposed to coevolution between mutualists. ??? We used a combination of principal component analyses and ecological niche modeling to determine whether varieties of Y. brevifolia associated with different pollinators specialize on different environments. ??? Yucca brevifolia occupies a diverse range of climates. When the two varieties can disperse to similar environments, they occupy similar habitats. ??? This suggests that the two varieties have not specialized on distinct habitats. In turn, this suggests that nonclimatic factors, such as the biotic interaction between Y. brevifolia and its pollinators, are responsible for evolutionary divergence in this system. ?? New Phytologist (2009).

  8. Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

    PubMed Central

    2011-01-01

    Background Genetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow linking diversification to geological, climatic, and ecological events, and thus disentangling the relative importance of different evolutionary drivers in generating and maintaining current species richness. Results Here, we use phylogenetic, phenotypic, geographic, and environmental data to investigate diversification in the Spanish sand racer (Psammodromus hispanicus). Phylogenetic, molecular clock dating, and phenotypic analyses show that P. hispanicus consists of three lineages. One lineage from Western Spain diverged 8.3 (2.9-14.7) Mya from the ancestor of Psammodromus hispanicus edwardsianus and P. hispanicus hispanicus Central lineage. The latter diverged 4.8 (1.5-8.7) Mya. Molecular clock dating, together with population genetic analyses, indicate that the three lineages experienced northward range expansions from southern Iberian refugia during Pleistocene glacial periods. Ecological niche modelling shows that suitable habitat of the Western lineage and P. h. edwardsianus overlap over vast areas, but that a barrier may hinder dispersal and genetic mixing of populations of both lineages. P. h. hispanicus Central lineage inhabits an ecological niche that overlaps marginally with the other two lineages. Conclusions Our results provide evidence for divergence in allopatry and niche conservatism between the Western lineage and the ancestor of P. h. edwardsianus and P. h. hispanicus Central lineage, whereas they suggest that niche divergence is involved in the origin of the latter two lineages. Both processes were temporally separated and may be responsible for the here documented genetic and phenotypic diversity of P. hispanicus. The temporal pattern is in line with those proposed for other animal lineages. It suggests that geographic isolation and

  9. Genomic landscape of liposarcoma.

    PubMed

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B; Said, Jonathan W; Mohith, S; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A; Silberman, Allan W; Forscher, Charles; Tyner, Jeffrey W; Ogawa, Seishi; Koeffler, H Phillip

    2015-12-15

    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.

  10. Genomic landscape of liposarcoma

    PubMed Central

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B.; Said, Jonathan W.; Mohith, S.; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A.; Silberman, Allan W.; Forscher, Charles; Tyner, Jeffrey W.; Ogawa, Seishi; Koeffler, H. Phillip

    2015-01-01

    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach. PMID:26643872

  11. Genomic landscape of liposarcoma.

    PubMed

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B; Said, Jonathan W; Mohith, S; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A; Silberman, Allan W; Forscher, Charles; Tyner, Jeffrey W; Ogawa, Seishi; Koeffler, H Phillip

    2015-12-15

    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach. PMID:26643872

  12. Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

    PubMed Central

    Orihuela, Rodrigo L. L.; Peres, Carlos A.; Mendes, Gabriel; Jarenkow, João A.; Tabarelli, Marcelo

    2015-01-01

    We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

  13. Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

    PubMed

    Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

    2015-01-01

    We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

  14. Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

    PubMed

    Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

    2015-01-01

    We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide.

  15. General theorem on the divergence of vortex beams

    NASA Astrophysics Data System (ADS)

    Vallone, Giuseppe; Parisi, Giuseppe; Spinello, Fabio; Mari, Elettra; Tamburini, Fabrizio; Villoresi, Paolo

    2016-08-01

    The propagation and divergence properties of beams carrying orbital angular momentum (OAM) play a crucial role in many applications. Here we present a general study on the divergence of optical beams with OAM. We show that the mean absolute value of the OAM imposes a lower bound on the value of the beam divergence. We discuss our results for two different definitions of the divergence, the so-called rms or encircled energy. The bound on the rms divergence can be expressed as a generalized uncertainty principle, with applications in long-range communication, microscopy, and two-dimensional quantum systems.

  16. Highly divergent mussel lineages in isolated Indonesian marine lakes

    PubMed Central

    de Leeuw, Christiaan A.; Knegt, Bram; Maas, Diede L.; de Voogd, Nicole J.; Abdunnur; Suyatna, Iwan; Peijnenburg, Katja T.C.A.

    2016-01-01

    Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago. PMID:27761314

  17. A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria

    PubMed Central

    Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

    2014-01-01

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

  18. Deconstructing a Polygenetic Landscape Using LiDAR and Multi-Resolution Analysis

    NASA Astrophysics Data System (ADS)

    Houser, C.; Barrineau, C. P.; Dobreva, I. D.; Bishop, M. P.

    2015-12-01

    In many earth surface systems characteristic morphologies are associated with various regimes both past and present. Aeolian systems contain a variety of features differentiated largely by morphometric differences, which in turn reflect age and divergent process regimes. Using quantitative analysis of high-resolution elevation data to generate detailed information regarding these characteristic morphometries enables geomorphologists to effectively map process regimes from a distance. Combined with satellite imagery and other types of remotely sensed data, the outputs can even help to delineate phases of activity within aeolian systems. The differentiation of regimes and identification of relict features together enables a greater level of rigor to analyses leading to field-based investigations, which are highly dependent on site-specific historical contexts that often obscure distinctions between separate process-form regimes. We present results from a Principal Components Analysis (PCA) performed on a LiDAR-derived elevation model of a largely stabilized aeolian system in South Texas. The resulting components are layered and classified to generate a map of aeolian morphometric signatures for a portion of the landscape. Several of these areas do not immediately appear to be aeolian in nature in satellite imagery or LiDAR-derived models, yet field observations and historical imagery reveal the PCA did in fact identify stabilized and relict dune features. This methodology enables researchers to generate a morphometric classification of the land surface. We believe this method is a valuable and innovative tool for researchers identifying process regimes within a study area, particularly in field-based investigations that rely heavily on site-specific context.

  19. Landscape response to base-level fall in extensional settings: Amargosa River, Basin and Range, USA

    NASA Astrophysics Data System (ADS)

    Smith, J.; Brocklehurst, S. H.; Gawthorpe, R. L.; Finch, E.

    2012-12-01

    area is characterised by three distinct, well-defined geomorphic domains: (i) little-modified Lake Tecopa-time fan surfaces (ii); an intermediate domain of gently incised streams and rounded hilltops; and (iii) incised canyons, featuring <50m knickpoints. An important control upon these domains is lithological contrasts within the Mio-Pliocene bedrock, with the large knickpoints corresponding to resistant horizons and unconsolidated lithologies corresponding to the subdued domain (ii). In addition to the large knickpoints which separate domains (ii) and (iii), a downstream divergence between (i) and (ii) also indicates a base-level fall and implies a scenario where the migrating erosional signal has been split by the lithological contrasts. As such, the vast majority of the catchment is disconnected from base-level in the Amargosa Gorge. While most of the sediments associated with the internally-drained phase of the Amargosa River will ultimately be removed, understanding how and when this occurs is important for both landscape evolution and sediment delivery to basins. This study shows that the erosional response is strongly modulated by lithological contrasts and that the base-level fall associated with integration can drive further drainage rearrangement, both of which have implications for sediment delivery to depocentres.

  20. Some Divergence Properties of Asset Price Models

    NASA Astrophysics Data System (ADS)

    Stummer, Wolfgang

    2001-12-01

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

  1. Robust Hypothesis Testing with alpha -Divergence

    NASA Astrophysics Data System (ADS)

    Gul, Gokhan; Zoubir, Abdelhak M.

    2016-09-01

    A robust minimax test for two composite hypotheses, which are determined by the neighborhoods of two nominal distributions with respect to a set of distances - called $\\alpha-$divergence distances, is proposed. Sion's minimax theorem is adopted to characterize the saddle value condition. Least favorable distributions, the robust decision rule and the robust likelihood ratio test are derived. If the nominal probability distributions satisfy a symmetry condition, the design procedure is shown to be simplified considerably. The parameters controlling the degree of robustness are bounded from above and the bounds are shown to be resulting from a solution of a set of equations. The simulations performed evaluate and exemplify the theoretical derivations.

  2. Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence

    PubMed Central

    Romero, Miguel; Ximenez, Cecilia

    2016-01-01

    Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasite Entamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genus Entamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of some Entamoeba species was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence between E. histolytica and E. nuttallii probably occurred 5.93 million years ago (Mya); this lineage diverged from E. dispar 9.97 Mya, while the ancestor of the latter separated from E. invadens 68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of the Entamoeba genus. PMID:27239333

  3. Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence.

    PubMed

    Romero, Miguel; Cerritos, R; Ximenez, Cecilia

    2016-01-01

    Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasite Entamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genus Entamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of some Entamoeba species was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence between E. histolytica and E. nuttallii probably occurred 5.93 million years ago (Mya); this lineage diverged from E. dispar 9.97 Mya, while the ancestor of the latter separated from E. invadens 68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of the Entamoeba genus. PMID:27239333

  4. Islands within an island: repeated adaptive divergence in a single population.

    PubMed

    Langin, Kathryn M; Sillett, T Scott; Funk, W Chris; Morrison, Scott A; Desrosiers, Michelle A; Ghalambor, Cameron K

    2015-03-01

    Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km(2) Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener. Variation in both bill measurements was heritable, and island scrub-jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale--environmental heterogeneity and localized dispersal--are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.

  5. Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral.

    PubMed

    Prada, Carlos; Hellberg, Michael E

    2013-03-01

    Long-lived corals, the foundation of modern reefs, often follow ecological gradients, so that populations or sister species segregate by habitat. Adaptive divergence maintains sympatric congeners after secondary contact or may even generate species by natural selection in the face of gene flow. Such ecological divergence, initially between alternative phenotypes within populations, may be aided by immigrant inviability, especially when a long period separates larval dispersal and the onset of reproduction, during which selection can sort lineages to match different habitats. Here, we evaluate the strength of one ecological factor (depth) to isolate populations by comparing the genes and morphologies of pairs of depth-segregated populations of the candelabrum coral Eunicea flexuosa across the Caribbean. Eunicea is endemic to the Caribbean and all sister species co-occur. Eunicea flexuosa is widespread both geographically and across reef habitats. Our genetic analysis revealed two depth-segregated lineages. Field survivorship data, combined with estimates of selection coefficients based on transplant experiments, suggest that selection is strong enough to segregate these two lineages. Genetic exchange between the Shallow and Deep lineages occurred either immediately after divergence or the two have diverged with gene flow. Migration occurs asymmetrically from the Shallow to Deep lineage. Limited recruitment to reproductive age, even under weak annual selection advantage, is sufficient to generate habitat segregation because of the cumulative prolonged prereproductive selection. Ecological factors associated with depth can act as filters generating strong barriers to gene flow, altering morphologies, and contributing to the potential for speciation in the sea.

  6. Parallel and non-parallel morphological divergence among foraging specialists in European whitefish (Coregonus lavaretus)

    PubMed Central

    Siwertsson, Anna; Knudsen, Rune; Adams, Colin E; Præbel, Kim; Amundsen, Per-Arne

    2013-01-01

    Parallel phenotypic evolution occurs when independent populations evolve similar traits in response to similar selective regimes. However, populations inhabiting similar environments also frequently show some phenotypic differences that result from non-parallel evolution. In this study, we quantified the relative importance of parallel evolution to similar foraging regimes and non-parallel lake-specific effects on morphological variation in European whitefish (Coregonus lavaretus). We found evidence for both lake-specific morphological characteristics and parallel morphological divergence between whitefish specializing in feeding on profundal and littoral resources in three separate lakes. Foraging specialists expressed similar phenotypes in different lakes in both overall body shape and selected measured morphological traits. The morphology of the two whitefish specialists resembled that predicted from other fish species, supporting the conclusion of an adaptive significance of the observed morphological characteristics. Our results indicate that divergent natural selection resulting from foraging specialization is driving and/or maintaining the observed parallel morphological divergence. Whitefish in this study may represent an early stage of divergence towards the evolution of specialized morphs. PMID:23789070

  7. Feedbacks Between Channel Adjustment, Sediment Calibre and Landscape Dynamics in Tectonically Perturbed Landscapes (Invited)

    NASA Astrophysics Data System (ADS)

    Attal, M.; Cowie, P. A.; Whittaker, A. C.; Tucker, G. E.; Mudd, S. M.; Hurst, M. D.

    2010-12-01

    Knowledge of the coupling between channel geometry and sediment input to rivers is central to understanding the mechanisms and timescales over which landscapes respond to a tectonic perturbation. Here, we document changes to channel geometry and sediment calibre in catchments experiencing a well-constrained increase in relative uplift rate in the Central Apennines (Italy) and the Sierra Nevada (California). In both landscapes, channels and hillslopes steepen and knickpoints propagate upstream through the catchments, leading to the formation of a break in both hillslope and channel gradient that separates the steepened landscape from lower relief topography which has not yet responded to the change in uplift rate. Downstream of this break in slope, channels narrow markedly as river gradient increases. In addition, they are supplied with coarser sediment from the steepened hillslopes, in particular when sediment is supplied via landslides and debris fans. In Italy, channel narrowing can be explained using the equation proposed by Finnegan et al. [2005]: W = kQ3/8S-3/16, where W is channel width, k is a constant, Q is river discharge and S is channel slope. However, to model our field data, the prefactor k must be strongly dependent on uplift rate: the higher the uplift rate, the smaller the prefactor k. Using the Channel-Hillslope Integrated Landscape Development (CHILD) model, we show that the location of the main break in slope along the river profiles in Italy (in terms of height and along stream distance) can be fitted using a detachment-limited model with dynamic channel adjustment (equation above), k dependent on uplift rate and a threshold for erosion. A threshold corresponding to the shear stress required to entrain the median grain size of the sediment along the steepened reaches of the channels best fits the data. Our modelling results show that the response time of the landscape in this setting is strongly dependent on relative uplift rate, since

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

    PubMed

    Clark, Rob

    2011-02-01

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

  9. Generation of low-divergence laser beams

    DOEpatents

    Kronberg, James W.

    1993-01-01

    Apparatus for transforming a conventional beam of coherent light, having a Gaussian energy distribution and relatively high divergence, into a beam in which the energy distribution approximates a single, non-zero-order Bessel function and which therefore has much lower divergence. The apparatus comprises a zone plate having transmitting and reflecting zones defined by the pattern of light interference produced by the combination of a beam of coherent light with a Gaussian energy distribution and one having such a Bessel distribution. The interference pattern between the two beams is a concentric array of multiple annuli, and is preferably recorded as a hologram. The hologram is then used to form the transmitting and reflecting zones by photo-etching portions of a reflecting layer deposited on a plate made of a transmitting material. A Bessel beam, containing approximately 50% of the energy of the incident beam, is produced by passing a Gaussian beam through such a Bessel zone plate. The reflected beam, also containing approximately 50% of the incident beam energy and having a Bessel energy distribution, can be redirected in the same direction and parallel to the transmitted beam. Alternatively, a filter similar to the Bessel zone plate can be placed within the resonator cavity of a conventional laser system having a front mirror and a rear mirror, preferably axially aligned with the mirrors and just inside the front mirror to generate Bessel energy distribution light beams at the laser source.

  10. Generation of low-divergence laser beams

    DOEpatents

    Kronberg, J.W.

    1993-09-14

    Apparatus for transforming a conventional beam of coherent light, having a Gaussian energy distribution and relatively high divergence, into a beam in which the energy distribution approximates a single, non-zero-order Bessel function and which therefore has much lower divergence. The apparatus comprises a zone plate having transmitting and reflecting zones defined by the pattern of light interference produced by the combination of a beam of coherent light with a Gaussian energy distribution and one having such a Bessel distribution. The interference pattern between the two beams is a concentric array of multiple annuli, and is preferably recorded as a hologram. The hologram is then used to form the transmitting and reflecting zones by photo-etching portions of a reflecting layer deposited on a plate made of a transmitting material. A Bessel beam, containing approximately 50% of the energy of the incident beam, is produced by passing a Gaussian beam through such a Bessel zone plate. The reflected beam, also containing approximately 50% of the incident beam energy and having a Bessel energy distribution, can be redirected in the same direction and parallel to the transmitted beam. Alternatively, a filter similar to the Bessel zone plate can be placed within the resonator cavity of a conventional laser system having a front mirror and a rear mirror, preferably axially aligned with the mirrors and just inside the front mirror to generate Bessel energy distribution light beams at the laser source. 11 figures.

  11. Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

    PubMed

    Kretzschmar, Martin; Kuhnt, Andreas; Bonkowski, Michael; Fiore-Donno, Anna Maria

    2016-07-01

    Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update.

  12. History repeats itself: genomic divergence in copepods.

    PubMed

    Renaut, Sébastien; Dion-Côté, Anne-Marie

    2016-04-01

    Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the tape would lead evolution down a pathway radically different from the road actually taken (Gould 1989). This thought experiment has puzzled evolutionary biologists for a long time: how repeatable are evolutionary events? And if history does indeed repeat itself, what are the factors that may help us predict the path taken? A powerful means to address these questions at a small evolutionary scale is to study closely related populations that have evolved independently, under similar environmental conditions. This is precisely what Pereira et al. (2016) set out to do using marine copepods Tigriopus californicus, and present their results in this issue of Molecular Ecology. They show that evolution can be repeatable and even partly predictable, at least at the molecular level. As expected from theory, patterns of divergence were shaped by natural selection. At the same time, strong genetic drift due to small population sizes also constrained evolution down a similar evolutionary road, and probably contributed to repeatable patterns of genomic divergence. PMID:27012819

  13. Genetic divergence of tomato ringspot virus.

    PubMed

    Rivera, Lucia; Zamorano, Alan; Fiore, Nicola

    2016-05-01

    Tomato ringspot virus (ToRSV) has been detected in Chile, causing economically important diseases in a wide range of hosts. A ToRSV isolate was obtained from raspberry cv Heritage (Rasp-CL) showing leaf yellowing and stunting. The complete genome of Rasp-CL was sequenced by deep sequencing. The Rasp-CL RNA1 sequence shared 97.4 % nucleotide sequence identity with divergent RNA1 of isolate Rasp1-2014, while Rasp-CL RNA2 showed high divergence from all four isolates available in the database, sharing only 63.9-72.7 % nucleotide sequence identity. This difference was mainly based on the X4 coding region, which has been reported to be a high-variability region. Moreover, based on differences in the X4 region, three Rasp-CL RNA2 variants of different length were identified in the same host. One putative recombination event was identified between the Rasp-CL and GYV-2014 X4 genes. Phylogenetic analysis suggested that ToRSV isolates with currently available sequences form three distinct groups. Our results suggest that, for an accurate phylogenetic classification of ToRSV, it is necessary to obtain sequences of both RNAs. This is the first report of a complete ToRSV genome sequence from South America.

  14. Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

    PubMed

    Kretzschmar, Martin; Kuhnt, Andreas; Bonkowski, Michael; Fiore-Donno, Anna Maria

    2016-07-01

    Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update. PMID:26663217

  15. Occurrence of Knudsen minima in diverging microchannels

    SciTech Connect

    Hemadri, Vadiraj; Bhandarkar, Upendra; Agrawal, Amit

    2014-12-09

    Rarefied gas flow is gaining increasing importance with the emergence of Micro Electro Mechanical Systems (MEMS). Knudsen minima is one of the characteristic feature of such rarefied flows and has been observed in uniform cross section channels such as plane channel, cylindrical tube and annulus. However, data pertaining to gaseous flow in varying cross section channel is relatively sparse. Channels of varying cross section are frequently encountered in MEMS devices and are fundamental to the design of micro-scale nozzles and micro-valves. In this context, rarefied gas flow through a diverging microchannel (divergence angle – 12 degree) is studied experimentally with three different gases (argon, nitrogen and oxygen). The experiments are performed over a wide range with the mean Knudsen number varying from slip to the transitional regime (0.07 to 1.2). It is found that the effect of molecular weight of the gas on the non-dimensional mass flow rate is negligible. The Knudsen minima is experimentally observed for the first time in microchannel of non-uniform cross section.

  16. How pervasive is biotic homogenization in human-modified tropical forest landscapes?

    PubMed

    Solar, Ricardo Ribeiro de Castro; Barlow, Jos; Ferreira, Joice; Berenguer, Erika; Lees, Alexander C; Thomson, James R; Louzada, Júlio; Maués, Márcia; Moura, Nárgila G; Oliveira, Victor H F; Chaul, Júlio C M; Schoereder, José Henrique; Vieira, Ima Célia Guimarães; Mac Nally, Ralph; Gardner, Toby A

    2015-10-01

    Land-cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi-taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape-scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among-site and among-landscape β-diversity appeared to attenuate species loss at larger scales. We found consistently high levels of β-diversity among landscapes for all land cover classes, providing support for landscape-scale divergence in species composition. Our findings support concerns that β-diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota. PMID:26299405

  17. How pervasive is biotic homogenization in human-modified tropical forest landscapes?

    PubMed

    Solar, Ricardo Ribeiro de Castro; Barlow, Jos; Ferreira, Joice; Berenguer, Erika; Lees, Alexander C; Thomson, James R; Louzada, Júlio; Maués, Márcia; Moura, Nárgila G; Oliveira, Victor H F; Chaul, Júlio C M; Schoereder, José Henrique; Vieira, Ima Célia Guimarães; Mac Nally, Ralph; Gardner, Toby A

    2015-10-01

    Land-cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi-taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape-scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among-site and among-landscape β-diversity appeared to attenuate species loss at larger scales. We found consistently high levels of β-diversity among landscapes for all land cover classes, providing support for landscape-scale divergence in species composition. Our findings support concerns that β-diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota.

  18. Establishment of new mutations under divergence and genome hitchhiking

    PubMed Central

    Feder, Jeffrey L.; Gejji, Richard; Yeaman, Sam; Nosil, Patrik

    2012-01-01

    Theoretical models addressing genome-wide patterns of divergence during speciation are needed to help us understand the evolutionary processes generating empirical patterns. Here, we examine a critical issue concerning speciation-with-gene flow: to what degree does physical linkage (r < 0.5) of new mutations to already diverged genes aid the build-up of genomic islands of differentiation? We used simulation and analytical approaches to partition the probability of establishment for a new divergently selected mutation when the mutation (i) is the first to arise in an undifferentiated genome (the direct effect of selection), (ii) arises unlinked to any selected loci (r = 0.5), but within a genome that has some already diverged genes (the effect of genome-wide reductions in gene flow for facilitating divergence, which we term ‘genome hitchhiking’), and (iii) arises in physical linkage to a diverged locus (divergence hitchhiking). We find that the strength of selection acting directly on a new mutation is generally the most important predictor for establishment, with divergence and genomic hitchhiking having smaller effects. We outline the specific conditions under which divergence and genome hitchhiking can aid mutation establishment. The results generate predictions about genome divergence at different points in the speciation process and avenues for further work. PMID:22201175

  19. Energy Landscape of Social Balance

    NASA Astrophysics Data System (ADS)

    Marvel, Seth A.; Strogatz, Steven H.; Kleinberg, Jon M.

    2009-11-01

    We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social “balance” allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

  20. Martian Landscapes in Motion

    NASA Astrophysics Data System (ADS)

    Mattson, Sarah; McEwen, Alfred; Kirk, Randolph; Howington-Kraus, Elpitha; Chojnacki, Matthew; Runyon, Kirby; Cremonese, Gabriele; Re, Cristina

    2014-05-01

    RISE orthorectified image sequences makes it possible to conduct accurate change detection studies of active processes on Mars. Some examples of studies of active landscapes on Mars using HiRISE DTMs and orthoimage sequences include: dune and ripple motion (Bridges et al., 2012, Nature), recurring slope lineae (RSL) (McEwen et al., 2011, Science; McEwen et al., 2013, Nature Geoscience), gully activity (Dundas et al., 2012, Icarus), and polar processes (Hansen et al., 2011, Science; Portyankina et al. 2013, Icarus,). These studies encompass images from multiple Mars years and seasons. Sequences of orthoimages make it possible to generate animated gifs or movies to visualize temporal changes (http://www.uahirise.org/sim/). They can also be brought into geospatial software to quantitatively map and record changes. The ability to monitor the surface of Mars at high spatial resolution with frequent repeat images has opened up our insight into seasonal and interannual changes, further increasing our understanding of Mars as an active planet.

  1. Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

    PubMed Central

    McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

    2013-01-01

    Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

  2. Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

    PubMed

    McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

    2013-01-01

    Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

  3. Population divergence in fish elemental phenotypes associated with trophic phenotypes and lake trophic state.

    PubMed

    Tuckett, Quenton M; Kinnison, Michael T; Saros, Jasmine E; Simon, Kevin S

    2016-11-01

    Studies of ecological stoichiometry typically emphasize the role of interspecific variation in body elemental content and the effects of species or family identity. Recent work suggests substantial variation in body stoichiometry can also exist within species. The importance of this variation will depend on insights into its origins and consequences at various ecological scales, including the distribution of elemental phenotypes across landscapes and their role in nutrient recycling. We investigated whether trophic divergence can produce predictable patterns of elemental phenotypes among populations of an invasive fish, the white perch (Morone americana), and whether elemental phenotypes predict nutrient excretion. White perch populations exhibited a gradient of trophic phenotypes associated with landscape-scale variation in lake trophic state. Perch body chemistry varied considerably among lakes (from 0.09 for % C to 0.31-fold for % P) casting doubt on the assumption of homogenous elemental phenotypes. This variation was correlated with divergence in fish body shape and other trophic traits. Elemental phenotypes covaried (r (2) up to 0.84) with lake trophic state. This covariation likely arose in contemporary time since many of these perch populations were introduced in the last century and the trophic state in many of the lakes has changed in the past few decades. Nutrient excretion varied extensively among populations, but was not readily related to fish body chemistry or lake trophic state. This suggests that predictable patterns of fish body composition can arise quickly through trophic specialization to lake conditions, but such elemental phenotypes may not translate to altered nutrient recycling by fish.

  4. Wildlife disease prevalence in human-modified landscapes.

    PubMed

    Brearley, Grant; Rhodes, Jonathan; Bradley, Adrian; Baxter, Greg; Seabrook, Leonie; Lunney, Daniel; Liu, Yan; McAlpine, Clive

    2013-05-01

    have been based on a one-dimensional comparison between unmodified and modified sites. What is lacking are spatially and temporally explicit quantitative approaches which are required to enable an understanding of the range of key causal mechanisms and the reasons for variability. This is particularly important for replicated studies across different host-pathogen systems. Furthermore, there are few studies that have attempted to separate the independent effects of habitat loss and fragmentation on wildlife disease, which are the major determinants of wildlife population dynamics in human-modified landscapes. There is an urgent need to understand better the potential causal links between the processes of human-induced landscape change and the associated influences of habitat fragmentation, matrix hostility and loss of connectivity on an animal's physiological stress, immune response and disease susceptibility. This review identified no study that had assessed the influence of human-induced landscape change on the prevalence of a wildlife sexually transmitted disease. A better understanding of the various mechanisms linking human-induced landscape change and the prevalence of wildlife disease will lead to more successful conservation management outcomes.

  5. Microevolutionary processes generate phylogenomic discordance at ancient divergences.

    PubMed

    Oliver, Jeffrey C

    2013-06-01

    Stochastic population processes may cause differences between species histories and gene histories. These processes are assumed to only influence the most recent divergences in the tree of life; however, there may be underappreciated potential for microevolutionary processes to impact deep divergences. I used multispecies coalescent models to determine the impact of stochastic processes on deep phylogenomic histories. Here I show phylogenomic discordance between gene histories and species histories is expected at deep divergences for many eukaryotic taxa, and the probability of discordance increases with population size, generation time, and the number of species in the tree. Five eukaryotic clades (angiosperms, birds, harpaline beetles, mammals, and nymphalid butterflies) demonstrate significant discordance potential at divergences over 50 million years old, and this discordance potential is independent of the age of divergence. These findings demonstrate population processes acting over very short timescales will leave a lasting impact on genomic histories, even for divergence events occurring tens to hundreds of millions of years ago.

  6. Bioenergy in a Multifunctional Landscape

    SciTech Connect

    Watts, Chad; Negri, Cristina; Ssegane, Herbert

    2015-10-23

    How can our landscapes be managed most effectively to produce crops for food, feed, and bioenergy, while also protecting our water resources by preventing the loss of nutrients from the soil? Dr. Cristina Negri and her team at the U.S. Department of Energy’s Argonne National Laboratory are tackling this question at an agricultural research site located in Fairbury, Illinois.

  7. SAVANNAH RIVER BASIN LANDSCAPE ANALYSIS

    EPA Science Inventory

    Scientists from the U.S. Environmental Protection Agency (EPA), Region 4, Science and Ecosystem Support Division, enlisted the assistance of the landscape ecology group of U.S. EPA, Office of Research and Development (ORD), National Exposure Research Laboratory, Environmental Sci...

  8. [Meadow maris: a genetic landscape].

    PubMed

    El'chinova, G I; Startseva, E A; Moshkina, I S; Ginter, E K

    1998-05-01

    The distribution of the most frequent family names was analyzed in five regions of the Marii El republic, and diagrams of their genetic landscape were constructed. Based on the diagrams, conclusions were drawn regarding the genetic subdivision of the corresponding populations and the boundary between elementary populations within them.

  9. Linguistic Landscape and Minority Languages

    ERIC Educational Resources Information Center

    Cenoz, Jasone; Gorter, Durk

    2006-01-01

    This paper focuses on the linguistic landscape of two streets in two multilingual cities in Friesland (Netherlands) and the Basque Country (Spain) where a minority language is spoken, Basque or Frisian. The paper analyses the use of the minority language (Basque or Frisian), the state language (Spanish or Dutch) and English as an international…

  10. Language's Landscape of the Mind.

    ERIC Educational Resources Information Center

    Tracy, Janet

    2000-01-01

    Describes how the author's 6 middle school students living in a village in the Yukon, 100 miles off the road system just below the arctic circle, enthusiastically wrote stories or poems about their lives. The students shared their works via an online electronic conferencing system with students from the unimaginably different landscape of the…

  11. Flowers and Landscape by Serendipity.

    ERIC Educational Resources Information Center

    Pippin, Sandi

    2003-01-01

    Describes an art lesson in which students sketch drawings of flowers and use watercolor paper and other materials to paint a landscape. Explains that the students also learn about impressionism in this lesson. Discusses how the students prepare the paper and create their artwork. (CMK)

  12. Assessing the New Competitive Landscape.

    ERIC Educational Resources Information Center

    Blustain, Harvey; Goldstein, Philip; Lozier, Gregory

    1998-01-01

    Argues that complex forces (new delivery technologies, changing demographics, emergence of corporate universities, global economy) have created a new, competitive landscape for higher education that forces institutions to think methodically about how to respond. A framework for college planning, incorporating three critical components, is…

  13. Selected Landscape Plants. Slide Script.

    ERIC Educational Resources Information Center

    McCann, Kevin

    This slide script, part of a series of slide scripts designed for use in vocational agriculture classes, deals with commercially important woody ornamental landscape plants. Included in the script are narrations for use with a total of 253 slides illustrating 92 different plants. Several slides are used to illustrate each plant: besides a view of…

  14. Ornamental Landscape Grasses. Slide Script.

    ERIC Educational Resources Information Center

    Still, Steven M.; Adams, Denise W.

    This slide script to accompany the slide series, Ornamental Landscape Grasses, contains photographs of the 167 slides and accompanying narrative text intended for use in the study and identification of commercially important ornamental grasses and grasslike plants. Narrative text is provided for slides of 62 different perennial and annual species…

  15. Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula.

    PubMed

    Crews, Sarah C; Hedin, Marshal

    2006-02-01

    Comparative phylogenetic and phylogeographic analyses have revealed a pervasive midpeninsular divergence in the mitochondrial genealogies of numerous vertebrate taxa distributed on the Baja California Peninsula. In this study, we extend the investigation of regional vicariance in Baja California to an arthropod taxon by examining patterns of phylogenetic and morphological divergence in the spider genus Homalonychus (Araneae, Homalonychidae). We analyzed data from two mtDNA genes (16S rRNA and NADH dehydrogenase subunit (1) and a nuclear gene (28S rRNA) using maximum parsimony and Bayesian phylogenetic analyses, and also conducted geometric morphometric analyses employing landmark data on male and female genitalia. Genes and morphology both reveal a deep split across the Colorado River and Gulf of California, separating Homalonychus selenopoides on the east side of river from its congener Homalonychus theologus on the west side of the river, including the Baja California Peninsula. Along the north-south axis of the Baja Peninsula, an apparently more recent midpeninsular phylogenetic break is evident within H. theologus in the mitochondrial genome and in female genitalia. However, there is no measurable divergence between northern and southern populations in either nuclear DNA or male genitalia. We suggest that this discordance between datasets reflects either a difference in rates of evolution between male versus female systems, or that male-based nuclear gene flow is obscuring a phylogenetic split that is fixed in the female-based systems. Our findings provide additional support for a midpeninsular Baja divergence event, although the timing and geological evidence for such an event remain elusive.

  16. An Analysis of the Landscaping Occupation.

    ERIC Educational Resources Information Center

    Stemple, Lynn L.; Dilley, John E.

    The general purpose of the occupational analysis is to provide workable, basic information dealing with the many and varied duties performed in the landscape services occupation. Depending on the preparation and abilities of the individual student, he may enter the landscape area as (1) nursery worker, (2) landscape planter, (3) landscape…

  17. 23 CFR 752.4 - Landscape development.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... landscaping and environmental design. (b) Landscape development should have provisions for plant establishment periods of a duration sufficient for expected survival in the highway environment. Normal 1-year plant... for natural regeneration of native growth and the management of that growth. (e) Landscaping...

  18. Thoughts concerning the economic valuation of landscapes.

    PubMed

    Schaeffer, Peter V

    2008-11-01

    The incorporation of economic thinking into the valuation of landscapes is still relatively new. It is an approach that yields valuable new insights and can help with prioritizing the use of scarce resources to improve and/or preserve landscapes. This paper explores and discusses the uses and limitations of economic valuation of landscapes from market failure, policy process, and theoretical and philosophical perspectives.

  19. The Changing Landscape of Higher Education

    ERIC Educational Resources Information Center

    Staley, David J.; Trinkle, Dennis A.

    2011-01-01

    The landscape of higher education--the growing variety of higher education institutions, the cultural environment, the competitive ecosystem--is changing rapidly and disruptively. The higher education landscape is metaphorically crossed with fault lines, those fissures in the landscape creating potential areas of dramatic change, and is as…

  20. Space Strategies for the New Learning Landscape

    ERIC Educational Resources Information Center

    Dugdale, Shirley

    2009-01-01

    The Learning Landscape is the total context for students' learning experiences and the diverse landscape of learning settings available today--from specialized to multipurpose, from formal to informal, and from physical to virtual. The goal of the Learning Landscape approach is to acknowledge this richness and maximize encounters among people,…

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

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

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

    PubMed

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

    2014-10-15

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

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

    PubMed

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

    2014-10-15

    Environmental changes, such as changes in the coastal topography due to Eurasian plate movements, climate oscillation during the Pleistocene, and alteration of ocean currents, have complicated the geographical structure of marine species and deepened their divergence between populations. As two widely distributed species of crustacean (Oratosquilla oratoria and Eriocheir japonica), weak differences were expected due to their high dispersal potential of planktonic larvae with ocean currents. However, results showed a significant genetic divergence between north of China and south of China in the study. In addition, the estimated north-south divergence time (27-30.5 Myr) of mantis shrimp was near the time of the Himalayan movement, and the China-Japan clade divergence time (10.5-11.9 Myr) of mitten crabs was also coincident with the time of the opening of the Sea of Japan. Thus, we hypothesized that environmental changes in the coastal topography contributed to the marine species divergence. Furthermore, based on phylogenetic analysis, network analysis and haplotype distribution, we surmised that mitten crabs originated from a population with the oldest haplotype (H6) and then divided into the north and south populations due to the recent Eurasian plate movements and ocean currents. And lineage of Japan originated from the north population for the opening of the Sea of Japan. While O. oratoria was guessed to originate from two separate populations in the China Sea. The results of "star-like" network, negative values in neutral test, and Tajima's D statistics of two marine species supported a recent rapid population expansion event after the Pleistocene glaciations. PMID:25106858

  4. Evidence for divergent plate-boundary characteristics and crustal spreading on venus.

    PubMed

    Head, J W; Crumpler, L S

    1987-12-01

    Detailed examination of the topography and morphology of western Aphrodite Terra reveals numerous features that are similar to terrestrial divergent plate-boundary characteristics. Individual domains between fracturezone-like discontinuities contain a variety of bilaterally symmetrical topographic elements that suggest that topographic features have been created at rise crests, rifted and separated, and moved laterally to their present symmetrical positions. The topographic and morphologic similarities, together with strikingly similar mirror-image map patterns on both sides of the rise axis, suggest that western Aphrodite Terra shares the characteristics of oceanic divergent plate boundaries, and is the site of crustal spreading on Venus. Topographic profiles are consistent with spreading rates of the order of several centimeters per year.

  5. Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

    PubMed Central

    Ciofi, C.; Beaumont, M. A.; Swingland, I. R.; Bruford, M. W.

    1999-01-01

    In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world's largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.

  6. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    SciTech Connect

    Larionov, V.; Kouprina, N. |; Edlarov, M. |; Perkins, E.; Porter, G.; Resnick, M.A.

    1993-12-31

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic growth. The frequency of recombination is partly dependent on the method of transformation in that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RADS2, RADI and the RNCI genes,

  7. Rapid Diversity Loss of Competing Animal Species in Well-Connected Landscapes.

    PubMed

    Schippers, Peter; Hemerik, Lia; Baveco, Johannes M; Verboom, Jana

    2015-01-01

    Population viability of a single species, when evaluated with metapopulation based landscape evaluation tools, always increases when the connectivity of the landscape increases. However, when interactions between species are taken into account, results can differ. We explore this issue using a stochastic spatially explicit meta-community model with 21 competing species in five different competitive settings: (1) weak, coexisting competition, (2) neutral competition, (3) strong, excluding competition, (4) hierarchical competition and (5) random species competition. The species compete in randomly generated landscapes with various fragmentation levels. With this model we study species loss over time. Simulation results show that overall diversity, the species richness in the entire landscape, decreases slowly in fragmented landscapes whereas in well-connected landscapes rapid species losses occur. These results are robust with respect to changing competitive settings, species parameters and spatial configurations. They indicate that optimal landscape configuration for species conservation differs between metapopulation approaches, modelling species separately and meta-community approaches allowing species interactions. The mechanism behind this is that species in well-connected landscapes rapidly outcompete each other. Species that become abundant, by chance or by their completive strength, send out large amounts of dispersers that colonize and take over other patches that are occupied by species that are less abundant. This mechanism causes rapid species loss. In fragmented landscapes the colonization rate is lower, and it is difficult for a new species to establish in an already occupied patch. So, here dominant species cannot easily take over patches occupied by other species and higher diversity is maintained for a longer time. These results suggest that fragmented landscapes have benefits for species conservation previously unrecognized by the landscape ecology

  8. Rapid Diversity Loss of Competing Animal Species in Well-Connected Landscapes

    PubMed Central

    Schippers, Peter; Hemerik, Lia; Baveco, Johannes M.; Verboom, Jana

    2015-01-01

    Population viability of a single species, when evaluated with metapopulation based landscape evaluation tools, always increases when the connectivity of the landscape increases. However, when interactions between species are taken into account, results can differ. We explore this issue using a stochastic spatially explicit meta-community model with 21 competing species in five different competitive settings: (1) weak, coexisting competition, (2) neutral competition, (3) strong, excluding competition, (4) hierarchical competition and (5) random species competition. The species compete in randomly generated landscapes with various fragmentation levels. With this model we study species loss over time. Simulation results show that overall diversity, the species richness in the entire landscape, decreases slowly in fragmented landscapes whereas in well-connected landscapes rapid species losses occur. These results are robust with respect to changing competitive settings, species parameters and spatial configurations. They indicate that optimal landscape configuration for species conservation differs between metapopulation approaches, modelling species separately and meta-community approaches allowing species interactions. The mechanism behind this is that species in well-connected landscapes rapidly outcompete each other. Species that become abundant, by chance or by their completive strength, send out large amounts of dispersers that colonize and take over other patches that are occupied by species that are less abundant. This mechanism causes rapid species loss. In fragmented landscapes the colonization rate is lower, and it is difficult for a new species to establish in an already occupied patch. So, here dominant species cannot easily take over patches occupied by other species and higher diversity is maintained for a longer time. These results suggest that fragmented landscapes have benefits for species conservation previously unrecognized by the landscape ecology

  9. Dating Tips for Divergence-Time Estimation.

    PubMed

    O'Reilly, Joseph E; dos Reis, Mario; Donoghue, Philip C J

    2015-11-01

    The molecular clock is the only viable means of establishing an accurate timescale for Life on Earth, but it remains reliant on a capricious fossil record for calibration. 'Tip-dating' promises a conceptual advance, integrating fossil species among their living relatives using molecular/morphological datasets and evolutionary models. Fossil species of known age establish calibration directly, and their phylogenetic uncertainty is accommodated through the co-estimation of time and topology. However, challenges remain, including a dearth of effective models of morphological evolution, rate correlation, the non-random nature of missing characters in fossil data, and, most importantly, accommodating uncertainty in fossil age. We show uncertainty in fossil-dating propagates to divergence-time estimates, yielding estimates that are older and less precise than those based on traditional node calibration. Ultimately, node and tip calibrations are not mutually incompatible and may be integrated to achieve more accurate and precise evolutionary timescales.

  10. Divergent clonal selection dominates medulloblastoma at recurrence.

    PubMed

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

    2016-01-21

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

  11. IR divergences in inflation and entropy perturbations

    SciTech Connect

    Xue, Wei; Brandenberger, Robert; Gao, Xian E-mail: xgao@apc.univ-paris7.fr

    2012-06-01

    We study leading order perturbative corrections to the two point correlation function of the scalar field describing the curvature perturbation in a slow-roll inflationary background, paying particular attention to the contribution of entropy mode loops. We find that the infrared divergences are worse than in pure de Sitter space: they are power law rather than logarithmic. The validity of perturbation theory and thus of the effective field theory of cosmological perturbations leads to stringent constraints on the coupling constants describing the interactions, in our model the quartic self-interaction coupling constant of the entropy field. If the self coupling constant is larger than some critical value which depends in particular on the duration of the inflationary phase, then perturbation theory breaks down. Our analysis may have implications for the stability of de Sitter space: the quantum effects which lead to an instability of de Sitter space will be larger in magnitude in the presence of entropy fluctuations.

  12. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes

    PubMed Central

    Affaticati, Pierre E.; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C.; Tittmann, Kai; Dalby, Paul A.

    2016-01-01

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies. PMID:27767080

  13. The information-divergence hypothesis of informational masking

    PubMed Central

    Lutfi, Robert A.; Gilbertson, Lynn; Heo, Inseok; Chang, An-Chieh; Stamas, Jacob

    2013-01-01

    In recent years there has been growing interest in masking that cannot be attributed to interactions in the cochlea—so-called informational masking (IM). Similarity in the acoustic properties of target and masker and uncertainty regarding the masker are the two major factors identified with IM. These factors involve quite different manipulations of signals and are believed to entail fundamentally different processes resulting in IM. Here, however, evidence is presented that these factors affect IM through their mutual influence on a single factor—the information divergence of target and masker given by Simpson–Fitter's da [Lutfi et al. (2012). J. Acoust. Soc. Am. 132, EL109–113]. Four experiments are described involving multitone pattern discrimination, multi-talker word recognition, sound-source identification, and sound localization. In each case standard manipulations of masker uncertainty and target-masker similarity (including the covariation of target-masker frequencies) are found to have the same effect on performance provided they produce the same change in da. The function relating d′ performance to da, moreover, appears to be linear with constant slope across listeners. The overriding dependence of IM on da is taken to reflect a general principle of perception that exploits differences in the statistical structure of signals to separate figure from ground. PMID:23967946

  14. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence.

    PubMed

    Org, Tõnis; Duan, Dan; Ferrari, Roberto; Montel-Hagen, Amelie; Van Handel, Ben; Kerényi, Marc A; Sasidharan, Rajkumar; Rubbi, Liudmilla; Fujiwara, Yuko; Pellegrini, Matteo; Orkin, Stuart H; Kurdistani, Siavash K; Mikkola, Hanna Ka

    2015-03-12

    Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic marks. Our data suggest that, rather than recruiting corepressors to enhancers, Scl prevents ectopic cardiogenesis by occupying enhancers that cardiac factors, such as Gata4 and Hand1, use for gene activation. Although hematopoietic Gata factors bind with Scl to both activated and repressed genes, they are dispensable for cardiac repression, but necessary for activating genes that enable hematopoietic stem/progenitor cell development. These results suggest that a unique subset of enhancers in lineage-specific genes that are accessible for regulators of opposing fates during the time of the fate decision provide a platform where the divergence of mutually exclusive fates is orchestrated.

  15. Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator.

    PubMed

    Twomey, Evan; Vestergaard, Jacob S; Venegas, Pablo J; Summers, Kyle

    2016-02-01

    While divergent ecological adaptation can drive speciation, understanding the factors that facilitate or constrain this process remains a major goal in speciation research. Here, we study two mimetic transition zones in the poison frog Ranitomeya imitator, a species that has undergone a Müllerian mimetic radiation to establish four morphs in Peru. We find that mimetic morphs are strongly phenotypically differentiated, producing geographic clines with varying widths. However, distinct morphs show little neutral genetic divergence, and landscape genetic analyses implicate isolation by distance as the primary determinant of among-population genetic differentiation. Mate choice experiments suggest random mating at the transition zones, although certain allopatric populations show a preference for their own morph. We present evidence that this preference may be mediated by color pattern specifically. These results contrast with an earlier study of a third transition zone, in which a mimetic shift was associated with reproductive isolation. Overall, our results suggest that the three known mimetic transition zones in R. imitator reflect a speciation continuum, which we have characterized at the geographic, phenotypic, behavioral, and genetic levels. We discuss possible explanations for variable progress toward speciation, suggesting that multifarious selection on both mimetic color pattern and body size may be responsible for generating reproductive isolation.

  16. Separation of Lift-Generated Vortex Wakes Into Two Diverging Parts

    NASA Technical Reports Server (NTRS)

    Rossow, Vernon J.; Brown, Anthony P.

    2010-01-01

    As part of an ongoing study of the spreading rate of lift-generated vortex wakes, the present investigation considers possible reasons as to why segments of lift-generated wakes sometimes depart from the main part of the wake to move rapidly in either an upward or downward direction. It is assumed that deficiencies or enhancements of the lift carry over across the fuselage-shrouded wing are the driving mechanism for departures of wake-segments. The computations presented first indicate that upwardly departing wake segments that were observed and photographed could have been produced by a deficiency in lift carryover across the fuselage-shrouded part of the wing. Computations made of idealized vortex wakes indicate that upward departure of a wake segment requires a centerline reduction in the span loading of 70% or more, whether the engines are at idle or robust thrust. Similarly, it was found that downward departure of wake segments is produced when the lift over the center part of the wing is enhanced. However, it was also found that downward departures do not occur without the presence of robust engine-exhaust streams (i.e., engines must NOT be at idle). In those cases, downward departures of a wake segment occurs when the centerline value of the loading is enhanced by any amount between about 10% to 100%. Observations of condensation trails indicate that downward departure of wake segments is rare. Upward departures of wake segments appears to be more common but still rare. A study to determine the part of the aircraft that causes wake departures has not been carried out. However, even though departures of wake segments rarely occur, some aircraft do regularly shed these wake structures. If aircraft safety is to be assured to a high degree of reliability, and a solution for eliminating them is not implemented, existing guidelines for the avoidance of vortex wakes [1,3] may need to be broadened to include possible increases in wake sizes caused by vertical departures of wake segments. Further study may indicate that it is not possible to modify existing aircraft enough to prevent wake departures. Wake-avoidance guidelines must then be adjusted to provide the desired degree of safety. It appears that steps to avoid upwardly moving wake segments have already been incorporated into the avoidance procedures used for aircraft on approach to runways at the Frankfurt Airport [6,7]. The uncertainty in the prospects for compromises in flight safety caused by rapidly upwardly or downwardly moving wake segments suggest that it be specified that aircraft do not fly above or below each other during operations in the airport vicinity where aircraft are likely to be closely spaced [20].

  17. The farmer as a landscape steward: Comparing local understandings of landscape stewardship, landscape values, and land management actions.

    PubMed

    Raymond, Christopher M; Bieling, Claudia; Fagerholm, Nora; Martin-Lopez, Berta; Plieninger, Tobias

    2016-03-01

    We develop a landscape stewardship classification which distinguishes between farmers' understanding of landscape stewardship, their landscape values, and land management actions. Forty semi-structured interviews were conducted with small-holder (<5 acres), medium-holders (5-100 acres), and large-holders (>100 acres) in South-West Devon, UK. Thematic analysis revealed four types of stewardship understandings: (1) an environmental frame which emphasized the farmers' role in conserving or restoring wildlife; (2) a primary production frame which emphasized the farmers' role in taking care of primary production assets; (3) a holistic frame focusing on farmers' role as a conservationist, primary producer, and manager of a range of landscape values, and; (4) an instrumental frame focusing on the financial benefits associated with compliance with agri-environmental schemes. We compare the landscape values and land management actions that emerged across stewardship types, and discuss the global implications of the landscape stewardship classification for the engagement of farmers in landscape management.

  18. Ferrofluid separator for nonferrous scrap separation

    NASA Technical Reports Server (NTRS)

    Kaiser, R.; Mir, L.

    1974-01-01

    Behavior of nonmagnetic objects within separator is essentially function of density, and independent of size or shape of objects. Results show close agreement between density of object and apparent density of ferrofluid required to float it. Results also demonstrate that very high separation rates are achievable by ferrofluid sink-float separation.

  19. Evolution of pollination niches and floral divergence in the generalist plant Erysimum mediohispanicum

    PubMed Central

    Gómez, J. M.; Muñoz-Pajares, A. J.; Abdelaziz, M.; Lorite, J.; Perfectti, F.

    2014-01-01

    Background and Aims How generalist plants diverge in response to pollinator selection without becoming specialized is still unknown. This study explores this question, focusing on the evolution of the pollination system in the pollination generalist Erysimum mediohispanicum (Brassicaceae). Methods Pollinator assemblages were surveyed from 2001 to 2010 in 48 geo-referenced populations covering the entire geographic distribution of E. mediohispanicum. Bipartite modularity, a complex network tool, was used to find the pollination niche of each population. Evolution of the pollination niches and the correlated evolution of floral traits and pollination niches were explored using within-species comparative analyses. Key Results Despite being generalists, the E. mediohispanicum populations studied can be classified into five pollination niches. The boundaries between niches were not sharp, the niches differing among them in the relative frequencies of the floral visitor functional groups. The absence of spatial autocorrelation and phylogenetic signal indicates that the niches were distributed in a phylogeographic mosaic. The ancestral E. mediohispanicum populations presumably belonged to the niche defined by a high number of beetle and ant visits. A correlated evolution was found between pollination niches and some floral traits, suggesting the existence of generalist pollination ecotypes. Conclusions It is conjectured that the geographic variation in pollination niches has contributed to the observed floral divergence in E. mediohispanicum. The process mediating this floral divergence presumably has been adaptive wandering, but the adaptation to the local pollinator faunas has been not universal. The outcome is a landscape where a few populations locally adapted to their pollination environment (generalist pollination ecotypes) coexist with many populations where this local adaptation has failed and where the plant phenotype is not primarily shaped by pollinators. PMID

  20. Landscape changes have greater effects than climate changes on six insect pests in China.

    PubMed

    Zhao, Zihua; Sandhu, Hardev S; Ouyang, Fang; Ge, Feng

    2016-06-01

    In recent years, global changes are the major causes of frequent, widespread outbreaks of pests in mosaic landscapes, which have received substantial attention worldwide. We collected data on global changes (landscape and climate) and economic damage caused by six main insect pests during 1951-2010 in China. Landscape changes had significant effects on all six insect pests. Pest damage increased significantly with increasing arable land area in agricultural landscapes. However, climate changes had no effect on damage caused by pests, except for the rice leaf roller (Cnaphalocrocis medinalis Guenee) and armyworm (Mythimna separate (Walker)), which caused less damage to crops with increasing mean temperature. Our results indicate that there is slight evidence of possible offset effects of climate changes on the increasing damage from these two agricultural pests. Landscape changes have caused serious outbreaks of several species, which suggests the possibility of the use of landscape design for the control of pest populations through habitat rearrangement. Landscape manipulation may be used as a green method to achieve sustainable pest management with minimal use of insecticides and herbicides. PMID:26825944

  1. Pastoral wildfires in the Mediterranean: understanding their linkages to land cover patterns in managed landscapes.

    PubMed

    Ruiz-Mirazo, Jabier; Martínez-Fernández, Jesús; Vega-García, Cristina

    2012-05-15

    The pastoral use of fire to regenerate rangelands is a major cause of wildfires in many Mediterranean countries. Despite producing important environmental impacts, this phenomenon has hardly ever been studied separately from other wildfire ignition causes. As extensive livestock breeding relies on the available pasture resources, we hypothesised that a higher rate of pastoral wildfire ignitions could be associated with land cover patterns, as these reflect the spatial arrangement of human activities in managed landscapes. To investigate these patterns, we studied landscape structure and the pastoral wildfires recorded between 1988 and 2000 in 24 Nature Park landscapes in Andalusia (Spain). The CORINE Land Cover map was reclassified according to five levels of grazing use and landscape metrics were calculated. Neural networks were developed to model the relationship between landscape metrics and pastoral wildfires, obtaining a set of significant variables which are discussed in the frame of land and livestock management in the region. We conclude that pastoral wildfire ignitions are more likely in landscapes where the pattern of being dominated by a matrix composed of several large patches of low to moderate grazing use, and having abundant small and elongated patches of higher grazing use, is more extreme. This pattern could be reflecting the persistence of numerous small livestock farms within an increasingly abandoned agrarian landscape. To prevent pastoral wildfires, land management could attempt to enlarge and merge those small patches of higher grazing use, reducing the amount of interface and their intermixture with the surrounding poorer pasture resources. PMID:22245863

  2. Pastoral wildfires in the Mediterranean: understanding their linkages to land cover patterns in managed landscapes.

    PubMed

    Ruiz-Mirazo, Jabier; Martínez-Fernández, Jesús; Vega-García, Cristina

    2012-05-15

    The pastoral use of fire to regenerate rangelands is a major cause of wildfires in many Mediterranean countries. Despite producing important environmental impacts, this phenomenon has hardly ever been studied separately from other wildfire ignition causes. As extensive livestock breeding relies on the available pasture resources, we hypothesised that a higher rate of pastoral wildfire ignitions could be associated with land cover patterns, as these reflect the spatial arrangement of human activities in managed landscapes. To investigate these patterns, we studied landscape structure and the pastoral wildfires recorded between 1988 and 2000 in 24 Nature Park landscapes in Andalusia (Spain). The CORINE Land Cover map was reclassified according to five levels of grazing use and landscape metrics were calculated. Neural networks were developed to model the relationship between landscape metrics and pastoral wildfires, obtaining a set of significant variables which are discussed in the frame of land and livestock management in the region. We conclude that pastoral wildfire ignitions are more likely in landscapes where the pattern of being dominated by a matrix composed of several large patches of low to moderate grazing use, and having abundant small and elongated patches of higher grazing use, is more extreme. This pattern could be reflecting the persistence of numerous small livestock farms within an increasingly abandoned agrarian landscape. To prevent pastoral wildfires, land management could attempt to enlarge and merge those small patches of higher grazing use, reducing the amount of interface and their intermixture with the surrounding poorer pasture resources.

  3. Landscape changes have greater effects than climate changes on six insect pests in China.

    PubMed

    Zhao, Zihua; Sandhu, Hardev S; Ouyang, Fang; Ge, Feng

    2016-06-01

    In recent years, global changes are the major causes of frequent, widespread outbreaks of pests in mosaic landscapes, which have received substantial attention worldwide. We collected data on global changes (landscape and climate) and economic damage caused by six main insect pests during 1951-2010 in China. Landscape changes had significant effects on all six insect pests. Pest damage increased significantly with increasing arable land area in agricultural landscapes. However, climate changes had no effect on damage caused by pests, except for the rice leaf roller (Cnaphalocrocis medinalis Guenee) and armyworm (Mythimna separate (Walker)), which caused less damage to crops with increasing mean temperature. Our results indicate that there is slight evidence of possible offset effects of climate changes on the increasing damage from these two agricultural pests. Landscape changes have caused serious outbreaks of several species, which suggests the possibility of the use of landscape design for the control of pest populations through habitat rearrangement. Landscape manipulation may be used as a green method to achieve sustainable pest management with minimal use of insecticides and herbicides.

  4. Gray Box Optimization for Mk Landscapes (NK Landscapes and MAX-kSAT).

    PubMed

    Whitley, L Darrell; Chicano, Francisco; Goldman, Brian W

    2016-01-01

    This article investigates Gray Box Optimization for pseudo-Boolean optimization problems composed of M subfunctions, where each subfunction accepts at most k variables. We will refer to these as Mk Landscapes. In Gray Box Optimization, the optimizer is given access to the set of M subfunctions. We prove Gray Box Optimization can efficiently compute hyperplane averages to solve non-deceptive problems in [Formula: see text] time. Bounded separable problems are also solved in [Formula: see text] time. As a result, Gray Box Optimization is able to solve many commonly used problems from the evolutional computation literature in [Formula: see text] evaluations. We also introduce a more general class of Mk Landscapes that can be solved using dynamic programming and discuss properties of these functions. For certain type of problems Gray Box Optimization makes it possible to enumerate all local optima faster than brute force methods. We also provide evidence that randomly generated test problems are far less structured than those found in real-world problems. PMID:27120114

  5. Gray Box Optimization for Mk Landscapes (NK Landscapes and MAX-kSAT).

    PubMed

    Whitley, L Darrell; Chicano, Francisco; Goldman, Brian W

    2016-01-01

    This article investigates Gray Box Optimization for pseudo-Boolean optimization problems composed of M subfunctions, where each subfunction accepts at most k variables. We will refer to these as Mk Landscapes. In Gray Box Optimization, the optimizer is given access to the set of M subfunctions. We prove Gray Box Optimization can efficiently compute hyperplane averages to solve non-deceptive problems in [Formula: see text] time. Bounded separable problems are also solved in [Formula: see text] time. As a result, Gray Box Optimization is able to solve many commonly used problems from the evolutional computation literature in [Formula: see text] evaluations. We also introduce a more general class of Mk Landscapes that can be solved using dynamic programming and discuss properties of these functions. For certain type of problems Gray Box Optimization makes it possible to enumerate all local optima faster than brute force methods. We also provide evidence that randomly generated test problems are far less structured than those found in real-world problems.

  6. Localization on the landscape and eternal inflation

    NASA Astrophysics Data System (ADS)

    Mersini-Houghton, Laura; Perry, Malcolm J.

    2014-11-01

    We investigate the validity of the assertion that eternal inflation populates the landscape of string theory. We verify that bubble solutions do not satisfy the Klein-Gordon equation for the landscape potential. Solutions to the landscape potential within the formalism of quantum cosmology are Anderson localized wavefunctions. These are inconsistent with inflating bubble solutions. The physical reasons behind the failure of a relation between eternal inflation and the landscape are rooted in quantum phenomena such as interference between wavefunction concentrated around the various vacua in the landscape.

  7. Children's and adolescents' tolerance for divergent beliefs: exploring the cognitive and affective dimensions of moral conviction in our youth.

    PubMed

    Wright, Jennifer C

    2012-11-01

    Moral conviction predicts interpersonal tolerance in adults, but its role in children and adolescents is not as well understood. This study measured moral conviction for a variety of issues along two separate dimensions - cognitive and affective - in children and adolescents (4th-12th grade). Results showed that, like adults, when children and adolescents view an issue as moral, this is strongly predictive of both age groups' discomfort with divergent beliefs. But only for adolescents, and not children, did moral conviction play a role in that discomfort, as had previously been found with adults. The context in which the divergent beliefs were encountered also mattered, but more for adolescents than for children - both groups were most comfortable with divergent beliefs when they were encountered in distal relations. PMID:23039329

  8. Steepened channels upstream of knickpoints: Controls on relict landscape response

    NASA Astrophysics Data System (ADS)

    Berlin, Maureen M.; Anderson, Robert S.

    2009-09-01

    The morphology of a relict landscape provides important insight into erosion rates and processes prior to base level fall. Fluvial knickpoints are commonly thought to form a leak-proof moving boundary between a rejuvenated landscape below and a relict landscape above. We argue that fluvial rejuvenation may leak farther upstream, depending on the rate and style of knickpoint migration. The outer margin of a relict landscape should therefore be used with caution in tectonic geomorphology studies, as channel steepening upstream of knickpoints could reduce the relict area. We explore the response of the Roan Plateau to knickpoint retreat triggered by late Cenozoic upper Colorado River incision. Multiple knickpoints (100-m waterfalls) separate a low-relief, upper landscape from incised canyons below. Two digital elevation model data sets (10-m U.S. Geological Survey and 1-m Airborne Laser Swath Mapping) indicate steeper channels above waterfalls relative to concave channels farther upstream. The steepened reaches are several kilometers long, correspond to doubling of slope, and exhibit channel narrowing and an increase in hillslope angle. We compare two mechanisms for generating steepened reaches. The first uses a recent model for erosion amplification due to flow acceleration at the waterfall lip. The second acknowledges that waterfall lips may be limited to the outcrop of a resistant formation. Subtle structural warping of the stratigraphy can lead to lowering of the waterfall lip as it retreats, thus lowering base level for upstream channels. Results of numerical modeling experiments suggest the latter mechanism is more consistent with our observations of long, mildly steepened reaches.

  9. Divergence of the entanglement range in low-dimensional quantum systems

    SciTech Connect

    Amico, L.; Patane, D.; Baroni, F.; Fubini, A.; Tognetti, V.; Verrucchi, Paola

    2006-08-15

    We study the pairwise entanglement close to separable ground states of a class of one-dimensional quantum spin models. At T=0 we find that such ground states separate regions, in the space of the Hamiltonian parameters, which are characterized by qualitatively different types of entanglement, namely parallel and antiparallel entanglement; we further demonstrate that the range of the concurrence diverges while approaching separable ground states, therefore evidencing that such states, with uncorrelated fluctuations, are reached by a long range reshuffling of the entanglement. We generalize our results to the analysis of quantum phase transitions occurring in bosonic and fermionic systems. Finally, the effects of finite temperature are considered: At T>0 we evidence the existence of a region where no pairwise entanglement survives, so that entanglement, if present, is genuinely multipartite.

  10. Isotope separation apparatus and method

    DOEpatents

    Cotter, Theodore P.

    1982-12-28

    The invention relates to a method and apparatus for laser isotope separation by photodeflection. A molecular beam comprising at least two isotopes to be separated intersects, preferable substantially perpendicular to one broad side of the molecular beam, with a laser beam traveling in a first direction. The laser beam is reflected back through the molecular beam, preferably in a second direction essentially opposite to the first direction. The laser beam comprises .pi.-pulses of a selected wavelength which excite unexcited molecules, or cause stimulated emission of excited molecules of one of the isotopes. Excitation caused by first direction .pi.-pulses moves molecules of the isotope excited thereby in the first direction. Stimulated emission of excited molecules of the isotope is brought about by returning .pi.-pulses traveling in the second direction. Stimulated emission moves emitting molecules in a direction opposite to the photon emitted. Because emitted photons travel in the second direction, emitting molecules move in the first direction. Substantial molecular movement is accomplished by a large number of .pi.-pulse-molecule interactions. A beam corer collects the molecules in the resulting enriched divergent portions of the beam.

  11. Isotope separation apparatus and method

    DOEpatents

    Feldman, Barry J.

    1985-01-01

    The invention relates to an improved method and apparatus for laser isotope separation by photodeflection. A molecular beam comprising at least two isotopes to be separated intersects, preferably substantially perpendicular to one broad side of the molecular beam, with a laser beam traveling in a first direction. The laser beam is reflected back through the molecular beam, preferably in a second direction essentially opposite to the first direction. Because the molecules in the beam occupy various degenerate energy levels, if the laser beam comprises chirped pulses comprising selected wavelengths, the laser beam will very efficiently excite substantially all unexcited molecules and will cause stimulated emission of substantially all excited molecules of a selected one of the isotopes in the beam which such pulses encounter. Excitation caused by first direction chirped pulses moves molecules of the isotope excited thereby in the first direction. Stimulated emission of excited molecules of the isotope is brought about by returning chirped pulses traveling in the second direction. Stimulated emission moves emitting molecules in a direction opposite to the photon emitted. Because emitted photons travel in the second direction, emitting molecules move in the first direction. Substantial molecular movement of essentially all the molecules containing the one isotope is accomplished by a large number of chirped pulse-molecule interactions. A beam corer collects the molecules in the resulting enriched divergent portions of the beam.

  12. Evaluation of Landsat Multispectral Scanner data for mapping vegetated soil landscapes

    USGS Publications Warehouse

    Thompson, D. R.; Haas, Robert H.; Milford, M. H.

    1981-01-01

    Landsat multispectral scanner data for Brazos County, Texas, were evaluated in terms of effectiveness for classifying soils on vegetated landscapes at three times during the year: a time of normally adequate soil water, a time of expected soil water deficit, and a time when soil water is normally being replenished. Six test sites were used to evaluate LARSYS supervised and unsupervised classification of vegetated soil landscapes. Open grassland soils were best separated in the fall during a period when soil moisture was being replenished after the summer period of soil water deficit. Woodland soils were separated by Landsat data in late spring when adequate moisture was available. However, a high degree of accuracy was not achieved using Landsat for separating soil map units. Accurate separation of soil mapping units on vegetated landscapes was not possible during late summer when soil water was deficient. Selected soil properties important to plant growth were separable on the test sites using June and October Landsat data. Particle size and soil moisture regime were separated at both dates. Soils with argillic horizons were separated from soils without argillic horizons.

  13. Properties of classical and quantum Jensen-Shannon divergence

    SciTech Connect

    Brieet, Jop; Harremoees, Peter

    2009-05-15

    Jensen-Shannon divergence (JD) is a symmetrized and smoothed version of the most important divergence measure of information theory, Kullback divergence. As opposed to Kullback divergence it determines in a very direct way a metric; indeed, it is the square of a metric. We consider a family of divergence measures (JD{sub {alpha}} for {alpha}>0), the Jensen divergences of order {alpha}, which generalize JD as JD{sub 1}=JD. Using a result of Schoenberg, we prove that JD{sub {alpha}} is the square of a metric for {alpha} is an element of (0,2], and that the resulting metric space of probability distributions can be isometrically embedded in a real Hilbert space. Quantum Jensen-Shannon divergence (QJD) is a symmetrized and smoothed version of quantum relative entropy and can be extended to a family of quantum Jensen divergences of order {alpha} (QJD{sub {alpha}}). We strengthen results by Lamberti and co-workers by proving that for qubits and pure states, QJD{sub {alpha}}{sup 1/2} is a metric space which can be isometrically embedded in a real Hilbert space when {alpha} is an element of (0,2]. In analogy with Burbea and Rao's generalization of JD, we also define general QJD by associating a Jensen-type quantity to any weighted family of states. Appropriate interpretations of quantities introduced are discussed and bounds are derived in terms of the total variation and trace distance.

  14. Parametric R-norm directed-divergence convex function

    NASA Astrophysics Data System (ADS)

    Garg, Dhanesh; Kumar, Satish

    2016-06-01

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

  15. Cultural Divergence Related to Urban Proximity on American Indian Reservations.

    ERIC Educational Resources Information Center

    Price, John A.

    The scattered reservation segments of a single U.S. or Canadian Indian tribe have often culturally diverged from one another in recent historical times. This divergence is particularly marked in more urban regions, such as California, and among tribes where some of the reservations are near cities. As tribalism has become less important and urban…

  16. Divergent Thinking and Creative Ideation of High School Students

    ERIC Educational Resources Information Center

    Ramzan, Shaikh Imran; Perveen, Shaheen

    2011-01-01

    Divergent thinking is an integral process in creativity. Openness to experience is a personality trait that relates to divergent thinking and, therefore, is hypothesized to be related to creative performance among the students. The effects of openness to experience are likely to be partially mediated by an individual's attitude toward divergent…

  17. Maps on Quantum States Preserving Bregman and Jensen Divergences

    NASA Astrophysics Data System (ADS)

    Virosztek, Dániel

    2016-09-01

    We describe the structure of the bijective transformations on the set of density operators which preserve the Bregman f-divergence for an arbitrary differentiable strictly convex function f. Furthermore, we determine the preservers of the Jensen f-divergence in the case when the generating function f belongs to a recently introduced function class called Matrix Entropy Class.

  18. Predicting Work Activities with Divergent Thinking Tests: A Longitudinal Study

    ERIC Educational Resources Information Center

    Clapham, Maria M.; Cowdery, Edwina M.; King, Kelly E.; Montang, Melissa A.

    2005-01-01

    This study examined whether divergent thinking test scores obtained from engineering students during college predicted creative work activities fifteen years later. Results showed that a subscore of the "Owens Creativity Test", which assesses divergent thinking about mechanical objects, correlated significantly with self-ratings of creative work…

  19. Cultivating Divergent Thinking: Conceptualization as a Critical Component of Artmaking

    ERIC Educational Resources Information Center

    Chin, Christina

    2013-01-01

    Discussing various perspectives of artists' influences and experiences can develop students' divergent thinking skills. Fostering students' divergent thinking skills is integral to developing creativity, and the Arts are a ripe forum for this. In contrast to convergent thinking, which focuses in on one "correct"…

  20. Convergent and Divergent Thinking in the Context of Narrative Mysteries

    ERIC Educational Resources Information Center

    Wenzel, William G.; Gerrig, Richard J.

    2015-01-01

    This project demonstrates how narrative mysteries provide a context in which readers engage in creative cognition. Drawing on the concepts of convergent and divergent thinking, we wrote stories that had either convergent or divergent outcomes. For example, one story had a character give his girlfriend a ring (a convergent outcome), whereas the…

  1. Measurements of Wind Divergence with Volume Imaging Lidar

    NASA Technical Reports Server (NTRS)

    Young, P. W.; Eloranta, E. W.

    1992-01-01

    Mesoscale horizontal divergence and vertical motion in the boundary layer are key ingredients in atmospheric and climate modeling. These quantities are very difficult to measure. This paper presents a technique for determining the divergence over a 10 km x 5 km area from lidar images depicting the spatial distribution of the naturally occurring atmospheric aerosols.

  2. Divergent Thinking and Evaluation Skills: Do They Always Go Together?

    ERIC Educational Resources Information Center

    Grohman, Magdalena; Wodniecka, Zofia; Klusak, Marcin

    2006-01-01

    The aim of the present study was to explore the hypothesized relationship between divergent thinking (DT) and two types of evaluation: interpersonal (judgments about others' ideas) and intrapersonal (judgments about one's own ideas). Divergent thinking and evaluation skills were measured by means of a GenEva (Generation and Evaluation) task. There…

  3. Dynamic Investigation of Static Divergence: Analysis and Testing

    NASA Technical Reports Server (NTRS)

    Heeg, Jennifer

    2000-01-01

    The phenomenon known as aeroelastic divergence is the focus of this work. The analyses and experiment presented here show that divergence can occur without a structural dynamic mode losing its oscillatory nature. Aeroelastic divergence occurs when the structural restorative capability or stiffness of a structure is overwhelmed by the static aerodynamic moment. This static aeroelastic coupling does not require the structural dynamic system behavior to cease, however. Aeroelastic changes in the dynamic mode behavior are governed not only by the stiffness, but by damping and inertial properties. The work presented here supports these fundamental assertions by examining a simple system: a typical section airfoil with only a rotational structural degree of freedom. Analytical results identified configurations that exhibit different types of dynamic mode behavior as the system encounters divergence. A wind tunnel model was designed and tested to examine divergence experimentally. The experimental results validate the analytical calculations and explicitly examine the divergence phenomenon where the dynamic mode persists. Three configurations of the wind tunnel model were tested. The experimental results agree very well with the analytical predictions of subcritical characteristics, divergence velocity, and behavior of the noncritical dynamic mode at divergence.

  4. Divergent selection for muscle color in broilers.

    PubMed

    Harford, I D; Pavlidis, H O; Anthony, N B

    2014-05-01

    One consumer-related physiological abnormality that is a recent concern for the poultry industry is atypical meat quality. Currently in the processing plant, meat is characterized on appearance such as tears, bruises, discoloration, or missing parts. Unfortunately, this method ignores physical properties such as palatability, texture, tenderness, taste, color, pH, and water-holding capacity (WHC). The growing demand for a convenient, economical, and palatable product has shifted the market toward value-added poultry products. The effect of a meat's physical properties on its marketability and versatility has become apparent to processors attempting to utilize poor quality meat. After 8 generations of divergent selection for muscle color or lightness (L*) in broilers, muscle quality parameters were investigated. The 2 broiler lines divergently selected for high (HMC) and low (LMC) muscle color along with their randombred control line (RBC) were included in the study. Heritability estimates for L* were 0.47 ± 0.05 and 0.51 ± 0.05 in the HMC and LMC lines, respectively. For generation 8, the mean L* for the HMC, RBC, and LMC lines were 53.91, 49.70, and 46.86, respectively. Selection for increased L* was found to result in increased breast fillet yellowness (b*), whereas selection for decreased L* resulted in an increase in breast fillet redness (a*). Selection for increased L* has resulted in increased rate of pH decline over time, whereas selection for decreased L* has resulted in a decreased rate of pH decline. The HMC line exhibited a higher percentage fillet drip loss than both the LMC and RBC lines, which did not differ from each other. Overall selection for L* was effective in modifying breast muscle color as well as correlated responses associated with atypical poultry meat such as drip loss and postmortem muscle pH. These selected lines can serve as resource populations for the study of PSE and DFD-like meat in poultry and demonstrate that L* selection

  5. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

    USGS Publications Warehouse

    Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

    2007-01-01

    Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

  6. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms.

    PubMed

    Nei, M; Xu, P; Glazko, G

    2001-02-27

    When many protein sequences are available for estimating the time of divergence between two species, it is customary to estimate the time for each protein separately and then use the average for all proteins as the final estimate. However, it can be shown that this estimate generally has an upward bias, and that an unbiased estimate is obtained by using distances based on concatenated sequences. We have shown that two concatenation-based distances, i.e., average gamma distance weighted with sequence length (d(2)) and multiprotein gamma distance (d(3)), generally give more satisfactory results than other concatenation-based distances. Using these two distance measures for 104 protein sequences, we estimated the time of divergence between mice and rats to be approximately 33 million years ago. Similarly, the time of divergence between humans and rodents was estimated to be approximately 96 million years ago. We also investigated the dependency of time estimates on statistical methods and various assumptions made by using sequence data from eubacteria, protists, plants, fungi, and animals. Our best estimates of the times of divergence between eubacteria and eukaryotes, between protists and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc.

  7. Reserves, resilience and dynamic landscapes.

    PubMed

    Bengtsson, Janne; Angelstam, Per; Elmqvist, Thomas; Emanuelsson, Urban; Folke, Carl; Ihse, Margareta; Moberg, Fredrik; Nyström, Magnus

    2003-09-01

    In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding landscape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level.

  8. Reserves, resilience and dynamic landscapes.

    PubMed

    Bengtsson, Janne; Angelstam, Per; Elmqvist, Thomas; Emanuelsson, Urban; Folke, Carl; Ihse, Margareta; Moberg, Fredrik; Nyström, Magnus

    2003-09-01

    In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding landscape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level. PMID:14627367

  9. Designer landscapes for sustainable biofuels.

    PubMed

    Koh, Lian Pin; Levang, Patrice; Ghazoul, Jaboury

    2009-08-01

    Oil palm is one of the most extensively cultivated biodiesel feedstocks worldwide, and expansion of its cultivation poses a significant threat to ecosystems, biodiversity and potentially the global climate. We evaluate the prospects of land sparing and wildlife-friendly farming, two contrasting approaches for reducing the impacts of oil palm agriculture. We draw on concepts from both approaches to suggest more sustainable production systems and argue that landscapes under threat from oil palm expansion need to be designed in recognition of biodiversity, economic and livelihood needs. Specifically, we advocate agroforestry zones between high conservation value areas and intensive oil palm plantations to create a more heterogeneous landscape benefiting both biodiversity and rural communities. Similar principles could apply to biofuel systems elsewhere.

  10. Shoulder separation - aftercare

    MedlinePlus

    Separated shoulder - aftercare; Acromioclavicular joint separation - aftercare; A/C separation - aftercare ... slower if you have: Arthritis in your shoulder joint Damaged cartilage (cushioning tissue) between your collarbone and ...

  11. Separation Anxiety (For Parents)

    MedlinePlus

    ... 5 Things to Know About Zika & Pregnancy Separation Anxiety KidsHealth > For Parents > Separation Anxiety Print A A ... both of you get through it. How Separation Anxiety Develops Babies adapt pretty well to other caregivers. ...

  12. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    PubMed

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence. PMID:24948738

  13. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    PubMed

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

  14. Niche divergence accelerates evolution in Asian endemic Procapra gazelles

    PubMed Central

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system–based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species’ bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

  15. Niche divergence accelerates evolution in Asian endemic Procapra gazelles.

    PubMed

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system-based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species' bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

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

    PubMed

    Runco, M A; Albert, R S

    1986-08-01

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

  17. Using remote sensing products to classify landscape. A multi-spatial resolution approach

    NASA Astrophysics Data System (ADS)

    García-Llamas, Paula; Calvo, Leonor; Álvarez-Martínez, José Manuel; Suárez-Seoane, Susana

    2016-08-01

    The European Landscape Convention encourages the inventory and characterization of landscapes for environmental management and planning actions. Among the range of data sources available for landscape classification, remote sensing has substantial applicability, although difficulties might arise when available data are not at the spatial resolution of operational interest. We evaluated the applicability of two remote sensing products informing on land cover (the categorical CORINE map at 30 m resolution and the continuous NDVI spectral index at 1 km resolution) in landscape classification across a range of spatial resolutions (30 m, 90 m, 180 m, 1 km), using the Cantabrian Mountains (NW Spain) as study case. Separate landscape classifications (using topography, urban influence and land cover as inputs) were accomplished, one per each land cover dataset and spatial resolution. Classification accuracy was estimated through confusion matrixes and uncertainty in terms of both membership probability and confusion indices. Regarding landscape classifications based on CORINE, both typology and number of landscape classes varied across spatial resolutions. Classification accuracy increased from 30 m (the original resolution of CORINE) to 90m, decreasing towards coarser resolutions. Uncertainty followed the opposite pattern. In the case of landscape classifications based on NDVI, the identified landscape patterns were geographically structured and showed little sensitivity to changes across spatial resolutions. Only the change from 1 km (the original resolution of NDVI) to 180 m improved classification accuracy. The value of confusion indices increased with resolution. We highlight the need for greater effort in selecting data sources at the suitable spatial resolution, matching regional peculiarities and minimizing error and uncertainty.

  18. Making molehills out of mountains: landscape genetics of the Mojave desert tortoise

    USGS Publications Warehouse

    Hagerty, Bridgette E.; Nussear, Kenneth E.; Esque, Todd C.; Tracy, C. Richard

    2010-01-01

    Heterogeneity in habitat often influences how organisms traverse the landscape matrix that connects populations. Understanding landscape connectivity is important to determine the ecological processes that influence those movements, which lead to evolutionary change due to gene flow. Here, we used landscape genetics and statistical models to evaluate hypotheses that could explain isolation among locations of the threatened Mojave desert tortoise (Gopherus agassizii). Within a causal modeling framework, we investigated three factors that can influence landscape connectivity: geographic distance, barriers to dispersal, and landscape friction. A statistical model of habitat suitability for the Mojave desert tortoise, based on topography, vegetation, and climate variables, was used as a proxy for landscape friction and barriers to dispersal. We quantified landscape friction with least-cost distances and with resistance distances among sampling locations. A set of diagnostic partial Mantel tests statistically separated the hypotheses of potential causes of genetic isolation. The best-supported model varied depending upon how landscape friction was quantified. Patterns of genetic structure were related to a combination of geographic distance and barriers as defined by least-cost distances, suggesting that mountain ranges and extremely low-elevation valleys influence connectivity at the regional scale beyond the tortoises' ability to disperse. However, geographic distance was the only influence detected using resistance distances, which we attributed to fundamental differences between the two ways of quantifying friction. Landscape friction, as we measured it, did not influence the observed patterns of genetic distances using either quantification. Barriers and distance may be more valuable predictors of observed population structure for species like the desert tortoise, which has high dispersal capability and a long generation time.

  19. The landscape epidemiology of echinococcoses.

    PubMed

    Cadavid Restrepo, Angela M; Yang, Yu Rong; McManus, Donald P; Gray, Darren J; Giraudoux, Patrick; Barnes, Tamsin S; Williams, Gail M; Soares Magalhães, Ricardo J; Hamm, Nicholas A S; Clements, Archie C A

    2016-01-01

    Echinococcoses are parasitic diseases of major public health importance globally. Human infection results in chronic disease with poor prognosis and serious medical, social and economic consequences for vulnerable populations. According to recent estimates, the geographical distribution of Echinococcus spp. infections is expanding and becoming an emerging and re-emerging problem in several regions of the world. Echinococcosis endemicity is geographically heterogeneous and over time it may be affected by global environmental change. Therefore, landscape epidemiology offers a unique opportunity to quantify and predict the ecological risk of infection at multiple spatial and temporal scales. Here, we review the most relevant environmental sources of spatial variation in human echinococcosis risk, and describe the potential applications of landscape epidemiological studies to characterise the current patterns of parasite transmission across natural and human-altered landscapes. We advocate future work promoting the use of this approach as a support tool for decision-making that facilitates the design, implementation and monitoring of spatially targeted interventions to reduce the burden of human echinococcoses in disease-endemic areas. PMID:26895758

  20. Energy landscapes and persistent minima

    NASA Astrophysics Data System (ADS)

    Carr, Joanne M.; Mazauric, Dorian; Cazals, Frédéric; Wales, David J.

    2016-02-01

    We consider a coarse-graining of high-dimensional potential energy landscapes based upon persistences, which correspond to lowest barrier heights to lower-energy minima. Persistences can be calculated efficiently for local minima in kinetic transition networks that are based on stationary points of the prevailing energy landscape. The networks studied here represent peptides, proteins, nucleic acids, an atomic cluster, and a glassy system. Minima with high persistence values are likely to represent some form of alternative structural morphology, which, if appreciably populated at the prevailing temperature, could compete with the global minimum (defined as infinitely persistent). Threshold values on persistences (and in some cases equilibrium occupation probabilities) have therefore been used in this work to select subsets of minima, which were then analysed to see how well they can represent features of the full network. Simplified disconnectivity graphs showing only the selected minima can convey the funnelling (including any multiple-funnel) characteristics of the corresponding full graphs. The effect of the choice of persistence threshold on the reduced disconnectivity graphs was considered for a system with a hierarchical, glassy landscape. Sets of persistent minima were also found to be useful in comparing networks for the same system sampled under different conditions, using minimum oriented spanning forests.

  1. Bromine and Chlorine Go Separate Ways

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This graph shows the relative concentrations of bromine and chlorine at various locations on Earth and Mars. Typically, bromine and chlorine stick together in a fixed ratio, as in martian meteorites and Earth seawater. But sometimes the elements split apart and their relative quantities diverge. This separation is usually caused by evaporation processes, as in the Dead Sea on Earth. On Mars, at Meridiani Planum and Gusev Crater, this split has been observed to an even greater degree than seen on Earth. This puzzling result is currently being further explored by Mars Exploration Rover scientists. Data for the Mars locations were taken by the rover's alpha particle X-ray spectrometer.

  2. Spacecraft -- Capsule Separation (Animation)

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Click on the image for Spacecraft -- Capsule Separation animation

    This animation shows the return capsule separating from the Stardust spacecraft.

  3. Diversity and Divergence of Dinoflagellate Histone Proteins

    PubMed Central

    Marinov, Georgi K.; Lynch, Michael

    2015-01-01

    Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed. PMID:26646152

  4. Radar imaging of intense nonlinear Ekman divergence

    NASA Astrophysics Data System (ADS)

    Liu, Guoqiang; Perrie, William; Kudryavtsev, Vladimir; He, Yijun; Shen, Hui; Zhang, Biao; Hu, Haibo

    2016-09-01

    In general, given an oceanic thermal front, there is a strong positive correlation between sea surface temperature (SST) gradients and surface winds, and the marine atmospheric boundary layer is unstable over the warm side of the oceanic thermal front. The Gulf Stream is a notable example of an oceanic thermal front, and its warm side is often detected as enhanced backscatter in synthetic aperture radar (SAR) images. However, in some "anomalous" SAR images, low backscatter is sometimes observed on the warm side of the front, which seems inconsistent. Therefore, we propose a mechanism to interpret the generation of the low backscatter, based on interactions between ocean surface wind waves and intense nonlinear Ekman divergence. This mechanism is verified by showing that patterns in an observed anomalous SAR image are in good agreement with those in the simulated radar signature. In addition, this methodology and analysis demonstrate that SAR is potentially important for detecting and diagnosing small scale air-sea interactions and upper ocean dynamics with strong vertical transports induced by submesoscale processes.

  5. Divergent clonal selection dominates medulloblastoma at recurrence.

    PubMed

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

    2016-01-21

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

  6. Remarkable ancient divergences amongst neglected lorisiform primates

    PubMed Central

    Nekaris, K. Anne‐Isola; Perkin, Andrew; Bearder, Simon K.; Pimley, Elizabeth R.; Schulze, Helga; Streicher, Ulrike; Nadler, Tilo; Kitchener, Andrew; Zischler, Hans; Zinner, Dietmar; Roos, Christian

    2015-01-01

    Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub‐Saharan Africa and South/South‐East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. © 2015 The Linnean Society of London PMID:26900177

  7. Diversity and Divergence of Dinoflagellate Histone Proteins.

    PubMed

    Marinov, Georgi K; Lynch, Michael

    2015-12-08

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

  8. On the divergences of inflationary superhorizon perturbations

    SciTech Connect

    Enqvist, K; Nurmi, S; Podolsky, D; Rigopoulos, G I E-mail: sami.nurmi@helsinki.fi E-mail: gerasimos.rigopoulos@helsinki.fi

    2008-04-15

    We discuss the infrared divergences that appear to plague cosmological perturbation theory. We show that, within the stochastic framework, they are regulated by eternal inflation so that the theory predicts finite fluctuations. Using the {Delta}N formalism to one loop, we demonstrate that the infrared modes can be absorbed into additive constants and the coefficients of the diagrammatic expansion for the connected parts of two-and three-point functions of the curvature perturbation. As a result, the use of any infrared cutoff below the scale of eternal inflation is permitted, provided that the background fields are appropriately redefined. The natural choice for the infrared cutoff would, of course, be the present horizon; other choices manifest themselves in the running of the correlators. We also demonstrate that it is possible to define observables that are renormalization-group-invariant. As an example, we derive a non-perturbative, infrared finite and renormalization point-independent relation between the two-point correlators of the curvature perturbation for the case of the free single field.

  9. Clock gene evolution and functional divergence.

    PubMed

    Tauber, Eran; Last, Kim S; Olive, Peter J W; Kyriacou, C P

    2004-10-01

    In considering the impact of the earth's changing geophysical conditions during the history of life, it is surprising to learn that the earth's rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the "protoclock" in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.

  10. Divergent clonal selection dominates medulloblastoma at recurrence

    PubMed Central

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

    2016-01-01

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

  11. The Divergent K-Plane Transform

    NASA Astrophysics Data System (ADS)

    Keinert, Fritz

    The divergent k-plane transform of a function f on an n-dimensional real vector space V is the function Df(a,(alpha)) = D(,a)f((alpha)) which assigns to each point a (ELEM) V and each (alpha) (ELEM) G(,k)(V) the integral of f over the translate of (pi)((alpha)) passing through a. Here (pi)((alpha)) is the non-oriented k-dimensional subspace of V associated with (alpha) and G(,k)(V) the Grassmann manifold of unit k-vectors on V. It is generally assumed that f (ELEM) L(,0)('2)((OMEGA)), where (OMEGA) is a bounded open subset of V, and that a is outside the closure of (OMEGA). It is shown that under these conditions D(,a)f (ELEM) L('2)(G(,k)(V)), and the adjoint is calculated. If D(,a)f is known for infinitely many sources a, this determines f uniquely, while for finitely many sources f is essentially arbitrary. Exact and approximate inversion formulas are derived. Some formulas for integration on the Grassmannian may have independent interest.

  12. Divergence and Convergence in Enzyme Evolution*

    PubMed Central

    Galperin, Michael Y.; Koonin, Eugene V.

    2012-01-01

    Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes. PMID:22069324

  13. Landscape influences on dispersal behaviour: a theoretical model and empirical test using the fire salamander, Salamandra infraimmaculata.

    PubMed

    Kershenbaum, Arik; Blank, Lior; Sinai, Iftach; Merilä, Juha; Blaustein, Leon; Templeton, Alan R

    2014-06-01

    When populations reside within a heterogeneous landscape, isolation by distance may not be a good predictor of genetic divergence if dispersal behaviour and therefore gene flow depend on landscape features. Commonly used approaches linking landscape features to gene flow include the least cost path (LCP), random walk (RW), and isolation by resistance (IBR) models. However, none of these models is likely to be the most appropriate for all species and in all environments. We compared the performance of LCP, RW and IBR models of dispersal with the aid of simulations conducted on artificially generated landscapes. We also applied each model to empirical data on the landscape genetics of the endangered fire salamander, Salamandra infraimmaculata, in northern Israel, where conservation planning requires an understanding of the dispersal corridors. Our simulations demonstrate that wide dispersal corridors of the low-cost environment facilitate dispersal in the IBR model, but inhibit dispersal in the RW model. In our empirical study, IBR explained the genetic divergence better than the LCP and RW models (partial Mantel correlation 0.413 for IBR, compared to 0.212 for LCP, and 0.340 for RW). Overall dispersal cost in salamanders was also well predicted by landscape feature slope steepness (76%), and elevation (24%). We conclude that fire salamander dispersal is well characterised by IBR predictions. Together with our simulation findings, these results indicate that wide dispersal corridors facilitate, rather than hinder, salamander dispersal. Comparison of genetic data to dispersal model outputs can be a useful technique in inferring dispersal behaviour from population genetic data.

  14. Applying landscape genetics to the microbial world.

    PubMed

    Dudaniec, Rachael Y; Tesson, Sylvie V M

    2016-07-01

    Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.

  15. Modern warfare as a significant form of zoogeomorphic disturbance upon the landscape

    NASA Astrophysics Data System (ADS)

    Hupy, Joseph P.; Koehler, Thomas

    2012-07-01

    The damage exerted by warfare on the physical landscape is one, of many, anthropogenic impacts upon the environment. Bombturbation is a term that describes the impacts of explosive munitions upon the landscape. Bombturbation, like many other forms of zoogeomorphology, is a disruptive force, capable of moving large amounts of sediments, and denuding landscapes to the point where changes in micro and mesotopography have long-term implications. The long term implication of bombturbative actions depends on the type and duration of explosive device that rendered the disturbance, and the geographic context of the landscape disturbed; i.e. cultural and physical factors. Recovery from bombturbative activity, in the context of this research, is measured by vegetative regrowth and soil development in cratered disturbances. A comparison and contrast between the two battlefields of Verdun, France and Khe Sanh, Vietnam show that bombturbative actions have significantly altered the topography at each location, thus influencing surface runoff and processes of soil development. Principals of the Runge pedogenic model, or the energy of water moving through the soil profile, best explain how the varying climate and parent material at each location influence post disturbance soil development rates. Whereas the data collected at Verdun suggest that explosive munitions have put that landscape on diverging path of development, thus rendering it much different post-disturbance landscape, Khe Sanh displays much different recovery patterns. Preliminary research at Khe Sanh indicates that reforestation and soil development following disturbance are not so much influenced by bombturbative patterns as land use activities in the area of study.

  16. Topographic Signature of Climate Change- insights into climatic controls on landscape evolution under permafrost and non-permafrost environments

    NASA Astrophysics Data System (ADS)

    Gangodagamage, C.; Rowland, J. C.; Wilson, C. J.; Brumby, S.; Prancevic, J. P.; Crosby, B. T.; Marsh, P.; Altmann, G.

    2012-12-01

    Climate gradient across the deglaciated North American continental landscape has been a major control on the trajectory of landscape evolution following the Last Glacial Maximum (LGM) (~19-25 ka BP). Following deglaciation, landscapes in the Arctic and subarctic regions have been subject to climatic conditions favoring the development and/or preservation of permafrost. In more southerly latitudes, warmer conditions have favored non-permafrost conditions. A comparison of formerly glaciated landscapes in both permafrost and non-permafrost settings offers a unique natural experiment to explore the influence of climate on landscape evolution. Additionally, by comparing formerly glaciated terrains under both permafrost and non-permafrost conditions to landscapes never having undergone glaciation it may be possible to identify unique signatures of glaciation on hillslope morphology and processes. After glaciers retreated, newly exposed landscapes were exposed to both fluvial and hillslope mass wasting processes, the relative balance and influence of these processes on landscape evolution varied depending on Holocene climatic conditions (permafrost versus non-permaforst environments). Using analysis of high resolution Digital Elevation Model (DEM ~ 1m) data we show that the topographic denudation on these landscapes over the past Holocene has imprinted a unique climatic signature. Major differences are observed in landscape regimes and regime transitions. These differences are quantified mainly by introducing a new index, Normalized Directed Distance for Relief (NDDR), that treats the landscape relief differences and successfully identify the climate induced landscape responses. Previously glaciated permafrost landscapes are primarily characterized by narrow divergent hilltops (NDDR < 0.3), longer convergent flow paths (~500-1000 m) in hillslopes, and abrupt hillslope to fluvial transitions (< 100 m). Previously glaciated non-permafrost landscapes characterized by

  17. Conserving tigers in working landscapes.

    PubMed

    Chanchani, Pranav; Noon, Barry R; Bailey, Larissa L; Warrier, Rekha A

    2016-06-01

    Tiger (Panthera tigris) conservation efforts in Asia are focused on protected areas embedded in human-dominated landscapes. A system of protected areas is an effective conservation strategy for many endangered species if the network is large enough to support stable metapopulations. The long-term conservation of tigers requires that the species be able to meet some of its life-history needs beyond the boundaries of small protected areas and within the working landscape, including multiple-use forests with logging and high human use. However, understanding of factors that promote or limit the occurrence of tigers in working landscapes is incomplete. We assessed the relative influence of protection status, prey occurrence, extent of grasslands, intensity of human use, and patch connectivity on tiger occurrence in the 5400 km(2) Central Terai Landscape of India, adjacent to Nepal. Two observer teams independently surveyed 1009 km of forest trails and water courses distributed across 60 166-km(2) cells. In each cell, the teams recorded detection of tiger signs along evenly spaced trail segments. We used occupancy models that permitted multiscale analysis of spatially correlated data to estimate cell-scale occupancy and segment-scale habitat use by tigers as a function of management and environmental covariates. Prey availability and habitat quality, rather than protected-area designation, influenced tiger occupancy. Tiger occupancy was low in some protected areas in India that were connected to extensive areas of tiger habitat in Nepal, which brings into question the efficacy of current protection and management strategies in both India and Nepal. At a finer spatial scale, tiger habitat use was high in trail segments associated with abundant prey and large grasslands, but it declined as human and livestock use increased. We speculate that riparian grasslands may provide tigers with critical refugia from human activity in the daytime and thereby promote tiger occurrence

  18. Conserving tigers in working landscapes.

    PubMed

    Chanchani, Pranav; Noon, Barry R; Bailey, Larissa L; Warrier, Rekha A

    2016-06-01

    Tiger (Panthera tigris) conservation efforts in Asia are focused on protected areas embedded in human-dominated landscapes. A system of protected areas is an effective conservation strategy for many endangered species if the network is large enough to support stable metapopulations. The long-term conservation of tigers requires that the species be able to meet some of its life-history needs beyond the boundaries of small protected areas and within the working landscape, including multiple-use forests with logging and high human use. However, understanding of factors that promote or limit the occurrence of tigers in working landscapes is incomplete. We assessed the relative influence of protection status, prey occurrence, extent of grasslands, intensity of human use, and patch connectivity on tiger occurrence in the 5400 km(2) Central Terai Landscape of India, adjacent to Nepal. Two observer teams independently surveyed 1009 km of forest trails and water courses distributed across 60 166-km(2) cells. In each cell, the teams recorded detection of tiger signs along evenly spaced trail segments. We used occupancy models that permitted multiscale analysis of spatially correlated data to estimate cell-scale occupancy and segment-scale habitat use by tigers as a function of management and environmental covariates. Prey availability and habitat quality, rather than protected-area designation, influenced tiger occupancy. Tiger occupancy was low in some protected areas in India that were connected to extensive areas of tiger habitat in Nepal, which brings into question the efficacy of current protection and management strategies in both India and Nepal. At a finer spatial scale, tiger habitat use was high in trail segments associated with abundant prey and large grasslands, but it declined as human and livestock use increased. We speculate that riparian grasslands may provide tigers with critical refugia from human activity in the daytime and thereby promote tiger occurrence

  19. Focusing of intense and divergent ion beams in a magnetic mass analyzer

    SciTech Connect

    Jianlin, Ke; Changgeng, Zhou; Rui, Qiu; Yonghong, Hu

    2014-07-15

    A magnetic mass analyzer is used to determine the beam composition of a vacuum arc ion source. In the analyzer, we used the concentric multi-ring electrodes to focus the intense and divergent ion beams. We describe the principle, design, and the test results of the focusing device. The diameter of the beam profile is less than 20 mm when the accelerating voltage is 30 kV and the focusing voltage is about 2.0 kV. The focusing device has been successfully used in the magnetic mass analyzer to separate Ti{sup +}, Ti{sup 2+}, and Ti{sup 3+}.

  20. A general and concise enantioselective divergent approach to 13-alkyl-substituted ionones.

    PubMed

    Bugoni, Serena; Merlini, Valentina; Porta, Alessio; Zanoni, Giuseppe; Vidari, Giovanni

    2014-10-01

    A novel enantioselective divergent route to 13-alkyl derivatives of α- and γ-ionone, important components of perfumes and fragrances, is reported. This relatively short and convenient methodology takes advantage of the use of a common intermediate, easily obtained from highly enantiomerically enriched (S)-α-ionone, which avoids the separate installation of the butenone side chain at C(6) for each analog. Olfactory evaluation of synthesized compounds reconfirmed the influence of the hydrophobic interactions of alkyl substituents at C(5) with olfactory receptors (ORs) in the chemoreception of ionones, and suggested that a synperiplanar orientation of C(13) and the lateral chain is the better geometry fitting OR's cavity.

  1. Connecting thermal and mechanical protein (un)folding landscapes

    NASA Astrophysics Data System (ADS)

    Sun, Li; Noel, Jeffrey; Sulkowska, Joanna; Levine, Herbert; Onuchic, José

    2015-03-01

    Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying force at both termini. The unfolding time-force relation τ(F) indicates that the unfolding behavior can be characterized into three regimes: barrier-limited low- and intermediate-force regimes, and a barrierless high-force regime. Slope changes of τ(F) separate the three regimes. We show that the behavior of τ(F) can be understood from a two-dimensional free energy landscape projected onto the extension X and the fraction of native contacts Q. In the low-force regime, the unfolding rate is roughly force-independent due to the small (even negative) separation in X between the native ensemble and transition state ensemble (TSE). In the intermediate-force regime, force sufficiently separates the TSE from the native ensemble such that τ(F) roughly follows an exponential relation. The TSE becomes increasingly structured with force. The high-force regime is characterized by barrierless unfolding, approaching a time limit of around 10 μs.

  2. Social and natural sciences differ in their research strategies, adapted to work for different knowledge landscapes.

    PubMed

    Jaffe, Klaus

    2014-01-01

    Do different fields of knowledge require different research strategies? A numerical model exploring different virtual knowledge landscapes, revealed two diverging optimal search strategies. Trend following is maximized when the popularity of new discoveries determine the number of individuals researching it. This strategy works best when many researchers explore few large areas of knowledge. In contrast, individuals or small groups of researchers are better in discovering small bits of information in dispersed knowledge landscapes. Bibliometric data of scientific publications showed a continuous bipolar distribution of these strategies, ranging from natural sciences, with highly cited publications in journals containing a large number of articles, to the social sciences, with rarely cited publications in many journals containing a small number of articles. The natural sciences seem to adapt their research strategies to landscapes with large concentrated knowledge clusters, whereas social sciences seem to have adapted to search in landscapes with many small isolated knowledge clusters. Similar bipolar distributions were obtained when comparing levels of insularity estimated by indicators of international collaboration and levels of country-self citations: researchers in academic areas with many journals such as social sciences, arts and humanities, were the most isolated, and that was true in different regions of the world. The work shows that quantitative measures estimating differences between academic disciplines improve our understanding of different research strategies, eventually helping interdisciplinary research and may be also help improve science policies worldwide.

  3. Social and Natural Sciences Differ in Their Research Strategies, Adapted to Work for Different Knowledge Landscapes

    PubMed Central

    Jaffe, Klaus

    2014-01-01

    Do different fields of knowledge require different research strategies? A numerical model exploring different virtual knowledge landscapes, revealed two diverging optimal search strategies. Trend following is maximized when the popularity of new discoveries determine the number of individuals researching it. This strategy works best when many researchers explore few large areas of knowledge. In contrast, individuals or small groups of researchers are better in discovering small bits of information in dispersed knowledge landscapes. Bibliometric data of scientific publications showed a continuous bipolar distribution of these strategies, ranging from natural sciences, with highly cited publications in journals containing a large number of articles, to the social sciences, with rarely cited publications in many journals containing a small number of articles. The natural sciences seem to adapt their research strategies to landscapes with large concentrated knowledge clusters, whereas social sciences seem to have adapted to search in landscapes with many small isolated knowledge clusters. Similar bipolar distributions were obtained when comparing levels of insularity estimated by indicators of international collaboration and levels of country-self citations: researchers in academic areas with many journals such as social sciences, arts and humanities, were the most isolated, and that was true in different regions of the world. The work shows that quantitative measures estimating differences between academic disciplines improve our understanding of different research strategies, eventually helping interdisciplinary research and may be also help improve science policies worldwide. PMID:25426723

  4. Decision tree algorithm for detection of spatial processes in landscape transformation.

    PubMed

    Bogaert, Jan; Ceulemans, Reinhart; Salvador-Van Eysenrode, David

    2004-01-01

    The conversion of landscapes by human activities results in widespread changes in landscape spatial structure. Regardless of the type of land conversion, there appears to be a limited number of common spatial configurations that result from such land transformation processes. Some of these configurations are considered optimal or more desirable than others. Based on pattern geometry, we define ten processes responsible for pattern change: aggregation, attrition, creation, deformation, dissection, enlargement, fragmentation, perforation, shift, and shrinkage. A novelty in this contribution is the inclusion of transformation processes causing expansion of the land cover of interest. Consequently, we propose a decision tree algorithm that enables detection of these processes, based on three parameters that have to be determined before and after the transformation of the landscape: area, perimeter length, and number of patches of the focal landscape class. As an example, the decision tree algorithm is applied to determine the transformation processes of three divergent land cover change scenarios: deciduous woodland degradation in Cadiz Township (Wisconsin, USA) 1831-1950, canopy gap formation in a terra firme rain forest at the Tiputini Biodiversity Station (Amazonian Ecuador) 1997-1998, and forest regrowth in Petersham Township (Massachusetts, USA) 1830-1985. The examples signal the importance of the temporal resolution of the data, since long-term pattern conversions can be subdivided in stadia in which particular pattern components are altered by specific transformation processes.

  5. A Holistic Landscape Description Reveals That Landscape Configuration Changes More over Time than Composition: Implications for Landscape Ecology Studies

    PubMed Central

    Mimet, Anne; Pellissier, Vincent; Houet, Thomas; Julliard, Romain; Simon, Laurent

    2016-01-01

    Background Space-for-time substitution—that is, the assumption that spatial variations of a system can explain and predict the effect of temporal variations—is widely used in ecology. However, it is questionable whether it can validly be used to explain changes in biodiversity over time in response to land-cover changes. Hypothesis Here, we hypothesize that different temporal vs spatial trajectories of landscape composition and configuration may limit space-for-time substitution in landscape ecology. Land-cover conversion changes not just the surface areas given over to particular types of land cover, but also affects isolation, patch size and heterogeneity. This means that a small change in land cover over time may have only minor repercussions on landscape composition but potentially major consequences for landscape configuration. Methods Using land-cover maps of the Paris region for 1982 and 2003, we made a holistic description of the landscape disentangling landscape composition from configuration. After controlling for spatial variations, we analyzed and compared the amplitudes of changes in landscape composition and configuration over time. Results For comparable spatial variations, landscape configuration varied more than twice as much as composition over time. Temporal changes in composition and configuration were not always spatially matched. Significance The fact that landscape composition and configuration do not vary equally in space and time calls into question the use of space-for-time substitution in landscape ecology studies. The instability of landscapes over time appears to be attributable to configurational changes in the main. This may go some way to explaining why the landscape variables that account for changes over time in biodiversity are not the same ones that account for the spatial distribution of biodiversity. PMID:26959363

  6. Development of hydrologic landscape regions for classifying hydrologic permanace and hydrological-ecological interactions

    EPA Science Inventory

    In a 2001 paper, Winter proposed the concept of the hydrologic landscape unit as a fundamental unit composed of an upland and lowland separated by a steeper slope. Winter suggested that this concept could be useful for hydrologic research, data analysis, and comparing hydrologic...

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

    PubMed Central

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

    2016-01-01

    Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically ‘leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs. PMID:27010670

  8. The effects of inheritance in tetraploids on genetic diversity and population divergence.

    PubMed

    Meirmans, P G; Van Tienderen, P H

    2013-02-01

    Polyploids are traditionally classified into allopolyploids and autopolyploids, based on their evolutionary origin and their disomic or multisomic mode of inheritance. Over the past decade it has become increasingly clear that there is a continuum between disomic and multisomic inheritance, with the rate of tetrasomy differing among species and among chromosomes within species. Here, we use a simple population genetic model to study the impact of the mode of inheritance on the genetic diversity and population divergence of tetraploids. We found that under almost strict disomic inheritance the tetraploid genome is divided into two separate subgenomes, such as found in classical allopolyploids. In those cases, assuming full tetrasomy in the analysis of polyploid genetic data will lead to an important bias in estimates of genetic diversity and population divergence. However, we found that even a low rate of allele exchange between the two subgenomes, at about one event per generation, is sufficient to homogenise the allele frequencies over the subgenomes, and the estimates become essentially unbiased. The inbreeding coefficient F(IS) can then be used to detect whether the estimates of diversity and divergence will be biased when full multisomy is assumed. Finally, we found that different summary statistics for measuring the strength of population differentiation are differentially affected by a deviation from full tetrasomy. Our model results provide several useful guidelines for the analysis of polyploid data, helping researchers to determine when their inferences are biased and which summary statistics to use.

  9. Molecular phylogeny, divergence times and biogeography of spiders of the subfamily Euophryinae (Araneae: Salticidae).

    PubMed

    Zhang, Jun-Xia; Maddison, Wayne P

    2013-07-01

    We investigate phylogenetic relationships of the jumping spider subfamily Euophryinae, diverse in species and genera in both the Old World and New World. DNA sequence data of four gene regions (nuclear: 28S, Actin 5C; mitochondrial: 16S-ND1, COI) were collected from 263 jumping spider species. The molecular phylogeny obtained by Bayesian, likelihood and parsimony methods strongly supports the monophyly of a Euophryinae re-delimited to include 85 genera. Diolenius and its relatives are shown to be euophryines. Euophryines from different continental regions generally form separate clades on the phylogeny, with few cases of mixture. Known fossils of jumping spiders were used to calibrate a divergence time analysis, which suggests most divergences of euophryines were after the Eocene. Given the divergence times, several intercontinental dispersal events are required to explain the distribution of euophryines. Early transitions of continental distribution between the Old and New World may have been facilitated by the Antarctic land bridge, which euophryines may have been uniquely able to exploit because of their apparent cold tolerance. Two hot-spots of diversity of euophryines are discovered: New Guinea and the Caribbean Islands. Implications of the molecular phylogeny on the taxonomy of euophryines, and on the evolution of unusual genitalic forms and myrmecophagy, are also briefly discussed. PMID:23542001

  10. Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

    PubMed Central

    Brown, Emily A; Chain, Frédéric J J; Crease, Teresa J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high-throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and “populations” of various species in our communities, we examine the impact of intra- and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59–84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31–63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group-specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs. PMID:26078859

  11. Single-input divergent flow IEF for preparative analysis of proteins.

    PubMed

    Stastna, Miroslava; Slais, Karel

    2008-11-01

    The instrument for continuous divergent flow IEF based on our principles set and outlined previously was further extended and tested. The separation and focusing area of a trapezoidal shape had a porous bed made from a nonwoven textile material with thickness decreasing from narrow input to wide output. A narrow end was used as a single input to continuously bring a single solution into separation space with a flow rate of 0.18 mL/min. Two pairs of electrodes were positioned close to both narrow and wide ends of the separation area with equilibrium state voltage of 75 V at the narrow input and 384 V at the wide output. Under dynamic equilibrium state, the zones of both pH gradient components and analytes were separated close to the input point and focused with increasing resolution while transporting through the separation space. The long-term stability experiments had shown the suitability of the device for preparative analysis; the zones of pI markers, hemoglobin and cytochrome C remained focused and separated over 15 h with deviations from the mean focusing positions ranging from 1.26 to 3.96% of the bed output width.

  12. [Wetland landscape ecological classification: research progress].

    PubMed

    Cao, Yu; Mo, Li-jiang; Li, Yan; Zhang, Wen-mei

    2009-12-01

    Wetland landscape ecological classification, as a basis for the studies of wetland landscape ecology, directly affects the precision and effectiveness of wetland-related research. Based on the history, current status, and latest progress in the studies on the theories, indicators, and methods of wetland landscape classification, some scientific wetland classification systems, e.g., NWI, Ramsar, and HGM, were introduced and discussed in this paper. It was suggested that a comprehensive classification method based on HGM and on the integral consideration of wetlands spatial structure, ecological function, ecological process, topography, soil, vegetation, hydrology, and human disturbance intensity should be the major future direction in this research field. Furthermore, the integration of 3S technologies, quantitative mathematics, landscape modeling, knowledge engineering, and artificial intelligence to enhance the automatization and precision of wetland landscape ecological classification would be the key issues and difficult topics in the studies of wetland landscape ecological classification.

  13. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka)

    USGS Publications Warehouse

    Pavey, Scott A.; Nielsen, Jennifer L.; Hamon, Troy R.

    2010-01-01

    Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (~500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000–15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier.

  14. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka).

    PubMed

    Pavey, Scott A; Nielsen, Jennifer L; Hamon, Troy R

    2010-06-01

    Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (approximately 500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000-15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier.

  15. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka).

    PubMed

    Pavey, Scott A; Nielsen, Jennifer L; Hamon, Troy R

    2010-06-01

    Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (approximately 500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000-15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier. PMID:20030707

  16. Genetic Structure Is Associated with Phenotypic Divergence in Floral Traits and Reproductive Investment in a High-Altitude Orchid from the Iron Quadrangle, Southeastern Brazil

    PubMed Central

    Leles, Bruno; Chaves, Anderson V.; Russo, Philip; Batista, João A. N.; Lovato, Maria Bernadete

    2015-01-01

    Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops. PMID:25756994

  17. Divergent and Convergent Evolution of Fungal Pathogenicity

    PubMed Central

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-01-01

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen–host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus–animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. PMID:27071652

  18. Shifting distributions and speciation: species divergence during rapid climate change.

    PubMed

    Carstens, Bryan C; Knowles, L Lacey

    2007-02-01

    Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species

  19. Shifting distributions and speciation: species divergence during rapid climate change.

    PubMed

    Carstens, Bryan C; Knowles, L Lacey

    2007-02-01

    Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species

  20. Lineage divergence in Odorrana graminea complex (Anura: Ranidae: Odorrana).

    PubMed

    Xiong, Rongchuan; Li, Cheng; Jiang, Jianping

    2015-05-26

    The confusing and unstable taxonomy of Odorrana livida (Rana livida) since its first record has made it a focal frog complex for systematics. In China, four species, Odorrana nebulosa, O. graminea, O. sinica, O. leporipes, were described to closely resemble O. livida or O. chloronota based on their morphological similarities, accompanied by much taxonomic confusion because of ambiguities in the wide distribution and morphological variations. Currently O. graminea is being used as the name of a provisional monotypic species group to include all the populations in China that closely resemble O. livida or O. chloronota. Here, we conducted a range-wide molecular phylogeographic analysis of the large green odorous frog (Odorrana graminea) complex across the majority of its range in China, based on 2780 bp DNA sequences of three mitochondrial genes (12S, 16S, ND2) in 107 samples from 20 sites. Our data recognized three distinct phylogeographic lineages of the Odorrana graminea (lato sensu) complex in China, and they together with a Thailand lineage formed a monophyletic group. Among the four lineages within O. graminea complex, the average genetic distances based on the concatenated sequences of 12S, 16S and ND2 were 7.5-8.8% and those based on 16S rRNA alone were 4.2-5.5%. Furthermore, canonical discriminant functions in morphometric analyses showed significant separations of all the paired lineage comparisons in China. The aforementioned genetic divergence and mismatched phenotypes among the lineages within the Odorrana graminea complex, in addition to their non-overlapping geographic distributions, imply extensive lineage diversification. However, precise taxonomic status of these lineages needs more studies based on adequate type information and more thorough species delimitation based on analysis of differentiation in bioacoustic and nuclear genetic characters especially regarding gene flow and admixture in geographical contact zones.

  1. Toward a comprehensive landscape vegetation monitoring framework

    NASA Astrophysics Data System (ADS)

    Kennedy, Robert; Hughes, Joseph; Neeti, Neeti; Larrue, Tara; Gregory, Matthew; Roberts, Heather; Ohmann, Janet; Kane, Van; Kane, Jonathan; Hooper, Sam; Nelson, Peder; Cohen, Warren; Yang, Zhiqiang

    2016-04-01

    Blossoming Earth observation resources provide great opportunity to better understand land vegetation dynamics, but also require new techniques and frameworks to exploit their potential. Here, I describe several parallel projects that leverage time-series Landsat imagery to describe vegetation dynamics at regional and continental scales. At the core of these projects are the LandTrendr algorithms, which distill time-series earth observation data into periods of consistent long or short-duration dynamics. In one approach, we built an integrated, empirical framework to blend these algorithmically-processed time-series data with field data and lidar data to ascribe yearly change in forest biomass across the US states of Washington, Oregon, and California. In a separate project, we expanded from forest-only monitoring to full landscape land cover monitoring over the same regional scale, including both categorical class labels and continuous-field estimates. In these and other projects, we apply machine-learning approaches to ascribe all changes in vegetation to driving processes such as harvest, fire, urbanization, etc., allowing full description of both disturbance and recovery processes and drivers. Finally, we are moving toward extension of these same techniques to continental and eventually global scales using Google Earth Engine. Taken together, these approaches provide one framework for describing and understanding processes of change in vegetation communities at broad scales.

  2. Active walker models: tracks and landscapes

    NASA Astrophysics Data System (ADS)

    Kayser, D. R.; Aberle, L. K.; Pochy, R. D.; Lam, L.

    1992-12-01

    The track patterns from the active walker models (AWMs) are compared with experimental retinal neuron and dielectric breakdown of liquid patterns, respectively. Excellent qualitative and quantitative agreements are obtained. The landscapes from the Boltzmann AWM in 1 + 1 dimensions form rough surfaces, with a first-order phase transition as the height of the landscaping function W0 is varied. Landscapes and statistics of the tracks from the probabilistic AWM in 2 + 1 dimensions are presented.

  3. LANDSCAPE INFLUENCES ON LAKE CHEMISTRY OF SMALL DIMICTIC LAKES IN THE HUMAN DOMINATED SOUTHERN WISCONSIN LANDSCAPE

    EPA Science Inventory

    Changes in landscape heterogeneity, historic landcover change, and human disturbance regimes are governed by complex interrelated landscape processes that modify lake water quality through the addition of nutrients, sediment, anthropogenic chemicals, and changes in major ion conc...

  4. Entropy landscape of solutions in the binary perceptron problem

    NASA Astrophysics Data System (ADS)

    Huang, Haiping; Wong, K. Y. Michael; Kabashima, Yoshiyuki

    2013-09-01

    The statistical picture of the solution space for a binary perceptron is studied. The binary perceptron learns a random classification of input random patterns by a set of binary synaptic weights. The learning of this network is difficult especially when the pattern (constraint) density is close to the capacity, which is supposed to be intimately related to the structure of the solution space. The geometrical organization is elucidated by the entropy landscape from a reference configuration and of solution-pairs separated by a given Hamming distance in the solution space. We evaluate the entropy at the annealed level as well as replica symmetric level and the mean field result is confirmed by the numerical simulations on single instances using the proposed message passing algorithms. From the first landscape (a random configuration as a reference), we see clearly how the solution space shrinks as more constraints are added. From the second landscape of solution-pairs, we deduce the coexistence of clustering and freezing in the solution space.

  5. Clustering and Phase Transitions on a Neutral Landscape

    NASA Astrophysics Data System (ADS)

    Scott, Adam; King, Dawn; Maric, Nevena; Bahar, Sonya

    2012-02-01

    The problem of speciation and species aggregation on a neutral landscape, subject to random mutational fluctuations rather than selective drive, has been a focus of research since the seminal work of Kimura on genetic drift. These ideas have received increased attention due to the more recent development of a neutral ecological theory by Hubbell. De Aguiar et al. recently demonstrated, in a computational model, that speciation can occur under neutral conditions; this study bears some comparison with more mathematical studies of clustering on neutral landscapes in the context of branching and annihilating random walks. Here, we show that clustering can occur on a neutral landscape where the dimensions specify the simulated organisms' phenotypes. Unlike the De Aguiar et al. model, we simulate sympatric speciation: the organisms cluster phenotypically, but are not spatially separated. Moreover, we find that clustering occurs not only in the case of assortative mating, but also in the case of asexual fission. Clustering is not observed in a control case where organisms can mate randomly. We find that the population size and the number of clusters undergo phase-transition-like behavior as the maximum mutation size is varied.

  6. The development of quick, robust, quantitative phenotypic assays for describing the host–nonhost landscape to stripe rust

    PubMed Central

    Dawson, Andrew M.; Bettgenhaeuser, Jan; Gardiner, Matthew; Green, Phon; Hernández-Pinzón, Inmaculada; Hubbard, Amelia; Moscou, Matthew J.

    2015-01-01

    Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host–nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen’s ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon. PMID:26579142

  7. Divergence and diversity: lessons from an arctic-alpine distribution (Pardosa saltuaria group, Lycosidae).

    PubMed

    Muster, Christoph; Berendonk, Thomas U

    2006-09-01

    The relationship of interpopulation genetic divergence and within-population diversity has been studied for many temperate species in Europe, but not for the cold-adapted fauna. Here we present the first European-wide phylogeographical study of an arctic-alpine distribution in invertebrates, focusing on wolf spiders of the Pardosa saltuaria group. One hundred twenty-seven (127) specimens from 14 populations were examined. Within Europe, these populations were distributed among six high mountain ranges and Scandinavia. We sequenced the whole 921 base pair mitochondrial (mt) ND1 gene. The resulting 55 unique haplotypes form three monophyletic phylogroups of deep divergence: a Pyrenean, a Balkan and a 'northern' clade. Genetic distances (3.6-4.0%) between the major clades indicate that the arctic-alpine range disjunction was initiated by vicariance events, which precede the four major Alpine glaciations. However, low divergence and incomplete lineage sorting within the 'northern clade' suggest a late Pleistocene separation of the Alpine, Scandinavian, Carpathian and Sudetian populations. Thus, we provide evidence for a multiglacial origin of arctic-alpine distributions in Europe, i.e. the current disjunction results from range fragmentation in several glacial cycles. The pattern of genetic diversity within populations seems predominantly determined by historical factors, but is modified by contemporary aspects. Overall, diversity and divergence are negatively correlated. We suggest that low diversity values might result from (i) ancient bottlenecking during warm interglacial periods, as seen in the Pyrenees and Balkans; (ii) recent bottlenecking in small modern areas, as seen in the Giant Mountains and Bohemian Forest; and (iii) dispersal bottlenecking in northern Scandinavia. PMID:16911211

  8. Divergence and diversity: lessons from an arctic-alpine distribution (Pardosa saltuaria group, Lycosidae).

    PubMed

    Muster, Christoph; Berendonk, Thomas U

    2006-09-01

    The relationship of interpopulation genetic divergence and within-population diversity has been studied for many temperate species in Europe, but not for the cold-adapted fauna. Here we present the first European-wide phylogeographical study of an arctic-alpine distribution in invertebrates, focusing on wolf spiders of the Pardosa saltuaria group. One hundred twenty-seven (127) specimens from 14 populations were examined. Within Europe, these populations were distributed among six high mountain ranges and Scandinavia. We sequenced the whole 921 base pair mitochondrial (mt) ND1 gene. The resulting 55 unique haplotypes form three monophyletic phylogroups of deep divergence: a Pyrenean, a Balkan and a 'northern' clade. Genetic distances (3.6-4.0%) between the major clades indicate that the arctic-alpine range disjunction was initiated by vicariance events, which precede the four major Alpine glaciations. However, low divergence and incomplete lineage sorting within the 'northern clade' suggest a late Pleistocene separation of the Alpine, Scandinavian, Carpathian and Sudetian populations. Thus, we provide evidence for a multiglacial origin of arctic-alpine distributions in Europe, i.e. the current disjunction results from range fragmentation in several glacial cycles. The pattern of genetic diversity within populations seems predominantly determined by historical factors, but is modified by contemporary aspects. Overall, diversity and divergence are negatively correlated. We suggest that low diversity values might result from (i) ancient bottlenecking during warm interglacial periods, as seen in the Pyrenees and Balkans; (ii) recent bottlenecking in small modern areas, as seen in the Giant Mountains and Bohemian Forest; and (iii) dispersal bottlenecking in northern Scandinavia.

  9. First divergence time estimate of spiders, scorpions, mites and ticks (subphylum: Chelicerata) inferred from mitochondrial phylogeny.

    PubMed

    Jeyaprakash, Ayyamperumal; Hoy, Marjorie A

    2009-01-01

    Spiders, scorpions, mites and ticks (chelicerates) form one of the most diverse groups of arthropods on land, but their origin and times of diversification are not yet established. We estimated, for the first time, the molecular divergence times for these chelicerates using complete mitochondrial sequences from 25 taxa. All mitochondrial genes were evaluated individually or after concatenation. Sequences belonging to three missing genes (ND3, 6, and tRNA-Asp) from three taxa, as well as the faster-evolving ribosomal RNAs (12S and 16S), tRNAs, and the third base of each codon from 11 protein-coding genes (PCGs) (COI-III, CYTB, ATP8, 6, ND1-2, 4L, and 4-5), were identified and removed. The remaining concatenated sequences from 11 PCGs produced a completely resolved phylogenetic tree and confirmed that all chelicerates are monophyletic. Removing the third base from each codon was essential to resolve the phylogeny, which allowed deep divergence times to be calculated using three nodes calibrated with upper and lower priors. Our estimates indicate that the orders and classes of spiders, scorpions, mites, and ticks diversified in the late Paleozoic, much earlier than previously reported from fossil date estimates. The divergence time estimated for ticks suggests that their first land hosts could have been amphibians rather than reptiles. Using molecular data, we separated the spider-scorpion clades and estimated their divergence times at 397 +/- 23 million years ago. Algae, fungi, plants, and animals, including insects, were well established on land when these chelicerates diversified. Future analyses, involving mitochondrial sequences from additional chelicerate taxa and the inclusion of nuclear genes (or entire genomes) will provide a more complete picture of the evolution of the Chelicerata, the second most abundant group of animals on earth.

  10. Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?

    PubMed

    Breitkopf, H; Schlüter, P M; Xu, S; Schiestl, F P; Cozzolino, S; Scopece, G

    2013-10-01

    Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic distance among populations with contrasting predominant pollinators. We analysed floral hydrocarbons as a proxy for floral divergence between populations. Floral adoption of pollinators and their fidelity was tested using pollinator choice experiments. Interpopulation gene flow and population differentiation levels were estimated using AFLP markers. The Tyrrhenian O. sphegodes population preferentially attracted the pollinator bee Andrena bimaculata, whereas the Adriatic O. sphegodes population exclusively attracted A. nigroaenea. Significant differences in scent component proportions were identified in O. sphegodes populations that attracted different preferred pollinators. High interpopulation gene flow was detected, but populations were genetically structured at species level. The high interpopulation gene flow levels independent of preferred pollinators suggest that local adaptation to different pollinators has not (yet) generated detectable genome-wide separation. Alternatively, despite extensive gene flow, few genes underlying floral isolation remain differentiated as a consequence of divergent selection. Different pollination ecotypes in O. sphegodes might represent a local selective response imposed by temporal variation in a geographical mosaic of pollinators as a consequence of the frequent disturbance regimes typical of Ophrys habitats.

  11. Different atmospheric moisture divergence responses to extreme and moderate El Niños

    NASA Astrophysics Data System (ADS)

    Xu, Guangzhi; Osborn, Timothy J.; Matthews, Adrian J.; Joshi, Manoj M.

    2016-07-01

    On seasonal and inter-annual time scales, vertically integrated moisture divergence provides a useful measure of the tropical atmospheric hydrological cycle. It reflects the combined dynamical and thermodynamical effects, and is not subject to the limitations that afflict observations of evaporation minus precipitation. An empirical orthogonal function (EOF) analysis of the tropical Pacific moisture divergence fields calculated from the ERA-Interim reanalysis reveals the dominant effects of the El Niño-Southern Oscillation (ENSO) on inter-annual time scales. Two EOFs are necessary to capture the ENSO signature, and regression relationships between their Principal Components and indices of equatorial Pacific sea surface temperature (SST) demonstrate that the transition from strong La Niña through to extreme El Niño events is not a linear one. The largest deviation from linearity is for the strongest El Niños, and we interpret that this arises at least partly because the EOF analysis cannot easily separate different patterns of responses that are not orthogonal to each other. To overcome the orthogonality constraints, a self-organizing map (SOM) analysis of the same moisture divergence fields was performed. The SOM analysis captures the range of responses to ENSO, including the distinction between the moderate and strong El Niños identified by the EOF analysis. The work demonstrates the potential for the application of SOM to large scale climatic analysis, by virtue of its easier interpretation, relaxation of orthogonality constraints and its versatility for serving as an alternative classification method. Both the EOF and SOM analyses suggest a classification of "moderate" and "extreme" El Niños by their differences in the magnitudes of the hydrological cycle responses, spatial patterns and evolutionary paths. Classification from the moisture divergence point of view shows consistency with results based on other physical variables such as SST.

  12. High-brightness diode lasers with very narrow vertical divergence

    NASA Astrophysics Data System (ADS)

    Erbert, Götz; Bugge, Frank; Eppich, Bernd; Fricke, Joerg; Hasler, Karl-Heinz; Paschke, Katrin; Pietrzak, Agnieszka; Wenzel, Hans; Tränkle, Günther

    2008-02-01

    A narrow vertical divergence of about 30° including 95% of power is highly desired in many applications. Principal designs for narrow divergence diode lasers like simple broad waveguide and more sophisticated resonant waveguide structures are discussed. Devices with narrow divergence could be realized in the wavelength range 800nm to 1060nm using very broad waveguide structures. More than 1W in fundamental mode and about 5W nearly diffraction limited output could be achieved from ridge waveguide laser and from diode lasers with tapered resonator structure, respectively.

  13. Divergences in the vacuum energy for frequency-dependent interactions

    NASA Astrophysics Data System (ADS)

    Vassilevich, D. V.

    2009-03-01

    We propose a method for determining ultraviolet divergences in the vacuum energy for systems whose spectrum of perturbations is defined through a nonlinear spectrum problem, i.e., when the fluctuation operator itself depends on the frequency. The method is applied to the plasma shell model, which describes some properties of the interaction of electromagnetic field with fullerenes. We formulate a scalar model, which simplifies the matrix structure, but keeps the frequency dependence of the plasma shell, and calculate the ultraviolet divergences in the case when the plasma sheet is slightly curved. The divergent terms are expressed in terms of surface integrals of corresponding invariants.

  14. Quantitative analyses of empirical fitness landscapes

    NASA Astrophysics Data System (ADS)

    Szendro, Ivan G.; Schenk, Martijn F.; Franke, Jasper; Krug, Joachim; de Visser, J. Arjan G. M.

    2013-01-01

    The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes was lacking, but since it became feasible to construct all possible genotypes containing combinations of a limited set of mutations, the number of studies has grown to a point where a classification of landscapes becomes possible. The aim of this review is to identify measures of epistasis that allow a meaningful comparison of fitness landscapes and then apply them to the empirical landscapes in order to discern factors that affect ruggedness. The various measures of epistasis that have been proposed in the literature appear to be equivalent. Our comparison shows that the ruggedness of the empirical landscape is affected by whether the included mutations are beneficial or deleterious and by whether intragenic or intergenic epistasis is involved. Finally, the empirical landscapes are compared to landscapes generated with the rough Mt Fuji model. Despite the simplicity of this model, it captures the features of the experimental landscapes remarkably well.

  15. Incorporating bioenergy into sustainable landscape designs

    DOE PAGESBeta

    Dale, Virginia H.; Kline, Keith L.; Buford, Marilyn A.; Volk, Timothy A.; Smith, C. Tattersall; Stupak, Inge

    2015-12-30

    In this paper, we describe an approach to landscape design that focuses on integrating bioenergy production with other components of environmental, social and economic systems. Landscape design as used here refers to a spatially explicit, collaborative plan for management of landscapes and supply chains. Landscape design can involve multiple scales and build on existing practices to reduce costs or enhance services. Appropriately applied to a specific context, landscape design can help people assess trade-offs when making choices about locations, types of feedstock, transport, refining and distribution of bioenergy products and services. The approach includes performance monitoring and reporting along themore » bioenergy supply chain. Examples of landscape design applied to bioenergy production systems are presented. Barriers to implementation of landscape design include high costs, the need to consider diverse land-management objectives from a wide array of stakeholders, up-front planning requirements, and the complexity and level of effort needed for successful stakeholder involvement. A landscape design process may be stymied by insufficient data or participation. An impetus for coordination is critical, and incentives may be required to engage landowners and the private sector. In conclusion, devising and implementing landscape designs for more sustainable outcomes require clear communication of environmental, social, and economic opportunities and concerns.« less

  16. Multidisciplinary modeling and GIS for landscape management

    SciTech Connect

    Flamm, R.O.; Turner, M.G.

    1993-12-31

    Ecological dynamics in human-influenced landscapes are strongly affected by the socioeconomic factors that influence land-use decisions. Incorporating these factors into a spatially-explicit landscape-change model requires the integration of multidisciplinary data. We developed a model that simulates the effects of land use on landscape structure in the Little Tennessee River Basin in western North Carolina. This model uses a variety of data, including interpreted remotely-sensed imagery, census and ownership maps, topography, and results from econometric models. Data are integrated by using a geographic information system and translated into a common format, maps. Simulations generate new maps of land cover representing the amount of land-cover change that occurs. With spatially-explicit projections of landscape change, issues such as biodiversity conservation, the importance of specific landscape elements to conservation goals, and long-term landscape integrity can be addressed. In order for management to use the model to address these issues, a computer-based landscape-management decision aid is being developed. This tool integrates the models, associated data bases, and a geographic information system to facilitate the evaluation of land-use decisions and management plans. This system will estimate landscape-level consequences of alternative actions and will serve to focus coordination among different land-owners and land-use interests in managing the regional landscape.

  17. Incorporating bioenergy into sustainable landscape designs

    SciTech Connect

    Dale, Virginia H.; Kline, Keith L.; Buford, Marilyn A.; Volk, Timothy A.; Smith, C. Tattersall; Stupak, Inge

    2015-12-30

    In this paper, we describe an approach to landscape design that focuses on integrating bioenergy production with other components of environmental, social and economic systems. Landscape design as used here refers to a spatially explicit, collaborative plan for management of landscapes and supply chains. Landscape design can involve multiple scales and build on existing practices to reduce costs or enhance services. Appropriately applied to a specific context, landscape design can help people assess trade-offs when making choices about locations, types of feedstock, transport, refining and distribution of bioenergy products and services. The approach includes performance monitoring and reporting along the bioenergy supply chain. Examples of landscape design applied to bioenergy production systems are presented. Barriers to implementation of landscape design include high costs, the need to consider diverse land-management objectives from a wide array of stakeholders, up-front planning requirements, and the complexity and level of effort needed for successful stakeholder involvement. A landscape design process may be stymied by insufficient data or participation. An impetus for coordination is critical, and incentives may be required to engage landowners and the private sector. In conclusion, devising and implementing landscape designs for more sustainable outcomes require clear communication of environmental, social, and economic opportunities and concerns.

  18. Adaptation and extinction in experimentally fragmented landscapes.

    PubMed

    Fakheran, Sima; Paul-Victor, Cloé; Heichinger, Christian; Schmid, Bernhard; Grossniklaus, Ueli; Turnbull, Lindsay A

    2010-11-01

    Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes.

  19. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

    PubMed Central

    Burri, Reto; Nater, Alexander; Kawakami, Takeshi; Mugal, Carina F.; Olason, Pall I.; Smeds, Linnea; Suh, Alexander; Dutoit, Ludovic; Bureš, Stanislav; Garamszegi, Laszlo Z.; Hogner, Silje; Moreno, Juan; Qvarnström, Anna; Ružić, Milan; Sæther, Stein-Are; Sætre, Glenn-Peter; Török, Janos; Ellegren, Hans

    2015-01-01

    Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation. PMID:26355005

  20. River Capture in Disequilibrium Landscapes

    NASA Astrophysics Data System (ADS)

    McCoy, S. W.; Perron, J.; Willett, S.; Goren, L.

    2013-12-01

    The process of river piracy or river capture has long drawn interest as a potential mechanism by which drainage basins large and small evolve towards an equilibrium state. River capture transfers both drainage area and drainage lines from one river basin to another, which can cause large, abrupt shifts in network topology, drainage divide positions, and river incision rates. Despite numerous case studies in which river capture has been proposed to have occurred, there is no general, mechanistic framework for understanding the controls on river capture, nor are there quantitative criteria for determining if capture has occurred. Here we use new metrics of landscape disequilibrium to first identify landscapes in which drainage reorganization is occurring. These metrics are based on a balance between an integral of the contributing drainage area and elevation. In an analysis of rivers in the Eastern United States we find that many rivers are in a state of disequilibrium and are experiencing recent or ongoing area exchange between basins. In these disequilibrium basins we find widespread evidence for network rearrangement via river capture at multiple scales. We then conduct numerical experiments with a 2-D landscape evolution model to explore the conditions in which area exchange among drainage basins is likely to occur as discrete capture events as opposed to continuous divide migration. These experiments indicate that: (1) capture activity increases with the degree of disequilibrium induced by persistent spatial gradients in tectonic forcing or by temporal changes in climate or tectonic forcing; (2) capture activity is strongly controlled by the initial planform drainage network geometry; and (3) capture activity scales with the fluvial incision rate constant in the river power erosion law.

  1. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  2. A computational framework for generalized moving windows and its application to landscape pattern analysis

    NASA Astrophysics Data System (ADS)

    Hagen-Zanker, Alex

    2016-02-01

    Land cover products based on remotely sensed data are commonly investigated in terms of landscape composition and configuration; i.e. landscape pattern. Traditional landscape pattern indicators summarize an aspect of landscape pattern over the full study area. Increasingly, the advantages of representing the scale-specific spatial variation of landscape patterns as continuous surfaces are being recognized. However, technical and computational barriers hinder the uptake of this approach. This article reduces such barriers by introducing a computational framework for moving window analysis that separates the tasks of tallying pixels, patches and edges as a window moves over the map from the internal logic of landscape indicators. The framework is applied on data covering the UK and Ireland at 250 m resolution, evaluating a variety of indicators including mean patch size, edge density and Shannon diversity at window sizes ranging from 2.5 km to 80 km. The required computation time is in the order of seconds to minutes on a regular personal computer. The framework supports rapid development of indicators requiring little coding. The computational efficiency means that methods can be integrated in iterative computational tasks such as multi-scale analysis, optimization, sensitivity analysis and simulation modelling.

  3. Modeling Forest Understory Fires in an Eastern Amazonian Landscape

    NASA Technical Reports Server (NTRS)

    Alencar, A. A. C.; Solorzano, L. A.; Nepstad, D. C.

    2004-01-01

    Forest understory fires are an increasingly important cause of forest impoverishment in Ammonia, but little is known of the landscape characteristics and climatic phenomena that determine their occurrence. We developed empirical functions relating the occurrence of understory fires to landscape features near Paragominas, a 35- yr-old ranching and logging center in eastern Ammonia. An historical sequence of maps of forest understory fire was created based on field interviews With local farmers and Landsat TM images. Several landscape features that might explain spatial variations in the occurrence of understory fires were also mapped and co-registered for each of the sample dates, including: forest fragment size and shape, forest impoverishment through logging and understory fires, source of ignition (settlements and charcoal pits), roads, forest edges, and others. The spatial relationship between forest understory fire and each landscape characteristic was tested by regression analyses. Fire probability models were then developed for various combinations of landscape characteristics. The analyses were conducted separately for years of the El Nino Southern Oscillation (ENSO), which are associated with severe drought in eastern Amazonia, and non-ENS0 years. Most (91 %) of the forest area that burned during the 10-yr sequence caught fire during ENSO years, when severe drought may have increased both forest flammability and the escape of agricultural management fires. Forest understory fires were associated with forest edges, as reported in previous studies from Ammonia. But the strongest predictor of forest fire was the percentage of the forest fragment that had been previously logged or burned. Forest fragment size, distance to charcoal pits, distance to agricultural settlement, proximity to forest edge, and distance to roads were also correlated with forest understory fire. Logistic regression models using information on fragment degradation and distance to ignition

  4. Martian Arctic Landscape Panorama Video

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation

    Typical view if you were standing on Mars and slowly turned around for a look. Starting at the north, SSI sees its shadow and turns its head viewing solar arrays, the lander deck and landscape. Note very few rocks on the hummocky terrain and network of troughs, typical of polar surfaces here on Earth.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  5. Ecological separation in a polymorphic terrestrial salamander.

    PubMed

    Anthony, Carl D; Venesky, Matthew D; Hickerson, Cari-Ann M

    2008-07-01

    1. When studying speciation, researchers commonly examine reproductive isolation in recently diverged populations. Polymorphic species provide an opportunity to examine the role of reproductive isolation in populations that may be in the process of divergence. 2. We examined a polymorphic population of Plethodon cinereus (red-backed salamanders) for evidence of sympatric ecological separation by colour morphology. Recent studies have correlated temperature and climate with colour morphology in this species, but no studies have looked at differences in diet or mate choice between colour morphs. We used artificial cover objects to assess salamander diet, mating preference and surface activity over a 2-year period at a field site in north-eastern Ohio. 3. We detected differences in diet between two colour morphs, striped and unstriped. The diets of striped individuals were significantly more diverse and were made up of more profitable prey than the diets of unstriped salamanders. 4. Opposite sex pairs were made up of individuals of the same colour morph and striped males were found more often with larger females than were unstriped males. 5. We corroborate findings of earlier studies suggesting that the unstriped form is adapted to warmer conditions. Unstriped individuals were the first to withdraw from the forest floor as temperatures fell in the late fall. We found no evidence that the colour morphs responded differently to abiotic factors such as soil moisture and relative humidity, and responses to surface temperatures were also equivocal. 6. We conclude that the two colour morphs exhibit some degree of ecological separation and tend to mate assortatively, but are unlikely to be undergoing divergence given the observed frequency of intermorph pairings.

  6. Numerical study of the spontaneous nucleation of self-rotational moist gas in a converging-diverging nozzle

    NASA Astrophysics Data System (ADS)

    Ma, Qing-Fen; Hu, Da-Peng; Jiang, Jing-Zhi; Qiu, Zhong-Hua

    2010-01-01

    Spontaneous nucleation is the primary way of droplet formation in the supersonic gas separation technology, and the converging-diverging nozzle is the condensation and separation unit of supersonic gas separation devices. A three-dimensional geometrical model for the generation of self-rotational transonic gas flow is set up, based on which, the spontaneous nucleation of self-rotational transonic moist gas in the converging-diverging nozzle is carried out using an Eulerian multi-fluid model. The simulated results of the main flow and nucleation parameters indicate that the spontaneous nucleation can occur in the diverging part of the nozzle. However, different from the nucleation flow without self-rotation, the distributions of these parameters are unsymmetrical about the nozzle axis due to the irregular flow form caused by the self-rotation of gas flow. The nucleation region is located on the position where gas flows with intense rotation and the self-rotation impacts much on the nucleation process. Stronger rotation delays the onset of spontaneous nucleation and yields lower nucleation rate and narrow nucleation region. In addition, influences of other factors such as inlet total pressure p 0, inlet total temperature T 0, the nozzle-expanding ratio Ȧ and the inlet relative humidity ф 0 on the nucleation of self-rotational moist gas flow in the nozzle are also discussed.

  7. A comparative investigation of methods for logistic regression with separated or nearly separated data.

    PubMed

    Heinze, Georg

    2006-12-30

    In logistic regression analysis of small or sparse data sets, results obtained by classical maximum likelihood methods cannot be generally trusted. In such analyses it may even happen that the likelihood meets the convergence criteria while at least one parameter estimate diverges to +/-infinity. This situation has been termed 'separation', and it typically occurs whenever no events are observed in one of the two groups defined by a dichotomous covariate. More generally, separation is caused by a linear combination of continuous or dichotomous covariates that perfectly separates events from non-events. Separation implies infinite or zero maximum likelihood estimates of odds ratios, which are usually considered unrealistic. I provide some examples of separation and near-separation in clinical data sets and discuss some options to analyse such data, including exact logistic regression analysis and a penalized likelihood approach. Both methods supply finite point estimates in case of separation. Profile penalized likelihood confidence intervals for parameters show excellent behaviour in terms of coverage probability and provide higher power than exact confidence intervals. General advantages of the penalized likelihood approach are discussed.

  8. Highly Divergent Hepaciviruses from African Cattle

    PubMed Central

    Corman, Victor Max; Grundhoff, Adam; Baechlein, Christine; Fischer, Nicole; Gmyl, Anatoly; Wollny, Robert; Dei, Dickson; Ritz, Daniel; Binger, Tabea; Adankwah, Ernest; Marfo, Kwadwo Sarfo; Annison, Lawrence; Annan, Augustina; Adu-Sarkodie, Yaw; Oppong, Samuel; Becher, Paul; Drosten, Christian

    2015-01-01

    ABSTRACT The hepatitis C virus (HCV; genus Hepacivirus) is a highly relevant human pathogen. Unique hepaciviruses (HV) were discovered recently in animal hosts. The direct ancestor of HCV has not been found, but the genetically most closely related animal HVs exist in horses. To investigate whether other peridomestic animals also carry HVs, we analyzed sera from Ghanaian cattle for HVs by reverse transcription-PCR (RT-PCR). Nine of 106 specimens from different sampling sites contained HV RNA (8.5%) at median viral loads of 1.6 × 105 copies/ml. Infection seemed unrelated to cattle age and gender. Near-full-genome sequencing of five representative viruses confirmed taxonomic classifications. Cattle HVs formed two distinct phylogenetic lineages that differed by up to 17.7% on the nucleotide level in the polyprotein-encoding region, suggesting cocirculation of different virus subtypes. A conserved microRNA122-binding site in the 5′ internal ribosomal entry site suggested liver tropism of cattle HVs. Phylogenetic analyses suggested the circulation of HVs in cattle for several centuries. Cattle HVs were genetically highly divergent from all other HVs, including HCV. HVs from genetically related equine and bovine hosts were not monophyletic, corroborating host shifts during the evolution of the genus Hepacivirus. Similar to equine HVs, the genetic diversity of cattle HVs was low compared to that of HCV genotypes. This suggests an influence of the human-modified ecology of peridomestic animals on virus diversity. Further studies should investigate the occurrence of cattle HVs in other geographic areas and breeds, virus pathogenicity in cattle, and the potential exposure of human risk groups, such as farmers, butchers, and abattoir workers. IMPORTANCE HCV (genus Hepacivirus) is a major human pathogen, causing liver failure and cancer. Unique hepaciviruses (HVs) were discovered over the last few years in animals, but the direct ancestor of HCV has not been found. The

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  10. Honeybee foraging in differentially structured landscapes.

    PubMed

    Steffan-Dewenter, Ingolf; Kuhn, Arno

    2003-03-22

    Honeybees communicate the distance and location of resource patches by bee dances, but this spatial information has rarely been used to study their foraging ecology. We analysed, for the first time to the best of the authors' knowledge, foraging distances and dance activities of honeybees in relation to landscape structure, season and colony using a replicated experimental approach on a landscape scale. We compared three structurally simple landscapes characterized by a high proportion of arable land and large patches, with three complex landscapes with a high proportion of semi-natural perennial habitats and low mean patch size. Four observation hives were placed in the centre of the landscapes and switched at regular intervals between the six landscapes from the beginning of May to the end of July. A total of 1137 bee dances were observed and decoded. Overall mean foraging distance was 1526.1 +/- 37.2 m, the median 1181.5 m and range 62.1-10037.1 m. Mean foraging distances of all bees and foraging distances of nectar-collecting bees did not significantly differ between simple and complex landscapes, but varied between month and colonies. Foraging distances of pollen-collecting bees were significantly larger in simple (1743 +/- 95.6 m) than in complex landscapes (1543.4 +/- 71 m) and highest in June when resources were scarce. Dancing activity, i.e. the number of observed bee dances per unit time, was significantly higher in complex than in simple landscapes, presumably because of larger spatial and temporal variability of resource patches in complex landscapes. The results facilitate an understanding of how human landscape modification may change the evolutionary significance of bee dances and ecological interactions, such as pollination and competition between honeybees and other bee species.

  11. The effects of landscape fragmentation on pollination dynamics: absence of evidence not evidence of absence.

    PubMed

    Hadley, Adam S; Betts, Matthew G

    2012-08-01

    Animal-mediated pollination is essential for both ecosystem services and conservation of global biodiversity, but a growing body of work reveals that it is negatively affected by anthropogenic disturbance. Landscape-scale disturbance results in two often inter-related processes: (1) habitat loss, (2) disruptions of habitat configuration (i.e. fragmentation). Understanding the relative effects of such processes is critical in designing effective management strategies to limit pollination and pollinator decline. We reviewed existing published work from 1989 to 2009 and found that only six of 303 studies considering the influence of landscape context on pollination separated the effects of habitat loss from fragmentation. We provide a synthesis of the current landscape, behavioural, and pollination ecology literature in order to present preliminary multiple working hypotheses explaining how these two landscape processes might independently influence pollination dynamics. Landscape disturbance primarily influences three components of pollination interactions: pollinator density, movement, and plant demography. We argue that effects of habitat loss on each of these components are likely to differ substantially from the effects of fragmentation, which is likely to be more complex and may influence each pollination component in contrasting ways. The interdependency between plants and animals inherent to pollination systems also has the possibility to drive cumulative effects of fragmentation, initiating negative feedback loops between animals and the plants they pollinate. Alternatively, due to their asymmetrical structure, pollination networks may be relatively robust to fragmentation. Despite the potential importance of independent effects of habitat fragmentation, its effects on pollination remain largely untested. We postulate that variation across studies in the effects of 'fragmentation' owes much to artifacts of the sampling regimes adopted, particularly (1

  12. The Landscape of the Gibbet

    PubMed Central

    Tarlow, Sarah; Dyndor, Zoe

    2015-01-01

    ABSTRACT From the Murder Act of 1752 until the Anatomy Act of 1832 it was forbidden to bury the bodies of executed murderers unless they had first been anatomised or ‘hung in chains’ (gibbeted). This paper considers some of the observations of the Wellcome-funded project ‘Harnessing the Power of the Criminal Corpse’ as they relate to the practice of gibbeting. The nature of hanging in chains is briefly described before an extensive discussion of the criteria by which gibbets, which often remained standing for many decades, were selected. These are: proximity to the scene of crime, visibility, and practicality. Exceptions, in the forms of those sentenced by the Admiralty Courts, and those sentenced in and around London, are briefly considered. Hanging in chains was an infrequent punishment (anatomical dissection was far more frequently practised) but it was the subject of huge public interest and attracted thousands of people. There was no specified time for which a body should remain hanging, and the gibbet often became a known landmark and a significant place in the landscape. There is a remarkable contrast between anatomical dissection, which obliterates and anonymises the body of the individual malefactor, and hanging in chains, which leaves a highly personalised and enduring imprint on the actual and imaginative landscape. PMID:27335506

  13. Multiple-channel, total-reflection optic with controllable divergence

    DOEpatents

    Gibson, David M.; Downing, Robert G.

    1997-01-01

    An apparatus and method for providing focused x-ray, gamma-ray, charged particle and neutral particle, including neutron, radiation beams with a controllable amount of divergence are disclosed. The apparatus features a novel use of a radiation blocking structure, which, when combined with multiple-channel total reflection optics, increases the versatility of the optics by providing user-controlled output-beam divergence.

  14. Multiple-channel, total-reflection optic with controllable divergence

    DOEpatents

    Gibson, D.M.; Downing, R.G.

    1997-02-18

    An apparatus and method for providing focused x-ray, gamma-ray, charged particle and neutral particle, including neutron, radiation beams with a controllable amount of divergence are disclosed. The apparatus features a novel use of a radiation blocking structure, which, when combined with multiple-channel total reflection optics, increases the versatility of the optics by providing user-controlled output-beam divergence. 11 figs.

  15. Negative ion source with low temperature transverse divergence optical system

    DOEpatents

    Whealton, John H.; Stirling, William L.

    1986-01-01

    A negative ion source is provided which has extremely low transverse divergence as a result of a unique ion focusing system in which the focal line of an ion beam emanating from an elongated, concave converter surface is outside of the ion exit slit of the source and the path of the exiting ions. The beam source operates with a minimum ion temperature which makes possible a sharply focused (extremely low transverse divergence) ribbon like negative ion beam.

  16. Negative ion source with low temperature transverse divergence optical system

    DOEpatents

    Whealton, J.H.; Stirling, W.L.

    1985-03-04

    A negative ion source is provided which has extremely low transverse divergence as a result of a unique ion focusing system in which the focal line of an ion beam emanating from an elongated, concave converter surface is outside of the ion exit slit of the source and the path of the exiting ions. The beam source operates with a minimum ion temperature which makes possible a sharply focused (extremely low transverse divergence) ribbon like negative ion beam.

  17. Tsallis and Rényi divergences of generalized Jacobi polynomials

    NASA Astrophysics Data System (ADS)

    Sfetcu, Răzvan-Cornel

    2016-10-01

    We consider some discrete probability distribution ψn(x) =(ψn,1(x) ,ψn,2(x) , … ,ψn,n(x)) . We show that, under suitable conditions, the sequence of Tsallis divergence (DT(ψn(x))) n and the sequence of Rényi divergence (DR(ψn(x))) n are convergent for any x ∈(- 1 , 1) .

  18. Varying the Divergence of Multiple Parallel Laser Beams

    NASA Technical Reports Server (NTRS)

    Kovalik, Joseph M.; Wright, Malcolm W.

    2008-01-01

    A provision for controlled variation of the divergence of a laser beam or of multiple parallel laser beams has been incorporated into the design of a conceptual free-space optical-communication station from which the transmitted laser beam(s) would be launched via a telescope. The original purpose to be served by this provision was to enable optimization, under various atmospheric optical conditions, of the divergence of a laser beam or beams transmitted from a ground station to a spacecraft.

  19. Measurement of divergence of co/sub 2/-laser radiation

    SciTech Connect

    Shepelenko, A.A.; Shulyat'ev, V.B.

    1986-04-01

    This paper presents a modification of the Foucault method for measuring the radiation divergence of high-power CW lasers in which the limiting diaphram is produced by an aperture burned through by the laser radiation itself. The method is suitable for beams with any cross-sectional intensitiy distribution. Results of divergence measurements of a CO/sub 2/ production laser with power to 2 kW are presented.

  20. Numerical Optimization of converging diverging miniature cavitating nozzles

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  1. Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora".

    PubMed

    Douady, Christophe J; Douzery, Emmanuel J P

    2003-08-01

    "Insectivores" are one of the key groups in understanding mammalian origins. For years, systematics of "Lipotyphla" taxa remained extremely unstable and challenged. Today, with the application of molecular techniques, "Lipotyphla" appears to be a paraphyletic assemblage that encompasses hedgehogs, shrews, and moles (i.e., Eulipotyphla-a member of Laurasiatheria), and golden moles and tenrecs (i.e., Afrosoricida-a member of Afrotheria). Based on nuclear genes and on this well-established phylogenetic framework, we estimated Bayesian relaxed molecular clock divergence times among major lineages of "Lipotyphla." Crown placental mammals are shown to diversify 102+/-6 million years ago (Mya; mean+/-one standard-deviation), followed by Boreoeutheria (94+/-6 Mya), Laurasiatheria (85+/-5 Mya), and Eulipotyphla (73+/-5), with moles separating from hedgehogs+shrews just at the K/T boundary (65+/-5 Mya). During the Early and Middle Eocene, all extant eulipotyphlan subfamilies originated: Uropsilinae (52+/-5 Mya), and Desmaninae, Talpinae, Erinaceinae, Hylomyinae, Soricinae, and Crocidurinae (38-42+/-5 Mya). Afrosoricida separated from Macroscelidae 69+/-5 Mya, golden moles from tenrecs 63+/-5 Mya, and the diversification within tenrecs occurred 43+/-5 Mya. Divergence times are shown to be in reasonably good agreement with the fossil record of eulipotyphlans, but not with the one of afrosoricid "insectivores." Eulipotyphlans diversification might have been sculpted by variations in paleoclimates of the cenozoic era.

  2. Evolutionary Divergence of the Genetic Architecture Underlying Photoperiodism in the Pitcher-Plant Mosquito, Wyeomyia Smithii

    PubMed Central

    Lair, K. P.; Bradshaw, W. E.; Holzapfel, C. M.

    1997-01-01

    We determine the contribution of composite additive, dominance, and epistatic effects to the genetic divergence of photoperiodic response along latitudinal, altitudinal, and longitudinal gradients in the pitcher-plant mosquito, Wyeomyia smithii. Joint scaling tests of crosses between populations showed wide-spread epistasis as well as additive and dominance differences among populations. There were differences due to epistasis between an alpine population in North Carolina and populations in Florida, lowland North Carolina, and Maine. Longitudinal displacement resulted in differences due to epistasis between Florida and Alabama populations separated by 300 km but not between Maine and Wisconsin populations separated by 2000 km. Genetic differences between New Jersey and Ontario did not involve either dominance or epistasis and we estimated the minimum number of effective factors contributing to a difference in mean critical photoperiod of 5 SD between them as n(E) = 5. We propose that the genetic similarity of populations within a broad northern region is due to their more recent origin since recession of the Laurentide Ice Sheet and that the unique genetic architecture of each population is the result of both mutation and repeated migration-founder-flush episodes during the dispersal of W. smithii in North America. Our results suggest that differences in composite additive and dominance effects arise early in the genetic divergence of populations while differences due to epistasis accumulate after more prolonged isolation. PMID:9409843

  3. 76 FR 61666 - Collaborative Forest Landscape Restoration Program Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-05

    ... Forest Service Collaborative Forest Landscape Restoration Program Advisory Committee AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The Collaborative Forest Landscape Restoration Program... members. However, persons who wish to bring Collaborative Forest Landscape Restoration Program matters...

  4. 75 FR 10204 - Collaborative Forest Landscape Restoration Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-05

    ...; ] DEPARTMENT OF AGRICULTURE Office of the Secretary Collaborative Forest Landscape Restoration Advisory... Forest Landscape Restoration Advisory Committee and call for nominations. SUMMARY: The Secretary of Agriculture intends to establish the Collaborative Forest Landscape Restoration Advisory Committee...

  5. 75 FR 38456 - Collaborative Forest Landscape Restoration Program Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-02

    ... Forest Service Collaborative Forest Landscape Restoration Program Advisory Committee AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The Collaborative Forest Landscape Restoration Program..., persons who wish to bring Collaborative Forest Landscape Restoration Program matters to the attention...

  6. 76 FR 3605 - Collaborative Forest Landscape Restoration Program Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-20

    ... Forest Service Collaborative Forest Landscape Restoration Program Advisory Committee AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The Collaborative Forest Landscape Restoration Program... Forest Landscape Restoration Program matters to the attention of the Committee may file...

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

    NASA Astrophysics Data System (ADS)

    Wilmking, M.; Singh, J.

    2008-06-01

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

  8. The Evolution of Ribosomal DNA: Divergent Paralogues and Phylogenetic Implications

    PubMed Central

    Buckler-IV, E. S.; Ippolito, A.; Holtsford, T. P.

    1997-01-01

    Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies. PMID:9055091

  9. Energy landscapes of resting-state brain networks.

    PubMed

    Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

    2014-01-01

    During rest, the human brain performs essential functions such as memory maintenance, which are associated with resting-state brain networks (RSNs) including the default-mode network (DMN) and frontoparietal network (FPN). Previous studies based on spiking-neuron network models and their reduced models, as well as those based on imaging data, suggest that resting-state network activity can be captured as attractor dynamics, i.e., dynamics of the brain state toward an attractive state and transitions between different attractors. Here, we analyze the energy landscapes of the RSNs by applying the maximum entropy model, or equivalently the Ising spin model, to human RSN data. We use the previously estimated parameter values to define the energy landscape, and the disconnectivity graph method to estimate the number of local energy minima (equivalent to attractors in attractor dynamics), the basin size, and hierarchical relationships among the different local minima. In both of the DMN and FPN, low-energy local minima tended to have large basins. A majority of the network states belonged to a basin of one of a few local minima. Therefore, a small number of local minima constituted the backbone of each RSN. In the DMN, the energy landscape consisted of two groups of low-energy local minima that are separated by a relatively high energy barrier. Within each group, the activity patterns of the local minima were similar, and different minima were connected by relatively low energy barriers. In the FPN, all dominant local minima were separated by relatively low energy barriers such that they formed a single coarse-grained global minimum. Our results indicate that multistable attractor dynamics may underlie the DMN, but not the FPN, and assist memory maintenance with different memory states.

  10. Assessing Landscapes to Support Watershed Management

    EPA Science Inventory

    As we change the face of the landscape in the United States with urban development and agriculture practices, the alterations can cause stormwater runoff, soil erosion and water pollution. Therefore, evaluating or assessing natural landscapes and providing the tools to do the...

  11. Oregon Hydrologic Landscapes: A Classification Framework

    EPA Science Inventory

    There is a growing need for hydrologic classification systems that can provide a basis for broad-scale assessments of the hydrologic functions of landscapes and watersheds and their responses to stressors such as climate change. We developed a hydrologic landscape (HL) classifica...

  12. Experiencing Landscape: Orkney Hill Land and Farming

    ERIC Educational Resources Information Center

    Lee, Jo

    2007-01-01

    This paper is about how rural landscape is experienced according to combinations of practical engagements with land and the ways meaning is made in relation to it. It presents the case of the ambiguous position of the Orkney Islands within categorisations of Highland and Lowland landscapes in Scotland. Through a discussion of the physical and…

  13. Comparative Rural Landscapes: A Conceptual Geographic Model.

    ERIC Educational Resources Information Center

    Steinbrink, John E.

    The geography unit is designed for use in upper elementary grades. The unit objective is to help the student learn facts about the landscapes of the United States, the Netherlands, Australia, Russia, and Central Africa, and acquire generic ideas which he can apply to the analysis and comparison of other landscapes. The unit is an attempt to apply…

  14. Magnetic separation of algae

    DOEpatents

    Nath, Pulak; Twary, Scott N.

    2016-04-26

    Described herein are methods and systems for harvesting, collecting, separating and/or dewatering algae using iron based salts combined with a magnetic field gradient to separate algae from an aqueous solution.

  15. Wildlife tradeoffs based on landscape models of habitat

    USGS Publications Warehouse

    Loehle, C.; Mitchell, M.S.

    2000-01-01

    It is becoming increasingly clear that the spatial structure of landscapes affects the habitat choices and abundance of wildlife. In contrast to wildlife management based on preservation of critical habitat features such as nest sites on a beach or mast trees, it has not been obvious how to incorporate spatial structure into management plans. We present techniques to accomplish this goal. We used multiscale logistic regression models developed previously for neotropical migrant bird species habitat use in South Carolina (USA) as a basis for these techniques. Based on these models we used a spatial optimization technique to generate optimal maps (probability of occurrence, P = 1.0) for each of seven species. To emulate management of a forest for maximum species diversity, we defined the objective function of the algorithm as the sum of probabilities over the seven species, resulting in a complex map that allowed all seven species to coexist. The map that allowed for coexistence is not obvious, must be computed algorithmically, and would be difficult to realize using rules of thumb for habitat management. To assess how management of a forest for a single species of interest might affect other species, we analyzed tradeoffs by gradually increasing the weighting on a single species in the objective function over a series of simulations. We found that as habitat was increasingly modified to favor that species, the probability of presence for two of the other species was driven to zero. This shows that whereas it is not possible to simultaneously maximize the likelihood of presence for multiple species with divergent habitat preferences, compromise solutions are possible at less than maximal likelihood in many cases. Our approach suggests that efficiency of habitat management for species diversity can by maximized for even small landscapes by incorporating spatial context. The methods we present are suitable for wildlife management, endangered species conservation, and

  16. Topology of cyclo-octane energy landscape

    NASA Astrophysics Data System (ADS)

    Martin, Shawn; Thompson, Aidan; Coutsias, Evangelos A.; Watson, Jean-Paul

    2010-06-01

    Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.

  17. Longwave infrared observation of urban landscapes

    NASA Technical Reports Server (NTRS)

    Goward, S. N.

    1981-01-01

    An investigation is conducted regarding the feasibility to develop improved methods for the identification and analysis of urban landscapes on the basis of a utilization of longwave infrared observations. Attention is given to landscape thermal behavior, urban thermal properties, modeled thermal behavior of pavements and buildings, and observed urban landscape thermal emissions. The differential thermal behavior of buildings, pavements, and natural areas within urban landscapes is found to suggest that integrated multispectral solar radiant reflectance and terrestrial radiant emissions data will significantly increase potentials for analyzing urban landscapes. In particular, daytime satellite observations of the considered type should permit better identification of urban areas and an analysis of the density of buildings and pavements within urban areas. This capability should enhance the utility of satellite remote sensor data in urban applications.

  18. Separation in Binary Alloys

    NASA Technical Reports Server (NTRS)

    Frazier, D. O.; Facemire, B. R.; Kaukler, W. F.; Witherow, W. K.; Fanning, U.

    1986-01-01

    Studies of monotectic alloys and alloy analogs reviewed. Report surveys research on liquid/liquid and solid/liquid separation in binary monotectic alloys. Emphasizes separation processes in low gravity, such as in outer space or in free fall in drop towers. Advances in methods of controlling separation in experiments highlighted.

  19. Meniscus Membranes For Separation

    DOEpatents

    Dye, Robert C.; Jorgensen, Betty; Pesiri, David R.

    2005-09-20

    Gas separation membranes, especially meniscus-shaped membranes for gas separations are disclosed together with the use of such meniscus-shaped membranes for applications such as thermal gas valves, pre-concentration of a gas stream, and selective pre-screening of a gas stream. In addition, a rapid screening system for simultaneously screening polymer materials for effectiveness in gas separation is provided.

  20. Space shuttle separation mechanisms

    NASA Technical Reports Server (NTRS)

    Rogers, W. F.

    1978-01-01

    The development of space shuttle separation devices is reviewed to illustrate the mechanisms involved in separating the Orbiter from the Boeing 747 carrier aircraft and from the externally mounted propellant tank. Other aspects of the separation device development discussed include design evolution, operational experience during the orbiter approach and landing tests, and the work required to produce an operational system.

  1. Space Shuttle separation mechanisms

    NASA Technical Reports Server (NTRS)

    Rogers, W. F.

    1979-01-01

    The development of space shuttle separation devices is reviewed to illustrate the mechanisms involved in separating the orbiter from the Boeing 747 carrier aircraft and from the externally mounted propellant tank. Other aspects of the separation device development discussed include design evolution, operational experience during the orbiter approach and landing tests, and the work to be accomplished before an operational system becomes a reality.

  2. Meniscus membranes for separations

    DOEpatents

    Dye, Robert C.; Jorgensen, Betty; Pesiri, David R.

    2004-01-27

    Gas separation membranes, especially meniscus-shaped membranes for gas separations are disclosed together with the use of such meniscus-shaped membranes for applications such as thermal gas valves, pre-concentration of a gas stream, and selective pre-screening of a gas stream. In addition, a rapid screening system for simultaneously screening polymer materials for effectiveness in gas separation is provided.

  3. The Contribution of Vegetation and Landscape Configuration for Predicting Environmental Change Impacts on Iberian Birds

    PubMed Central

    Triviño, Maria; Thuiller, Wilfried; Cabeza, Mar; Hickler, Thomas; Araújo, Miguel B.

    2011-01-01

    Although climate is known to be one of the key factors determining animal species distributions amongst others, projections of global change impacts on their distributions often rely on bioclimatic envelope models. Vegetation structure and landscape configuration are also key determinants of distributions, but they are rarely considered in such assessments. We explore the consequences of using simulated vegetation structure and composition as well as its associated landscape configuration in models projecting global change effects on Iberian bird species distributions. Both present-day and future distributions were modelled for 168 bird species using two ensemble forecasting methods: Random Forests (RF) and Boosted Regression Trees (BRT). For each species, several models were created, differing in the predictor variables used (climate, vegetation, and landscape configuration). Discrimination ability of each model in the present-day was then tested with four commonly used evaluation methods (AUC, TSS, specificity and sensitivity). The different sets of predictor variables yielded similar spatial patterns for well-modelled species, but the future projections diverged for poorly-modelled species. Models using all predictor variables were not significantly better than models fitted with climate variables alone for ca. 50% of the cases. Moreover, models fitted with climate data were always better than models fitted with landscape configuration variables, and vegetation variables were found to correlate with bird species distributions in 26–40% of the cases with BRT, and in 1–18% of the cases with RF. We conclude that improvements from including vegetation and its landscape configuration variables in comparison with climate only variables might not always be as great as expected for future projections of Iberian bird species. PMID:22216263

  4. statement of significance, location map, site plan, landscape plan, site ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA

  5. The interplay between local ecology, divergent selection, and genetic drift in population divergence of a sexually antagonistic female trait.

    PubMed

    Green, Kristina Karlsson; Svensson, Erik I; Bergsten, Johannes; Härdling, Roger; Hansson, Bengt

    2014-07-01

    Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic mating trait in an insect group; the dorsal structures (either rough or smooth) of female diving beetles. Our recent work suggests that the rough structures have a sexually antagonistic function in reducing male mating attempts. For two species (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic drift as an explanation for population divergence in morph frequencies, whereas for the third (Hygrotus impressopunctatus) we found that divergent selection pulls morph frequencies apart across populations. Furthermore, population morph frequencies in H. impressopunctatus were significantly related to local bioclimatic factors, providing an additional line of evidence for local adaptation in this species. These data, therefore, suggest that local ecological factors and sexual conflict interact over larger spatial scales to shape population divergence in the polymorphism.

  6. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals.

    PubMed

    Nishihara, Hidenori; Maruyama, Shigenori; Okada, Norihiro

    2009-03-31

    As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 +/- 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148-138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, approximately 120 Ma.

  7. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

    PubMed Central

    Nishihara, Hidenori; Maruyama, Shigenori; Okada, Norihiro

    2009-01-01

    As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 ± 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148–138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, ≈120 Ma. PMID:19286970

  8. High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Beta genes

    PubMed Central

    2008-01-01

    selection on LHB and CGB8, and a positive evolution of CGB1. Conclusion If generalized, our data suggests that in addition to species-specific deletions and duplications, parallel duplication events may have contributed to genetic differences separating humans from their closest relatives. Compared to unique genomic segments, duplicated regions are characterized by high divergence promoted by intraspecies gene conversion and species-specific chromosomal rearrangements, including the alterations in gene copy number. PMID:18606016

  9. Safety shutdown separators

    SciTech Connect

    Carlson, Steven Allen; Anakor, Ifenna Kingsley; Farrell, Greg Robert

    2015-06-30

    The present invention pertains to electrochemical cells which comprise (a) an anode; (b) a cathode; (c) a solid porous separator, such as a polyolefin, xerogel, or inorganic oxide separator; and (d) a nonaqueous electrolyte, wherein the separator comprises a porous membrane having a microporous coating comprising polymer particles which have not coalesced to form a continuous film. This microporous coating on the separator acts as a safety shutdown layer that rapidly increases the internal resistivity and shuts the cell down upon heating to an elevated temperature, such as 110.degree. C. Also provided are methods for increasing the safety of an electrochemical cell by utilizing such separators with a safety shutdown layer.

  10. Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment.

    PubMed

    McCairns, R J Scott; Bernatchez, Louis

    2008-09-01

    Disentangling the relative contributions of selective and neutral processes underlying phenotypic and genetic variation under natural, environmental conditions remains a central challenge in evolutionary ecology. However, much of the variation that could be informative in this area of research is likely to be cryptic in nature; thus, the identification of wild populations suitable for study may be problematic. We use a landscape genetics approach to identify such populations of three-spined stickleback inhabiting the Saint Lawrence River estuary. We sampled 1865 adult fish over multiple years. Individuals were genotyped for nine microsatellite loci, and georeferenced multilocus data were used to infer population groupings, as well as locations of genetic discontinuities, under a Bayesian model framework (geneland). We modelled environmental data using nonparametric multiple regression to explain genetic differentiation as a function of spatio-ecological effects. Additionally, we used genotype data to estimate dispersal and gene flow to parameterize a simple model predicting adaptive vs. plastic divergence between demes. We demonstrate a bipartite division of the genetic landscape into freshwater and maritime zones, independent of geographical distance. Moreover, we show that the greatest proportion of genetic variation (31.5%) is explained by environmental differences. However, the potential for either adaptive or plastic divergence between demes is highly dependent upon the strength of migration and selection. Consequently, we highlight the utility of landscape genetics as a tool for hypothesis generation and experimental design, to identify focal populations and putative selection gradients, in order to distinguish between phenotypic plasticity and local adaptation.

  11. Aptamers in Affinity Separations: Stationary Separation

    NASA Astrophysics Data System (ADS)

    Ravelet, Corinne; Peyrin, Eric

    The use of DNA or RNA aptamers as tools in analytical chemistry is a very promising field of research because of their capabilities to bind specifically the target molecules with an affinity similar to that of antibodies. Notably, they appear to be of great interest as target-specific ligands for the separation and capture of various analytes in affinity chromatography and related affinity-based methods such as magnetic bead technology. In this chapter, the recent developments of these aptamer-based separation/capture approaches are addressed.

  12. DAST in Flight Showing Diverging Wingtip Oscillations

    NASA Technical Reports Server (NTRS)

    1980-01-01

    normal stiffness. This was done because stiffness requires structural weight but ensures freedom from flutter-an uncontrolled, divergent oscillation of the structure, driven by aerodynamic forces and resulting in structural failure. The program used refined theoretical tools to predict at what speed flutter would occur. It then designed a high-response control system to counteract the motion and permit a much lighter wing structure. The wing had, in effect, 'electronic stiffness.' Flight research with this concept was extremely hazardous because an error in either the flutter prediction or control system implementation would result in wing structural failure and the loss of the vehicle. Because of this, flight demonstration of a sub-scale vehicle made sense from the standpoint of both safety and cost. The program anticipated structural failure during the course of the flight research. The Firebee II was a supersonic drone selected as the DAST testbed because its wing could be easily replaced, it used only tail-mounted control surfaces, and it was available as surplus from the U. S. Air Force. It was capable of 5-g turns (that is, turns producing acceleration equal to 5 times that of gravity). Langley outfitted a drone with an aeroelastic, supercritical research wing suitable for a Mach 0.98 cruise transport with a predicted flutter speed of Mach 0.95 at an altitude of 25,000 feet. Dryden and Langley, in conjunction with Boeing, designed and fabricated a digital flutter suppression system (FSS). Dryden developed an RPRV (remotely piloted research vehicle) flight control system; integrated the wing, FSS, and vehicle systems; and conducted the flight program. In addition to a digital flight control system and aeroelastic wings, each DAST drone had research equipment mounted in its nose and a mid-air retrieval system in its tail. The drones were originally launched from the NASA B-52 bomber and later from a DC-130. The DAST vehicle's flight was monitored from the sky by an F

  13. The Aeroacoustics of Slowly Diverging Supersonic Jets

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.; Leib, S. J.

    2008-01-01

    This paper is concerned with utilizing the acoustic analogy approach to predict the sound from unheated supersonic jets. Previous attempts have been unsuccessful at making such predictions over the Mach number range of practical interest. The present paper, therefore, focuses on implementing the necessary refinements needed to accomplish this objective. The important effects influencing peak supersonic noise turn out to be source convection, mean flow refraction, mean flow amplification, and source non-compactness. It appears that the last two effects have not been adequately dealt with in the literature. The first of these because the usual parallel flow models produce most of the amplification in the so called critical layer where the solution becomes singular and, therefore, causes the predicted sound field to become infinite as well. We deal with this by introducing a new weakly non parallel flow analysis that eliminates the critical layer singularity. This has a strong effect on the shape of the peak noise spectrum. The last effect places severe demands on the source models at the higher Mach numbers because the retarded time variations significantly increase the sensitivity of the radiated sound to the source structure in this case. A highly refined (non-separable) source model is, therefore, introduced in this paper.

  14. Defining the landscape of adaptive genetic diversity.

    PubMed

    Eckert, Andrew J; Dyer, Rodney J

    2012-06-01

    Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). PMID:22676074

  15. Landscape co-evolution and river discharge.

    NASA Astrophysics Data System (ADS)

    van der Velde, Ype; Temme, Arnaud

    2015-04-01

    Fresh water is crucial for society and ecosystems. However, our ability to secure fresh water resources under climatic and anthropogenic change is impaired by the complexity of interactions between human society, ecosystems, soils, and topography. These interactions cause landscape properties to co-evolve, continuously changing the flow paths of water through the landscape. These co-evolution driven flow path changes and their effect on river runoff are, to-date, poorly understood. In this presentation we introduce a spatially distributed landscape evolution model that incorporates growing vegetation and its effect on evapotranspiration, interception, infiltration, soil permeability, groundwater-surface water exchange and erosion. This landscape scale (10km2) model is calibrated to evolve towards well known empirical organising principles such as the Budyko curve and Hacks law under different climate conditions. To understand how positive and negative feedbacks within the model structure form complex landscape patterns of forests and peat bogs that resemble observed landscapes under humid and boreal climates, we analysed the effects of individual processes on the spatial distribution of vegetation and river peak and mean flows. Our results show that especially river peak flows and droughts decrease with increasing evolution of the landscape, which is a result that has direct implications for flood management.

  16. Do geographically isolated wetlands influence landscape functions?

    PubMed

    Cohen, Matthew J; Creed, Irena F; Alexander, Laurie; Basu, Nandita B; Calhoun, Aram J K; Craft, Christopher; D'Amico, Ellen; DeKeyser, Edward; Fowler, Laurie; Golden, Heather E; Jawitz, James W; Kalla, Peter; Kirkman, L Katherine; Lane, Charles R; Lang, Megan; Leibowitz, Scott G; Lewis, David Bruce; Marton, John; McLaughlin, Daniel L; Mushet, David M; Raanan-Kiperwas, Hadas; Rains, Mark C; Smith, Lora; Walls, Susan C

    2016-02-23

    Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bodies to create spatial and temporal heterogeneity in the timing, flow paths, and magnitude of network connectivity. These attributes signal a critical role for GIWs in sustaining a portfolio of landscape functions, but legal protections remain weak despite preferential loss from many landscapes. GIWs lack persistent surface water connections, but this condition does not imply the absence of hydrological, biogeochemical, and biological exchanges with nearby and downstream waters. Although hydrological and biogeochemical connectivity is often episodic or slow (e.g., via groundwater), hydrologic continuity and limited evaporative solute enrichment suggest both flow generation and solute and sediment retention. Similarly, whereas biological connectivity usually requires overland dispersal, numerous organisms, including many rare or threatened species, use both GIWs and downstream waters at different times or life stages, suggesting that GIWs are critical elements of landscape habitat mosaics. Indeed, weaker hydrologic connectivity with downstream waters and constrained biological connectivity with other landscape elements are precisely what enhances some GIW functions and enables others. Based on analysis of wetland geography and synthesis of wetland functions, we argue that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs.

  17. Metapopulation capacity of evolving fluvial landscapes

    NASA Astrophysics Data System (ADS)

    Bertuzzo, Enrico; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

    2015-04-01

    The form of fluvial landscapes is known to attain stationary network configurations that settle in dynamically accessible minima of total energy dissipation by landscape-forming discharges. Recent studies have highlighted the role of the dendritic structure of river networks in controlling population dynamics of the species they host and large-scale biodiversity patterns. Here, we systematically investigate the relation between energy dissipation, the physical driver for the evolution of river networks, and the ecological dynamics of their embedded biota. To that end, we use the concept of metapopulation capacity, a measure to link landscape structures with the population dynamics they host. Technically, metapopulation capacity is the leading eigenvalue λM of an appropriate "landscape" matrix subsuming whether a given species is predicted to persist in the long run. λM can conveniently be used to rank different landscapes in terms of their capacity to support viable metapopulations. We study how λM changes in response to the evolving network configurations of spanning trees. Such sequence of configurations is theoretically known to relate network selection to general landscape evolution equations through imperfect searches for dynamically accessible states frustrated by the vagaries of Nature. Results show that the process shaping the metric and the topological properties of river networks, prescribed by physical constraints, leads to a progressive increase in the corresponding metapopulation capacity and therefore on the landscape capacity to support metapopulations—with implications on biodiversity in fluvial ecosystems.

  18. Do geographically isolated wetlands influence landscape functions?

    USGS Publications Warehouse

    Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie C.; Basu, Nandita; Calhoun, Aram J. K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward S.; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan; Leibowitz, Scott G.; Lewis, David Bruce; Marton, John; McLaughlin, Daniel L.; Mushet, David M.; Raanan-Kiperwas, Hadas; Rains, Mark C.; Smith, Lora; Walls, Susan C.

    2015-01-01

    Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bodies to create spatial and temporal heterogeneity in the timing, flow paths, and magnitude of network connectivity. These attributes signal a critical role for GIWs in sustaining a portfolio of landscape functions, but legal protections remain weak despite preferential loss from many landscapes. GIWs lack persistent surface water connections, but this condition does not imply the absence of hydrological, biogeochemical, and biological exchanges with nearby and downstream waters. Although hydrological and biogeochemical connectivity is often episodic or slow (e.g., via groundwater), hydrologic continuity and limited evaporative solute enrichment suggest both flow generation and solute and sediment retention. Similarly, whereas biological connectivity usually requires overland dispersal, numerous organisms, including many rare or threatened species, use both GIWs and downstream waters at different times or life stages, suggesting that GIWs are critical elements of landscape habitat mosaics. Indeed, weaker hydrologic connectivity with downstream waters and constrained biological connectivity with other landscape elements are precisely what enhances some GIW functions and enables others. Based on analysis of wetland geography and synthesis of wetland functions, we argue that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs.

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

    ERIC Educational Resources Information Center

    Bijvoet-van den Berg, Simone; Hoicka, Elena

    2014-01-01

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

  20. Scalar field quantization without divergences in all spacetime dimensions

    NASA Astrophysics Data System (ADS)

    Klauder, John R.

    2011-07-01

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